Daily Papers

We present UniPLV, a powerful framework that unifies point clouds, images and text in a single learning paradigm for open-world 3D scene understanding. UniPLV employs the image modal as a bridge to co-embed 3D points with pre-aligned images and text in a shared feature space without requiring carefully crafted point cloud text pairs. To accomplish multi-modal alignment, we propose two key strategies:(i) logit and feature distillation modules between images and point clouds, and (ii) a vison-point matching module is given to explicitly correct the misalignment caused by points to pixels projection. To further improve the performance of our unified framework, we adopt four task-specific losses and a two-stage training strategy. Extensive experiments show that our method outperforms the state-of-the-art methods by an average of 15.6% and 14.8% for semantic segmentation over Base-Annotated and Annotation-Free tasks, respectively. The code will be released later.

In this paper, we investigate Open-Vocabulary 3D Instance Segmentation (OV-3DIS) with free-form language instructions. Earlier works that rely on only annotated base categories for training suffer from limited generalization to unseen novel categories. Recent works mitigate poor generalizability to novel categories by generating class-agnostic masks or projecting generalized masks from 2D to 3D, but disregard semantic or geometry information, leading to sub-optimal performance. Instead, generating generalizable but semantic-related masks directly from 3D point clouds would result in superior outcomes. In this paper, we introduce Segment any 3D Object with LanguagE (SOLE), which is a semantic and geometric-aware visual-language learning framework with strong generalizability by generating semantic-related masks directly from 3D point clouds. Specifically, we propose a multimodal fusion network to incorporate multimodal semantics in both backbone and decoder. In addition, to align the 3D segmentation model with various language instructions and enhance the mask quality, we introduce three types of multimodal associations as supervision. Our SOLE outperforms previous methods by a large margin on ScanNetv2, ScanNet200, and Replica benchmarks, and the results are even close to the fully-supervised counterpart despite the absence of class annotations in the training. Furthermore, extensive qualitative results demonstrate the versatility of our SOLE to language instructions.

Vision Language Models (VLMs) often struggle with culture-specific knowledge, particularly in languages other than English and in underrepresented cultural contexts. To evaluate their understanding of such knowledge, we introduce WorldCuisines, a massive-scale benchmark for multilingual and multicultural, visually grounded language understanding. This benchmark includes a visual question answering (VQA) dataset with text-image pairs across 30 languages and dialects, spanning 9 language families and featuring over 1 million data points, making it the largest multicultural VQA benchmark to date. It includes tasks for identifying dish names and their origins. We provide evaluation datasets in two sizes (12k and 60k instances) alongside a training dataset (1 million instances). Our findings show that while VLMs perform better with correct location context, they struggle with adversarial contexts and predicting specific regional cuisines and languages. To support future research, we release a knowledge base with annotated food entries and images along with the VQA data.

The Four-Element Theory is a fundamental framework in criminal law, defining the constitution of crime through four dimensions: Subject, Object, Subjective aspect, and Objective aspect. This theory is widely referenced in legal reasoning, and many Large Language Models (LLMs) attempt to incorporate it when handling legal tasks. However, current approaches rely on LLMs' internal knowledge to incorporate this theory, often lacking completeness and representativeness. To address this limitation, we introduce JUREX-4E, an expert-annotated knowledge base covering 155 criminal charges. It is structured through a progressive hierarchical annotation framework that prioritizes legal source validity and employs diverse legal interpretation methods to ensure comprehensiveness and authority. We evaluate JUREX-4E on the Similar Charge Distinction task and apply it to Legal Case Retrieval, demonstrating its effectiveness in improving LLM performance. Experimental results validate the high quality of JUREX-4E and its substantial impact on downstream legal tasks, underscoring its potential for advancing legal AI applications. Code: https://github.com/THUlawtech/JUREX

Understanding objects is a central building block of artificial intelligence, especially for embodied AI. Even though object recognition excels with deep learning, current machines still struggle to learn higher-level knowledge, e.g., what attributes an object has, and what can we do with an object. In this work, we propose a challenging Object Concept Learning (OCL) task to push the envelope of object understanding. It requires machines to reason out object affordances and simultaneously give the reason: what attributes make an object possesses these affordances. To support OCL, we build a densely annotated knowledge base including extensive labels for three levels of object concept (category, attribute, affordance), and the causal relations of three levels. By analyzing the causal structure of OCL, we present a baseline, Object Concept Reasoning Network (OCRN). It leverages causal intervention and concept instantiation to infer the three levels following their causal relations. In experiments, OCRN effectively infers the object knowledge while following the causalities well. Our data and code are available at https://mvig-rhos.com/ocl.

We present a new resource for the NLP community, namely a large (3.5M+ sentence) knowledge base of *generic statements*, e.g., "Trees remove carbon dioxide from the atmosphere", collected from multiple corpora. This is the first large resource to contain *naturally occurring* generic sentences, as opposed to extracted or crowdsourced triples, and thus is rich in high-quality, general, semantically complete statements. All GenericsKB sentences are annotated with their topical term, surrounding context (sentences), and a (learned) confidence. We also release GenericsKB-Best (1M+ sentences), containing the best-quality generics in GenericsKB augmented with selected, synthesized generics from WordNet and ConceptNet. In tests on two existing datasets requiring multihop reasoning (OBQA and QASC), we find using GenericsKB can result in higher scores and better explanations than using a much larger corpus. This demonstrates that GenericsKB can be a useful resource for NLP applications, as well as providing data for linguistic studies of generics and their semantics. GenericsKB is available at https://allenai.org/data/genericskb.

Turkish Wikipedia Named-Entity Recognition and Text Categorization (TWNERTC) dataset is a collection of automatically categorized and annotated sentences obtained from Wikipedia. We constructed large-scale gazetteers by using a graph crawler algorithm to extract relevant entity and domain information from a semantic knowledge base, Freebase. The constructed gazetteers contains approximately 300K entities with thousands of fine-grained entity types under 77 different domains. Since automated processes are prone to ambiguity, we also introduce two new content specific noise reduction methodologies. Moreover, we map fine-grained entity types to the equivalent four coarse-grained types: person, loc, org, misc. Eventually, we construct six different dataset versions and evaluate the quality of annotations by comparing ground truths from human annotators. We make these datasets publicly available to support studies on Turkish named-entity recognition (NER) and text categorization (TC).

The task of Question Generation over Knowledge Bases (KBQG) aims to convert a logical form into a natural language question. For the sake of expensive cost of large-scale question annotation, the methods of KBQG under low-resource scenarios urgently need to be developed. However, current methods heavily rely on annotated data for fine-tuning, which is not well-suited for few-shot question generation. The emergence of Large Language Models (LLMs) has shown their impressive generalization ability in few-shot tasks. Inspired by Chain-of-Thought (CoT) prompting, which is an in-context learning strategy for reasoning, we formulate KBQG task as a reasoning problem, where the generation of a complete question is splitted into a series of sub-question generation. Our proposed prompting method KQG-CoT first retrieves supportive logical forms from the unlabeled data pool taking account of the characteristics of the logical form. Then, we write a prompt to explicit the reasoning chain of generating complicated questions based on the selected demonstrations. To further ensure prompt quality, we extend KQG-CoT into KQG-CoT+ via sorting the logical forms by their complexity. We conduct extensive experiments over three public KBQG datasets. The results demonstrate that our prompting method consistently outperforms other prompting baselines on the evaluated datasets. Remarkably, our KQG-CoT+ method could surpass existing few-shot SoTA results of the PathQuestions dataset by 18.25, 10.72, and 10.18 absolute points on BLEU-4, METEOR, and ROUGE-L, respectively.

Humans can watch a continuous video stream and effortlessly perform continual acquisition and transfer of new knowledge with minimal supervision yet retaining previously learnt experiences. In contrast, existing continual learning (CL) methods require fully annotated labels to effectively learn from individual frames in a video stream. Here, we examine a more realistic and challenging problemx2014Label-Efficient Online Continual Object Detection (LEOCOD) in streaming video. We propose a plug-and-play module, Efficient-CLS, that can be easily inserted into and improve existing continual learners for object detection in video streams with reduced data annotation costs and model retraining time. We show that our method has achieved significant improvement with minimal forgetting across all supervision levels on two challenging CL benchmarks for streaming real-world videos. Remarkably, with only 25% annotated video frames, our method still outperforms the base CL learners, which are trained with 100% annotations on all video frames. The data and source code will be publicly available at https://github.com/showlab/Efficient-CLS.

Transformer-based language models, more specifically BERT-based architectures have achieved state-of-the-art performance in many downstream tasks. However, for a relatively low-resource language such as Thai, the choices of models are limited to training a BERT-based model based on a much smaller dataset or finetuning multi-lingual models, both of which yield suboptimal downstream performance. Moreover, large-scale multi-lingual pretraining does not take into account language-specific features for Thai. To overcome these limitations, we pretrain a language model based on RoBERTa-base architecture on a large, deduplicated, cleaned training set (78GB in total size), curated from diverse domains of social media posts, news articles and other publicly available datasets. We apply text processing rules that are specific to Thai most importantly preserving spaces, which are important chunk and sentence boundaries in Thai before subword tokenization. We also experiment with word-level, syllable-level and SentencePiece tokenization with a smaller dataset to explore the effects on tokenization on downstream performance. Our model wangchanberta-base-att-spm-uncased trained on the 78.5GB dataset outperforms strong baselines (NBSVM, CRF and ULMFit) and multi-lingual models (XLMR and mBERT) on both sequence classification and token classification tasks in human-annotated, mono-lingual contexts.

We introduce Paralinguistic Speech Captions (ParaSpeechCaps), a large-scale dataset that annotates speech utterances with rich style captions. While rich abstract tags (e.g. guttural, nasal, pained) have been explored in small-scale human-annotated datasets, existing large-scale datasets only cover basic tags (e.g. low-pitched, slow, loud). We combine off-the-shelf text and speech embedders, classifiers and an audio language model to automatically scale rich tag annotations for the first time. ParaSpeechCaps covers a total of 59 style tags, including both speaker-level intrinsic tags and utterance-level situational tags. It consists of 342 hours of human-labelled data (PSC-Base) and 2427 hours of automatically annotated data (PSC-Scaled). We finetune Parler-TTS, an open-source style-prompted TTS model, on ParaSpeechCaps, and achieve improved style consistency (+7.9% Consistency MOS) and speech quality (+15.5% Naturalness MOS) over the best performing baseline that combines existing rich style tag datasets. We ablate several of our dataset design choices to lay the foundation for future work in this space. Our dataset, models and code are released at https://github.com/ajd12342/paraspeechcaps .

Post-training of Large Language Models often involves a pipeline of Supervised Finetuning (SFT) followed by Preference Finetuning (PFT) using methods like Direct Preference Optimization. Both stages require annotated data that are very different in structure and costs. We study how to optimally allocate a fixed training data budget between the two stages, through extensive experiments spanning four diverse tasks, multiple model sizes and various data annotation costs. Our findings reveal that just SFT on the base model dominates performance in low-data regimes (<1,000 annotated examples). With larger data-budgets, we observe that a combination of SFT and PFT, often with increasing portions allocated towards preference data yields optimal performance. However, completely eliminating SFT and running PFT directly on the base model yields suboptimal performance, described as the cold start problem on tasks like mathematics. We observe that this is due to the distribution shift arising from using DPO directly on the base model to elicit step-by-step reasoning. This limitation can be effectively addressed by allocating even a small portion (<10%) of the budget to SFT first, resulting in performance improvements of 15-20% on analytical benchmarks like GSM8k. These results provide actionable insights for researchers and practitioners optimizing model development under budget constraints, where high-quality data curation often represents a significant portion of the total costs of model development.

Multimodal Large Language Models (MLLMs) have recently demonstrated impressive capabilities in multimodal understanding, reasoning, and interaction. However, existing MLLMs prevalently suffer from serious hallucination problems, generating text that is not factually grounded in associated images. The problem makes existing MLLMs untrustworthy and thus impractical in real-world (especially high-stakes) applications. To address the challenge, we present RLHF-V, which enhances MLLM trustworthiness via behavior alignment from fine-grained correctional human feedback. Specifically, RLHF-V collects human preference in the form of segment-level corrections on hallucinations, and performs dense direct preference optimization over the human feedback. Comprehensive experiments on five benchmarks in both automatic and human evaluation show that, RLHF-V can enable substantially more trustworthy MLLM behaviors with promising data and computation efficiency. Remarkably, using 1.4k annotated data samples, RLHF-V significantly reduces the hallucination rate of the base MLLM by 34.8%, outperforming the concurrent LLaVA-RLHF trained on 10k annotated data. The final model achieves state-of-the-art performance in trustworthiness among open-source MLLMs, and shows better robustness than GPT-4V in preventing hallucinations aroused from over-generalization. We open-source our code, model, and data at https://github.com/RLHF-V/RLHF-V.

We propose Masked Siamese Networks (MSN), a self-supervised learning framework for learning image representations. Our approach matches the representation of an image view containing randomly masked patches to the representation of the original unmasked image. This self-supervised pre-training strategy is particularly scalable when applied to Vision Transformers since only the unmasked patches are processed by the network. As a result, MSNs improve the scalability of joint-embedding architectures, while producing representations of a high semantic level that perform competitively on low-shot image classification. For instance, on ImageNet-1K, with only 5,000 annotated images, our base MSN model achieves 72.4% top-1 accuracy, and with 1% of ImageNet-1K labels, we achieve 75.7% top-1 accuracy, setting a new state-of-the-art for self-supervised learning on this benchmark. Our code is publicly available.

Large Language Models (LLMs) face significant challenges at inference time due to their high computational demands. To address this, we present Performance-Guided Knowledge Distillation (PGKD), a cost-effective and high-throughput solution for production text classification applications. PGKD utilizes teacher-student Knowledge Distillation to distill the knowledge of LLMs into smaller, task-specific models. PGKD establishes an active learning routine between the student model and the LLM; the LLM continuously generates new training data leveraging hard-negative mining, student model validation performance, and early-stopping protocols to inform the data generation. By employing a cyclical, performance-aware approach tailored for highly multi-class, sparsely annotated datasets prevalent in industrial text classification, PGKD effectively addresses training challenges and outperforms traditional BERT-base models and other knowledge distillation methods on several multi-class classification datasets. Additionally, cost and latency benchmarking reveals that models fine-tuned with PGKD are up to 130X faster and 25X less expensive than LLMs for inference on the same classification task. While PGKD is showcased for text classification tasks, its versatile framework can be extended to any LLM distillation task, including language generation, making it a powerful tool for optimizing performance across a wide range of AI applications.

The automatic evaluation of instruction following typically involves using large language models (LLMs) to assess response quality. However, there is a lack of comprehensive evaluation of these LLM-based evaluators across two dimensions: the base LLMs and the evaluation protocols. Therefore, we present a thorough meta-evaluation of instruction following, including 25 base LLMs and 15 recently proposed evaluation protocols, on 4 human-annotated datasets, assessing the evaluation accuracy of the LLM-evaluators. Our evaluation allows us to identify the best-performing base LLMs and evaluation protocols with a high degree of robustness. Moreover, our large-scale evaluation reveals: (1) Base LLM performance ranking remains largely consistent across evaluation protocols, with less capable LLMs showing greater improvement from protocol enhancements; (2) Robust evaluation of evaluation protocols requires many base LLMs with varying capability levels, as protocol effectiveness can depend on the base LLM used; (3) Evaluation results on different datasets are not always consistent, so a rigorous evaluation requires multiple datasets with distinctive features. We release our meta-evaluation suite ReIFE, which provides the codebase and evaluation result collection for more than 500 LLM-evaluator configurations, to support future research in instruction-following evaluation.

To bridge the gap between supervised semantic segmentation and real-world applications that acquires one model to recognize arbitrary new concepts, recent zero-shot segmentation attracts a lot of attention by exploring the relationships between unseen and seen object categories, yet requiring large amounts of densely-annotated data with diverse base classes. In this paper, we propose a new open-world semantic segmentation pipeline that makes the first attempt to learn to segment semantic objects of various open-world categories without any efforts on dense annotations, by purely exploiting the image-caption data that naturally exist on the Internet. Our method, Vision-language-driven Semantic Segmentation (ViL-Seg), employs an image and a text encoder to generate visual and text embeddings for the image-caption data, with two core components that endow its segmentation ability: First, the image encoder is jointly trained with a vision-based contrasting and a cross-modal contrasting, which encourage the visual embeddings to preserve both fine-grained semantics and high-level category information that are crucial for the segmentation task. Furthermore, an online clustering head is devised over the image encoder, which allows to dynamically segment the visual embeddings into distinct semantic groups such that they can be classified by comparing with various text embeddings to complete our segmentation pipeline. Experiments show that without using any data with dense annotations, our method can directly segment objects of arbitrary categories, outperforming zero-shot segmentation methods that require data labeling on three benchmark datasets.

Medical visual question answering (Med-VQA) has tremendous potential in healthcare. However, the development of this technology is hindered by the lacking of publicly-available and high-quality labeled datasets for training and evaluation. In this paper, we present a large bilingual dataset, SLAKE, with comprehensive semantic labels annotated by experienced physicians and a new structural medical knowledge base for Med-VQA. Besides, SLAKE includes richer modalities and covers more human body parts than the currently available dataset. We show that SLAKE can be used to facilitate the development and evaluation of Med-VQA systems. The dataset can be downloaded from http://www.med-vqa.com/slake.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Data annotation is the labeling or tagging of raw data with relevant information, essential for improving the efficacy of machine learning models. The process, however, is labor-intensive and expensive. The emergence of advanced Large Language Models (LLMs), exemplified by GPT-4, presents an unprecedented opportunity to revolutionize and automate the intricate process of data annotation. While existing surveys have extensively covered LLM architecture, training, and general applications, this paper uniquely focuses on their specific utility for data annotation. This survey contributes to three core aspects: LLM-Based Data Annotation, Assessing LLM-generated Annotations, and Learning with LLM-generated annotations. Furthermore, the paper includes an in-depth taxonomy of methodologies employing LLMs for data annotation, a comprehensive review of learning strategies for models incorporating LLM-generated annotations, and a detailed discussion on primary challenges and limitations associated with using LLMs for data annotation. As a key guide, this survey aims to direct researchers and practitioners in exploring the potential of the latest LLMs for data annotation, fostering future advancements in this critical domain. We provide a comprehensive papers list at https://github.com/Zhen-Tan-dmml/LLM4Annotation.git.

Diderot's Encyclop\'edie is a reference work from XVIIIth century in Europe that aimed at collecting the knowledge of its era. Wikipedia has the same ambition with a much greater scope. However, the lack of digital connection between the two encyclopedias may hinder their comparison and the study of how knowledge has evolved. A key element of Wikipedia is Wikidata that backs the articles with a graph of structured data. In this paper, we describe the annotation of more than 10,300 of the Encyclop\'edie entries with Wikidata identifiers enabling us to connect these entries to the graph. We considered geographic and human entities. The Encyclop\'edie does not contain biographic entries as they mostly appear as subentries of locations. We extracted all the geographic entries and we completely annotated all the entries containing a description of human entities. This represents more than 2,600 links referring to locations or human entities. In addition, we annotated more than 9,500 entries having a geographic content only. We describe the annotation process as well as application examples. This resource is available at https://github.com/pnugues/encyclopedie_1751

The HuggingFace Datasets Hub hosts thousands of datasets. This provides exciting opportunities for language model training and evaluation. However, the datasets for a given type of task are stored with different schemas, and harmonization is harder than it seems (https://xkcd.com/927/). Multi-task training or evaluation requires manual work to fit data into task templates. Various initiatives independently address this problem by releasing the harmonized datasets or harmonization codes to preprocess datasets to the same format. We identify patterns across previous preprocessings, e.g. mapping of column names, and extraction of a specific sub-field from structured data in a column, and propose a structured annotation framework that makes our annotations fully exposed and not buried in unstructured code. We release a dataset annotation framework and dataset annotations for more than 400 English tasks (https://github.com/sileod/tasksource). These annotations provide metadata, like the name of the columns that should be used as input or labels for all datasets, and can save time for future dataset preprocessings, even if they do not use our framework. We fine-tune a multi-task text encoder on all tasksource tasks, outperforming every publicly available text encoder of comparable size on an external evaluation https://hf.co/sileod/deberta-v3-base-tasksource-nli.

The NLP pipeline has evolved dramatically in the last few years. The first step in the pipeline is to find suitable annotated datasets to evaluate the tasks we are trying to solve. Unfortunately, most of the published datasets lack metadata annotations that describe their attributes. Not to mention, the absence of a public catalogue that indexes all the publicly available datasets related to specific regions or languages. When we consider low-resource dialectical languages, for example, this issue becomes more prominent. In this paper we create Masader, the largest public catalogue for Arabic NLP datasets, which consists of 200 datasets annotated with 25 attributes. Furthermore, We develop a metadata annotation strategy that could be extended to other languages. We also make remarks and highlight some issues about the current status of Arabic NLP datasets and suggest recommendations to address them.

Relevant information in documents is often summarized in tables, helping the reader to identify useful facts. Most benchmark datasets support either document layout analysis or table understanding, but lack in providing data to apply both tasks in a unified way. We define the task of Contextualized Table Extraction (CTE), which aims to extract and define the structure of tables considering the textual context of the document. The dataset comprises 75k fully annotated pages of scientific papers, including more than 35k tables. Data are gathered from PubMed Central, merging the information provided by annotations in the PubTables-1M and PubLayNet datasets. The dataset can support CTE and adds new classes to the original ones. The generated annotations can be used to develop end-to-end pipelines for various tasks, including document layout analysis, table detection, structure recognition, and functional analysis. We formally define CTE and evaluation metrics, showing which subtasks can be tackled, describing advantages, limitations, and future works of this collection of data. Annotations and code will be accessible a https://github.com/AILab-UniFI/cte-dataset.

This paper presents NorNE, a manually annotated corpus of named entities which extends the annotation of the existing Norwegian Dependency Treebank. Comprising both of the official standards of written Norwegian (Bokm{\aa}l and Nynorsk), the corpus contains around 600,000 tokens and annotates a rich set of entity types including persons, organizations, locations, geo-political entities, products, and events, in addition to a class corresponding to nominals derived from names. We here present details on the annotation effort, guidelines, inter-annotator agreement and an experimental analysis of the corpus using a neural sequence labeling architecture.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

In the absence of readily available labeled data for a given sequence labeling task and language, annotation projection has been proposed as one of the possible strategies to automatically generate annotated data. Annotation projection has often been formulated as the task of transporting, on parallel corpora, the labels pertaining to a given span in the source language into its corresponding span in the target language. In this paper we present T-Projection, a novel approach for annotation projection that leverages large pretrained text-to-text language models and state-of-the-art machine translation technology. T-Projection decomposes the label projection task into two subtasks: (i) A candidate generation step, in which a set of projection candidates using a multilingual T5 model is generated and, (ii) a candidate selection step, in which the generated candidates are ranked based on translation probabilities. We conducted experiments on intrinsic and extrinsic tasks in 5 Indo-European and 8 low-resource African languages. We demostrate that T-projection outperforms previous annotation projection methods by a wide margin. We believe that T-Projection can help to automatically alleviate the lack of high-quality training data for sequence labeling tasks. Code and data are publicly available.

