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Sep 3

Human-Aligned Faithfulness in Toxicity Explanations of LLMs

The discourse around toxicity and LLMs in NLP largely revolves around detection tasks. This work shifts the focus to evaluating LLMs' reasoning about toxicity -- from their explanations that justify a stance -- to enhance their trustworthiness in downstream tasks. Despite extensive research on explainability, it is not straightforward to adopt existing methods to evaluate free-form toxicity explanation due to their over-reliance on input text perturbations, among other challenges. To account for these, we propose a novel, theoretically-grounded multi-dimensional criterion, Human-Aligned Faithfulness (HAF), that measures the extent to which LLMs' free-form toxicity explanations align with those of a rational human under ideal conditions. We develop six metrics, based on uncertainty quantification, to comprehensively evaluate \haf of LLMs' toxicity explanations with no human involvement, and highlight how "non-ideal" the explanations are. We conduct several experiments on three Llama models (of size up to 70B) and an 8B Ministral model on five diverse toxicity datasets. Our results show that while LLMs generate plausible explanations to simple prompts, their reasoning about toxicity breaks down when prompted about the nuanced relations between the complete set of reasons, the individual reasons, and their toxicity stances, resulting in inconsistent and nonsensical responses. We open-source our code and LLM-generated explanations at https://github.com/uofthcdslab/HAF.

Automated Identification of Toxic Code Reviews Using ToxiCR

Toxic conversations during software development interactions may have serious repercussions on a Free and Open Source Software (FOSS) development project. For example, victims of toxic conversations may become afraid to express themselves, therefore get demotivated, and may eventually leave the project. Automated filtering of toxic conversations may help a FOSS community to maintain healthy interactions among its members. However, off-the-shelf toxicity detectors perform poorly on Software Engineering (SE) datasets, such as one curated from code review comments. To encounter this challenge, we present ToxiCR, a supervised learning-based toxicity identification tool for code review interactions. ToxiCR includes a choice to select one of the ten supervised learning algorithms, an option to select text vectorization techniques, eight preprocessing steps, and a large-scale labeled dataset of 19,571 code review comments. Two out of those eight preprocessing steps are SE domain specific. With our rigorous evaluation of the models with various combinations of preprocessing steps and vectorization techniques, we have identified the best combination for our dataset that boosts 95.8% accuracy and 88.9% F1 score. ToxiCR significantly outperforms existing toxicity detectors on our dataset. We have released our dataset, pre-trained models, evaluation results, and source code publicly available at: https://github.com/WSU-SEAL/ToxiCR

Toxicity of the Commons: Curating Open-Source Pre-Training Data

Open-source large language models are becoming increasingly available and popular among researchers and practitioners. While significant progress has been made on open-weight models, open training data is a practice yet to be adopted by the leading open-weight models creators. At the same time, there researchers are working to make language models safer. We propose a data curation pipeline to reduce harmful outputs by models trained on public domain data. There are unique challenges to working with public domain data, as these sources differ from web text in both form and content. Many sources are historical documents and are the result of Optical Character Recognition (OCR). Consequently, current state-of-the-art approaches to toxicity filtering are often infeasible or inappropriate for open data models. In this paper, we introduce a new fully open-source pipeline for open-data toxicity filtering. Our contributions are threefold. We create a custom training dataset, ToxicCommons, which is composed of texts which have been classified across five different dimensions (racial/origin-based, gender/sex-based, religious, ability-based discrimination, and violence). We use this dataset to train a custom classifier, Celadon, that can be used to detect toxic content in open data more efficiently at a larger scale. Finally, we describe the balanced approach to content filtration that optimizes safety filtering with respect to the filtered data available for training.

IndicLLMSuite: A Blueprint for Creating Pre-training and Fine-Tuning Datasets for Indian Languages

Despite the considerable advancements in English LLMs, the progress in building comparable models for other languages has been hindered due to the scarcity of tailored resources. Our work aims to bridge this divide by introducing an expansive suite of resources specifically designed for the development of Indic LLMs, covering 22 languages, containing a total of 251B tokens and 74.8M instruction-response pairs. Recognizing the importance of both data quality and quantity, our approach combines highly curated manually verified data, unverified yet valuable data, and synthetic data. We build a clean, open-source pipeline for curating pre-training data from diverse sources, including websites, PDFs, and videos, incorporating best practices for crawling, cleaning, flagging, and deduplication. For instruction-fine tuning, we amalgamate existing Indic datasets, translate/transliterate English datasets into Indian languages, and utilize LLaMa2 and Mixtral models to create conversations grounded in articles from Indian Wikipedia and Wikihow. Additionally, we address toxicity alignment by generating toxic prompts for multiple scenarios and then generate non-toxic responses by feeding these toxic prompts to an aligned LLaMa2 model. We hope that the datasets, tools, and resources released as a part of this work will not only propel the research and development of Indic LLMs but also establish an open-source blueprint for extending such efforts to other languages. The data and other artifacts created as part of this work are released with permissive licenses.