This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. In addition to the full corpus, a sub-corpus of MedMentions is also presented, comprising annotations for a subset of UMLS 2017 targeted towards document retrieval. To encourage research in Biomedical Named Entity Recognition and Linking, data splits for training and testing are included in the release, and a baseline model and its metrics for entity linking are also described.

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved F_1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

Very-High Resolution (VHR) remote sensing imagery is increasingly accessible, but often lacks annotations for effective machine learning applications. Recent foundation models like GroundingDINO and Segment Anything (SAM) provide opportunities to automatically generate annotations. This study introduces FMARS (Foundation Model Annotations in Remote Sensing), a methodology leveraging VHR imagery and foundation models for fast and robust annotation. We focus on disaster management and provide a large-scale dataset with labels obtained from pre-event imagery over 19 disaster events, derived from the Maxar Open Data initiative. We train segmentation models on the generated labels, using Unsupervised Domain Adaptation (UDA) techniques to increase transferability to real-world scenarios. Our results demonstrate the effectiveness of leveraging foundation models to automatically annotate remote sensing data at scale, enabling robust downstream models for critical applications. Code and dataset are available at https://github.com/links-ads/igarss-fmars.

The success of deep learning has sparked interest in improving relational table tasks, like data preparation and search, with table representation models trained on large table corpora. Existing table corpora primarily contain tables extracted from HTML pages, limiting the capability to represent offline database tables. To train and evaluate high-capacity models for applications beyond the Web, we need resources with tables that resemble relational database tables. Here we introduce GitTables, a corpus of 1M relational tables extracted from GitHub. Our continuing curation aims at growing the corpus to at least 10M tables. Analyses of GitTables show that its structure, content, and topical coverage differ significantly from existing table corpora. We annotate table columns in GitTables with semantic types, hierarchical relations and descriptions from Schema.org and DBpedia. The evaluation of our annotation pipeline on the T2Dv2 benchmark illustrates that our approach provides results on par with human annotations. We present three applications of GitTables, demonstrating its value for learned semantic type detection models, schema completion methods, and benchmarks for table-to-KG matching, data search, and preparation. We make the corpus and code available at https://gittables.github.io.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

We introduce FindingEmo, a new image dataset containing annotations for 25k images, specifically tailored to Emotion Recognition. Contrary to existing datasets, it focuses on complex scenes depicting multiple people in various naturalistic, social settings, with images being annotated as a whole, thereby going beyond the traditional focus on faces or single individuals. Annotated dimensions include Valence, Arousal and Emotion label, with annotations gathered using Prolific. Together with the annotations, we release the list of URLs pointing to the original images, as well as all associated source code.

The process of annotating data within the legal sector is filled with distinct challenges that differ from other fields, primarily due to the inherent complexities of legal language and documentation. The initial task usually involves selecting an appropriate raw dataset that captures the intricate aspects of legal texts. Following this, extracting text becomes a complicated task, as legal documents often have complex structures, footnotes, references, and unique terminology. The importance of data cleaning is magnified in this context, ensuring that redundant information is eliminated while maintaining crucial legal details and context. Creating comprehensive yet straightforward annotation guidelines is imperative, as these guidelines serve as the road map for maintaining uniformity and addressing the subtle nuances of legal terminology. Another critical aspect is the involvement of legal professionals in the annotation process. Their expertise is valuable in ensuring that the data not only remains contextually accurate but also adheres to prevailing legal standards and interpretations. This paper provides an expanded view of these challenges and aims to offer a foundational understanding and guidance for researchers and professionals engaged in legal data annotation projects. In addition, we provide links to our created and fine-tuned datasets and language models. These resources are outcomes of our discussed projects and solutions to challenges faced while working on them.

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

We introduce S2ORC, a large corpus of 81.1M English-language academic papers spanning many academic disciplines. The corpus consists of rich metadata, paper abstracts, resolved bibliographic references, as well as structured full text for 8.1M open access papers. Full text is annotated with automatically-detected inline mentions of citations, figures, and tables, each linked to their corresponding paper objects. In S2ORC, we aggregate papers from hundreds of academic publishers and digital archives into a unified source, and create the largest publicly-available collection of machine-readable academic text to date. We hope this resource will facilitate research and development of tools and tasks for text mining over academic text.

Large-scale datasets are essential to modern day deep learning. Advocates argue that understanding these methods requires dataset transparency (e.g. "dataset curation, motivation, composition, collection process, etc..."). However, almost no one has suggested the release of the detailed definitions and visual category examples provided to annotators - information critical to understanding the structure of the annotations present in each dataset. These labels are at the heart of public datasets, yet few datasets include the instructions that were used to generate them. We introduce a new task, Labeling Instruction Generation, to address missing publicly available labeling instructions. In Labeling Instruction Generation, we take a reasonably annotated dataset and: 1) generate a set of examples that are visually representative of each category in the dataset; 2) provide a text label that corresponds to each of the examples. We introduce a framework that requires no model training to solve this task and includes a newly created rapid retrieval system that leverages a large, pre-trained vision and language model. This framework acts as a proxy to human annotators that can help to both generate a final labeling instruction set and evaluate its quality. Our framework generates multiple diverse visual and text representations of dataset categories. The optimized instruction set outperforms our strongest baseline across 5 folds by 7.06 mAP for NuImages and 12.9 mAP for COCO.

We present ShapeNet: a richly-annotated, large-scale repository of shapes represented by 3D CAD models of objects. ShapeNet contains 3D models from a multitude of semantic categories and organizes them under the WordNet taxonomy. It is a collection of datasets providing many semantic annotations for each 3D model such as consistent rigid alignments, parts and bilateral symmetry planes, physical sizes, keywords, as well as other planned annotations. Annotations are made available through a public web-based interface to enable data visualization of object attributes, promote data-driven geometric analysis, and provide a large-scale quantitative benchmark for research in computer graphics and vision. At the time of this technical report, ShapeNet has indexed more than 3,000,000 models, 220,000 models out of which are classified into 3,135 categories (WordNet synsets). In this report we describe the ShapeNet effort as a whole, provide details for all currently available datasets, and summarize future plans.

Foundation models, pre-trained on a large amount of data have demonstrated impressive zero-shot capabilities in various downstream tasks. However, in object detection and instance segmentation, two fundamental computer vision tasks heavily reliant on extensive human annotations, foundation models such as SAM and DINO struggle to achieve satisfactory performance. In this study, we reveal that the devil is in the object boundary, i.e., these foundation models fail to discern boundaries between individual objects. For the first time, we probe that CLIP, which has never accessed any instance-level annotations, can provide a highly beneficial and strong instance-level boundary prior in the clustering results of its particular intermediate layer. Following this surprising observation, we propose Zip which Zips up CLip and SAM in a novel classification-first-then-discovery pipeline, enabling annotation-free, complex-scene-capable, open-vocabulary object detection and instance segmentation. Our Zip significantly boosts SAM's mask AP on COCO dataset by 12.5% and establishes state-of-the-art performance in various settings, including training-free, self-training, and label-efficient finetuning. Furthermore, annotation-free Zip even achieves comparable performance to the best-performing open-vocabulary object detecters using base annotations. Code is released at https://github.com/ChengShiest/Zip-Your-CLIP

Column type annotation is the task of annotating the columns of a relational table with the semantic type of the values contained in each column. Column type annotation is an important pre-processing step for data search and data integration in the context of data lakes. State-of-the-art column type annotation methods either rely on matching table columns to properties of a knowledge graph or fine-tune pre-trained language models such as BERT for column type annotation. In this work, we take a different approach and explore using ChatGPT for column type annotation. We evaluate different prompt designs in zero- and few-shot settings and experiment with providing task definitions and detailed instructions to the model. We further implement a two-step table annotation pipeline which first determines the class of the entities described in the table and depending on this class asks ChatGPT to annotate columns using only the relevant subset of the overall vocabulary. Using instructions as well as the two-step pipeline, ChatGPT reaches F1 scores of over 85% in zero- and one-shot setups. To reach a similar F1 score a RoBERTa model needs to be fine-tuned with 356 examples. This comparison shows that ChatGPT is able deliver competitive results for the column type annotation task given no or only a minimal amount of task-specific demonstrations.

Foundational Hebrew NLP tasks such as segmentation, tagging and parsing, have relied to date on various versions of the Hebrew Treebank (HTB, Sima'an et al. 2001). However, the data in HTB, a single-source newswire corpus, is now over 30 years old, and does not cover many aspects of contemporary Hebrew on the web. This paper presents a new, freely available UD treebank of Hebrew stratified from a range of topics selected from Hebrew Wikipedia. In addition to introducing the corpus and evaluating the quality of its annotations, we deploy automatic validation tools based on grew (Guillaume, 2021), and conduct the first cross domain parsing experiments in Hebrew. We obtain new state-of-the-art (SOTA) results on UD NLP tasks, using a combination of the latest language modelling and some incremental improvements to existing transformer based approaches. We also release a new version of the UD HTB matching annotation scheme updates from our new corpus.

Despite the impressive performance on information-seeking tasks, large language models (LLMs) still struggle with hallucinations. Attributed LLMs, which augment generated text with in-line citations, have shown potential in mitigating hallucinations and improving verifiability. However, current approaches suffer from suboptimal citation quality due to their reliance on in-context learning. Furthermore, the practice of citing only coarse document identifiers makes it challenging for users to perform fine-grained verification. In this work, we introduce FRONT, a training framework designed to teach LLMs to generate Fine-Grained Grounded Citations. By grounding model outputs in fine-grained supporting quotes, these quotes guide the generation of grounded and consistent responses, not only improving citation quality but also facilitating fine-grained verification. Experiments on the ALCE benchmark demonstrate the efficacy of FRONT in generating superior grounded responses and highly supportive citations. With LLaMA-2-7B, the framework significantly outperforms all the baselines, achieving an average of 14.21% improvement in citation quality across all datasets, even surpassing ChatGPT.

Automatic medical text simplification can assist providers with patient-friendly communication and make medical texts more accessible, thereby improving health literacy. But curating a quality corpus for this task requires the supervision of medical experts. In this work, we present Med-EASi (textbf{Med}ical dataset for textbf{E}laborative and textbf{A}bstractive textbf{Si}mplification), a uniquely crowdsourced and finely annotated dataset for supervised simplification of short medical texts. Its expert-layman-AI collaborative annotations facilitate controllability over text simplification by marking four kinds of textual transformations: elaboration, replacement, deletion, and insertion. To learn medical text simplification, we fine-tune T5-large with four different styles of input-output combinations, leading to two control-free and two controllable versions of the model. We add two types of controllability into text simplification, by using a multi-angle training approach: position-aware, which uses in-place annotated inputs and outputs, and position-agnostic, where the model only knows the contents to be edited, but not their positions. Our results show that our fine-grained annotations improve learning compared to the unannotated baseline. Furthermore, position-aware control generates better simplification than the position-agnostic one. The data and code are available at https://github.com/Chandrayee/CTRL-SIMP.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

Many recent approaches to natural language tasks are built on the remarkable abilities of large language models. Large language models can perform in-context learning, where they learn a new task from a few task demonstrations, without any parameter updates. This work examines the implications of in-context learning for the creation of datasets for new natural language tasks. Departing from recent in-context learning methods, we formulate an annotation-efficient, two-step framework: selective annotation that chooses a pool of examples to annotate from unlabeled data in advance, followed by prompt retrieval that retrieves task examples from the annotated pool at test time. Based on this framework, we propose an unsupervised, graph-based selective annotation method, voke-k, to select diverse, representative examples to annotate. Extensive experiments on 10 datasets (covering classification, commonsense reasoning, dialogue, and text/code generation) demonstrate that our selective annotation method improves the task performance by a large margin. On average, vote-k achieves a 12.9%/11.4% relative gain under an annotation budget of 18/100, as compared to randomly selecting examples to annotate. Compared to state-of-the-art supervised finetuning approaches, it yields similar performance with 10-100x less annotation cost across 10 tasks. We further analyze the effectiveness of our framework in various scenarios: language models with varying sizes, alternative selective annotation methods, and cases where there is a test data domain shift. We hope that our studies will serve as a basis for data annotations as large language models are increasingly applied to new tasks. Our code is available at https://github.com/HKUNLP/icl-selective-annotation.

Empirical methods in geoparsing have thus far lacked a standard evaluation framework describing the task, metrics and data used to compare state-of-the-art systems. Evaluation is further made inconsistent, even unrepresentative of real-world usage by the lack of distinction between the different types of toponyms, which necessitates new guidelines, a consolidation of metrics and a detailed toponym taxonomy with implications for Named Entity Recognition (NER) and beyond. To address these deficiencies, our manuscript introduces a new framework in three parts. Part 1) Task Definition: clarified via corpus linguistic analysis proposing a fine-grained Pragmatic Taxonomy of Toponyms. Part 2) Metrics: discussed and reviewed for a rigorous evaluation including recommendations for NER/Geoparsing practitioners. Part 3) Evaluation Data: shared via a new dataset called GeoWebNews to provide test/train examples and enable immediate use of our contributions. In addition to fine-grained Geotagging and Toponym Resolution (Geocoding), this dataset is also suitable for prototyping and evaluating machine learning NLP models.

This paper introduces the first version of the NUBes corpus (Negation and Uncertainty annotations in Biomedical texts in Spanish). The corpus is part of an on-going research and currently consists of 29,682 sentences obtained from anonymised health records annotated with negation and uncertainty. The article includes an exhaustive comparison with similar corpora in Spanish, and presents the main annotation and design decisions. Additionally, we perform preliminary experiments using deep learning algorithms to validate the annotated dataset. As far as we know, NUBes is the largest publicly available corpus for negation in Spanish and the first that also incorporates the annotation of speculation cues, scopes, and events.

The web provides a rich, open-domain environment with textual, structural, and spatial properties. We propose a new task for grounding language in this environment: given a natural language command (e.g., "click on the second article"), choose the correct element on the web page (e.g., a hyperlink or text box). We collected a dataset of over 50,000 commands that capture various phenomena such as functional references (e.g. "find who made this site"), relational reasoning (e.g. "article by john"), and visual reasoning (e.g. "top-most article"). We also implemented and analyzed three baseline models that capture different phenomena present in the dataset.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

People often utilise online media (e.g., Facebook, Reddit) as a platform to express their psychological distress and seek support. State-of-the-art NLP techniques demonstrate strong potential to automatically detect mental health issues from text. Research suggests that mental health issues are reflected in emotions (e.g., sadness) indicated in a person's choice of language. Therefore, we developed a novel emotion-annotated mental health corpus (EmoMent), consisting of 2802 Facebook posts (14845 sentences) extracted from two South Asian countries - Sri Lanka and India. Three clinical psychology postgraduates were involved in annotating these posts into eight categories, including 'mental illness' (e.g., depression) and emotions (e.g., 'sadness', 'anger'). EmoMent corpus achieved 'very good' inter-annotator agreement of 98.3% (i.e. % with two or more agreement) and Fleiss' Kappa of 0.82. Our RoBERTa based models achieved an F1 score of 0.76 and a macro-averaged F1 score of 0.77 for the first task (i.e. predicting a mental health condition from a post) and the second task (i.e. extent of association of relevant posts with the categories defined in our taxonomy), respectively.

The Open Images Dataset contains approximately 9 million images and is a widely accepted dataset for computer vision research. As is common practice for large datasets, the annotations are not exhaustive, with bounding boxes and attribute labels for only a subset of the classes in each image. In this paper, we present a new set of annotations on a subset of the Open Images dataset called the MIAP (More Inclusive Annotations for People) subset, containing bounding boxes and attributes for all of the people visible in those images. The attributes and labeling methodology for the MIAP subset were designed to enable research into model fairness. In addition, we analyze the original annotation methodology for the person class and its subclasses, discussing the resulting patterns in order to inform future annotation efforts. By considering both the original and exhaustive annotation sets, researchers can also now study how systematic patterns in training annotations affect modeling.

Besides the COVID-19 pandemic and political upheaval in the US, 2020 was also the year in which neural volume rendering exploded onto the scene, triggered by the impressive NeRF paper by Mildenhall et al. (2020). Both of us have tried to capture this excitement, Frank on a blog post (Dellaert, 2020) and Yen-Chen in a Github collection (Yen-Chen, 2020). This note is an annotated bibliography of the relevant papers, and we posted the associated bibtex file on the repository.

Automated surgical instrument localization is an important technology to understand the surgical process and in order to analyze them to provide meaningful guidance during surgery or surgical index after surgery to the surgeon. We introduce a new dataset that reflects the kinematic characteristics of surgical instruments for automated surgical instrument localization of surgical videos. The hSDB(hutom Surgery DataBase)-instrument dataset consists of instrument localization information from 24 cases of laparoscopic cholecystecomy and 24 cases of robotic gastrectomy. Localization information for all instruments is provided in the form of a bounding box for object detection. To handle class imbalance problem between instruments, synthesized instruments modeled in Unity for 3D models are included as training data. Besides, for 3D instrument data, a polygon annotation is provided to enable instance segmentation of the tool. To reflect the kinematic characteristics of all instruments, they are annotated with head and body parts for laparoscopic instruments, and with head, wrist, and body parts for robotic instruments separately. Annotation data of assistive tools (specimen bag, needle, etc.) that are frequently used for surgery are also included. Moreover, we provide statistical information on the hSDB-instrument dataset and the baseline localization performances of the object detection networks trained by the MMDetection library and resulting analyses.

The task of annotating data into concise summaries poses a significant challenge across various domains, frequently requiring the allocation of significant time and specialized knowledge by human experts. Despite existing efforts to use large language models for annotation tasks, significant problems such as limited applicability to unlabeled data, the absence of self-supervised methods, and the lack of focus on complex structured data still persist. In this work, we propose a GPT self-supervision annotation method, which embodies a generating-recovering paradigm that leverages the one-shot learning capabilities of the Generative Pretrained Transformer (GPT). The proposed approach comprises a one-shot tuning phase followed by a generation phase. In the one-shot tuning phase, we sample a data from the support set as part of the prompt for GPT to generate a textual summary, which is then used to recover the original data. The alignment score between the recovered and original data serves as a self-supervision navigator to refine the process. In the generation stage, the optimally selected one-shot sample serves as a template in the prompt and is applied to generating summaries from challenging datasets. The annotation performance is evaluated by tuning several human feedback reward networks and by calculating alignment scores between original and recovered data at both sentence and structure levels. Our self-supervised annotation method consistently achieves competitive scores, convincingly demonstrating its robust strength in various data-to-summary annotation tasks.

During natural and man-made disasters, people use social media platforms such as Twitter to post textual and multime- dia content to report updates about injured or dead people, infrastructure damage, and missing or found people among other information types. Studies have revealed that this on- line information, if processed timely and effectively, is ex- tremely useful for humanitarian organizations to gain situational awareness and plan relief operations. In addition to the analysis of textual content, recent studies have shown that imagery content on social media can boost disaster response significantly. Despite extensive research that mainly focuses on textual content to extract useful information, limited work has focused on the use of imagery content or the combination of both content types. One of the reasons is the lack of labeled imagery data in this domain. Therefore, in this paper, we aim to tackle this limitation by releasing a large multi-modal dataset collected from Twitter during different natural disasters. We provide three types of annotations, which are useful to address a number of crisis response and management tasks for different humanitarian organizations.

Foundation Models (FMs) have demonstrated unprecedented capabilities including zero-shot learning, high fidelity data synthesis, and out of domain generalization. However, as we show in this paper, FMs still have poor out-of-the-box performance on expert tasks (e.g. retrieval of car manuals technical illustrations from language queries), data for which is either unseen or belonging to a long-tail part of the data distribution of the huge datasets used for FM pre-training. This underlines the necessity to explicitly evaluate and finetune FMs on such expert tasks, arguably ones that appear the most in practical real-world applications. In this paper, we propose a first of its kind FETA benchmark built around the task of teaching FMs to understand technical documentation, via learning to match their graphical illustrations to corresponding language descriptions. Our FETA benchmark focuses on text-to-image and image-to-text retrieval in public car manuals and sales catalogue brochures. FETA is equipped with a procedure for completely automatic annotation extraction (code would be released upon acceptance), allowing easy extension of FETA to more documentation types and application domains in the future. Our automatic annotation leads to an automated performance metric shown to be consistent with metrics computed on human-curated annotations (also released). We provide multiple baselines and analysis of popular FMs on FETA leading to several interesting findings that we believe would be very valuable to the FM community, paving the way towards real-world application of FMs for practical expert tasks currently 'overlooked' by standard benchmarks focusing on common objects.

We present the development of a dataset for Kazakh named entity recognition. The dataset was built as there is a clear need for publicly available annotated corpora in Kazakh, as well as annotation guidelines containing straightforward--but rigorous--rules and examples. The dataset annotation, based on the IOB2 scheme, was carried out on television news text by two native Kazakh speakers under the supervision of the first author. The resulting dataset contains 112,702 sentences and 136,333 annotations for 25 entity classes. State-of-the-art machine learning models to automatise Kazakh named entity recognition were also built, with the best-performing model achieving an exact match F1-score of 97.22% on the test set. The annotated dataset, guidelines, and codes used to train the models are freely available for download under the CC BY 4.0 licence from https://github.com/IS2AI/KazNERD.

Memes are the new-age conveyance mechanism for humor on social media sites. Memes often include an image and some text. Memes can be used to promote disinformation or hatred, thus it is crucial to investigate in details. We introduce Memotion 3, a new dataset with 10,000 annotated memes. Unlike other prevalent datasets in the domain, including prior iterations of Memotion, Memotion 3 introduces Hindi-English Codemixed memes while prior works in the area were limited to only the English memes. We describe the Memotion task, the data collection and the dataset creation methodologies. We also provide a baseline for the task. The baseline code and dataset will be made available at https://github.com/Shreyashm16/Memotion-3.0

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Annotated data plays a critical role in Natural Language Processing (NLP) in training models and evaluating their performance. Given recent developments in Large Language Models (LLMs), models such as ChatGPT demonstrate zero-shot capability on many text-annotation tasks, comparable with or even exceeding human annotators. Such LLMs can serve as alternatives for manual annotation, due to lower costs and higher scalability. However, limited work has leveraged LLMs as complementary annotators, nor explored how annotation work is best allocated among humans and LLMs to achieve both quality and cost objectives. We propose CoAnnotating, a novel paradigm for Human-LLM co-annotation of unstructured texts at scale. Under this framework, we utilize uncertainty to estimate LLMs' annotation capability. Our empirical study shows CoAnnotating to be an effective means to allocate work from results on different datasets, with up to 21% performance improvement over random baseline. For code implementation, see https://github.com/SALT-NLP/CoAnnotating.