RealToxicityPrompts: Evaluating Neural Toxic Degeneration in Language Models

Pretrained neural language models (LMs) are prone to generating racist, sexist, or otherwise toxic language which hinders their safe deployment. We investigate the extent to which pretrained LMs can be prompted to generate toxic language, and the effectiveness of controllable text generation algorithms at preventing such toxic degeneration. We create and release RealToxicityPrompts, a dataset of 100K naturally occurring, sentence-level prompts derived from a large corpus of English web text, paired with toxicity scores from a widely-used toxicity classifier. Using RealToxicityPrompts, we find that pretrained LMs can degenerate into toxic text even from seemingly innocuous prompts. We empirically assess several controllable generation methods, and find that while data- or compute-intensive methods (e.g., adaptive pretraining on non-toxic data) are more effective at steering away from toxicity than simpler solutions (e.g., banning "bad" words), no current method is failsafe against neural toxic degeneration. To pinpoint the potential cause of such persistent toxic degeneration, we analyze two web text corpora used to pretrain several LMs (including GPT-2; Radford et. al, 2019), and find a significant amount of offensive, factually unreliable, and otherwise toxic content. Our work provides a test bed for evaluating toxic generations by LMs and stresses the need for better data selection processes for pretraining.

HalluciDoctor: Mitigating Hallucinatory Toxicity in Visual Instruction Data

Multi-modal Large Language Models (MLLMs) tuned on machine-generated instruction-following data have demonstrated remarkable performance in various multi-modal understanding and generation tasks. However, the hallucinations inherent in machine-generated data, which could lead to hallucinatory outputs in MLLMs, remain under-explored. This work aims to investigate various hallucinations (i.e., object, relation, attribute hallucinations) and mitigate those hallucinatory toxicities in large-scale machine-generated visual instruction datasets. Drawing on the human ability to identify factual errors, we present a novel hallucination detection and elimination framework, HalluciDoctor, based on the cross-checking paradigm. We use our framework to identify and eliminate hallucinations in the training data automatically. Interestingly, HalluciDoctor also indicates that spurious correlations arising from long-tail object co-occurrences contribute to hallucinations. Based on that, we execute counterfactual visual instruction expansion to balance data distribution, thereby enhancing MLLMs' resistance to hallucinations. Comprehensive experiments on hallucination evaluation benchmarks show that our method successfully mitigates 44.6% hallucinations relatively and maintains competitive performance compared to LLaVA.The source code will be released at https://github.com/Yuqifan1117/HalluciDoctor.

CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction

Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated data and lack of interpretability limit their applicability. This limits their ability to capture organ-specific toxicities driven by complex biological mechanisms. Large language models (LLMs) offer a promising alternative through step-by-step reasoning and integration of textual data, yet prior approaches lack biological context and transparent rationale. To address this issue, we propose CoTox, a novel framework that integrates LLM with chain-of-thought (CoT) reasoning for multi-toxicity prediction. CoTox combines chemical structure data, biological pathways, and gene ontology (GO) terms to generate interpretable toxicity predictions through step-by-step reasoning. Using GPT-4o, we show that CoTox outperforms both traditional machine learning and deep learning model. We further examine its performance across various LLMs to identify where CoTox is most effective. Additionally, we find that representing chemical structures with IUPAC names, which are easier for LLMs to understand than SMILES, enhances the model's reasoning ability and improves predictive performance. To demonstrate its practical utility in drug development, we simulate the treatment of relevant cell types with drug and incorporated the resulting biological context into the CoTox framework. This approach allow CoTox to generate toxicity predictions aligned with physiological responses, as shown in case study. This result highlights the potential of LLM-based frameworks to improve interpretability and support early-stage drug safety assessment. The code and prompt used in this work are available at https://github.com/dmis-lab/CoTox.

BeanCounter: A low-toxicity, large-scale, and open dataset of business-oriented text

Many of the recent breakthroughs in language modeling have resulted from scaling effectively the same model architecture to larger datasets. In this vein, recent work has highlighted performance gains from increasing training dataset size and quality, suggesting a need for novel sources of large-scale datasets. In this work, we introduce BeanCounter, a public dataset consisting of more than 159B tokens extracted from businesses' disclosures. We show that this data is indeed novel: less than 0.1% of BeanCounter appears in Common Crawl-based datasets and it is an order of magnitude larger than datasets relying on similar sources. Given the data's provenance, we hypothesize that BeanCounter is comparatively more factual and less toxic than web-based datasets. Exploring this hypothesis, we find that many demographic identities occur with similar prevalence in BeanCounter but with significantly less toxic context relative to other datasets. To demonstrate the utility of BeanCounter, we evaluate and compare two LLMs continually pre-trained on BeanCounter with their base models. We find an 18-33% reduction in toxic generation and improved performance within the finance domain for the continually pretrained models. Collectively, our work suggests that BeanCounter is a novel source of low-toxicity and high-quality domain-specific data with sufficient scale to train multi-billion parameter LLMs.