Data annotation is an essential step for constructing new datasets. However, the conventional approach of data annotation through crowdsourcing is both time-consuming and expensive. In addition, the complexity of this process increases when dealing with low-resource languages owing to the difference in the language pool of crowdworkers. To address these issues, this study proposes an autonomous annotation method by utilizing large language models, which have been recently demonstrated to exhibit remarkable performance. Through our experiments, we demonstrate that the proposed method is not just cost-efficient but also applicable for low-resource language annotation. Additionally, we constructed an image captioning dataset using our approach and are committed to open this dataset for future study. We have opened our source code for further study and reproducibility.

In large organisations, identifying experts on a given topic is crucial in leveraging the internal knowledge spread across teams and departments. So-called enterprise expert retrieval systems automatically discover and structure employees' expertise based on the vast amount of heterogeneous data available about them and the work they perform. Evaluating these systems requires comprehensive ground truth expert annotations, which are hard to obtain. Therefore, the annotation process typically relies on automated recommendations of knowledge areas to validate. This case study provides an analysis of how these recommendations can impact the evaluation of expert finding systems. We demonstrate on a popular benchmark that system-validated annotations lead to overestimated performance of traditional term-based retrieval models and even invalidate comparisons with more recent neural methods. We also augment knowledge areas with synonyms to uncover a strong bias towards literal mentions of their constituent words. Finally, we propose constraints to the annotation process to prevent these biased evaluations, and show that this still allows annotation suggestions of high utility. These findings should inform benchmark creation or selection for expert finding, to guarantee meaningful comparison of methods.

Textual domain is a crucial property within the Natural Language Processing (NLP) community due to its effects on downstream model performance. The concept itself is, however, loosely defined and, in practice, refers to any non-typological property, such as genre, topic, medium or style of a document. We investigate the core notion of domains via human proficiency in identifying related intrinsic textual properties, specifically the concepts of genre (communicative purpose) and topic (subject matter). We publish our annotations in *TGeGUM*: A collection of 9.1k sentences from the GUM dataset (Zeldes, 2017) with single sentence and larger context (i.e., prose) annotations for one of 11 genres (source type), and its topic/subtopic as per the Dewey Decimal library classification system (Dewey, 1979), consisting of 10/100 hierarchical topics of increased granularity. Each instance is annotated by three annotators, for a total of 32.7k annotations, allowing us to examine the level of human disagreement and the relative difficulty of each annotation task. With a Fleiss' kappa of at most 0.53 on the sentence level and 0.66 at the prose level, it is evident that despite the ubiquity of domains in NLP, there is little human consensus on how to define them. By training classifiers to perform the same task, we find that this uncertainty also extends to NLP models.

Anthropogenic ecological crisis constitutes a significant challenge that all within the academy must urgently face, including the Natural Language Processing (NLP) community. While recent years have seen increasing work revolving around climate-centric discourse, crucial environmental and ecological topics outside of climate change remain largely unaddressed, despite their prominent importance. Mainstream NLP tasks, such as sentiment analysis, dominate the scene, but there remains an untouched space in the literature involving the analysis of environmental impacts of certain events and practices. To address this gap, this paper presents EcoVerse, an annotated English Twitter dataset of 3,023 tweets spanning a wide spectrum of environmental topics. We propose a three-level annotation scheme designed for Eco-Relevance Classification, Stance Detection, and introducing an original approach for Environmental Impact Analysis. We detail the data collection, filtering, and labeling process that led to the creation of the dataset. Remarkable Inter-Annotator Agreement indicates that the annotation scheme produces consistent annotations of high quality. Subsequent classification experiments using BERT-based models, including ClimateBERT, are presented. These yield encouraging results, while also indicating room for a model specifically tailored for environmental texts. The dataset is made freely available to stimulate further research.

Identification of named entities from legal texts is an essential building block for developing other legal Artificial Intelligence applications. Named Entities in legal texts are slightly different and more fine-grained than commonly used named entities like Person, Organization, Location etc. In this paper, we introduce a new corpus of 46545 annotated legal named entities mapped to 14 legal entity types. The Baseline model for extracting legal named entities from judgment text is also developed.

We introduce a large-scale dataset of math word problems and an interpretable neural math problem solver that learns to map problems to operation programs. Due to annotation challenges, current datasets in this domain have been either relatively small in scale or did not offer precise operational annotations over diverse problem types. We introduce a new representation language to model precise operation programs corresponding to each math problem that aim to improve both the performance and the interpretability of the learned models. Using this representation language, our new dataset, MathQA, significantly enhances the AQuA dataset with fully-specified operational programs. We additionally introduce a neural sequence-to-program model enhanced with automatic problem categorization. Our experiments show improvements over competitive baselines in our MathQA as well as the AQuA dataset. The results are still significantly lower than human performance indicating that the dataset poses new challenges for future research. Our dataset is available at: https://math-qa.github.io/math-QA/

We present an overview of the FIGNEWS shared task, organized as part of the ArabicNLP 2024 conference co-located with ACL 2024. The shared task addresses bias and propaganda annotation in multilingual news posts. We focus on the early days of the Israel War on Gaza as a case study. The task aims to foster collaboration in developing annotation guidelines for subjective tasks by creating frameworks for analyzing diverse narratives highlighting potential bias and propaganda. In a spirit of fostering and encouraging diversity, we address the problem from a multilingual perspective, namely within five languages: English, French, Arabic, Hebrew, and Hindi. A total of 17 teams participated in two annotation subtasks: bias (16 teams) and propaganda (6 teams). The teams competed in four evaluation tracks: guidelines development, annotation quality, annotation quantity, and consistency. Collectively, the teams produced 129,800 data points. Key findings and implications for the field are discussed.

This paper presents Wojood, a corpus for Arabic nested Named Entity Recognition (NER). Nested entities occur when one entity mention is embedded inside another entity mention. Wojood consists of about 550K Modern Standard Arabic (MSA) and dialect tokens that are manually annotated with 21 entity types including person, organization, location, event and date. More importantly, the corpus is annotated with nested entities instead of the more common flat annotations. The data contains about 75K entities and 22.5% of which are nested. The inter-annotator evaluation of the corpus demonstrated a strong agreement with Cohen's Kappa of 0.979 and an F1-score of 0.976. To validate our data, we used the corpus to train a nested NER model based on multi-task learning and AraBERT (Arabic BERT). The model achieved an overall micro F1-score of 0.884. Our corpus, the annotation guidelines, the source code and the pre-trained model are publicly available.

This handbook is a hands-on guide on how to approach text annotation tasks. It provides a gentle introduction to the topic, an overview of theoretical concepts as well as practical advice. The topics covered are mostly technical, but business, ethical and regulatory issues are also touched upon. The focus lies on readability and conciseness rather than completeness and scientific rigor. Experience with annotation and knowledge of machine learning are useful but not required. The document may serve as a primer or reference book for a wide range of professions such as team leaders, project managers, IT architects, software developers and machine learning engineers.

When a human requests an LLM to complete a coding task using functionality from a large code repository, how do we provide context from the repo to the LLM? One approach is to add the entire repo to the LLM's context window. However, most tasks involve only fraction of symbols from a repo, longer contexts are detrimental to the LLM's reasoning abilities, and context windows are not unlimited. Alternatively, we could emulate the human ability to navigate a large repo, pick out the right functionality, and form a plan to solve the task. We propose MutaGReP (Mutation-guided Grounded Repository Plan Search), an approach to search for plans that decompose a user request into natural language steps grounded in the codebase. MutaGReP performs neural tree search in plan space, exploring by mutating plans and using a symbol retriever for grounding. On the challenging LongCodeArena benchmark, our plans use less than 5% of the 128K context window for GPT-4o but rival the coding performance of GPT-4o with a context window filled with the repo. Plans produced by MutaGReP allow Qwen 2.5 Coder 32B and 72B to match the performance of GPT-4o with full repo context and enable progress on the hardest LongCodeArena tasks. Project page: zaidkhan.me/MutaGReP

Generative large language models (LLMs) can be a powerful tool for augmenting text annotation procedures, but their performance varies across annotation tasks due to prompt quality, text data idiosyncrasies, and conceptual difficulty. Because these challenges will persist even as LLM technology improves, we argue that any automated annotation process using an LLM must validate the LLM's performance against labels generated by humans. To this end, we outline a workflow to harness the annotation potential of LLMs in a principled, efficient way. Using GPT-4, we validate this approach by replicating 27 annotation tasks across 11 datasets from recent social science articles in high-impact journals. We find that LLM performance for text annotation is promising but highly contingent on both the dataset and the type of annotation task, which reinforces the necessity to validate on a task-by-task basis. We make available easy-to-use software designed to implement our workflow and streamline the deployment of LLMs for automated annotation.

Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) in order to answer correctly that "the person is riding a horse-drawn carriage". In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 100K images where each image has an average of 21 objects, 18 attributes, and 18 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answers.

Due to reasons of convenience and lack of tech literacy, transliteration (i.e., Romanizing native scripts instead of using localization tools) is eminently prevalent in the context of low-resource languages such as Sinhala, which have their own writing script. In this study, our focus is on Romanized Sinhala transliteration. We propose two methods to address this problem: Our baseline is a rule-based method, which is then compared against our second method where we approach the transliteration problem as a sequence-to-sequence task akin to the established Neural Machine Translation (NMT) task. For the latter, we propose a Transformer-based Encode-Decoder solution. We witnessed that the Transformer-based method could grab many ad-hoc patterns within the Romanized scripts compared to the rule-based method. The code base associated with this paper is available on GitHub - https://github.com/kasunw22/Sinhala-Transliterator/

Understanding causal narratives communicated in clinical notes can help make strides towards personalized healthcare. Extracted causal information from clinical notes can be combined with structured EHR data such as patients' demographics, diagnoses, and medications. This will enhance healthcare providers' ability to identify aspects of a patient's story communicated in the clinical notes and help make more informed decisions. In this work, we propose annotation guidelines, develop an annotated corpus and provide baseline scores to identify types and direction of causal relations between a pair of biomedical concepts in clinical notes; communicated implicitly or explicitly, identified either in a single sentence or across multiple sentences. We annotate a total of 2714 de-identified examples sampled from the 2018 n2c2 shared task dataset and train four different language model based architectures. Annotation based on our guidelines achieved a high inter-annotator agreement i.e. Fleiss' kappa (kappa) score of 0.72, and our model for identification of causal relations achieved a macro F1 score of 0.56 on the test data. The high inter-annotator agreement for clinical text shows the quality of our annotation guidelines while the provided baseline F1 score sets the direction for future research towards understanding narratives in clinical texts.

Scientific article summarization is challenging: large, annotated corpora are not available, and the summary should ideally include the article's impacts on research community. This paper provides novel solutions to these two challenges. We 1) develop and release the first large-scale manually-annotated corpus for scientific papers (on computational linguistics) by enabling faster annotation, and 2) propose summarization methods that integrate the authors' original highlights (abstract) and the article's actual impacts on the community (citations), to create comprehensive, hybrid summaries. We conduct experiments to demonstrate the efficacy of our corpus in training data-driven models for scientific paper summarization and the advantage of our hybrid summaries over abstracts and traditional citation-based summaries. Our large annotated corpus and hybrid methods provide a new framework for scientific paper summarization research.

There are substantial instructional videos on the Internet, which provide us tutorials for completing various tasks. Existing instructional video datasets only focus on specific steps at the video level, lacking experiential guidelines at the task level, which can lead to beginners struggling to learn new tasks due to the lack of relevant experience. Moreover, the specific steps without guidelines are trivial and unsystematic, making it difficult to provide a clear tutorial. To address these problems, we present the GUIDE (Guideline-Guided) dataset, which contains 3.5K videos of 560 instructional tasks in 8 domains related to our daily life. Specifically, we annotate each instructional task with a guideline, representing a common pattern shared by all task-related videos. On this basis, we annotate systematic specific steps, including their associated guideline steps, specific step descriptions and timestamps. Our proposed benchmark consists of three sub-tasks to evaluate comprehension ability of models: (1) Step Captioning: models have to generate captions for specific steps from videos. (2) Guideline Summarization: models have to mine the common pattern in task-related videos and summarize a guideline from them. (3) Guideline-Guided Captioning: models have to generate captions for specific steps under the guide of guideline. We evaluate plenty of foundation models with GUIDE and perform in-depth analysis. Given the diversity and practicality of GUIDE, we believe that it can be used as a better benchmark for instructional video comprehension.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

The DocRED dataset is one of the most popular and widely used benchmarks for document-level relation extraction (RE). It adopts a recommend-revise annotation scheme so as to have a large-scale annotated dataset. However, we find that the annotation of DocRED is incomplete, i.e., false negative samples are prevalent. We analyze the causes and effects of the overwhelming false negative problem in the DocRED dataset. To address the shortcoming, we re-annotate 4,053 documents in the DocRED dataset by adding the missed relation triples back to the original DocRED. We name our revised DocRED dataset Re-DocRED. We conduct extensive experiments with state-of-the-art neural models on both datasets, and the experimental results show that the models trained and evaluated on our Re-DocRED achieve performance improvements of around 13 F1 points. Moreover, we conduct a comprehensive analysis to identify the potential areas for further improvement. Our dataset is publicly available at https://github.com/tonytan48/Re-DocRED.

User interface understanding with vision-language models has received much attention due to its potential for enabling next-generation software automation. However, existing UI datasets either only provide large-scale context-free element annotations or contextualized functional descriptions for elements at a much smaller scale. In this work, we propose the pipeline for automatically annotating UI elements with detailed functionality descriptions at scale. Specifically, we leverage large language models (LLMs) to infer element functionality by comparing the UI content changes before and after simulated interactions with specific UI elements. To improve annotation quality, we propose LLM-aided rejection and verification, eliminating invalid and incorrect annotations without human labor. We construct an -704k dataset using the proposed pipeline, featuring multi-resolution, multi-device screenshots, diverse data domains, and detailed functionality annotations that have never been provided by previous datasets. Human evaluation shows that the AutoGUI pipeline achieves annotation correctness comparable to trained human annotators. Extensive experimental results show that our -704k dataset remarkably enhances VLM's UI grounding capabilities, exhibits significant scaling effects, and outperforms existing web pre-training data types. We envision AutoGUI as a scalable pipeline for generating massive data to build GUI-oriented VLMs. AutoGUI dataset can be viewed at this anonymous URL: https://autogui-project.github.io/.

Despite the huge success of Large Language Models (LLMs) in coding assistants like GitHub Copilot, these models struggle to understand the context present in the repository (e.g., imports, parent classes, files with similar names, etc.), thereby producing inaccurate code completions. This effect is more pronounced when using these assistants for repositories that the model has not seen during training, such as proprietary software or work-in-progress code projects. Recent work has shown the promise of using context from the repository during inference. In this work, we extend this idea and propose RepoFusion, a framework to train models to incorporate relevant repository context. Experiments on single-line code completion show that our models trained with repository context significantly outperform much larger code models as CodeGen-16B-multi (sim73times larger) and closely match the performance of the sim 70times larger StarCoderBase model that was trained with the Fill-in-the-Middle objective. We find these results to be a novel and compelling demonstration of the gains that training with repository context can bring. We carry out extensive ablation studies to investigate the impact of design choices such as context type, number of contexts, context length, and initialization within our framework. Lastly, we release Stack-Repo, a dataset of 200 Java repositories with permissive licenses and near-deduplicated files that are augmented with three types of repository contexts. Additionally, we are making available the code and trained checkpoints for our work. Our released resources can be found at https://huggingface.co/RepoFusion.

Named entity recognition is one of the cornerstones of Danish NLP, essential for language technology applications within both industry and research. However, Danish NER is inhibited by a lack of available datasets. As a consequence, no current models are capable of fine-grained named entity recognition, nor have they been evaluated for potential generalizability issues across datasets and domains. To alleviate these limitations, this paper introduces: 1) DANSK: a named entity dataset providing for high-granularity tagging as well as within-domain evaluation of models across a diverse set of domains; 2) DaCy 2.6.0 that includes three generalizable models with fine-grained annotation; and 3) an evaluation of current state-of-the-art models' ability to generalize across domains. The evaluation of existing and new models revealed notable performance discrepancies across domains, which should be addressed within the field. Shortcomings of the annotation quality of the dataset and its impact on model training and evaluation are also discussed. Despite these limitations, we advocate for the use of the new dataset DANSK alongside further work on the generalizability within Danish NER.

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of errorful and error-free parallel corpora. We design custom token-level transformations to map input tokens to target corrections. Our best single-model/ensemble GEC tagger achieves an F_{0.5} of 65.3/66.5 on CoNLL-2014 (test) and F_{0.5} of 72.4/73.6 on BEA-2019 (test). Its inference speed is up to 10 times as fast as a Transformer-based seq2seq GEC system. The code and trained models are publicly available.

Social Media platforms have offered invaluable opportunities for linguistic research. The availability of up-to-date data, coming from any part in the world, and coming from natural contexts, has allowed researchers to study language in real time. One of the fields that has made great use of social media platforms is Corpus Linguistics. There is currently a wide range of projects which have been able to successfully create corpora from social media. In this paper, we present the development and deployment of a linguistic corpus from Twitter posts in English, coming from 26 news agencies and 27 individuals. The main goal was to create a fully annotated English corpus for linguistic analysis. We include information on morphology and syntax, as well as NLP features such as tokenization, lemmas, and n- grams. The information is presented through a range of powerful visualisations for users to explore linguistic patterns in the corpus. With this tool, we aim to contribute to the area of language technologies applied to linguistic research.

This paper presents a new challenging information extraction task in the domain of materials science. We develop an annotation scheme for marking information on experiments related to solid oxide fuel cells in scientific publications, such as involved materials and measurement conditions. With this paper, we publish our annotation guidelines, as well as our SOFC-Exp corpus consisting of 45 open-access scholarly articles annotated by domain experts. A corpus and an inter-annotator agreement study demonstrate the complexity of the suggested named entity recognition and slot filling tasks as well as high annotation quality. We also present strong neural-network based models for a variety of tasks that can be addressed on the basis of our new data set. On all tasks, using BERT embeddings leads to large performance gains, but with increasing task complexity, adding a recurrent neural network on top seems beneficial. Our models will serve as competitive baselines in future work, and analysis of their performance highlights difficult cases when modeling the data and suggests promising research directions.

State-of-the-art language models (LMs) are notoriously susceptible to generating hallucinated information. Such inaccurate outputs not only undermine the reliability of these models but also limit their use and raise serious concerns about misinformation and propaganda. In this work, we focus on hallucinated book and article references and present them as the "model organism" of language model hallucination research, due to their frequent and easy-to-discern nature. We posit that if a language model cites a particular reference in its output, then it should ideally possess sufficient information about its authors and content, among other relevant details. Using this basic insight, we illustrate that one can identify hallucinated references without ever consulting any external resources, by asking a set of direct or indirect queries to the language model about the references. These queries can be considered as "consistency checks." Our findings highlight that while LMs, including GPT-4, often produce inconsistent author lists for hallucinated references, they also often accurately recall the authors of real references. In this sense, the LM can be said to "know" when it is hallucinating references. Furthermore, these findings show how hallucinated references can be dissected to shed light on their nature. Replication code and results can be found at https://github.com/microsoft/hallucinated-references.

Colonial archives are at the center of increased interest from a variety of perspectives, as they contain traces of historically marginalized people. Unfortunately, like most archives, they remain difficult to access due to significant persisting barriers. We focus here on one of them: the biases to be found in historical findings aids, such as indexes of person names, which remain in use to this day. In colonial archives, indexes can perpetuate silences by omitting to include mentions of historically marginalized persons. In order to overcome such limitations and pluralize the scope of existing finding aids, we propose using automated entity recognition. To this end, we contribute a fit-for-purpose annotation typology and apply it on the colonial archive of the Dutch East India Company (VOC). We release a corpus of nearly 70,000 annotations as a shared task, for which we provide baselines using state-of-the-art neural network models. Our work intends to stimulate further contributions in the direction of broadening access to (colonial) archives, integrating automation as a possible means to this end.

We present ToTTo, an open-domain English table-to-text dataset with over 120,000 training examples that proposes a controlled generation task: given a Wikipedia table and a set of highlighted table cells, produce a one-sentence description. To obtain generated targets that are natural but also faithful to the source table, we introduce a dataset construction process where annotators directly revise existing candidate sentences from Wikipedia. We present systematic analyses of our dataset and annotation process as well as results achieved by several state-of-the-art baselines. While usually fluent, existing methods often hallucinate phrases that are not supported by the table, suggesting that this dataset can serve as a useful research benchmark for high-precision conditional text generation.

Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several datasets have been released for the yet understudied materials science domain. However, these datasets focus on sub-problems such as parsing synthesis procedures or on sub-domains, e.g., solid oxide fuel cells. In this resource paper, we present MuLMS, a new dataset of 50 open-access articles, spanning seven sub-domains of materials science. The corpus has been annotated by domain experts with several layers ranging from named entities over relations to frame structures. We present competitive neural models for all tasks and demonstrate that multi-task training with existing related resources leads to benefits.

Online active learning is a paradigm in machine learning that aims to select the most informative data points to label from a data stream. The problem of minimizing the cost associated with collecting labeled observations has gained a lot of attention in recent years, particularly in real-world applications where data is only available in an unlabeled form. Annotating each observation can be time-consuming and costly, making it difficult to obtain large amounts of labeled data. To overcome this issue, many active learning strategies have been proposed in the last decades, aiming to select the most informative observations for labeling in order to improve the performance of machine learning models. These approaches can be broadly divided into two categories: static pool-based and stream-based active learning. Pool-based active learning involves selecting a subset of observations from a closed pool of unlabeled data, and it has been the focus of many surveys and literature reviews. However, the growing availability of data streams has led to an increase in the number of approaches that focus on online active learning, which involves continuously selecting and labeling observations as they arrive in a stream. This work aims to provide an overview of the most recently proposed approaches for selecting the most informative observations from data streams in real time. We review the various techniques that have been proposed and discuss their strengths and limitations, as well as the challenges and opportunities that exist in this area of research.

Quotation extraction and attribution are challenging tasks, aiming at determining the spans containing quotations and attributing each quotation to the original speaker. Applying this task to news data is highly related to fact-checking, media monitoring and news tracking. Direct quotations are more traceable and informative, and therefore of great significance among different types of quotations. Therefore, this paper introduces DirectQuote, a corpus containing 19,760 paragraphs and 10,279 direct quotations manually annotated from online news media. To the best of our knowledge, this is the largest and most complete corpus that focuses on direct quotations in news texts. We ensure that each speaker in the annotation can be linked to a specific named entity on Wikidata, benefiting various downstream tasks. In addition, for the first time, we propose several sequence labeling models as baseline methods to extract and attribute quotations simultaneously in an end-to-end manner.

Recent work has shown exciting promise in updating large language models with new memories, so as to replace obsolete information or add specialized knowledge. However, this line of work is predominantly limited to updating single associations. We develop MEMIT, a method for directly updating a language model with many memories, demonstrating experimentally that it can scale up to thousands of associations for GPT-J (6B) and GPT-NeoX (20B), exceeding prior work by orders of magnitude. Our code and data are at https://memit.baulab.info.