IndoToxic2024: A Demographically-Enriched Dataset of Hate Speech and Toxicity Types for Indonesian Language

Hate speech poses a significant threat to social harmony. Over the past two years, Indonesia has seen a ten-fold increase in the online hate speech ratio, underscoring the urgent need for effective detection mechanisms. However, progress is hindered by the limited availability of labeled data for Indonesian texts. The condition is even worse for marginalized minorities, such as Shia, LGBTQ, and other ethnic minorities because hate speech is underreported and less understood by detection tools. Furthermore, the lack of accommodation for subjectivity in current datasets compounds this issue. To address this, we introduce IndoToxic2024, a comprehensive Indonesian hate speech and toxicity classification dataset. Comprising 43,692 entries annotated by 19 diverse individuals, the dataset focuses on texts targeting vulnerable groups in Indonesia, specifically during the hottest political event in the country: the presidential election. We establish baselines for seven binary classification tasks, achieving a macro-F1 score of 0.78 with a BERT model (IndoBERTweet) fine-tuned for hate speech classification. Furthermore, we demonstrate how incorporating demographic information can enhance the zero-shot performance of the large language model, gpt-3.5-turbo. However, we also caution that an overemphasis on demographic information can negatively impact the fine-tuned model performance due to data fragmentation.

Red teaming ChatGPT via Jailbreaking: Bias, Robustness, Reliability and Toxicity

Recent breakthroughs in natural language processing (NLP) have permitted the synthesis and comprehension of coherent text in an open-ended way, therefore translating the theoretical algorithms into practical applications. The large language models (LLMs) have significantly impacted businesses such as report summarization software and copywriters. Observations indicate, however, that LLMs may exhibit social prejudice and toxicity, posing ethical and societal dangers of consequences resulting from irresponsibility. Large-scale benchmarks for accountable LLMs should consequently be developed. Although several empirical investigations reveal the existence of a few ethical difficulties in advanced LLMs, there is little systematic examination and user study of the risks and harmful behaviors of current LLM usage. To further educate future efforts on constructing ethical LLMs responsibly, we perform a qualitative research method called ``red teaming'' on OpenAI's ChatGPTIn this paper, ChatGPT refers to the version released on Dec 15th. to better understand the practical features of ethical dangers in recent LLMs. We analyze ChatGPT comprehensively from four perspectives: 1) Bias 2) Reliability 3) Robustness 4) Toxicity. In accordance with our stated viewpoints, we empirically benchmark ChatGPT on multiple sample datasets. We find that a significant number of ethical risks cannot be addressed by existing benchmarks, and hence illustrate them via additional case studies. In addition, we examine the implications of our findings on AI ethics and harmal behaviors of ChatGPT, as well as future problems and practical design considerations for responsible LLMs. We believe that our findings may give light on future efforts to determine and mitigate the ethical hazards posed by machines in LLM applications.

Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?

Toxicity remains a leading cause of early-stage drug development failure. Despite advances in molecular design and property prediction, the task of molecular toxicity repair - generating structurally valid molecular alternatives with reduced toxicity - has not yet been systematically defined or benchmarked. To fill this gap, we introduce ToxiMol, the first benchmark task for general-purpose Multimodal Large Language Models (MLLMs) focused on molecular toxicity repair. We construct a standardized dataset covering 11 primary tasks and 560 representative toxic molecules spanning diverse mechanisms and granularities. We design a prompt annotation pipeline with mechanism-aware and task-adaptive capabilities, informed by expert toxicological knowledge. In parallel, we propose an automated evaluation framework, ToxiEval, which integrates toxicity endpoint prediction, synthetic accessibility, drug-likeness, and structural similarity into a high-throughput evaluation chain for repair success. We systematically assess nearly 30 mainstream general-purpose MLLMs and design multiple ablation studies to analyze key factors such as evaluation criteria, candidate diversity, and failure attribution. Experimental results show that although current MLLMs still face significant challenges on this task, they begin to demonstrate promising capabilities in toxicity understanding, semantic constraint adherence, and structure-aware molecule editing.