The comic domain is rapidly advancing with the development of single- and multi-page analysis and synthesis models. Recent benchmarks and datasets have been introduced to support and assess models' capabilities in tasks such as detection (panels, characters, text), linking (character re-identification and speaker identification), and analysis of comic elements (e.g., dialog transcription). However, to provide a comprehensive understanding of the storyline, a model must not only extract elements but also understand their relationships and generate highly informative captions. In this work, we propose a pipeline that leverages Vision-Language Models (VLMs) to obtain dense, grounded captions. To construct our pipeline, we introduce an attribute-retaining metric that assesses whether all important attributes are identified in the caption. Additionally, we created a densely annotated test set to fairly evaluate open-source VLMs and select the best captioning model according to our metric. Our pipeline generates dense captions with bounding boxes that are quantitatively and qualitatively superior to those produced by specifically trained models, without requiring any additional training. Using this pipeline, we annotated over 2 million panels across 13,000 books, which will be available on the project page https://github.com/emanuelevivoli/ComiCap.

Long-form article generation (LFAG) presents challenges such as maintaining logical consistency, comprehensive topic coverage, and narrative coherence across extended articles. Existing datasets often lack both the hierarchical structure and fine-grained annotation needed to effectively decompose tasks, resulting in shallow, disorganized article generation. To address these limitations, we introduce DeFine, a Decomposed and Fine-grained annotated dataset for long-form article generation. DeFine is characterized by its hierarchical decomposition strategy and the integration of domain-specific knowledge with multi-level annotations, ensuring granular control and enhanced depth in article generation. To construct the dataset, a multi-agent collaborative pipeline is proposed, which systematically segments the generation process into four parts: Data Miner, Cite Retreiver, Q&A Annotator and Data Cleaner. To validate the effectiveness of DeFine, we designed and tested three LFAG baselines: the web retrieval, the local retrieval, and the grounded reference. We fine-tuned the Qwen2-7b-Instruct model using the DeFine training dataset. The experimental results showed significant improvements in text quality, specifically in topic coverage, depth of information, and content fidelity. Our dataset publicly available to facilitate future research.

A database of images of approximately 960 unique plants belonging to 12 species at several growth stages is made publicly available. It comprises annotated RGB images with a physical resolution of roughly 10 pixels per mm. To standardise the evaluation of classification results obtained with the database, a benchmark based on f_{1} scores is proposed. The dataset is available at https://vision.eng.au.dk/plant-seedlings-dataset

We introduce RealKIE, a benchmark of five challenging datasets aimed at advancing key information extraction methods, with an emphasis on enterprise applications. The datasets include a diverse range of documents including SEC S1 Filings, US Non-disclosure Agreements, UK Charity Reports, FCC Invoices, and Resource Contracts. Each presents unique challenges: poor text serialization, sparse annotations in long documents, and complex tabular layouts. These datasets provide a realistic testing ground for key information extraction tasks like investment analysis and legal data processing. In addition to presenting these datasets, we offer an in-depth description of the annotation process, document processing techniques, and baseline modeling approaches. This contribution facilitates the development of NLP models capable of handling practical challenges and supports further research into information extraction technologies applicable to industry-specific problems. The annotated data and OCR outputs are available to download at https://indicodatasolutions.github.io/RealKIE/ code to reproduce the baselines will be available shortly.

The large amount of data available in social media, forums and websites motivates researches in several areas of Natural Language Processing, such as sentiment analysis. The popularity of the area due to its subjective and semantic characteristics motivates research on novel methods and approaches for classification. Hence, there is a high demand for datasets on different domains and different languages. This paper introduces TweetSentBR, a sentiment corpora for Brazilian Portuguese manually annotated with 15.000 sentences on TV show domain. The sentences were labeled in three classes (positive, neutral and negative) by seven annotators, following literature guidelines for ensuring reliability on the annotation. We also ran baseline experiments on polarity classification using three machine learning methods, reaching 80.99% on F-Measure and 82.06% on accuracy in binary classification, and 59.85% F-Measure and 64.62% on accuracy on three point classification.

We present DictaLM, a large-scale language model tailored for Modern Hebrew. Boasting 7B parameters, this model is predominantly trained on Hebrew-centric data. As a commitment to promoting research and development in the Hebrew language, we release both the foundation model and the instruct-tuned model under a Creative Commons license. Concurrently, we introduce DictaLM-Rab, another foundation model geared towards Rabbinic/Historical Hebrew. These foundation models serve as ideal starting points for fine-tuning various Hebrew-specific tasks, such as instruction, Q&A, sentiment analysis, and more. This release represents a preliminary step, offering an initial Hebrew LLM model for the Hebrew NLP community to experiment with.

The vast majority of existing datasets for Named Entity Recognition (NER) are built primarily on news, research papers and Wikipedia with a few exceptions, created from historical and literary texts. What is more, English is the main source for data for further labelling. This paper aims to fill in multiple gaps by creating a novel dataset "Razmecheno", gathered from the diary texts of the project "Prozhito" in Russian. Our dataset is of interest for multiple research lines: literary studies of diary texts, transfer learning from other domains, low-resource or cross-lingual named entity recognition. Razmecheno comprises 1331 sentences and 14119 tokens, sampled from diaries, written during the Perestroika. The annotation schema consists of five commonly used entity tags: person, characteristics, location, organisation, and facility. The labelling is carried out on the crowdsourcing platfrom Yandex.Toloka in two stages. First, workers selected sentences, which contain an entity of particular type. Second, they marked up entity spans. As a result 1113 entities were obtained. Empirical evaluation of Razmecheno is carried out with off-the-shelf NER tools and by fine-tuning pre-trained contextualized encoders. We release the annotated dataset for open access.

Continuity of care is crucial to ensuring positive health outcomes for patients discharged from an inpatient hospital setting, and improved information sharing can help. To share information, caregivers write discharge notes containing action items to share with patients and their future caregivers, but these action items are easily lost due to the lengthiness of the documents. In this work, we describe our creation of a dataset of clinical action items annotated over MIMIC-III, the largest publicly available dataset of real clinical notes. This dataset, which we call CLIP, is annotated by physicians and covers 718 documents representing 100K sentences. We describe the task of extracting the action items from these documents as multi-aspect extractive summarization, with each aspect representing a type of action to be taken. We evaluate several machine learning models on this task, and show that the best models exploit in-domain language model pre-training on 59K unannotated documents, and incorporate context from neighboring sentences. We also propose an approach to pre-training data selection that allows us to explore the trade-off between size and domain-specificity of pre-training datasets for this task.

We present a new dataset, Functional Map of the World (fMoW), which aims to inspire the development of machine learning models capable of predicting the functional purpose of buildings and land use from temporal sequences of satellite images and a rich set of metadata features. The metadata provided with each image enables reasoning about location, time, sun angles, physical sizes, and other features when making predictions about objects in the image. Our dataset consists of over 1 million images from over 200 countries. For each image, we provide at least one bounding box annotation containing one of 63 categories, including a "false detection" category. We present an analysis of the dataset along with baseline approaches that reason about metadata and temporal views. Our data, code, and pretrained models have been made publicly available.

The research described in this paper concerns automatic cyberbullying detection in social media. There are two goals to achieve: building a gold standard cyberbullying detection dataset and measuring the performance of the Samurai cyberbullying detection system. The Formspring dataset provided in a Kaggle competition was re-annotated as a part of the research. The annotation procedure is described in detail and, unlike many other recent data annotation initiatives, does not use Mechanical Turk for finding people willing to perform the annotation. The new annotation compared to the old one seems to be more coherent since all tested cyberbullying detection system performed better on the former. The performance of the Samurai system is compared with 5 commercial systems and one well-known machine learning algorithm, used for classifying textual content, namely Fasttext. It turns out that Samurai scores the best in all measures (accuracy, precision and recall), while Fasttext is the second-best performing algorithm.

Plant diseases pose significant threats to agriculture. It necessitates proper diagnosis and effective treatment to safeguard crop yields. To automate the diagnosis process, image segmentation is usually adopted for precisely identifying diseased regions, thereby advancing precision agriculture. Developing robust image segmentation models for plant diseases demands high-quality annotations across numerous images. However, existing plant disease datasets typically lack segmentation labels and are often confined to controlled laboratory settings, which do not adequately reflect the complexity of natural environments. Motivated by this fact, we established PlantSeg, a large-scale segmentation dataset for plant diseases. PlantSeg distinguishes itself from existing datasets in three key aspects. (1) Annotation type: Unlike the majority of existing datasets that only contain class labels or bounding boxes, each image in PlantSeg includes detailed and high-quality segmentation masks, associated with plant types and disease names. (2) Image source: Unlike typical datasets that contain images from laboratory settings, PlantSeg primarily comprises in-the-wild plant disease images. This choice enhances the practical applicability, as the trained models can be applied for integrated disease management. (3) Scale: PlantSeg is extensive, featuring 11,400 images with disease segmentation masks and an additional 8,000 healthy plant images categorized by plant type. Extensive technical experiments validate the high quality of PlantSeg's annotations. This dataset not only allows researchers to evaluate their image classification methods but also provides a critical foundation for developing and benchmarking advanced plant disease segmentation algorithms.

Precise geocoding and time normalization for text requires that location and time phrases be identified. Many state-of-the-art geoparsers and temporal parsers suffer from low recall. Categories commonly missed by parsers are: nouns used in a non- spatiotemporal sense, adjectival and adverbial phrases, prepositional phrases, and numerical phrases. We collected and annotated data set by querying commercial web searches API with such spatiotemporal expressions as were missed by state-of-the- art parsers. Due to the high cost of sentence annotation, active learning was used to label training data, and a new strategy was designed to better select training examples to reduce labeling cost. For the learning algorithm, we applied an average perceptron trained Featurized Hidden Markov Model (FHMM). Five FHMM instances were used to create an ensemble, with the output phrase selected by voting. Our ensemble model was tested on a range of sequential labeling tasks, and has shown competitive performance. Our contributions include (1) an new dataset annotated with named entities and expanded spatiotemporal expressions; (2) a comparison of inference algorithms for ensemble models showing the superior accuracy of Belief Propagation over Viterbi Decoding; (3) a new example re-weighting method for active ensemble learning that 'memorizes' the latest examples trained; (4) a spatiotemporal parser that jointly recognizes expanded spatiotemporal expressions as well as named entities.

In real-world data labeling applications, annotators often provide imperfect labels. It is thus common to employ multiple annotators to label data with some overlap between their examples. We study active learning in such settings, aiming to train an accurate classifier by collecting a dataset with the fewest total annotations. Here we propose ActiveLab, a practical method to decide what to label next that works with any classifier model and can be used in pool-based batch active learning with one or multiple annotators. ActiveLab automatically estimates when it is more informative to re-label examples vs. labeling entirely new ones. This is a key aspect of producing high quality labels and trained models within a limited annotation budget. In experiments on image and tabular data, ActiveLab reliably trains more accurate classifiers with far fewer annotations than a wide variety of popular active learning methods.

News headline generation is a crucial task in increasing productivity for both the readers and producers of news. This task can easily be aided by automated News headline-generation models. However, the presence of irrelevant headlines in scraped news articles results in sub-optimal performance of generation models. We propose that relevance-based headline classification can greatly aid the task of generating relevant headlines. Relevance-based headline classification involves categorizing news headlines based on their relevance to the corresponding news articles. While this task is well-established in English, it remains under-explored in low-resource languages like Telugu due to a lack of annotated data. To address this gap, we present TeClass, the first-ever human-annotated Telugu news headline classification dataset, containing 78,534 annotations across 26,178 article-headline pairs. We experiment with various baseline models and provide a comprehensive analysis of their results. We further demonstrate the impact of this work by fine-tuning various headline generation models using TeClass dataset. The headlines generated by the models fine-tuned on highly relevant article-headline pairs, showed about a 5 point increment in the ROUGE-L scores. To encourage future research, the annotated dataset as well as the annotation guidelines will be made publicly available.

In this paper we introduce a new publicly available dataset for verification against textual sources, FEVER: Fact Extraction and VERification. It consists of 185,445 claims generated by altering sentences extracted from Wikipedia and subsequently verified without knowledge of the sentence they were derived from. The claims are classified as Supported, Refuted or NotEnoughInfo by annotators achieving 0.6841 in Fleiss kappa. For the first two classes, the annotators also recorded the sentence(s) forming the necessary evidence for their judgment. To characterize the challenge of the dataset presented, we develop a pipeline approach and compare it to suitably designed oracles. The best accuracy we achieve on labeling a claim accompanied by the correct evidence is 31.87%, while if we ignore the evidence we achieve 50.91%. Thus we believe that FEVER is a challenging testbed that will help stimulate progress on claim verification against textual sources.

Despite the success of the Universal Dependencies (UD) project exemplified by its impressive language breadth, there is still a lack in `within-language breadth': most treebanks focus on standard languages. Even for German, the language with the most annotations in UD, so far no treebank exists for one of its language varieties spoken by over 10M people: Bavarian. To contribute to closing this gap, we present the first multi-dialect Bavarian treebank (MaiBaam) manually annotated with part-of-speech and syntactic dependency information in UD, covering multiple text genres (wiki, fiction, grammar examples, social, non-fiction). We highlight the morphosyntactic differences between the closely-related Bavarian and German and showcase the rich variability of speakers' orthographies. Our corpus includes 15k tokens, covering dialects from all Bavarian-speaking areas spanning three countries. We provide baseline parsing and POS tagging results, which are lower than results obtained on German and vary substantially between different graph-based parsers. To support further research on Bavarian syntax, we make our dataset, language-specific guidelines and code publicly available.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Named Entity Recognition (NER) models play a crucial role in various NLP tasks, including information extraction (IE) and text understanding. In academic writing, references to machine learning models and datasets are fundamental components of various computer science publications and necessitate accurate models for identification. Despite the advancements in NER, existing ground truth datasets do not treat fine-grained types like ML model and model architecture as separate entity types, and consequently, baseline models cannot recognize them as such. In this paper, we release a corpus of 100 manually annotated full-text scientific publications and a first baseline model for 10 entity types centered around ML models and datasets. In order to provide a nuanced understanding of how ML models and datasets are mentioned and utilized, our dataset also contains annotations for informal mentions like "our BERT-based model" or "an image CNN". You can find the ground truth dataset and code to replicate model training at https://data.gesis.org/gsap/gsap-ner.

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp's number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as PolypGen) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation. Our dataset can be downloaded from https://doi.org/10.7303/syn26376615.

We tackle NED by comparing entities in short sentences with graphs. Creating a context vector from graphs through deep learning is a challenging problem that has never been applied to NED. Our main contribution is to present an experimental study of recent neural techniques, as well as a discussion about which graph features are most important for the disambiguation task. In addition, a new dataset () is created to allow a clean and scalable evaluation of NED with entries, and to be used as a reference in future research. In the end our results show that a Bi-LSTM encoding of the graph triplets performs best, improving upon the baseline models and scoring an F1 value of 91.6% on the test set

We present the system description for our submission towards the Key Point Analysis Shared Task at ArgMining 2021. Track 1 of the shared task requires participants to develop methods to predict the match score between each pair of arguments and keypoints, provided they belong to the same topic under the same stance. We leveraged existing state of the art pre-trained language models along with incorporating additional data and features extracted from the inputs (topics, key points, and arguments) to improve performance. We were able to achieve mAP strict and mAP relaxed score of 0.872 and 0.966 respectively in the evaluation phase, securing 5th place on the leaderboard. In the post evaluation phase, we achieved a mAP strict and mAP relaxed score of 0.921 and 0.982 respectively. All the codes to generate reproducible results on our models are available on Github.

We consider the problem of translating high-level textual descriptions to formal representations in technical documentation as part of an effort to model the meaning of such documentation. We focus specifically on the problem of learning translational correspondences between text descriptions and grounded representations in the target documentation, such as formal representation of functions or code templates. Our approach exploits the parallel nature of such documentation, or the tight coupling between high-level text and the low-level representations we aim to learn. Data is collected by mining technical documents for such parallel text-representation pairs, which we use to train a simple semantic parsing model. We report new baseline results on sixteen novel datasets, including the standard library documentation for nine popular programming languages across seven natural languages, and a small collection of Unix utility manuals.

This document provides the annotation guidelines for MaiBaam, a Bavarian corpus annotated with part-of-speech (POS) tags and syntactic dependencies. MaiBaam belongs to the Universal Dependencies (UD) project, and our annotations elaborate on the general and German UD version 2 guidelines. In this document, we detail how to preprocess and tokenize Bavarian data, provide an overview of the POS tags and dependencies we use, explain annotation decisions that would also apply to closely related languages like German, and lastly we introduce and motivate decisions that are specific to Bavarian grammar.

Software that contains machine learning algorithms is an integral part of automotive perception, for example, in driving automation systems. The development of such software, specifically the training and validation of the machine learning components, require large annotated datasets. An industry of data and annotation services has emerged to serve the development of such data-intensive automotive software components. Wide-spread difficulties to specify data and annotation needs challenge collaborations between OEMs (Original Equipment Manufacturers) and their suppliers of software components, data, and annotations. This paper investigates the reasons for these difficulties for practitioners in the Swedish automotive industry to arrive at clear specifications for data and annotations. The results from an interview study show that a lack of effective metrics for data quality aspects, ambiguities in the way of working, unclear definitions of annotation quality, and deficits in the business ecosystems are causes for the difficulty in deriving the specifications. We provide a list of recommendations that can mitigate challenges when deriving specifications and we propose future research opportunities to overcome these challenges. Our work contributes towards the on-going research on accountability of machine learning as applied to complex software systems, especially for high-stake applications such as automated driving.

Deep active learning in the presence of outlier examples poses a realistic yet challenging scenario. Acquiring unlabeled data for annotation requires a delicate balance between avoiding outliers to conserve the annotation budget and prioritizing useful inlier examples for effective training. In this work, we present an approach that leverages three highly synergistic components, which are identified as key ingredients: joint classifier training with inliers and outliers, semi-supervised learning through pseudo-labeling, and model ensembling. Our work demonstrates that ensembling significantly enhances the accuracy of pseudo-labeling and improves the quality of data acquisition. By enabling semi-supervision through the joint training process, where outliers are properly handled, we observe a substantial boost in classifier accuracy through the use of all available unlabeled examples. Notably, we reveal that the integration of joint training renders explicit outlier detection unnecessary; a conventional component for acquisition in prior work. The three key components align seamlessly with numerous existing approaches. Through empirical evaluations, we showcase that their combined use leads to a performance increase. Remarkably, despite its simplicity, our proposed approach outperforms all other methods in terms of performance. Code: https://github.com/vladan-stojnic/active-outliers

The introduction of computerized medical records in hospitals has reduced burdensome operations like manual writing and information fetching. However, the data contained in medical records are still far underutilized, primarily because extracting them from unstructured textual medical records takes time and effort. Information Extraction, a subfield of Natural Language Processing, can help clinical practitioners overcome this limitation, using automated text-mining pipelines. In this work, we created the first Italian neuropsychiatric Named Entity Recognition dataset, PsyNIT, and used it to develop a Large Language Model for this task. Moreover, we conducted several experiments with three external independent datasets to implement an effective multicenter model, with overall F1-score 84.77%, Precision 83.16%, Recall 86.44%. The lessons learned are: (i) the crucial role of a consistent annotation process and (ii) a fine-tuning strategy that combines classical methods with a "few-shot" approach. This allowed us to establish methodological guidelines that pave the way for future implementations in this field and allow Italian hospitals to tap into important research opportunities.

Legal tasks and datasets are often used as benchmarks for the capabilities of language models. However, openly available annotated datasets are rare. In this paper, we introduce AGB-DE, a corpus of 3,764 clauses from German consumer contracts that have been annotated and legally assessed by legal experts. Together with the data, we present a first baseline for the task of detecting potentially void clauses, comparing the performance of an SVM baseline with three fine-tuned open language models and the performance of GPT-3.5. Our results show the challenging nature of the task, with no approach exceeding an F1-score of 0.54. While the fine-tuned models often performed better with regard to precision, GPT-3.5 outperformed the other approaches with regard to recall. An analysis of the errors indicates that one of the main challenges could be the correct interpretation of complex clauses, rather than the decision boundaries of what is permissible and what is not.

We present a new knowledge-base of hasPart relationships, extracted from a large corpus of generic statements. Complementary to other resources available, it is the first which is all three of: accurate (90% precision), salient (covers relationships a person may mention), and has high coverage of common terms (approximated as within a 10 year old's vocabulary), as well as having several times more hasPart entries than in the popular ontologies ConceptNet and WordNet. In addition, it contains information about quantifiers, argument modifiers, and links the entities to appropriate concepts in Wikipedia and WordNet. The knowledge base is available at https://allenai.org/data/haspartkb

This paper proposes a novel named entity recognition (NER) technique specifically tailored for the open-source software systems. Our approach aims to address the scarcity of annotated software data by employing a comprehensive two-step distantly supervised annotation process. This process strategically leverages language heuristics, unique lookup tables, external knowledge sources, and an active learning approach. By harnessing these powerful techniques, we not only enhance model performance but also effectively mitigate the limitations associated with cost and the scarcity of expert annotators. It is noteworthy that our framework significantly outperforms the state-of-the-art LLMs by a substantial margin. We also show the effectiveness of NER in the downstream task of relation extraction.

Augmnety is a Python library for structured text augmentation. It is built on top of spaCy and allows for augmentation of both the text and its annotations. Augmenty provides a wide range of augmenters which can be combined in a flexible manner to create complex augmentation pipelines. It also includes a set of primitives that can be used to create custom augmenters such as word replacement augmenters. This functionality allows for augmentations within a range of applications such as named entity recognition (NER), part-of-speech tagging, and dependency parsing.

Skill Classification (SC) is the task of classifying job competences from job postings. This work is the first in SC applied to Danish job vacancy data. We release the first Danish job posting dataset: Kompetencer (en: competences), annotated for nested spans of competences. To improve upon coarse-grained annotations, we make use of The European Skills, Competences, Qualifications and Occupations (ESCO; le Vrang et al., 2014) taxonomy API to obtain fine-grained labels via distant supervision. We study two setups: The zero-shot and few-shot classification setting. We fine-tune English-based models and RemBERT (Chung et al., 2020) and compare them to in-language Danish models. Our results show RemBERT significantly outperforms all other models in both the zero-shot and the few-shot setting.

Online social media platforms, such as Twitter, provide valuable information during disaster events. Existing tweet disaster summarization approaches provide a summary of these events to aid government agencies, humanitarian organizations, etc., to ensure effective disaster response. In the literature, there are two types of approaches for disaster summarization, namely, supervised and unsupervised approaches. Although supervised approaches are typically more effective, they necessitate a sizable number of disaster event summaries for testing and training. However, there is a lack of good number of disaster summary datasets for training and evaluation. This motivates us to add more datasets to make supervised learning approaches more efficient. In this paper, we present ADSumm, which adds annotated ground-truth summaries for eight disaster events which consist of both natural and man-made disaster events belonging to seven different countries. Our experimental analysis shows that the newly added datasets improve the performance of the supervised summarization approaches by 8-28% in terms of ROUGE-N F1-score. Moreover, in newly annotated dataset, we have added a category label for each input tweet which helps to ensure good coverage from different categories in summary. Additionally, we have added two other features relevance label and key-phrase, which provide information about the quality of a tweet and explanation about the inclusion of the tweet into summary, respectively. For ground-truth summary creation, we provide the annotation procedure adapted in detail, which has not been described in existing literature. Experimental analysis shows the quality of ground-truth summary is very good with Coverage, Relevance and Diversity.

Retrieval models are often evaluated on partially-annotated datasets. Each query is mapped to a few relevant texts and the remaining corpus is assumed to be irrelevant. As a result, models that successfully retrieve false negatives are punished in evaluation. Unfortunately, completely annotating all texts for every query is not resource efficient. In this work, we show that using partially-annotated datasets in evaluation can paint a distorted picture. We curate D-MERIT, a passage retrieval evaluation set from Wikipedia, aspiring to contain all relevant passages for each query. Queries describe a group (e.g., ``journals about linguistics'') and relevant passages are evidence that entities belong to the group (e.g., a passage indicating that Language is a journal about linguistics). We show that evaluating on a dataset containing annotations for only a subset of the relevant passages might result in misleading ranking of the retrieval systems and that as more relevant texts are included in the evaluation set, the rankings converge. We propose our dataset as a resource for evaluation and our study as a recommendation for balance between resource-efficiency and reliable evaluation when annotating evaluation sets for text retrieval.

Named Entity Recognition (NER) is a foundational NLP task that aims to provide class labels like Person, Location, Organisation, Time, and Number to words in free text. Named Entities can also be multi-word expressions where the additional I-O-B annotation information helps label them during the NER annotation process. While English and European languages have considerable annotated data for the NER task, Indian languages lack on that front -- both in terms of quantity and following annotation standards. This paper releases a significantly sized standard-abiding Hindi NER dataset containing 109,146 sentences and 2,220,856 tokens, annotated with 11 tags. We discuss the dataset statistics in all their essential detail and provide an in-depth analysis of the NER tag-set used with our data. The statistics of tag-set in our dataset show a healthy per-tag distribution, especially for prominent classes like Person, Location and Organisation. Since the proof of resource-effectiveness is in building models with the resource and testing the model on benchmark data and against the leader-board entries in shared tasks, we do the same with the aforesaid data. We use different language models to perform the sequence labelling task for NER and show the efficacy of our data by performing a comparative evaluation with models trained on another dataset available for the Hindi NER task. Our dataset helps achieve a weighted F1 score of 88.78 with all the tags and 92.22 when we collapse the tag-set, as discussed in the paper. To the best of our knowledge, no available dataset meets the standards of volume (amount) and variability (diversity), as far as Hindi NER is concerned. We fill this gap through this work, which we hope will significantly help NLP for Hindi. We release this dataset with our code and models at https://github.com/cfiltnlp/HiNER

We introduce Latent Meaning Cells, a deep latent variable model which learns contextualized representations of words by combining local lexical context and metadata. Metadata can refer to granular context, such as section type, or to more global context, such as unique document ids. Reliance on metadata for contextualized representation learning is apropos in the clinical domain where text is semi-structured and expresses high variation in topics. We evaluate the LMC model on the task of zero-shot clinical acronym expansion across three datasets. The LMC significantly outperforms a diverse set of baselines at a fraction of the pre-training cost and learns clinically coherent representations. We demonstrate that not only is metadata itself very helpful for the task, but that the LMC inference algorithm provides an additional large benefit.

The advancement of aspect-based sentiment analysis (ABSA) has urged the lack of a user-friendly framework that can largely lower the difficulty of reproducing state-of-the-art ABSA performance, especially for beginners. To meet the demand, we present \our, a modularized framework built on PyTorch for reproducible ABSA. To facilitate ABSA research, PyABSA supports several ABSA subtasks, including aspect term extraction, aspect sentiment classification, and end-to-end aspect-based sentiment analysis. Concretely, PyABSA integrates 29 models and 26 datasets. With just a few lines of code, the result of a model on a specific dataset can be reproduced. With a modularized design, PyABSA can also be flexiblely extended to considered models, datasets, and other related tasks. Besides, PyABSA highlights its data augmentation and annotation features, which significantly address data scarity. All are welcome to have a try at https://github.com/yangheng95/PyABSA.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation. In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

Human annotated data plays a crucial role in machine learning (ML) research and development. However, the ethical considerations around the processes and decisions that go into dataset annotation have not received nearly enough attention. In this paper, we survey an array of literature that provides insights into ethical considerations around crowdsourced dataset annotation. We synthesize these insights, and lay out the challenges in this space along two layers: (1) who the annotator is, and how the annotators' lived experiences can impact their annotations, and (2) the relationship between the annotators and the crowdsourcing platforms, and what that relationship affords them. Finally, we introduce a novel framework, CrowdWorkSheets, for dataset developers to facilitate transparent documentation of key decisions points at various stages of the data annotation pipeline: task formulation, selection of annotators, platform and infrastructure choices, dataset analysis and evaluation, and dataset release and maintenance.

In this work, we focus on the problem of retrieving relevant arguments for a query claim covering diverse aspects. State-of-the-art methods rely on explicit mappings between claims and premises, and thus are unable to utilize large available collections of premises without laborious and costly manual annotation. Their diversity approach relies on removing duplicates via clustering which does not directly ensure that the selected premises cover all aspects. This work introduces a new multi-step approach for the argument retrieval problem. Rather than relying on ground-truth assignments, our approach employs a machine learning model to capture semantic relationships between arguments. Beyond that, it aims to cover diverse facets of the query, instead of trying to identify duplicates explicitly. Our empirical evaluation demonstrates that our approach leads to a significant improvement in the argument retrieval task even though it requires less data.

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied than NER in the general domain. Given that significant progress has been made on NER, we believe that scholarly domain-specific NER will receive increasing attention in the years to come. Currently, progress on CS NER -- the focus of this work -- is hampered in part by its recency and the lack of a standardized annotation aim for scientific entities/terms. This work proposes a standardized task by defining a set of seven contribution-centric scholarly entities for CS NER viz., research problem, solution, resource, language, tool, method, and dataset. Following which, its main contributions are: combines existing CS NER resources that maintain their annotation focus on the set or subset of contribution-centric scholarly entities we consider; further, noting the need for big data to train neural NER models, this work additionally supplies thousands of contribution-centric entity annotations from article titles and abstracts, thus releasing a cumulative large novel resource for CS NER; and, finally, trains a sequence labeling CS NER model inspired after state-of-the-art neural architectures from the general domain NER task. Throughout the work, several practical considerations are made which can be useful to information technology designers of the digital libraries.

Newspaper reports provide a rich source of information on the unfolding of public debate on specific policy fields that can serve as basis for inquiry in political science. Such debates are often triggered by critical events, which attract public attention and incite the reactions of political actors: crisis sparks the debate. However, due to the challenges of reliable annotation and modeling, few large-scale datasets with high-quality annotation are available. This paper introduces DebateNet2.0, which traces the political discourse on the European refugee crisis in the German quality newspaper taz during the year 2015. The core units of our annotation are political claims (requests for specific actions to be taken within the policy field) and the actors who make them (politicians, parties, etc.). The contribution of this paper is twofold. First, we document and release DebateNet2.0 along with its companion R package, mardyR, guiding the reader through the practical and conceptual issues related to the annotation of policy debates in newspapers. Second, we outline and apply a Discourse Network Analysis (DNA) to DebateNet2.0, comparing two crucial moments of the policy debate on the 'refugee crisis': the migration flux through the Mediterranean in April/May and the one along the Balkan route in September/October. Besides the released resources and the case-study, our contribution is also methodological: we talk the reader through the steps from a newspaper article to a discourse network, demonstrating that there is not just one discourse network for the German migration debate, but multiple ones, depending on the topic of interest (political actors, policy fields, time spans).

In this paper we present datasets of Facebook comment threads to mainstream media posts in Slovene and English developed inside the Slovene national project FRENK which cover two topics, migrants and LGBT, and are manually annotated for different types of socially unacceptable discourse (SUD). The main advantages of these datasets compared to the existing ones are identical sampling procedures, producing comparable data across languages and an annotation schema that takes into account six types of SUD and five targets at which SUD is directed. We describe the sampling and annotation procedures, and analyze the annotation distributions and inter-annotator agreements. We consider this dataset to be an important milestone in understanding and combating SUD for both languages.

Design biases in NLP systems, such as performance differences for different populations, often stem from their creator's positionality, i.e., views and lived experiences shaped by identity and background. Despite the prevalence and risks of design biases, they are hard to quantify because researcher, system, and dataset positionality is often unobserved. We introduce NLPositionality, a framework for characterizing design biases and quantifying the positionality of NLP datasets and models. Our framework continuously collects annotations from a diverse pool of volunteer participants on LabintheWild, and statistically quantifies alignment with dataset labels and model predictions. We apply NLPositionality to existing datasets and models for two tasks -- social acceptability and hate speech detection. To date, we have collected 16,299 annotations in over a year for 600 instances from 1,096 annotators across 87 countries. We find that datasets and models align predominantly with Western, White, college-educated, and younger populations. Additionally, certain groups, such as non-binary people and non-native English speakers, are further marginalized by datasets and models as they rank least in alignment across all tasks. Finally, we draw from prior literature to discuss how researchers can examine their own positionality and that of their datasets and models, opening the door for more inclusive NLP systems.

Although the problem of hallucinations in neural machine translation (NMT) has received some attention, research on this highly pathological phenomenon lacks solid ground. Previous work has been limited in several ways: it often resorts to artificial settings where the problem is amplified, it disregards some (common) types of hallucinations, and it does not validate adequacy of detection heuristics. In this paper, we set foundations for the study of NMT hallucinations. First, we work in a natural setting, i.e., in-domain data without artificial noise neither in training nor in inference. Next, we annotate a dataset of over 3.4k sentences indicating different kinds of critical errors and hallucinations. Then, we turn to detection methods and both revisit methods used previously and propose using glass-box uncertainty-based detectors. Overall, we show that for preventive settings, (i) previously used methods are largely inadequate, (ii) sequence log-probability works best and performs on par with reference-based methods. Finally, we propose DeHallucinator, a simple method for alleviating hallucinations at test time that significantly reduces the hallucinatory rate. To ease future research, we release our annotated dataset for WMT18 German-English data, along with the model, training data, and code.

Existing Text-to-SQL generators require the entire schema to be encoded with the user text. This is expensive or impractical for large databases with tens of thousands of columns. Standard dense retrieval techniques are inadequate for schema subsetting of a large structured database, where the correct semantics of retrieval demands that we rank sets of schema elements rather than individual elements. In response, we propose a two-stage process for effective coverage during retrieval. First, we instruct an LLM to hallucinate a minimal DB schema deemed adequate to answer the query. We use the hallucinated schema to retrieve a subset of the actual schema, by composing the results from multiple dense retrievals. Remarkably, hallucination x2013 generally considered a nuisance x2013 turns out to be actually useful as a bridging mechanism. Since no existing benchmarks exist for schema subsetting on large databases, we introduce three benchmarks. Two semi-synthetic datasets are derived from the union of schemas in two well-known datasets, SPIDER and BIRD, resulting in 4502 and 798 schema elements respectively. A real-life benchmark called SocialDB is sourced from an actual large data warehouse comprising 17844 schema elements. We show that our method1 leads to significantly higher recall than SOTA retrieval-based augmentation methods.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

We open-source a state-of-the-art 7.5B-parameter generative model series named PhoGPT for Vietnamese, which includes the base pre-trained monolingual model PhoGPT-7B5 and its instruction-following variant, PhoGPT-7B5-Instruct. In addition, we also demonstrate its superior performance compared to previous open-source models through a human evaluation experiment. GitHub: https://github.com/VinAIResearch/PhoGPT

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a meticulously curated, comprehensive instruction dataset expressly designed for the biomolecular realm. Mol-Instructions is composed of three pivotal components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions, each curated to enhance the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on the representative LLM, we underscore the potency of Mol-Instructions to enhance the adaptability and cognitive acuity of large models within the complex sphere of biomolecular studies, thereby promoting advancements in the biomolecular research community. Mol-Instructions is made publicly accessible for future research endeavors and will be subjected to continual updates for enhanced applicability.

Active Learning (AL) addresses the high costs of collecting human annotations by strategically annotating the most informative samples. However, for subjective NLP tasks, incorporating a wide range of perspectives in the annotation process is crucial to capture the variability in human judgments. We introduce Annotator-Centric Active Learning (ACAL), which incorporates an annotator selection strategy following data sampling. Our objective is two-fold: (1) to efficiently approximate the full diversity of human judgments, and (2) to assess model performance using annotator-centric metrics, which emphasize minority perspectives over a majority. We experiment with multiple annotator selection strategies across seven subjective NLP tasks, employing both traditional and novel, human-centered evaluation metrics. Our findings indicate that ACAL improves data efficiency and excels in annotator-centric performance evaluations. However, its success depends on the availability of a sufficiently large and diverse pool of annotators to sample from.

Modern language models are trained on large, unstructured datasets consisting of trillions of tokens and obtained by crawling the web. The unstructured nature makes it difficult to reason about their contents and develop systematic approaches to data curation. In this paper, we unpack monolithic web corpora by developing taxonomies of their contents and organizing them into domains. We introduce WebOrganizer, a framework for organizing web pages in terms of both their topic and format. Using these two complementary notions of domains, we automatically annotate pre-training data by distilling annotations from a large language model into efficient classifiers. This allows us to study how data from different domains should be mixed to improve models on downstream tasks, and we show that we can combine insights about effective topics and formats to further boost performance. We demonstrate that our domain mixing also improves existing methods that select data based on quality. Furthermore, we study and compare how quality-based methods will implicitly change the domain mixture. Overall, our work demonstrates that constructing and mixing domains provides a valuable complement to quality-based data curation methods, opening new avenues for effective and insightful pre-training data curation.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Annotation noise is widespread in datasets, but manually revising a flawed corpus is time-consuming and error-prone. Hence, given the prior knowledge in Pre-trained Language Models and the expected uniformity across all annotations, we attempt to reduce annotation noise in the corpus through two tasks automatically: (1) Annotation Inconsistency Detection that indicates the credibility of annotations, and (2) Annotation Error Correction that rectifies the abnormal annotations. We investigate how to acquire semantic sensitive annotation representations from Pre-trained Language Models, expecting to embed the examples with identical annotations to the mutually adjacent positions even without fine-tuning. We proposed a novel credibility score to reveal the likelihood of annotation inconsistencies based on the neighbouring consistency. Then, we fine-tune the Pre-trained Language Models based classifier with cross-validation for annotation correction. The annotation corrector is further elaborated with two approaches: (1) soft labelling by Kernel Density Estimation and (2) a novel distant-peer contrastive loss. We study the re-annotation in relation extraction and create a new manually revised dataset, Re-DocRED, for evaluating document-level re-annotation. The proposed credibility scores show promising agreement with human revisions, achieving a Binary F1 of 93.4 and 72.5 in detecting inconsistencies on TACRED and DocRED respectively. Moreover, the neighbour-aware classifiers based on distant-peer contrastive learning and uncertain labels achieve Macro F1 up to 66.2 and 57.8 in correcting annotations on TACRED and DocRED respectively. These improvements are not merely theoretical: Rather, automatically denoised training sets demonstrate up to 3.6% performance improvement for state-of-the-art relation extraction models.

Understanding the relations between entities denoted by NPs in a text is a critical part of human-like natural language understanding. However, only a fraction of such relations is covered by standard NLP tasks and benchmarks nowadays. In this work, we propose a novel task termed text-based NP enrichment (TNE), in which we aim to enrich each NP in a text with all the preposition-mediated relations -- either explicit or implicit -- that hold between it and other NPs in the text. The relations are represented as triplets, each denoted by two NPs related via a preposition. Humans recover such relations seamlessly, while current state-of-the-art models struggle with them due to the implicit nature of the problem. We build the first large-scale dataset for the problem, provide the formal framing and scope of annotation, analyze the data, and report the results of fine-tuned language models on the task, demonstrating the challenge it poses to current technology. A webpage with a data-exploration UI, a demo, and links to the code, models, and leaderboard, to foster further research into this challenging problem can be found at: yanaiela.github.io/TNE/.

The increased use of large language models (LLMs) across a variety of real-world applications calls for mechanisms to verify the factual accuracy of their outputs. In this work, we present a holistic end-to-end solution for annotating the factuality of LLM-generated responses, which encompasses a multi-stage annotation scheme designed to yield detailed labels concerning the verifiability and factual inconsistencies found in LLM outputs. We design and build an annotation tool to speed up the labelling procedure and ease the workload of raters. It allows flexible incorporation of automatic results in any stage, e.g. automatically-retrieved evidence. We further construct an open-domain document-level factuality benchmark in three-level granularity: claim, sentence and document. Preliminary experiments show that FacTool, FactScore and Perplexity.ai are struggling to identify false claims with the best F1=0.53. Annotation tool, benchmark and code are available at https://github.com/yuxiaw/Factcheck-GPT.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

We present MapReader, a free, open-source software library written in Python for analyzing large map collections (scanned or born-digital). This library transforms the way historians can use maps by turning extensive, homogeneous map sets into searchable primary sources. MapReader allows users with little or no computer vision expertise to i) retrieve maps via web-servers; ii) preprocess and divide them into patches; iii) annotate patches; iv) train, fine-tune, and evaluate deep neural network models; and v) create structured data about map content. We demonstrate how MapReader enables historians to interpret a collection of approx16K nineteenth-century Ordnance Survey map sheets (approx30.5M patches), foregrounding the challenge of translating visual markers into machine-readable data. We present a case study focusing on British rail infrastructure and buildings as depicted on these maps. We also show how the outputs from the MapReader pipeline can be linked to other, external datasets, which we use to evaluate as well as enrich and interpret the results. We release approx62K manually annotated patches used here for training and evaluating the models.

Media is full of false claims. Even Oxford Dictionaries named "post-truth" as the word of 2016. This makes it more important than ever to build systems that can identify the veracity of a story, and the kind of discourse there is around it. RumourEval is a SemEval shared task that aims to identify and handle rumours and reactions to them, in text. We present an annotation scheme, a large dataset covering multiple topics - each having their own families of claims and replies - and use these to pose two concrete challenges as well as the results achieved by participants on these challenges.

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

NLP benchmarks rely on standardized datasets for training and evaluating models and are crucial for advancing the field. Traditionally, expert annotations ensure high-quality labels; however, the cost of expert annotation does not scale well with the growing demand for larger datasets required by modern models. While crowd-sourcing provides a more scalable solution, it often comes at the expense of annotation precision and consistency. Recent advancements in large language models (LLMs) offer new opportunities to enhance the annotation process, particularly for detecting label errors in existing datasets. In this work, we consider the recent approach of LLM-as-a-judge, leveraging an ensemble of LLMs to flag potentially mislabeled examples. Through a case study of four datasets from the TRUE benchmark, covering different tasks and domains, we empirically analyze the labeling quality of existing datasets, and compare expert, crowd-sourced, and our LLM-based annotations in terms of agreement, label quality, and efficiency, demonstrating the strengths and limitations of each annotation method. Our findings reveal a substantial number of label errors, which, when corrected, induce a significant upward shift in reported model performance. This suggests that many of the LLMs so-called mistakes are due to label errors rather than genuine model failures. Additionally, we discuss the implications of mislabeled data and propose methods to mitigate them in training to improve model performance.

Massive amounts of unlabelled data are captured by Earth Observation (EO) satellites, with the Sentinel-2 constellation generating 1.6 TB of data daily. This makes Remote Sensing a data-rich domain well suited to Machine Learning (ML) solutions. However, a bottleneck in applying ML models to EO is the lack of annotated data as annotation is a labour-intensive and costly process. As a result, research in this domain has focused on Self-Supervised Learning and Foundation Model approaches. This paper addresses the need to evaluate different Foundation Models on a fair and uniform benchmark by introducing the PhilEO Bench, a novel evaluation framework for EO Foundation Models. The framework comprises of a testbed and a novel 400 GB Sentinel-2 dataset containing labels for three downstream tasks, building density estimation, road segmentation, and land cover classification. We present experiments using our framework evaluating different Foundation Models, including Prithvi and SatMAE, at multiple n-shots and convergence rates.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

The rise of large language models (LLMs) has brought a critical need for high-quality human-labeled data, particularly for processes like human feedback and evaluation. A common practice is to label data via consensus annotation over crowdworker judgments. However, annotators' judgments for subjective tasks can differ in many ways: they may have different qualitative judgments about an example, and they may map those to a labeling scheme in different ways. We show that these nuances can be captured by natural language explanations, and propose a method to rescale ordinal annotations and explanations using LLMs. Specifically, we feed annotators' Likert ratings and corresponding explanations into an LLM and prompt it to produce a numeric score anchored in a scoring rubric. These scores should reflect the annotators' underlying assessments of the example. The rubric can be designed or modified after annotation, and include distinctions that may not have been known when the original error taxonomy was devised. We explore our technique in the context of rating system outputs for a document-grounded question answering task, where LLMs achieve near-human performance. Our method rescales the raw judgments without impacting agreement and brings the scores closer to human judgments grounded in the same scoring rubric.

To address the risks of encountering inappropriate or harmful content, researchers managed to incorporate several harmful contents datasets with machine learning methods to detect harmful concepts. However, existing harmful datasets are curated by the presence of a narrow range of harmful objects, and only cover real harmful content sources. This hinders the generalizability of methods based on such datasets, potentially leading to misjudgments. Therefore, we propose a comprehensive harmful dataset, Visual Harmful Dataset 11K (VHD11K), consisting of 10,000 images and 1,000 videos, crawled from the Internet and generated by 4 generative models, across a total of 10 harmful categories covering a full spectrum of harmful concepts with nontrivial definition. We also propose a novel annotation framework by formulating the annotation process as a multi-agent Visual Question Answering (VQA) task, having 3 different VLMs "debate" about whether the given image/video is harmful, and incorporating the in-context learning strategy in the debating process. Therefore, we can ensure that the VLMs consider the context of the given image/video and both sides of the arguments thoroughly before making decisions, further reducing the likelihood of misjudgments in edge cases. Evaluation and experimental results demonstrate that (1) the great alignment between the annotation from our novel annotation framework and those from human, ensuring the reliability of VHD11K; (2) our full-spectrum harmful dataset successfully identifies the inability of existing harmful content detection methods to detect extensive harmful contents and improves the performance of existing harmfulness recognition methods; (3) VHD11K outperforms the baseline dataset, SMID, as evidenced by the superior improvement in harmfulness recognition methods. The complete dataset and code can be found at https://github.com/nctu-eva-lab/VHD11K.