ToxiGen: A Large-Scale Machine-Generated Dataset for Adversarial and Implicit Hate Speech Detection

Toxic language detection systems often falsely flag text that contains minority group mentions as toxic, as those groups are often the targets of online hate. Such over-reliance on spurious correlations also causes systems to struggle with detecting implicitly toxic language. To help mitigate these issues, we create ToxiGen, a new large-scale and machine-generated dataset of 274k toxic and benign statements about 13 minority groups. We develop a demonstration-based prompting framework and an adversarial classifier-in-the-loop decoding method to generate subtly toxic and benign text with a massive pretrained language model. Controlling machine generation in this way allows ToxiGen to cover implicitly toxic text at a larger scale, and about more demographic groups, than previous resources of human-written text. We conduct a human evaluation on a challenging subset of ToxiGen and find that annotators struggle to distinguish machine-generated text from human-written language. We also find that 94.5% of toxic examples are labeled as hate speech by human annotators. Using three publicly-available datasets, we show that finetuning a toxicity classifier on our data improves its performance on human-written data substantially. We also demonstrate that ToxiGen can be used to fight machine-generated toxicity as finetuning improves the classifier significantly on our evaluation subset. Our code and data can be found at https://github.com/microsoft/ToxiGen.

Efficient Detection of Toxic Prompts in Large Language Models

Large language models (LLMs) like ChatGPT and Gemini have significantly advanced natural language processing, enabling various applications such as chatbots and automated content generation. However, these models can be exploited by malicious individuals who craft toxic prompts to elicit harmful or unethical responses. These individuals often employ jailbreaking techniques to bypass safety mechanisms, highlighting the need for robust toxic prompt detection methods. Existing detection techniques, both blackbox and whitebox, face challenges related to the diversity of toxic prompts, scalability, and computational efficiency. In response, we propose ToxicDetector, a lightweight greybox method designed to efficiently detect toxic prompts in LLMs. ToxicDetector leverages LLMs to create toxic concept prompts, uses embedding vectors to form feature vectors, and employs a Multi-Layer Perceptron (MLP) classifier for prompt classification. Our evaluation on various versions of the LLama models, Gemma-2, and multiple datasets demonstrates that ToxicDetector achieves a high accuracy of 96.39\% and a low false positive rate of 2.00\%, outperforming state-of-the-art methods. Additionally, ToxicDetector's processing time of 0.0780 seconds per prompt makes it highly suitable for real-time applications. ToxicDetector achieves high accuracy, efficiency, and scalability, making it a practical method for toxic prompt detection in LLMs.

ROBBIE: Robust Bias Evaluation of Large Generative Language Models

As generative large language models (LLMs) grow more performant and prevalent, we must develop comprehensive enough tools to measure and improve their fairness. Different prompt-based datasets can be used to measure social bias across multiple text domains and demographic axes, meaning that testing LLMs on more datasets can potentially help us characterize their biases more fully, and better ensure equal and equitable treatment of marginalized demographic groups. In this work, our focus is two-fold: (1) Benchmarking: a comparison of 6 different prompt-based bias and toxicity metrics across 12 demographic axes and 5 families of generative LLMs. Out of those 6 metrics, AdvPromptSet and HolisticBiasR are novel datasets proposed in the paper. The comparison of those benchmarks gives us insights about the bias and toxicity of the compared models. Therefore, we explore the frequency of demographic terms in common LLM pre-training corpora and how this may relate to model biases. (2) Mitigation: we conduct a comprehensive study of how well 3 bias/toxicity mitigation techniques perform across our suite of measurements. ROBBIE aims to provide insights for practitioners while deploying a model, emphasizing the need to not only measure potential harms, but also understand how they arise by characterizing the data, mitigate harms once found, and balance any trade-offs. We open-source our analysis code in hopes of encouraging broader measurements of bias in future LLMs.

T2Vs Meet VLMs: A Scalable Multimodal Dataset for Visual Harmfulness Recognition

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.

ChineseWebText 2.0: Large-Scale High-quality Chinese Web Text with Multi-dimensional and fine-grained information

During the development of large language models (LLMs), pre-training data play a critical role in shaping LLMs' capabilities. In recent years several large-scale and high-quality pre-training datasets have been released to accelerate the research of LLMs, including ChineseWebText1.0, C4, Pile, WanJuan, MAPCC and others. However, as LLMs continue to evolve, focus has increasingly shifted to domain-specific capabilities and safety concerns, making those previous coarse-grained texts insufficient for meeting training requirements. Furthermore, fine-grained information, such as quality, domain and toxicity, is becoming increasingly important in building powerful and reliable LLMs for various scenarios. To address these challenges, in this paper we propose a new tool-chain called MDFG-tool for constructing large-scale and high-quality Chinese datasets with multi-dimensional and fine-grained information. First, we employ manually crafted rules to discard explicit noisy texts from raw contents. Second, the quality evaluation model, domain classifier, and toxicity evaluation model are well-designed to assess the remaining cleaned data respectively. Finally, we integrate these three types of fine-grained information for each text. With this approach, we release the largest, high-quality and fine-grained Chinese text ChineseWebText2.0, which consists of 3.8TB and each text is associated with a quality score, domain labels, a toxicity label and a toxicity score, facilitating the LLM researchers to select data based on various types of fine-grained information. The data, codes and the tool-chain are available on this website https://github.com/CASIA-LM/ChineseWebText-2.0