Extracting who says what to whom is a crucial part in analyzing human communication in today's abundance of data such as online news articles. Yet, the lack of annotated data for this task in German news articles severely limits the quality and usability of possible systems. To remedy this, we present a new, freely available, creative-commons-licensed dataset for quotation attribution in German news articles based on WIKINEWS. The dataset provides curated, high-quality annotations across 1000 documents (250,000 tokens) in a fine-grained annotation schema enabling various downstream uses for the dataset. The annotations not only specify who said what but also how, in which context, to whom and define the type of quotation. We specify our annotation schema, describe the creation of the dataset and provide a quantitative analysis. Further, we describe suitable evaluation metrics, apply two existing systems for quotation attribution, discuss their results to evaluate the utility of our dataset and outline use cases of our dataset in downstream tasks.

Recent work has shown that large language models (LLMs) are capable of generating summaries zero-shot (i.e., without explicit supervision) that, under human assessment, are often comparable or even preferred to manually composed reference summaries. However, this prior work has focussed almost exclusively on evaluating news article summarization. How do zero-shot summarizers perform in other (potentially more specialized) domains? In this work we evaluate zero-shot generated summaries across specialized domains including biomedical articles, and legal bills (in addition to standard news benchmarks for reference). We focus especially on the factuality of outputs. We acquire annotations from domain experts to identify inconsistencies in summaries and systematically categorize these errors. We analyze whether the prevalence of a given domain in the pretraining corpus affects extractiveness and faithfulness of generated summaries of articles in this domain. We release all collected annotations to facilitate additional research toward measuring and realizing factually accurate summarization, beyond news articles. The dataset can be downloaded from https://github.com/sanjanaramprasad/zero_shot_faceval_domains

To overcome the limitations and challenges of current automatic table data annotation methods and random table data synthesis approaches, we propose a novel method for synthesizing annotation data specifically designed for table recognition. This method utilizes the structure and content of existing complex tables, facilitating the efficient creation of tables that closely replicate the authentic styles found in the target domain. By leveraging the actual structure and content of tables from Chinese financial announcements, we have developed the first extensive table annotation dataset in this domain. We used this dataset to train several recent deep learning-based end-to-end table recognition models. Additionally, we have established the inaugural benchmark for real-world complex tables in the Chinese financial announcement domain, using it to assess the performance of models trained on our synthetic data, thereby effectively validating our method's practicality and effectiveness. Furthermore, we applied our synthesis method to augment the FinTabNet dataset, extracted from English financial announcements, by increasing the proportion of tables with multiple spanning cells to introduce greater complexity. Our experiments show that models trained on this augmented dataset achieve comprehensive improvements in performance, especially in the recognition of tables with multiple spanning cells.

We present NUBIA, a methodology to build automatic evaluation metrics for text generation using only machine learning models as core components. A typical NUBIA model is composed of three modules: a neural feature extractor, an aggregator and a calibrator. We demonstrate an implementation of NUBIA which outperforms metrics currently used to evaluate machine translation, summaries and slightly exceeds/matches state of the art metrics on correlation with human judgement on the WMT segment-level Direct Assessment task, sentence-level ranking and image captioning evaluation. The model implemented is modular, explainable and set to continuously improve over time.

We introduce TV show Retrieval (TVR), a new multimodal retrieval dataset. TVR requires systems to understand both videos and their associated subtitle (dialogue) texts, making it more realistic. The dataset contains 109K queries collected on 21.8K videos from 6 TV shows of diverse genres, where each query is associated with a tight temporal window. The queries are also labeled with query types that indicate whether each of them is more related to video or subtitle or both, allowing for in-depth analysis of the dataset and the methods that built on top of it. Strict qualification and post-annotation verification tests are applied to ensure the quality of the collected data. Further, we present several baselines and a novel Cross-modal Moment Localization (XML ) network for multimodal moment retrieval tasks. The proposed XML model uses a late fusion design with a novel Convolutional Start-End detector (ConvSE), surpassing baselines by a large margin and with better efficiency, providing a strong starting point for future work. We have also collected additional descriptions for each annotated moment in TVR to form a new multimodal captioning dataset with 262K captions, named TV show Caption (TVC). Both datasets are publicly available. TVR: https://tvr.cs.unc.edu, TVC: https://tvr.cs.unc.edu/tvc.html.

The availability of large public datasets and the increased amount of computing power have shifted the interest of the medical community to high-performance algorithms. However, little attention is paid to the quality of the data and their annotations. High performance on benchmark datasets may be reported without considering possible shortcuts or artifacts in the data, besides, models are not tested on subpopulation groups. With this work, we aim to raise awareness about shortcuts problems. We validate previous findings, and present a case study on chest X-rays using two publicly available datasets. We share annotations for a subset of pneumothorax images with drains. We conclude with general recommendations for medical image classification.

We focus on electronic theses and dissertations (ETDs), aiming to improve access and expand their utility, since more than 6 million are publicly available, and they constitute an important corpus to aid research and education across disciplines. The corpus is growing as new born-digital documents are included, and since millions of older theses and dissertations have been converted to digital form to be disseminated electronically in institutional repositories. In ETDs, as with other scholarly works, figures and tables can communicate a large amount of information in a concise way. Although methods have been proposed for extracting figures and tables from born-digital PDFs, they do not work well with scanned ETDs. Considering this problem, our assessment of state-of-the-art figure extraction systems is that the reason they do not function well on scanned PDFs is that they have only been trained on born-digital documents. To address this limitation, we present ScanBank, a new dataset containing 10 thousand scanned page images, manually labeled by humans as to the presence of the 3.3 thousand figures or tables found therein. We use this dataset to train a deep neural network model based on YOLOv5 to accurately extract figures and tables from scanned ETDs. We pose and answer important research questions aimed at finding better methods for figure extraction from scanned documents. One of those concerns the value for training, of data augmentation techniques applied to born-digital documents which are used to train models better suited for figure extraction from scanned documents. To the best of our knowledge, ScanBank is the first manually annotated dataset for figure and table extraction for scanned ETDs. A YOLOv5-based model, trained on ScanBank, outperforms existing comparable open-source and freely available baseline methods by a considerable margin.

The successes of foundation models such as ChatGPT and AlphaFold have spurred significant interest in building similar models for electronic medical records (EMRs) to improve patient care and hospital operations. However, recent hype has obscured critical gaps in our understanding of these models' capabilities. We review over 80 foundation models trained on non-imaging EMR data (i.e. clinical text and/or structured data) and create a taxonomy delineating their architectures, training data, and potential use cases. We find that most models are trained on small, narrowly-scoped clinical datasets (e.g. MIMIC-III) or broad, public biomedical corpora (e.g. PubMed) and are evaluated on tasks that do not provide meaningful insights on their usefulness to health systems. In light of these findings, we propose an improved evaluation framework for measuring the benefits of clinical foundation models that is more closely grounded to metrics that matter in healthcare.

Identifying, classifying, and analyzing arguments in legal discourse has been a prominent area of research since the inception of the argument mining field. However, there has been a major discrepancy between the way natural language processing (NLP) researchers model and annotate arguments in court decisions and the way legal experts understand and analyze legal argumentation. While computational approaches typically simplify arguments into generic premises and claims, arguments in legal research usually exhibit a rich typology that is important for gaining insights into the particular case and applications of law in general. We address this problem and make several substantial contributions to move the field forward. First, we design a new annotation scheme for legal arguments in proceedings of the European Court of Human Rights (ECHR) that is deeply rooted in the theory and practice of legal argumentation research. Second, we compile and annotate a large corpus of 373 court decisions (2.3M tokens and 15k annotated argument spans). Finally, we train an argument mining model that outperforms state-of-the-art models in the legal NLP domain and provide a thorough expert-based evaluation. All datasets and source codes are available under open lincenses at https://github.com/trusthlt/mining-legal-arguments.

TACRED is one of the largest and most widely used sentence-level relation extraction datasets. Proposed models that are evaluated using this dataset consistently set new state-of-the-art performance. However, they still exhibit large error rates despite leveraging external knowledge and unsupervised pretraining on large text corpora. A recent study suggested that this may be due to poor dataset quality. The study observed that over 50% of the most challenging sentences from the development and test sets are incorrectly labeled and account for an average drop of 8% f1-score in model performance. However, this study was limited to a small biased sample of 5k (out of a total of 106k) sentences, substantially restricting the generalizability and broader implications of its findings. In this paper, we address these shortcomings by: (i) performing a comprehensive study over the whole TACRED dataset, (ii) proposing an improved crowdsourcing strategy and deploying it to re-annotate the whole dataset, and (iii) performing a thorough analysis to understand how correcting the TACRED annotations affects previously published results. After verification, we observed that 23.9% of TACRED labels are incorrect. Moreover, evaluating several models on our revised dataset yields an average f1-score improvement of 14.3% and helps uncover significant relationships between the different models (rather than simply offsetting or scaling their scores by a constant factor). Finally, aside from our analysis we also release Re-TACRED, a new completely re-annotated version of the TACRED dataset that can be used to perform reliable evaluation of relation extraction models.

Multilingual pretrained language models (mPLMs) acquire valuable, generalizable linguistic information during pretraining and have advanced the state of the art on task-specific finetuning. To date, only ~31 out of ~2,000 African languages are covered in existing language models. We ameliorate this limitation by developing SERENGETI, a massively multilingual language model that covers 517 African languages and language varieties. We evaluate our novel models on eight natural language understanding tasks across 20 datasets, comparing to 4 mPLMs that cover 4-23 African languages. SERENGETI outperforms other models on 11 datasets across the eights tasks, achieving 82.27 average F_1. We also perform analyses of errors from our models, which allows us to investigate the influence of language genealogy and linguistic similarity when the models are applied under zero-shot settings. We will publicly release our models for research.\href{https://github.com/UBC-NLP/serengeti{https://github.com/UBC-NLP/serengeti}}

Obtaining text datasets with semantic annotations is an effortful process, yet crucial for supervised training in natural language processsing (NLP). In general, developing and applying new NLP pipelines in domain-specific contexts for tasks often requires custom designed datasets to address NLP tasks in supervised machine learning fashion. When operating in non-English languages for medical data processing, this exposes several minor and major, interconnected problems such as lack of task-matching datasets as well as task-specific pre-trained models. In our work we suggest to leverage pretrained language models for training data acquisition in order to retrieve sufficiently large datasets for training smaller and more efficient models for use-case specific tasks. To demonstrate the effectiveness of your approach, we create a custom dataset which we use to train a medical NER model for German texts, GPTNERMED, yet our method remains language-independent in principle. Our obtained dataset as well as our pre-trained models are publicly available at: https://github.com/frankkramer-lab/GPTNERMED

In this study, we introduce FEET, a standardized protocol designed to guide the development and benchmarking of foundation models. While numerous benchmark datasets exist for evaluating these models, we propose a structured evaluation protocol across three distinct scenarios to gain a comprehensive understanding of their practical performance. We define three primary use cases: frozen embeddings, few-shot embeddings, and fully fine-tuned embeddings. Each scenario is detailed and illustrated through two case studies: one in sentiment analysis and another in the medical domain, demonstrating how these evaluations provide a thorough assessment of foundation models' effectiveness in research applications. We recommend this protocol as a standard for future research aimed at advancing representation learning models.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

One common trend in recent studies of language models (LMs) is the use of standardized tests for evaluation. However, despite being the fifth most spoken language worldwide, few such evaluations have been conducted in Portuguese. This is mainly due to the lack of high-quality datasets available to the community for carrying out evaluations in Portuguese. To address this gap, we introduce the Brazilian Leading Universities Entrance eXams (BLUEX), a dataset of entrance exams from the two leading universities in Brazil: UNICAMP and USP. The dataset includes annotated metadata for evaluating the performance of NLP models on a variety of subjects. Furthermore, BLUEX includes a collection of recently administered exams that are unlikely to be included in the training data of many popular LMs as of 2023. The dataset is also annotated to indicate the position of images in each question, providing a valuable resource for advancing the state-of-the-art in multimodal language understanding and reasoning. We describe the creation and characteristics of BLUEX and establish a benchmark through experiments with state-of-the-art LMs, demonstrating its potential for advancing the state-of-the-art in natural language understanding and reasoning in Portuguese. The data and relevant code can be found at https://github.com/Portuguese-Benchmark-Datasets/BLUEX

This paper presents the first publicly available version of the Carolina Corpus and discusses its future directions. Carolina is a large open corpus of Brazilian Portuguese texts under construction using web-as-corpus methodology enhanced with provenance, typology, versioning, and text integrality. The corpus aims at being used both as a reliable source for research in Linguistics and as an important resource for Computer Science research on language models, contributing towards removing Portuguese from the set of low-resource languages. Here we present the construction of the corpus methodology, comparing it with other existing methodologies, as well as the corpus current state: Carolina's first public version has 653,322,577 tokens, distributed over 7 broad types. Each text is annotated with several different metadata categories in its header, which we developed using TEI annotation standards. We also present ongoing derivative works and invite NLP researchers to contribute with their own.

We introduce a new, highly challenging benchmark and a dataset -- FungiTastic -- based on data continuously collected over a twenty-year span. The dataset originates in fungal records labeled and curated by experts. It consists of about 350k multi-modal observations that include more than 650k photographs from 5k fine-grained categories and diverse accompanying information, e.g., acquisition metadata, satellite images, and body part segmentation. FungiTastic is the only benchmark that includes a test set with partially DNA-sequenced ground truth of unprecedented label reliability. The benchmark is designed to support (i) standard close-set classification, (ii) open-set classification, (iii) multi-modal classification, (iv) few-shot learning, (v) domain shift, and many more. We provide baseline methods tailored for almost all the use-cases. We provide a multitude of ready-to-use pre-trained models on HuggingFace and a framework for model training. A comprehensive documentation describing the dataset features and the baselines are available at https://bohemianvra.github.io/FungiTastic/ and https://www.kaggle.com/datasets/picekl/fungitastic.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

In this paper, we examine several methods of acquiring Czech data for automated fact-checking, which is a task commonly modeled as a classification of textual claim veracity w.r.t. a corpus of trusted ground truths. We attempt to collect sets of data in form of a factual claim, evidence within the ground truth corpus, and its veracity label (supported, refuted or not enough info). As a first attempt, we generate a Czech version of the large-scale FEVER dataset built on top of Wikipedia corpus. We take a hybrid approach of machine translation and document alignment; the approach and the tools we provide can be easily applied to other languages. We discuss its weaknesses and inaccuracies, propose a future approach for their cleaning and publish the 127k resulting translations, as well as a version of such dataset reliably applicable for the Natural Language Inference task - the CsFEVER-NLI. Furthermore, we collect a novel dataset of 3,097 claims, which is annotated using the corpus of 2.2M articles of Czech News Agency. We present its extended annotation methodology based on the FEVER approach, and, as the underlying corpus is kept a trade secret, we also publish a standalone version of the dataset for the task of Natural Language Inference we call CTKFactsNLI. We analyze both acquired datasets for spurious cues - annotation patterns leading to model overfitting. CTKFacts is further examined for inter-annotator agreement, thoroughly cleaned, and a typology of common annotator errors is extracted. Finally, we provide baseline models for all stages of the fact-checking pipeline and publish the NLI datasets, as well as our annotation platform and other experimental data.

We introduce Universal NER (UNER), an open, community-driven project to develop gold-standard NER benchmarks in many languages. The overarching goal of UNER is to provide high-quality, cross-lingually consistent annotations to facilitate and standardize multilingual NER research. UNER v1 contains 18 datasets annotated with named entities in a cross-lingual consistent schema across 12 diverse languages. In this paper, we detail the dataset creation and composition of UNER; we also provide initial modeling baselines on both in-language and cross-lingual learning settings. We release the data, code, and fitted models to the public.

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the continual influx of domain-specific terminologies in scholarly literature. Current research in Biomedical Method (BioMethod) NER suffers from a scarcity of resources, primarily attributed to the intricate nature of methodological concepts, which necessitate a profound understanding for precise delineation. In this study, we propose a novel dataset for biomedical method entity recognition, employing an automated BioMethod entity recognition and information retrieval system to assist human annotation. Furthermore, we comprehensively explore a range of conventional and contemporary open-domain NER methodologies, including the utilization of cutting-edge large-scale language models (LLMs) customised to our dataset. Our empirical findings reveal that the large parameter counts of language models surprisingly inhibit the effective assimilation of entity extraction patterns pertaining to biomedical methods. Remarkably, the approach, leveraging the modestly sized ALBERT model (only 11MB), in conjunction with conditional random fields (CRF), achieves state-of-the-art (SOTA) performance.

We release the Nemotron-4 340B model family, including Nemotron-4-340B-Base, Nemotron-4-340B-Instruct, and Nemotron-4-340B-Reward. Our models are open access under the NVIDIA Open Model License Agreement, a permissive model license that allows distribution, modification, and use of the models and its outputs. These models perform competitively to open access models on a wide range of evaluation benchmarks, and were sized to fit on a single DGX H100 with 8 GPUs when deployed in FP8 precision. We believe that the community can benefit from these models in various research studies and commercial applications, especially for generating synthetic data to train smaller language models. Notably, over 98% of data used in our model alignment process is synthetically generated, showcasing the effectiveness of these models in generating synthetic data. To further support open research and facilitate model development, we are also open-sourcing the synthetic data generation pipeline used in our model alignment process.

Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such models do not take into consideration expert domain knowledge. In this work, we introduced UmlsBERT, a contextual embedding model that integrates domain knowledge during the pre-training process via a novel knowledge augmentation strategy. More specifically, the augmentation on UmlsBERT with the Unified Medical Language System (UMLS) Metathesaurus was performed in two ways: i) connecting words that have the same underlying `concept' in UMLS, and ii) leveraging semantic group knowledge in UMLS to create clinically meaningful input embeddings. By applying these two strategies, UmlsBERT can encode clinical domain knowledge into word embeddings and outperform existing domain-specific models on common named-entity recognition (NER) and clinical natural language inference clinical NLP tasks.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

Scientific documents record research findings and valuable human knowledge, comprising a vast corpus of high-quality data. Leveraging multi-modality data extracted from these documents and assessing large models' abilities to handle scientific document-oriented tasks is therefore meaningful. Despite promising advancements, large models still perform poorly on multi-page scientific document extraction and understanding tasks, and their capacity to process within-document data formats such as charts and equations remains under-explored. To address these issues, we present DocGenome, a structured document benchmark constructed by annotating 500K scientific documents from 153 disciplines in the arXiv open-access community, using our custom auto-labeling pipeline. DocGenome features four key characteristics: 1) Completeness: It is the first dataset to structure data from all modalities including 13 layout attributes along with their LaTeX source codes. 2) Logicality: It provides 6 logical relationships between different entities within each scientific document. 3) Diversity: It covers various document-oriented tasks, including document classification, visual grounding, document layout detection, document transformation, open-ended single-page QA and multi-page QA. 4) Correctness: It undergoes rigorous quality control checks conducted by a specialized team. We conduct extensive experiments to demonstrate the advantages of DocGenome and objectively evaluate the performance of large models on our benchmark.

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

Recent advancements in NLP have witnessed the groundbreaking impact of pretrained models, yielding impressive outcomes across various tasks. This study seeks to extend the power of pretraining methodologies to facilitating the prediction over tables in data science, a domain traditionally overlooked, yet inherently challenging due to the plethora of table schemas intrinsic to different tasks. The primary research questions underpinning this work revolve around the establishment of a universal pretraining protocol for tables with varied structures, the generalizability and transferability of learned knowledge across tasks, the adaptation to diverse downstream applications, and the incorporation of incremental columns over time. In response to these challenges, we introduce UniTabE, a straightforward yet effective method designed to process tables in a uniform manner, devoid of constraints imposed by specific table structures. UniTabE's core concept relies on representing each basic table element with a module, termed TabUnit. This is subsequently followed by a Transformer encoder to refine the representation. Moreover, our model is designed to facilitate pretraining and finetuning through the utilization of free-form prompts. In order to implement the pretraining phase, we curated an expansive tabular dataset comprising approximately 13B samples, meticulously gathered from the Kaggle platform. This research primarily centers on classification and regression tasks involving tabular data, and conducts rigorous experimental testing and analyses to validate the effectiveness of our methodology. The experimental results demonstrate UniTabE's superior performance against several baselines across massive benchmarks. This, therefore, underscores UniTabE's potential to significantly enhance the semantic representation of tabular data, thereby marking a significant stride for tabular data analysis.

In-context learning is a promising paradigm that utilizes in-context examples as prompts for the predictions of large language models. These prompts are crucial for achieving strong performance. However, since the prompts need to be sampled from a large volume of annotated examples, finding the right prompt may result in high annotation costs. To address this challenge, this paper introduces an influence-driven selective annotation method that aims to minimize annotation costs while improving the quality of in-context examples. The essence of our method is to select a pivotal subset from a large-scale unlabeled data pool to annotate for the subsequent sampling of prompts. Specifically, a directed graph is first constructed to represent unlabeled data. Afterward, the influence of candidate unlabeled subsets is quantified with a diffusion process. A simple yet effective greedy algorithm for unlabeled data selection is lastly introduced. It iteratively selects the data if it provides a maximum marginal gain with respect to quantified influence. Compared with previous efforts on selective annotations, our influence-driven method works in an end-to-end manner, avoids an intractable explicit balance between data diversity and representativeness, and enjoys theoretical support. Experiments confirm the superiority of the proposed method on various benchmarks, achieving better performance under lower time consumption during subset selection. The project page is available at https://skzhang1.github.io/IDEAL/.

We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where the goal is to design novel proteins that are better (e.g., more stable) than existing sequences. Thus, by definition, the target sequences and their attribute values are out of the training distribution, posing challenges to existing methods that aim to directly generate the target sequence. Instead, in this work, we propose Iterative Controlled Extrapolation (ICE) which iteratively makes local edits to a sequence to enable extrapolation. We train the model on synthetically generated sequence pairs that demonstrate small improvement in the attribute value. Results on one natural language task (sentiment analysis) and two protein engineering tasks (ACE2 stability and AAV fitness) show that ICE considerably outperforms state-of-the-art approaches despite its simplicity. Our code and models are available at: https://github.com/vishakhpk/iter-extrapolation.

Sentiment analysis is a highly subjective and challenging task. Its complexity further increases when applied to the Arabic language, mainly because of the large variety of dialects that are unstandardized and widely used in the Web, especially in social media. While many datasets have been released to train sentiment classifiers in Arabic, most of these datasets contain shallow annotation, only marking the sentiment of the text unit, as a word, a sentence or a document. In this paper, we present the Arabic Sentiment Twitter Dataset for the Levantine dialect (ArSenTD-LEV). Based on findings from analyzing tweets from the Levant region, we created a dataset of 4,000 tweets with the following annotations: the overall sentiment of the tweet, the target to which the sentiment was expressed, how the sentiment was expressed, and the topic of the tweet. Results confirm the importance of these annotations at improving the performance of a baseline sentiment classifier. They also confirm the gap of training in a certain domain, and testing in another domain.