GeDi: Generative Discriminator Guided Sequence Generation

While large-scale language models (LMs) are able to imitate the distribution of natural language well enough to generate realistic text, it is difficult to control which regions of the distribution they generate. This is especially problematic because datasets used for training large LMs usually contain significant toxicity, hate, bias, and negativity. We propose GeDi as an efficient method for using smaller LMs as generative discriminators to guide generation from large LMs to make them safer and more controllable. GeDi guides generation at each step by computing classification probabilities for all possible next tokens via Bayes rule by normalizing over two class-conditional distributions; one conditioned on the desired attribute, or control code, and another conditioned on the undesired attribute, or anti control code. We find that GeDi gives stronger controllability than the state of the art method while also achieving generation speeds more than 30 times faster. Additionally, training GeDi on only four topics allows us to controllably generate new topics zero-shot from just a keyword, unlocking a new capability that previous controllable generation methods do not have. Lastly, we show that GeDi can make GPT-2 (1.5B parameters) significantly less toxic without sacrificing linguistic quality, making it by far the most practical existing method for detoxifying large language models while maintaining a fast generation speed.

IberBench: LLM Evaluation on Iberian Languages

Large Language Models (LLMs) remain difficult to evaluate comprehensively, particularly for languages other than English, where high-quality data is often limited. Existing benchmarks and leaderboards are predominantly English-centric, with only a few addressing other languages. These benchmarks fall short in several key areas: they overlook the diversity of language varieties, prioritize fundamental Natural Language Processing (NLP) capabilities over tasks of industrial relevance, and are static. With these aspects in mind, we present IberBench, a comprehensive and extensible benchmark designed to assess LLM performance on both fundamental and industry-relevant NLP tasks, in languages spoken across the Iberian Peninsula and Ibero-America. IberBench integrates 101 datasets from evaluation campaigns and recent benchmarks, covering 22 task categories such as sentiment and emotion analysis, toxicity detection, and summarization. The benchmark addresses key limitations in current evaluation practices, such as the lack of linguistic diversity and static evaluation setups by enabling continual updates and community-driven model and dataset submissions moderated by a committee of experts. We evaluate 23 LLMs ranging from 100 million to 14 billion parameters and provide empirical insights into their strengths and limitations. Our findings indicate that (i) LLMs perform worse on industry-relevant tasks than in fundamental ones, (ii) performance is on average lower for Galician and Basque, (iii) some tasks show results close to random, and (iv) in other tasks LLMs perform above random but below shared task systems. IberBench offers open-source implementations for the entire evaluation pipeline, including dataset normalization and hosting, incremental evaluation of LLMs, and a publicly accessible leaderboard.

VHELM: A Holistic Evaluation of Vision Language Models

Current benchmarks for assessing vision-language models (VLMs) often focus on their perception or problem-solving capabilities and neglect other critical aspects such as fairness, multilinguality, or toxicity. Furthermore, they differ in their evaluation procedures and the scope of the evaluation, making it difficult to compare models. To address these issues, we extend the HELM framework to VLMs to present the Holistic Evaluation of Vision Language Models (VHELM). VHELM aggregates various datasets to cover one or more of the 9 aspects: visual perception, knowledge, reasoning, bias, fairness, multilinguality, robustness, toxicity, and safety. In doing so, we produce a comprehensive, multi-dimensional view of the capabilities of the VLMs across these important factors. In addition, we standardize the standard inference parameters, methods of prompting, and evaluation metrics to enable fair comparisons across models. Our framework is designed to be lightweight and automatic so that evaluation runs are cheap and fast. Our initial run evaluates 22 VLMs on 21 existing datasets to provide a holistic snapshot of the models. We uncover new key findings, such as the fact that efficiency-focused models (e.g., Claude 3 Haiku or Gemini 1.5 Flash) perform significantly worse than their full models (e.g., Claude 3 Opus or Gemini 1.5 Pro) on the bias benchmark but not when evaluated on the other aspects. For transparency, we release the raw model generations and complete results on our website (https://crfm.stanford.edu/helm/vhelm/v2.0.1). VHELM is intended to be a living benchmark, and we hope to continue adding new datasets and models over time.

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

Detection of Somali-written Fake News and Toxic Messages on the Social Media Using Transformer-based Language Models

The fact that everyone with a social media account can create and share content, and the increasing public reliance on social media platforms as a news and information source bring about significant challenges such as misinformation, fake news, harmful content, etc. Although human content moderation may be useful to an extent and used by these platforms to flag posted materials, the use of AI models provides a more sustainable, scalable, and effective way to mitigate these harmful contents. However, low-resourced languages such as the Somali language face limitations in AI automation, including scarce annotated training datasets and lack of language models tailored to their unique linguistic characteristics. This paper presents part of our ongoing research work to bridge some of these gaps for the Somali language. In particular, we created two human-annotated social-media-sourced Somali datasets for two downstream applications, fake news \& toxicity classification, and developed a transformer-based monolingual Somali language model (named SomBERTa) -- the first of its kind to the best of our knowledge. SomBERTa is then fine-tuned and evaluated on toxic content, fake news and news topic classification datasets. Comparative evaluation analysis of the proposed model against related multilingual models (e.g., AfriBERTa, AfroXLMR, etc) demonstrated that SomBERTa consistently outperformed these comparators in both fake news and toxic content classification tasks while achieving the best average accuracy (87.99%) across all tasks. This research contributes to Somali NLP by offering a foundational language model and a replicable framework for other low-resource languages, promoting digital and AI inclusivity and linguistic diversity.

Single and Multi-Hop Question-Answering Datasets for Reticular Chemistry with GPT-4-Turbo

The rapid advancement in artificial intelligence and natural language processing has led to the development of large-scale datasets aimed at benchmarking the performance of machine learning models. Herein, we introduce 'RetChemQA,' a comprehensive benchmark dataset designed to evaluate the capabilities of such models in the domain of reticular chemistry. This dataset includes both single-hop and multi-hop question-answer pairs, encompassing approximately 45,000 Q&As for each type. The questions have been extracted from an extensive corpus of literature containing about 2,530 research papers from publishers including NAS, ACS, RSC, Elsevier, and Nature Publishing Group, among others. The dataset has been generated using OpenAI's GPT-4 Turbo, a cutting-edge model known for its exceptional language understanding and generation capabilities. In addition to the Q&A dataset, we also release a dataset of synthesis conditions extracted from the corpus of literature used in this study. The aim of RetChemQA is to provide a robust platform for the development and evaluation of advanced machine learning algorithms, particularly for the reticular chemistry community. The dataset is structured to reflect the complexities and nuances of real-world scientific discourse, thereby enabling nuanced performance assessments across a variety of tasks. The dataset is available at the following link: https://github.com/nakulrampal/RetChemQA

The Open Catalyst 2020 (OC20) Dataset and Community Challenges

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

AHELM: A Holistic Evaluation of Audio-Language Models

Evaluations of audio-language models (ALMs) -- multimodal models that take interleaved audio and text as input and output text -- are hindered by the lack of standardized benchmarks; most benchmarks measure only one or two capabilities and omit evaluative aspects such as fairness or safety. Furthermore, comparison across models is difficult as separate evaluations test a limited number of models and use different prompting methods and inference parameters. To address these shortfalls, we introduce AHELM, a benchmark that aggregates various datasets -- including 2 new synthetic audio-text datasets called PARADE, which evaluates the ALMs on avoiding stereotypes, and CoRe-Bench, which measures reasoning over conversational audio through inferential multi-turn question answering -- to holistically measure the performance of ALMs across 10 aspects we have identified as important to the development and usage of ALMs: audio perception, knowledge, reasoning, emotion detection, bias, fairness, multilinguality, robustness, toxicity, and safety. We also standardize the prompts, inference parameters, and evaluation metrics to ensure equitable comparisons across models. We test 14 open-weight and closed-API ALMs from 3 developers and 3 additional simple baseline systems each consisting of an automatic speech recognizer and a language model. Our results show that while Gemini 2.5 Pro ranks top in 5 out of 10 aspects, it exhibits group unfairness (p=0.01) on ASR tasks whereas most of the other models do not. We also find that the baseline systems perform reasonably well on AHELM, with one ranking 5th overall despite having only speech-to-text capabilities. For transparency, all raw prompts, model generations, and outputs are available on our website at https://crfm.stanford.edu/helm/audio/v1.0.0. AHELM is intended to be a living benchmark and new datasets and models will be added over time.