We describe the construction and evaluation of a part-of-speech tagger for Yiddish (the first one, to the best of our knowledge). This is the first step in a larger project of automatically assigning part-of-speech tags and syntactic structure to Yiddish text for purposes of linguistic research. We combine two resources for the current work - an 80K word subset of the Penn Parsed Corpus of Historical Yiddish (PPCHY) (Santorini, 2021) and 650 million words of OCR'd Yiddish text from the Yiddish Book Center (YBC). We compute word embeddings on the YBC corpus, and these embeddings are used with a tagger model trained and evaluated on the PPCHY. Yiddish orthography in the YBC corpus has many spelling inconsistencies, and we present some evidence that even simple non-contextualized embeddings are able to capture the relationships among spelling variants without the need to first "standardize" the corpus. We evaluate the tagger performance on a 10-fold cross-validation split, with and without the embeddings, showing that the embeddings improve tagger performance. However, a great deal of work remains to be done, and we conclude by discussing some next steps, including the need for additional annotated training and test data.

Language models (LMs) are no longer restricted to ML community, and instruction-tuned LMs have led to a rise in autonomous AI agents. As the accessibility of LMs grows, it is imperative that an understanding of their capabilities, intended usage, and development cycle also improves. Model cards are a popular practice for documenting detailed information about an ML model. To automate model card generation, we introduce a dataset of 500 question-answer pairs for 25 ML models that cover crucial aspects of the model, such as its training configurations, datasets, biases, architecture details, and training resources. We employ annotators to extract the answers from the original paper. Further, we explore the capabilities of LMs in generating model cards by answering questions. Our initial experiments with ChatGPT-3.5, LLaMa, and Galactica showcase a significant gap in the understanding of research papers by these aforementioned LMs as well as generating factual textual responses. We posit that our dataset can be used to train models to automate the generation of model cards from paper text and reduce human effort in the model card curation process. The complete dataset is available on https://osf.io/hqt7p/?view_only=3b9114e3904c4443bcd9f5c270158d37

Recently, it has been found that monolingual English language models can be used as knowledge bases. Instead of structural knowledge base queries, masked sentences such as "Paris is the capital of [MASK]" are used as probes. We translate the established benchmarks TREx and GoogleRE into 53 languages. Working with mBERT, we investigate three questions. (i) Can mBERT be used as a multilingual knowledge base? Most prior work only considers English. Extending research to multiple languages is important for diversity and accessibility. (ii) Is mBERT's performance as knowledge base language-independent or does it vary from language to language? (iii) A multilingual model is trained on more text, e.g., mBERT is trained on 104 Wikipedias. Can mBERT leverage this for better performance? We find that using mBERT as a knowledge base yields varying performance across languages and pooling predictions across languages improves performance. Conversely, mBERT exhibits a language bias; e.g., when queried in Italian, it tends to predict Italy as the country of origin.

Statically analyzing dynamically-typed code is a challenging endeavor, as even seemingly trivial tasks such as determining the targets of procedure calls are non-trivial without knowing the types of objects at compile time. Addressing this challenge, gradual typing is increasingly added to dynamically-typed languages, a prominent example being TypeScript that introduces static typing to JavaScript. Gradual typing improves the developer's ability to verify program behavior, contributing to robust, secure and debuggable programs. In practice, however, users only sparsely annotate types directly. At the same time, conventional type inference faces performance-related challenges as program size grows. Statistical techniques based on machine learning offer faster inference, but although recent approaches demonstrate overall improved accuracy, they still perform significantly worse on user-defined types than on the most common built-in types. Limiting their real-world usefulness even more, they rarely integrate with user-facing applications. We propose CodeTIDAL5, a Transformer-based model trained to reliably predict type annotations. For effective result retrieval and re-integration, we extract usage slices from a program's code property graph. Comparing our approach against recent neural type inference systems, our model outperforms the current state-of-the-art by 7.85% on the ManyTypes4TypeScript benchmark, achieving 71.27% accuracy overall. Furthermore, we present JoernTI, an integration of our approach into Joern, an open source static analysis tool, and demonstrate that the analysis benefits from the additional type information. As our model allows for fast inference times even on commodity CPUs, making our system available through Joern leads to high accessibility and facilitates security research.

This report describes the training dataset creation and recipe behind the family of arctic-embed text embedding models (a set of five models ranging from 22 to 334 million parameters with weights open-sourced under an Apache-2 license). At the time of their release, each model achieved state-of-the-art retrieval accuracy for models of their size on the MTEB Retrieval leaderboard, with the largest model, arctic-embed-l outperforming closed source embedding models such as Cohere's embed-v3 and Open AI's text-embed-3-large. In addition to the details of our training recipe, we have provided several informative ablation studies, which we believe are the cause of our model performance.

We present a statistical model for German medical natural language processing trained for named entity recognition (NER) as an open, publicly available model. The work serves as a refined successor to our first GERNERMED model which is substantially outperformed by our work. We demonstrate the effectiveness of combining multiple techniques in order to achieve strong results in entity recognition performance by the means of transfer-learning on pretrained deep language models (LM), word-alignment and neural machine translation. Due to the sparse situation on open, public medical entity recognition models for German texts, this work offers benefits to the German research community on medical NLP as a baseline model. Since our model is based on public English data, its weights are provided without legal restrictions on usage and distribution. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED-pp

Despite over a decade of legislative efforts to address modern slavery in the supply chains of large corporations, the effectiveness of government oversight remains hampered by the challenge of scrutinizing thousands of statements annually. While Large Language Models (LLMs) can be considered a well established solution for the automatic analysis and summarization of documents, recognizing concrete modern slavery countermeasures taken by companies and differentiating those from vague claims remains a challenging task. To help evaluate and fine-tune LLMs for the assessment of corporate statements, we introduce a dataset composed of 5,731 modern slavery statements taken from the Australian Modern Slavery Register and annotated at the sentence level. This paper details the construction steps for the dataset that include the careful design of annotation specifications, the selection and preprocessing of statements, and the creation of high-quality annotation subsets for effective model evaluations. To demonstrate our dataset's utility, we propose a machine learning methodology for the detection of sentences relevant to mandatory reporting requirements set by the Australian Modern Slavery Act. We then follow this methodology to benchmark modern language models under zero-shot and supervised learning settings.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

In this paper we address issues with image retrieval benchmarking on standard and popular Oxford 5k and Paris 6k datasets. In particular, annotation errors, the size of the dataset, and the level of challenge are addressed: new annotation for both datasets is created with an extra attention to the reliability of the ground truth. Three new protocols of varying difficulty are introduced. The protocols allow fair comparison between different methods, including those using a dataset pre-processing stage. For each dataset, 15 new challenging queries are introduced. Finally, a new set of 1M hard, semi-automatically cleaned distractors is selected. An extensive comparison of the state-of-the-art methods is performed on the new benchmark. Different types of methods are evaluated, ranging from local-feature-based to modern CNN based methods. The best results are achieved by taking the best of the two worlds. Most importantly, image retrieval appears far from being solved.

Distant supervision allows obtaining labeled training corpora for low-resource settings where only limited hand-annotated data exists. However, to be used effectively, the distant supervision must be easy to gather. In this work, we present ANEA, a tool to automatically annotate named entities in texts based on entity lists. It spans the whole pipeline from obtaining the lists to analyzing the errors of the distant supervision. A tuning step allows the user to improve the automatic annotation with their linguistic insights without labelling or checking all tokens manually. In six low-resource scenarios, we show that the F1-score can be increased by on average 18 points through distantly supervised data obtained by ANEA.

We describe a dataset developed for Named Entity Recognition in German federal court decisions. It consists of approx. 67,000 sentences with over 2 million tokens. The resource contains 54,000 manually annotated entities, mapped to 19 fine-grained semantic classes: person, judge, lawyer, country, city, street, landscape, organization, company, institution, court, brand, law, ordinance, European legal norm, regulation, contract, court decision, and legal literature. The legal documents were, furthermore, automatically annotated with more than 35,000 TimeML-based time expressions. The dataset, which is available under a CC-BY 4.0 license in the CoNNL-2002 format, was developed for training an NER service for German legal documents in the EU project Lynx.

Whether the media faithfully communicate scientific information has long been a core issue to the science community. Automatically identifying paraphrased scientific findings could enable large-scale tracking and analysis of information changes in the science communication process, but this requires systems to understand the similarity between scientific information across multiple domains. To this end, we present the SCIENTIFIC PARAPHRASE AND INFORMATION CHANGE DATASET (SPICED), the first paraphrase dataset of scientific findings annotated for degree of information change. SPICED contains 6,000 scientific finding pairs extracted from news stories, social media discussions, and full texts of original papers. We demonstrate that SPICED poses a challenging task and that models trained on SPICED improve downstream performance on evidence retrieval for fact checking of real-world scientific claims. Finally, we show that models trained on SPICED can reveal large-scale trends in the degrees to which people and organizations faithfully communicate new scientific findings. Data, code, and pre-trained models are available at http://www.copenlu.com/publication/2022_emnlp_wright/.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

French language models, such as CamemBERT, have been widely adopted across industries for natural language processing (NLP) tasks, with models like CamemBERT seeing over 4 million downloads per month. However, these models face challenges due to temporal concept drift, where outdated training data leads to a decline in performance, especially when encountering new topics and terminology. This issue emphasizes the need for updated models that reflect current linguistic trends. In this paper, we introduce two new versions of the CamemBERT base model-CamemBERTav2 and CamemBERTv2-designed to address these challenges. CamemBERTav2 is based on the DeBERTaV3 architecture and makes use of the Replaced Token Detection (RTD) objective for better contextual understanding, while CamemBERTv2 is built on RoBERTa, which uses the Masked Language Modeling (MLM) objective. Both models are trained on a significantly larger and more recent dataset with longer context length and an updated tokenizer that enhances tokenization performance for French. We evaluate the performance of these models on both general-domain NLP tasks and domain-specific applications, such as medical field tasks, demonstrating their versatility and effectiveness across a range of use cases. Our results show that these updated models vastly outperform their predecessors, making them valuable tools for modern NLP systems. All our new models, as well as intermediate checkpoints, are made openly available on Huggingface.

We provide a literature review about Automatic Text Summarization (ATS) systems. We consider a citation-based approach. We start with some popular and well-known papers that we have in hand about each topic we want to cover and we have tracked the "backward citations" (papers that are cited by the set of papers we knew beforehand) and the "forward citations" (newer papers that cite the set of papers we knew beforehand). In order to organize the different methods, we present the diverse approaches to ATS guided by the mechanisms they use to generate a summary. Besides presenting the methods, we also present an extensive review of the datasets available for summarization tasks and the methods used to evaluate the quality of the summaries. Finally, we present an empirical exploration of these methods using the CNN Corpus dataset that provides golden summaries for extractive and abstractive methods.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

EuroCrops contains geo-referenced polygons of agricultural croplands from 16 countries of the European Union (EU) as well as information on the respective crop species grown there. These semantic annotations are derived from self-declarations by farmers receiving subsidies under the Common Agriculture Policy (CAP) of the European Commission (EC). Over the last 1.5 years, the individual national crop datasets have been manually collected, the crop classes have been translated into the English language and transferred into the newly developed Hierarchical Crop and Agriculture Taxonomy (HCAT). EuroCrops is publicly available under continuous improvement through an active user community.

The recent integration of deep learning and pairwise similarity annotation-based constrained clustering -- i.e., deep constrained clustering (DCC) -- has proven effective for incorporating weak supervision into massive data clustering: Less than 1% of pair similarity annotations can often substantially enhance the clustering accuracy. However, beyond empirical successes, there is a lack of understanding of DCC. In addition, many DCC paradigms are sensitive to annotation noise, but performance-guaranteed noisy DCC methods have been largely elusive. This work first takes a deep look into a recently emerged logistic loss function of DCC, and characterizes its theoretical properties. Our result shows that the logistic DCC loss ensures the identifiability of data membership under reasonable conditions, which may shed light on its effectiveness in practice. Building upon this understanding, a new loss function based on geometric factor analysis is proposed to fend against noisy annotations. It is shown that even under unknown annotation confusions, the data membership can still be provably identified under our proposed learning criterion. The proposed approach is tested over multiple datasets to validate our claims.

We continue the investigation into the power of smaller Transformer-based language models as initiated by TinyStories -- a 10 million parameter model that can produce coherent English -- and the follow-up work on phi-1, a 1.3 billion parameter model with Python coding performance close to the state-of-the-art. The latter work proposed to use existing Large Language Models (LLMs) to generate ``textbook quality" data as a way to enhance the learning process compared to traditional web data. We follow the ``Textbooks Are All You Need" approach, focusing this time on common sense reasoning in natural language, and create a new 1.3 billion parameter model named phi-1.5, with performance on natural language tasks comparable to models 5x larger, and surpassing most non-frontier LLMs on more complex reasoning tasks such as grade-school mathematics and basic coding. More generally, phi-1.5 exhibits many of the traits of much larger LLMs, both good -- such as the ability to ``think step by step" or perform some rudimentary in-context learning -- and bad, including hallucinations and the potential for toxic and biased generations -- encouragingly though, we are seeing improvement on that front thanks to the absence of web data. We open-source phi-1.5 to promote further research on these urgent topics.

We introduce CheckEval, a novel evaluation framework using Large Language Models, addressing the challenges of ambiguity and inconsistency in current evaluation methods. CheckEval addresses these challenges by dividing evaluation criteria into detailed sub-aspects and constructing a checklist of Boolean questions for each, simplifying the evaluation. This approach not only renders the process more interpretable but also significantly enhances the robustness and reliability of results by focusing on specific evaluation dimensions. Validated through a focused case study using the SummEval benchmark, CheckEval indicates a strong correlation with human judgments. Furthermore, it demonstrates a highly consistent Inter-Annotator Agreement. These findings highlight the effectiveness of CheckEval for objective, flexible, and precise evaluations. By offering a customizable and interactive framework, CheckEval sets a new standard for the use of LLMs in evaluation, responding to the evolving needs of the field and establishing a clear method for future LLM-based evaluation.

Code comments can help in program comprehension and are considered as important artifacts to help developers in software maintenance. However, the comments are mostly missing or are outdated, specially in complex software projects. As a result, several automatic comment generation models are developed as a solution. The recent models explore the integration of external knowledge resources such as Unified Modeling Language class diagrams to improve the generated comments. In this paper, we propose API2Com, a model that leverages the Application Programming Interface Documentations (API Docs) as a knowledge resource for comment generation. The API Docs include the description of the methods in more details and therefore, can provide better context in the generated comments. The API Docs are used along with the code snippets and Abstract Syntax Trees in our model. We apply the model on a large Java dataset of over 130,000 methods and evaluate it using both Transformer and RNN-base architectures. Interestingly, when API Docs are used, the performance increase is negligible. We therefore run different experiments to reason about the results. For methods that only contain one API, adding API Docs improves the results by 4% BLEU score on average (BLEU score is an automatic evaluation metric used in machine translation). However, as the number of APIs that are used in a method increases, the performance of the model in generating comments decreases due to long documentations used in the input. Our results confirm that the API Docs can be useful in generating better comments, but, new techniques are required to identify the most informative ones in a method rather than using all documentations simultaneously.

Annotated data has become the most important bottleneck in training accurate machine learning models, especially for areas that require domain expertise. A recent approach to deal with the above issue proposes using natural language explanations instead of labeling individual data points, thereby increasing human annotators' efficiency as well as decreasing costs substantially. This paper focuses on the task of turning these natural language descriptions into Python labeling functions by following a novel approach to semantic parsing with pre-trained text-to-text Transformers. In a series of experiments our approach achieves a new state of the art on the semantic parsing benchmark CoNaLa, surpassing the previous best approach by 3.7 BLEU points. Furthermore, on a manually constructed dataset of natural language descriptions-labeling functions pairs we achieve a BLEU of 0.39. Our approach can be regarded as a stepping stone towards models that are taught how to label in natural language, instead of being provided specific labeled samples. Our code, constructed dataset and models are available at https://github.com/ypapanik/t5-for-code-generation.

One of the central tasks in software maintenance is being able to understand and develop code changes. Thus, given a natural language description of the desired new operation of a function, an agent (human or AI) might be asked to generate the set of edits to that function to implement the desired new operation; likewise, given a set of edits to a function, an agent might be asked to generate a changed description, of that function's new workings. Thus, there is an incentive to train a neural model for change-related tasks. Motivated by this, we offer a new, "natural", large dataset of coupled changes to code and documentation mined from actual high-quality GitHub projects, where each sample represents a single commit where the code and the associated docstring were changed together. We present the methodology for gathering the dataset, and some sample, challenging (but realistic) tasks where our dataset provides opportunities for both learning and evaluation. We find that current models (specifically Llama-3.1 405B, Mixtral 8times22B) do find these maintenance-related tasks challenging.

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

We present a new dataset for form understanding in noisy scanned documents (FUNSD) that aims at extracting and structuring the textual content of forms. The dataset comprises 199 real, fully annotated, scanned forms. The documents are noisy and vary widely in appearance, making form understanding (FoUn) a challenging task. The proposed dataset can be used for various tasks, including text detection, optical character recognition, spatial layout analysis, and entity labeling/linking. To the best of our knowledge, this is the first publicly available dataset with comprehensive annotations to address FoUn task. We also present a set of baselines and introduce metrics to evaluate performance on the FUNSD dataset, which can be downloaded at https://guillaumejaume.github.io/FUNSD/.

Recent advances in Large Language Models (LLMs) have achieved remarkable breakthroughs in understanding and responding to user intents. However, their performance lag behind general use cases in some expertise domains, such as Chinese medicine. Existing efforts to incorporate Chinese medicine into LLMs rely on Supervised Fine-Tuning (SFT) with single-turn and distilled dialogue data. These models lack the ability for doctor-like proactive inquiry and multi-turn comprehension and cannot align responses with experts' intentions. In this work, we introduce Zhongjing, the first Chinese medical LLaMA-based LLM that implements an entire training pipeline from continuous pre-training, SFT, to Reinforcement Learning from Human Feedback (RLHF). Additionally, we construct a Chinese multi-turn medical dialogue dataset of 70,000 authentic doctor-patient dialogues, CMtMedQA, which significantly enhances the model's capability for complex dialogue and proactive inquiry initiation. We also define a refined annotation rule and evaluation criteria given the unique characteristics of the biomedical domain. Extensive experimental results show that Zhongjing outperforms baselines in various capacities and matches the performance of ChatGPT in some abilities, despite the 100x parameters. Ablation studies also demonstrate the contributions of each component: pre-training enhances medical knowledge, and RLHF further improves instruction-following ability and safety. Our code, datasets, and models are available at https://github.com/SupritYoung/Zhongjing.

With the release of ever more capable large language models (LLMs), researchers in NLP and related disciplines have started to explore the usability of LLMs for a wide variety of different annotation tasks. Very recently, a lot of this attention has shifted to tasks that are subjective in nature. Given that the latest generations of LLMs have digested and encoded extensive knowledge about different human subpopulations and individuals, the hope is that these models can be trained, tuned or prompted to align with a wide range of different human perspectives. While researchers already evaluate the success of this alignment via surveys and tests, there is a lack of resources to evaluate the alignment on what oftentimes matters the most in NLP; the actual downstream tasks. To fill this gap we present SubData, a Python library that offers researchers working on topics related to subjectivity in annotation tasks a convenient way of collecting, combining and using a range of suitable datasets.

Clinical data in hospitals are increasingly accessible for research through clinical data warehouses, however these documents are unstructured. It is therefore necessary to extract information from medical reports to conduct clinical studies. Transfer learning with BERT-like models such as CamemBERT has allowed major advances, especially for named entity recognition. However, these models are trained for plain language and are less efficient on biomedical data. This is why we propose a new French public biomedical dataset on which we have continued the pre-training of CamemBERT. Thus, we introduce a first version of CamemBERT-bio, a specialized public model for the French biomedical domain that shows 2.54 points of F1 score improvement on average on different biomedical named entity recognition tasks. Our findings demonstrate the success of continual pre-training from a French model and contrast with recent proposals on the same domain and language. One of our key contributions highlights the importance of using a standard evaluation protocol that enables a clear view of the current state-of-the-art for French biomedical models.

The process of cyber mapping gives insights in relationships among financial entities and service providers. Centered around the outsourcing practices of companies within fund prospectuses in Germany, we introduce a dataset specifically designed for named entity recognition and relation extraction tasks. The labeling process on 948 sentences was carried out by three experts which yields to 5,969 annotations for four entity types (Outsourcing, Company, Location and Software) and 4,102 relation annotations (Outsourcing-Company, Company-Location). State-of-the-art deep learning models were trained to recognize entities and extract relations showing first promising results. An anonymized version of the dataset, along with guidelines and the code used for model training, are publicly available at https://www.dfki.uni-kl.de/cybermapping/data/CO-Fun-1.0-anonymized.zip.

Named Entity Disambiguation (NED) refers to the task of resolving multiple named entity mentions in a document to their correct references in a knowledge base (KB) (e.g., Wikipedia). In this paper, we propose a novel embedding method specifically designed for NED. The proposed method jointly maps words and entities into the same continuous vector space. We extend the skip-gram model by using two models. The KB graph model learns the relatedness of entities using the link structure of the KB, whereas the anchor context model aims to align vectors such that similar words and entities occur close to one another in the vector space by leveraging KB anchors and their context words. By combining contexts based on the proposed embedding with standard NED features, we achieved state-of-the-art accuracy of 93.1% on the standard CoNLL dataset and 85.2% on the TAC 2010 dataset.

Grammatical Error Detection and Correction (GEC) tools have proven useful for native speakers and second language learners. Developing such tools requires a large amount of parallel, annotated data, which is unavailable for most languages. Synthetic data generation is a common practice to overcome the scarcity of such data. However, it is not straightforward for morphologically rich languages like Turkish due to complex writing rules that require phonological, morphological, and syntactic information. In this work, we present a flexible and extensible synthetic data generation pipeline for Turkish covering more than 20 expert-curated grammar and spelling rules (a.k.a., writing rules) implemented through complex transformation functions. Using this pipeline, we derive 130,000 high-quality parallel sentences from professionally edited articles. Additionally, we create a more realistic test set by manually annotating a set of movie reviews. We implement three baselines formulating the task as i) neural machine translation, ii) sequence tagging, and iii) prefix tuning with a pretrained decoder-only model, achieving strong results. Furthermore, we perform exhaustive experiments on out-of-domain datasets to gain insights on the transferability and robustness of the proposed approaches. Our results suggest that our corpus, GECTurk, is high-quality and allows knowledge transfer for the out-of-domain setting. To encourage further research on Turkish GEC, we release our datasets, baseline models, and the synthetic data generation pipeline at https://github.com/GGLAB-KU/gecturk.