Accurate Chemistry Collection: Coupled cluster atomization energies for broad chemical space

Accurate thermochemical data with sub-chemical accuracy (i.e., within pm1 kcal mol^{-1} from sufficiently accurate experimental or theoretical reference data) is essential for the development and improvement of computational chemistry methods. Challenging thermochemical properties such as heats of formation and total atomization energies (TAEs) are of particular interest because they rigorously test the ability of computational chemistry methods to accurately describe complex chemical transformations involving multiple bond rearrangements. Yet, existing thermochemical datasets that confidently reach this level of accuracy are limited in either size or scope. Datasets with highly accurate reference values include a small number of data points, and larger datasets provide less accurate data or only cover a narrow portion of the chemical space. The existing datasets are therefore insufficient for developing data-driven methods with predictive accuracy over a large chemical space. The Microsoft Research Accurate Chemistry Collection (MSR-ACC) will address this challenge. Here, it offers the MSR-ACC/TAE25 dataset of 76,879 total atomization energies obtained at the CCSD(T)/CBS level via the W1-F12 thermochemical protocol. The dataset is constructed to exhaustively cover chemical space for all elements up to argon by enumerating and sampling chemical graphs, thus avoiding bias towards any particular subspace of the chemical space (such as drug-like, organic, or experimentally observed molecules). With this first dataset in MSR-ACC, we enable data-driven approaches for developing predictive computational chemistry methods with unprecedented accuracy and scope.

Dynamics of Toxicity in Political Podcasts

Toxicity in digital media poses significant challenges, yet little attention has been given to its dynamics within the rapidly growing medium of podcasts. This paper addresses this gap by analyzing political podcast data to study the emergence and propagation of toxicity, focusing on conversation chains-structured reply patterns within podcast transcripts. Leveraging state-of-the-art transcription models and advanced conversational analysis techniques, we systematically examine toxic discourse in over 30 popular political podcasts in the United States. Our key contributions include: (1) creating a comprehensive dataset of transcribed and diarized political podcasts, identifying thousands of toxic instances using Google's Perspective API, (2) uncovering concerning trends where a majority of episodes contain at least one toxic instance, (3) introducing toxic conversation chains and analyzing their structural and linguistic properties, revealing characteristics such as longer durations, repetitive patterns, figurative language, and emotional cues tied to anger and annoyance, (4) identifying demand-related words like 'want', 'like', and 'know' as precursors to toxicity, and (5) developing predictive models to anticipate toxicity shifts based on annotated change points. Our findings provide critical insights into podcast toxicity and establish a foundation for future research on real-time monitoring and intervention mechanisms to foster healthier discourse in this influential medium.

ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Models

Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry -- from educational foundations to specialized expertise -- spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code) -- mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

Enhancing Adverse Drug Event Detection with Multimodal Dataset: Corpus Creation and Model Development

The mining of adverse drug events (ADEs) is pivotal in pharmacovigilance, enhancing patient safety by identifying potential risks associated with medications, facilitating early detection of adverse events, and guiding regulatory decision-making. Traditional ADE detection methods are reliable but slow, not easily adaptable to large-scale operations, and offer limited information. With the exponential increase in data sources like social media content, biomedical literature, and Electronic Medical Records (EMR), extracting relevant ADE-related information from these unstructured texts is imperative. Previous ADE mining studies have focused on text-based methodologies, overlooking visual cues, limiting contextual comprehension, and hindering accurate interpretation. To address this gap, we present a MultiModal Adverse Drug Event (MMADE) detection dataset, merging ADE-related textual information with visual aids. Additionally, we introduce a framework that leverages the capabilities of LLMs and VLMs for ADE detection by generating detailed descriptions of medical images depicting ADEs, aiding healthcare professionals in visually identifying adverse events. Using our MMADE dataset, we showcase the significance of integrating visual cues from images to enhance overall performance. This approach holds promise for patient safety, ADE awareness, and healthcare accessibility, paving the way for further exploration in personalized healthcare.

Rethinking Benchmark and Contamination for Language Models with Rephrased Samples

Large language models are increasingly trained on all the data ever produced by humans. Many have raised concerns about the trustworthiness of public benchmarks due to potential contamination in pre-training or fine-tuning datasets. While most data decontamination efforts apply string matching (e.g., n-gram overlap) to remove benchmark data, we show that these methods are insufficient, and simple variations of test data (e.g., paraphrasing, translation) can easily bypass these decontamination measures. Furthermore, we demonstrate that if such variation of test data is not eliminated, a 13B model can easily overfit a test benchmark and achieve drastically high performance, on par with GPT-4. We validate such observations in widely used benchmarks such as MMLU, GSK8k, and HumanEval. To address this growing risk, we propose a stronger LLM-based decontamination method and apply it to widely used pre-training and fine-tuning datasets, revealing significant previously unknown test overlap. For example, in pre-training sets such as RedPajama-Data-1T and StarCoder-Data, we identified that 8-18\% of the HumanEval benchmark overlaps. Interestingly, we also find such contamination in synthetic dataset generated by GPT-3.5/4, suggesting a potential risk of unintentional contamination. We urge the community to adopt stronger decontamination approaches when using public benchmarks. Moreover, we call for the community to actively develop fresh one-time exams to evaluate models accurately. Our decontamination tool is publicly available at https://github.com/lm-sys/llm-decontaminator.