Metadata are general characteristics of the data in a well-curated and condensed format, and have been proven to be useful for decision making, knowledge discovery, and also heterogeneous data organization of biobank. Among all data types in the biobank, pathology is the key component of the biobank and also serves as the gold standard of diagnosis. To maximize the utility of biobank and allow the rapid progress of biomedical science, it is essential to organize the data with well-populated pathology metadata. However, manual annotation of such information is tedious and time-consuming. In the study, we develop a multimodal multitask learning framework to predict four major slide-level metadata of pathology images. The framework learns generalizable representations across tissue slides, pathology reports, and case-level structured data. We demonstrate improved performance across all four tasks with the proposed method compared to a single modal single task baseline on two test sets, one external test set from a distinct data source (TCGA) and one internal held-out test set (TTH). In the test sets, the performance improvements on the averaged area under receiver operating characteristic curve across the four tasks are 16.48% and 9.05% on TCGA and TTH, respectively. Such pathology metadata prediction system may be adopted to mitigate the effort of expert annotation and ultimately accelerate the data-driven research by better utilization of the pathology biobank.

Medication Extraction and Mining play an important role in healthcare NLP research due to its practical applications in hospital settings, such as their mapping into standard clinical knowledge bases (SNOMED-CT, BNF, etc.). In this work, we investigate state-of-the-art LLMs in text mining tasks on medications and their related attributes such as dosage, route, strength, and adverse effects. In addition, we explore different ensemble learning methods (Stack-Ensemble and Voting-Ensemble) to augment the model performances from individual LLMs. Our ensemble learning result demonstrated better performances than individually fine-tuned base models BERT, RoBERTa, RoBERTa-L, BioBERT, BioClinicalBERT, BioMedRoBERTa, ClinicalBERT, and PubMedBERT across general and specific domains. Finally, we build up an entity linking function to map extracted medical terminologies into the SNOMED-CT codes and the British National Formulary (BNF) codes, which are further mapped to the Dictionary of Medicines and Devices (dm+d), and ICD. Our model's toolkit and desktop applications are publicly available at https://github.com/HECTA-UoM/ensemble-NER.

In populous countries, pending legal cases have been growing exponentially. There is a need for developing techniques for processing and organizing legal documents. In this paper, we introduce a new corpus for structuring legal documents. In particular, we introduce a corpus of legal judgment documents in English that are segmented into topical and coherent parts. Each of these parts is annotated with a label coming from a list of pre-defined Rhetorical Roles. We develop baseline models for automatically predicting rhetorical roles in a legal document based on the annotated corpus. Further, we show the application of rhetorical roles to improve performance on the tasks of summarization and legal judgment prediction. We release the corpus and baseline model code along with the paper.

Large-scale data sets on scholarly publications are the basis for a variety of bibliometric analyses and natural language processing (NLP) applications. Especially data sets derived from publication's full-text have recently gained attention. While several such data sets already exist, we see key shortcomings in terms of their domain and time coverage, citation network completeness, and representation of full-text content. To address these points, we propose a new version of the data set unarXive. We base our data processing pipeline and output format on two existing data sets, and improve on each of them. Our resulting data set comprises 1.9 M publications spanning multiple disciplines and 32 years. It furthermore has a more complete citation network than its predecessors and retains a richer representation of document structure as well as non-textual publication content such as mathematical notation. In addition to the data set, we provide ready-to-use training/test data for citation recommendation and IMRaD classification. All data and source code is publicly available at https://github.com/IllDepence/unarXive.

The quality of the dataset is crucial for ensuring optimal performance and reliability of downstream task models. However, datasets often contain noisy data inadvertently included during the construction process. Numerous attempts have been made to correct this issue through human annotators. However, hiring and managing human annotators is expensive and time-consuming. As an alternative, recent studies are exploring the use of large language models (LLMs) for data annotation. In this study, we present a case study that extends the application of LLM-based data annotation to enhance the quality of existing datasets through a cleansing strategy. Specifically, we leverage approaches such as chain-of-thought (CoT) and majority voting to imitate human annotation and classify unrelated documents from the Multi-News dataset, which is widely used for the multi-document summarization task. Through our proposed cleansing method, we introduce an enhanced Multi-News+. By employing LLMs for data cleansing, we demonstrate an efficient and effective approach to improving dataset quality without relying on expensive human annotation efforts.

The proliferation of bias and propaganda on social media is an increasingly significant concern, leading to the development of techniques for automatic detection. This article presents a multilingual corpus of 12, 000 Facebook posts fully annotated for bias and propaganda. The corpus was created as part of the FigNews 2024 Shared Task on News Media Narratives for framing the Israeli War on Gaza. It covers various events during the War from October 7, 2023 to January 31, 2024. The corpus comprises 12, 000 posts in five languages (Arabic, Hebrew, English, French, and Hindi), with 2, 400 posts for each language. The annotation process involved 10 graduate students specializing in Law. The Inter-Annotator Agreement (IAA) was used to evaluate the annotations of the corpus, with an average IAA of 80.8% for bias and 70.15% for propaganda annotations. Our team was ranked among the bestperforming teams in both Bias and Propaganda subtasks. The corpus is open-source and available at https://sina.birzeit.edu/fada

Entities are at the center of how we represent and aggregate knowledge. For instance, Encyclopedias such as Wikipedia are structured by entities (e.g., one per Wikipedia article). The ability to retrieve such entities given a query is fundamental for knowledge-intensive tasks such as entity linking and open-domain question answering. Current approaches can be understood as classifiers among atomic labels, one for each entity. Their weight vectors are dense entity representations produced by encoding entity meta information such as their descriptions. This approach has several shortcomings: (i) context and entity affinity is mainly captured through a vector dot product, potentially missing fine-grained interactions; (ii) a large memory footprint is needed to store dense representations when considering large entity sets; (iii) an appropriately hard set of negative data has to be subsampled at training time. In this work, we propose GENRE, the first system that retrieves entities by generating their unique names, left to right, token-by-token in an autoregressive fashion. This mitigates the aforementioned technical issues since: (i) the autoregressive formulation directly captures relations between context and entity name, effectively cross encoding both; (ii) the memory footprint is greatly reduced because the parameters of our encoder-decoder architecture scale with vocabulary size, not entity count; (iii) the softmax loss is computed without subsampling negative data. We experiment with more than 20 datasets on entity disambiguation, end-to-end entity linking and document retrieval tasks, achieving new state-of-the-art or very competitive results while using a tiny fraction of the memory footprint of competing systems. Finally, we demonstrate that new entities can be added by simply specifying their names. Code and pre-trained models at https://github.com/facebookresearch/GENRE.

ROOTS is a 1.6TB multilingual text corpus developed for the training of BLOOM, currently the largest language model explicitly accompanied by commensurate data governance efforts. In continuation of these efforts, we present the ROOTS Search Tool: a search engine over the entire ROOTS corpus offering both fuzzy and exact search capabilities. ROOTS is the largest corpus to date that can be investigated this way. The ROOTS Search Tool is open-sourced and available on Hugging Face Spaces. We describe our implementation and the possible use cases of our tool.

Automatic Term Extraction deals with the extraction of terminology from a domain specific corpus, and has long been an established research area in data and knowledge acquisition. ATE remains a challenging task as it is known that there is no existing ATE methods that can consistently outperform others in any domain. This work adopts a refreshed perspective to this problem: instead of searching for such a 'one-size-fit-all' solution that may never exist, we propose to develop generic methods to 'enhance' existing ATE methods. We introduce SemRe-Rank, the first method based on this principle, to incorporate semantic relatedness - an often overlooked venue - into an existing ATE method to further improve its performance. SemRe-Rank incorporates word embeddings into a personalised PageRank process to compute 'semantic importance' scores for candidate terms from a graph of semantically related words (nodes), which are then used to revise the scores of candidate terms computed by a base ATE algorithm. Extensively evaluated with 13 state-of-the-art base ATE methods on four datasets of diverse nature, it is shown to have achieved widespread improvement over all base methods and across all datasets, with up to 15 percentage points when measured by the Precision in the top ranked K candidate terms (the average for a set of K's), or up to 28 percentage points in F1 measured at a K that equals to the expected real terms in the candidates (F1 in short). Compared to an alternative approach built on the well-known TextRank algorithm, SemRe-Rank can potentially outperform by up to 8 points in Precision at top K, or up to 17 points in F1.

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language foundation models, which thrive on substantially larger scales. Furthermore, genome understanding involves numerous downstream genome annotation tasks with inherent data heterogeneity, thereby necessitating more efficient and robust fine-tuning methods tailored for genomics. Here, we present Lingo: Language prefix fIne-tuning for GenOmes. Unlike DNA foundation models, Lingo strategically leverages natural language foundation models' contextual cues, recalibrating their linguistic knowledge to genomic sequences. Lingo further accommodates numerous, heterogeneous downstream fine-tune tasks by an adaptive rank sampling method that prunes and stochastically reintroduces pruned singular vectors within small computational budgets. Adaptive rank sampling outperformed existing fine-tuning methods on all benchmarked 14 genome understanding tasks, while requiring fewer than 2\% of trainable parameters as genomic-specific adapters. Impressively, applying these adapters on natural language foundation models matched or even exceeded the performance of DNA foundation models. Lingo presents a new paradigm of efficient and scalable genome understanding via genomic-specific adapters on language models.

Albeit Natural Language Processing has seen major breakthroughs in the last few years, transferring such advances into real-world business cases can be challenging. One of the reasons resides in the displacement between popular benchmarks and actual data. Lack of supervision, unbalanced classes, noisy data and long documents often affect real problems in vertical domains such as finance, law and health. To support industry-oriented research, we present BUSTER, a BUSiness Transaction Entity Recognition dataset. The dataset consists of 3779 manually annotated documents on financial transactions. We establish several baselines exploiting both general-purpose and domain-specific language models. The best performing model is also used to automatically annotate 6196 documents, which we release as an additional silver corpus to BUSTER.

Demand for image editing has been increasing as users' desire for expression is also increasing. However, for most users, image editing tools are not easy to use since the tools require certain expertise in photo effects and have complex interfaces. Hence, users might need someone to help edit their images, but having a personal dedicated human assistant for every user is impossible to scale. For that reason, an automated assistant system for image editing is desirable. Additionally, users want more image sources for diverse image editing works, and integrating an image search functionality into the editing tool is a potential remedy for this demand. Thus, we propose a dataset of an automated Conversational Agent for Image Search and Editing (CAISE). To our knowledge, this is the first dataset that provides conversational image search and editing annotations, where the agent holds a grounded conversation with users and helps them to search and edit images according to their requests. To build such a system, we first collect image search and editing conversations between pairs of annotators. The assistant-annotators are equipped with a customized image search and editing tool to address the requests from the user-annotators. The functions that the assistant-annotators conduct with the tool are recorded as executable commands, allowing the trained system to be useful for real-world application execution. We also introduce a generator-extractor baseline model for this task, which can adaptively select the source of the next token (i.e., from the vocabulary or from textual/visual contexts) for the executable command. This serves as a strong starting point while still leaving a large human-machine performance gap for useful future work. Our code and dataset are publicly available at: https://github.com/hyounghk/CAISE

While the general machine learning (ML) community has benefited from public datasets, tasks, and models, the progress of ML in healthcare has been hampered by a lack of such shared assets. The success of foundation models creates new challenges for healthcare ML by requiring access to shared pretrained models to validate performance benefits. We help address these challenges through three contributions. First, we publish a new dataset, EHRSHOT, which contains deidentified structured data from the electronic health records (EHRs) of 6,739 patients from Stanford Medicine. Unlike MIMIC-III/IV and other popular EHR datasets, EHRSHOT is longitudinal and not restricted to ICU/ED patients. Second, we publish the weights of CLMBR-T-base, a 141M parameter clinical foundation model pretrained on the structured EHR data of 2.57M patients. We are one of the first to fully release such a model for coded EHR data; in contrast, most prior models released for clinical data (e.g. GatorTron, ClinicalBERT) only work with unstructured text and cannot process the rich, structured data within an EHR. We provide an end-to-end pipeline for the community to validate and build upon its performance. Third, we define 15 few-shot clinical prediction tasks, enabling evaluation of foundation models on benefits such as sample efficiency and task adaptation. Our model and dataset are available via a research data use agreement from the Stanford AIMI Center. Code to reproduce our results are available at our Github repo: https://github.com/som-shahlab/ehrshot-benchmark

Recent studies have revealed a number of pathologies of neural machine translation (NMT) systems. Hypotheses explaining these mostly suggest there is something fundamentally wrong with NMT as a model or its training algorithm, maximum likelihood estimation (MLE). Most of this evidence was gathered using maximum a posteriori (MAP) decoding, a decision rule aimed at identifying the highest-scoring translation, i.e. the mode. We argue that the evidence corroborates the inadequacy of MAP decoding more than casts doubt on the model and its training algorithm. In this work, we show that translation distributions do reproduce various statistics of the data well, but that beam search strays from such statistics. We show that some of the known pathologies and biases of NMT are due to MAP decoding and not to NMT's statistical assumptions nor MLE. In particular, we show that the most likely translations under the model accumulate so little probability mass that the mode can be considered essentially arbitrary. We therefore advocate for the use of decision rules that take into account the translation distribution holistically. We show that an approximation to minimum Bayes risk decoding gives competitive results confirming that NMT models do capture important aspects of translation well in expectation.

Document layout analysis is a known problem to the documents research community and has been vastly explored yielding a multitude of solutions ranging from text mining, and recognition to graph-based representation, visual feature extraction, etc. However, most of the existing works have ignored the crucial fact regarding the scarcity of labeled data. With growing internet connectivity to personal life, an enormous amount of documents had been available in the public domain and thus making data annotation a tedious task. We address this challenge using self-supervision and unlike, the few existing self-supervised document segmentation approaches which use text mining and textual labels, we use a complete vision-based approach in pre-training without any ground-truth label or its derivative. Instead, we generate pseudo-layouts from the document images to pre-train an image encoder to learn the document object representation and localization in a self-supervised framework before fine-tuning it with an object detection model. We show that our pipeline sets a new benchmark in this context and performs at par with the existing methods and the supervised counterparts, if not outperforms. The code is made publicly available at: https://github.com/MaitySubhajit/SelfDocSeg

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

Annotator disagreement is ubiquitous in natural language processing (NLP) tasks. There are multiple reasons for such disagreements, including the subjectivity of the task, difficult cases, unclear guidelines, and so on. Rather than simply aggregating labels to obtain data annotations, we instead try to directly model the diverse perspectives of the annotators, and explicitly account for annotators' idiosyncrasies in the modeling process by creating representations for each annotator (annotator embeddings) and also their annotations (annotation embeddings). In addition, we propose TID-8, The Inherent Disagreement - 8 dataset, a benchmark that consists of eight existing language understanding datasets that have inherent annotator disagreement. We test our approach on TID-8 and show that our approach helps models learn significantly better from disagreements on six different datasets in TID-8 while increasing model size by fewer than 1% parameters. By capturing the unique tendencies and subjectivity of individual annotators through embeddings, our representations prime AI models to be inclusive of diverse viewpoints.

This study introduces the eFontes models for automatic linguistic annotation of Medieval Latin texts, focusing on lemmatization, part-of-speech tagging, and morphological feature determination. Using the Transformers library, these models were trained on Universal Dependencies (UD) corpora and the newly developed eFontes corpus of Polish Medieval Latin. The research evaluates the models' performance, addressing challenges such as orthographic variations and the integration of Latinized vernacular terms. The models achieved high accuracy rates: lemmatization at 92.60%, part-of-speech tagging at 83.29%, and morphological feature determination at 88.57%. The findings underscore the importance of high-quality annotated corpora and propose future enhancements, including extending the models to Named Entity Recognition.

We present a human-and-model-in-the-loop process for dynamically generating datasets and training better performing and more robust hate detection models. We provide a new dataset of ~40,000 entries, generated and labelled by trained annotators over four rounds of dynamic data creation. It includes ~15,000 challenging perturbations and each hateful entry has fine-grained labels for the type and target of hate. Hateful entries make up 54% of the dataset, which is substantially higher than comparable datasets. We show that model performance is substantially improved using this approach. Models trained on later rounds of data collection perform better on test sets and are harder for annotators to trick. They also perform better on HateCheck, a suite of functional tests for online hate detection. We provide the code, dataset and annotation guidelines for other researchers to use. Accepted at ACL 2021.

Benchmark datasets for table structure recognition (TSR) must be carefully processed to ensure they are annotated consistently. However, even if a dataset's annotations are self-consistent, there may be significant inconsistency across datasets, which can harm the performance of models trained and evaluated on them. In this work, we show that aligning these benchmarksx2014removing both errors and inconsistency between themx2014improves model performance significantly. We demonstrate this through a data-centric approach where we adopt a single model architecture, the Table Transformer (TATR), that we hold fixed throughout. Baseline exact match accuracy for TATR evaluated on the ICDAR-2013 benchmark is 65% when trained on PubTables-1M, 42% when trained on FinTabNet, and 69% combined. After reducing annotation mistakes and inter-dataset inconsistency, performance of TATR evaluated on ICDAR-2013 increases substantially to 75% when trained on PubTables-1M, 65% when trained on FinTabNet, and 81% combined. We show through ablations over the modification steps that canonicalization of the table annotations has a significantly positive effect on performance, while other choices balance necessary trade-offs that arise when deciding a benchmark dataset's final composition. Overall we believe our work has significant implications for benchmark design for TSR and potentially other tasks as well. All dataset processing and training code will be released.

We propose a new shared task for tactical data-to-text generation in the domain of source code libraries. Specifically, we focus on text generation of function descriptions from example software projects. Data is drawn from existing resources used for studying the related problem of semantic parser induction (Richardson and Kuhn, 2017b; Richardson and Kuhn, 2017a), and spans a wide variety of both natural languages and programming languages. In this paper, we describe these existing resources, which will serve as training and development data for the task, and discuss plans for building new independent test sets.

The role of sentiment analysis is increasingly emerging to study software developers' emotions by mining crowd-generated content within social software engineering tools. However, off-the-shelf sentiment analysis tools have been trained on non-technical domains and general-purpose social media, thus resulting in misclassifications of technical jargon and problem reports. Here, we present Senti4SD, a classifier specifically trained to support sentiment analysis in developers' communication channels. Senti4SD is trained and validated using a gold standard of Stack Overflow questions, answers, and comments manually annotated for sentiment polarity. It exploits a suite of both lexicon- and keyword-based features, as well as semantic features based on word embedding. With respect to a mainstream off-the-shelf tool, which we use as a baseline, Senti4SD reduces the misclassifications of neutral and positive posts as emotionally negative. To encourage replications, we release a lab package including the classifier, the word embedding space, and the gold standard with annotation guidelines.

Mathematical symbols and descriptions appear in various forms across document section boundaries without explicit markup. In this paper, we present a new large-scale dataset that emphasizes extracting symbols and descriptions in scientific documents. Symlink annotates scientific papers of 5 different domains (i.e., computer science, biology, physics, mathematics, and economics). Our experiments on Symlink demonstrate the challenges of the symbol-description linking task for existing models and call for further research effort in this area. We will publicly release Symlink to facilitate future research.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

The success of pre-trained contextualized representations has prompted researchers to analyze them for the presence of linguistic information. Indeed, it is natural to assume that these pre-trained representations do encode some level of linguistic knowledge as they have brought about large empirical improvements on a wide variety of NLP tasks, which suggests they are learning true linguistic generalization. In this work, we focus on intrinsic probing, an analysis technique where the goal is not only to identify whether a representation encodes a linguistic attribute but also to pinpoint where this attribute is encoded. We propose a novel latent-variable formulation for constructing intrinsic probes and derive a tractable variational approximation to the log-likelihood. Our results show that our model is versatile and yields tighter mutual information estimates than two intrinsic probes previously proposed in the literature. Finally, we find empirical evidence that pre-trained representations develop a cross-lingually entangled notion of morphosyntax.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly for applications in drug discovery, remains a challenge due to the complexity of RNA structures and interactions. While foundational models in biology have demonstrated success in modeling several biomolecules, especially proteins, achieving similar breakthroughs for RNA has proven more difficult. Current RNA models have yet to match the performance observed in the protein domain, leaving an important gap in computational biology. In this work, we present ChaRNABERT, a suite of sample and parameter-efficient RNA foundational models, that through a learnable tokenization process, are able to reach state-of-the-art performance on several tasks in established benchmarks. We extend its testing in relevant downstream tasks such as RNA-protein and aptamer-protein interaction prediction. Weights and inference code for ChaRNABERT-8M will be provided for academic research use. The other models will be available upon request.

This paper explores the use of open generative Large Language Models (LLMs) for annotation tasks in the social sciences. The study highlights the challenges associated with proprietary models, such as limited reproducibility and privacy concerns, and advocates for the adoption of open (source) models that can be operated on independent devices. Two examples of annotation tasks, sentiment analysis in tweets and identification of leisure activities in childhood aspirational essays are provided. The study evaluates the performance of different prompting strategies and models (neural-chat-7b-v3-2, Starling-LM-7B-alpha, openchat_3.5, zephyr-7b-alpha and zephyr-7b-beta). The results indicate the need for careful validation and tailored prompt engineering. The study highlights the advantages of open models for data privacy and reproducibility.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

Accurate mapping of the built asset information to established data classification systems and taxonomies is crucial for effective asset management, whether for compliance at project handover or ad-hoc data integration scenarios. Due to the complex nature of built asset data, which predominantly comprises technical text elements, this process remains largely manual and reliant on domain expert input. Recent breakthroughs in contextual text representation learning (text embedding), particularly through pre-trained large language models, offer promising approaches that can facilitate the automation of cross-mapping of the built asset data. However, no comprehensive evaluation has yet been conducted to assess these models' ability to effectively represent the complex semantics specific to built asset technical terminology. This study presents a comparative benchmark of state-of-the-art text embedding models to evaluate their effectiveness in aligning built asset information with domain-specific technical concepts. Our proposed datasets are derived from two renowned built asset data classification dictionaries. The results of our benchmarking across six proposed datasets, covering three tasks of clustering, retrieval, and reranking, highlight the need for future research on domain adaptation techniques. The benchmarking resources are published as an open-source library, which will be maintained and extended to support future evaluations in this field.

The CoNLL-03 corpus is arguably the most well-known and utilized benchmark dataset for named entity recognition (NER). However, prior works found significant numbers of annotation errors, incompleteness, and inconsistencies in the data. This poses challenges to objectively comparing NER approaches and analyzing their errors, as current state-of-the-art models achieve F1-scores that are comparable to or even exceed the estimated noise level in CoNLL-03. To address this issue, we present a comprehensive relabeling effort assisted by automatic consistency checking that corrects 7.0% of all labels in the English CoNLL-03. Our effort adds a layer of entity linking annotation both for better explainability of NER labels and as additional safeguard of annotation quality. Our experimental evaluation finds not only that state-of-the-art approaches reach significantly higher F1-scores (97.1%) on our data, but crucially that the share of correct predictions falsely counted as errors due to annotation noise drops from 47% to 6%. This indicates that our resource is well suited to analyze the remaining errors made by state-of-the-art models, and that the theoretical upper bound even on high resource, coarse-grained NER is not yet reached. To facilitate such analysis, we make CleanCoNLL publicly available to the research community.