Standardized Benchmark Dataset for Localized Exposure to a Realistic Source at 10-90 GHz

The lack of freely available standardized datasets represents an aggravating factor during the development and testing the performance of novel computational techniques in exposure assessment and dosimetry research. This hinders progress as researchers are required to generate numerical data (field, power and temperature distribution) anew using simulation software for each exposure scenario. Other than being time consuming, this approach is highly susceptible to errors that occur during the configuration of the electromagnetic model. To address this issue, in this paper, the limited available data on the incident power density and resultant maximum temperature rise on the skin surface considering various steady-state exposure scenarios at 10-90 GHz have been statistically modeled. The synthetic data have been sampled from the fitted statistical multivariate distribution with respect to predetermined dosimetric constraints. We thus present a comprehensive and open-source dataset compiled of the high-fidelity numerical data considering various exposures to a realistic source. Furthermore, different surrogate models for predicting maximum temperature rise on the skin surface were fitted based on the synthetic dataset. All surrogate models were tested on the originally available data where satisfactory predictive performance has been demonstrated. A simple technique of combining quadratic polynomial and tensor-product spline surrogates, each operating on its own cluster of data, has achieved the lowest mean absolute error of 0.058 {\deg}C. Therefore, overall experimental results indicate the validity of the proposed synthetic dataset.

Crowdsourcing Dermatology Images with Google Search Ads: Creating a Real-World Skin Condition Dataset

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

Reddit-Impacts: A Named Entity Recognition Dataset for Analyzing Clinical and Social Effects of Substance Use Derived from Social Media

Substance use disorders (SUDs) are a growing concern globally, necessitating enhanced understanding of the problem and its trends through data-driven research. Social media are unique and important sources of information about SUDs, particularly since the data in such sources are often generated by people with lived experiences. In this paper, we introduce Reddit-Impacts, a challenging Named Entity Recognition (NER) dataset curated from subreddits dedicated to discussions on prescription and illicit opioids, as well as medications for opioid use disorder. The dataset specifically concentrates on the lesser-studied, yet critically important, aspects of substance use--its clinical and social impacts. We collected data from chosen subreddits using the publicly available Application Programming Interface for Reddit. We manually annotated text spans representing clinical and social impacts reported by people who also reported personal nonmedical use of substances including but not limited to opioids, stimulants and benzodiazepines. Our objective is to create a resource that can enable the development of systems that can automatically detect clinical and social impacts of substance use from text-based social media data. The successful development of such systems may enable us to better understand how nonmedical use of substances affects individual health and societal dynamics, aiding the development of effective public health strategies. In addition to creating the annotated data set, we applied several machine learning models to establish baseline performances. Specifically, we experimented with transformer models like BERT, and RoBERTa, one few-shot learning model DANN by leveraging the full training dataset, and GPT-3.5 by using one-shot learning, for automatic NER of clinical and social impacts. The dataset has been made available through the 2024 SMM4H shared tasks.

Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

A Pretrainer's Guide to Training Data: Measuring the Effects of Data Age, Domain Coverage, Quality, & Toxicity

Pretraining is the preliminary and fundamental step in developing capable language models (LM). Despite this, pretraining data design is critically under-documented and often guided by empirically unsupported intuitions. To address this, we pretrain 28 1.5B parameter decoder-only models, training on data curated (1) at different times, (2) with varying toxicity and quality filters, and (3) with different domain compositions. First, we quantify the effect of pretraining data age. A temporal shift between evaluation data and pretraining data leads to performance degradation, which is not overcome by finetuning. Second, we explore the effect of quality and toxicity filters, showing a trade-off between performance on standard benchmarks and risk of toxic generations. Our findings indicate there does not exist a one-size-fits-all solution to filtering training data. We also find that the effects of different types of filtering are not predictable from text domain characteristics. Lastly, we empirically validate that the inclusion of heterogeneous data sources, like books and web, is broadly beneficial and warrants greater prioritization. These findings constitute the largest set of experiments to validate, quantify, and expose many undocumented intuitions about text pretraining, which we hope will help support more informed data-centric decisions in LM development.

Patherea: Cell Detection and Classification for the 2020s

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

Agent-based Learning of Materials Datasets from Scientific Literature

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and rich resource of such data. However, manual dataset creation from these resources is challenging due to issues in maintaining quality and consistency, scalability limitations, and the risk of human error and bias. Therefore, in this work, we develop a chemist AI agent, powered by large language models (LLMs), to overcome these challenges by autonomously creating structured datasets from natural language text, ranging from sentences and paragraphs to extensive scientific research articles. Our chemist AI agent, Eunomia, can plan and execute actions by leveraging the existing knowledge from decades of scientific research articles, scientists, the Internet and other tools altogether. We benchmark the performance of our approach in three different information extraction tasks with various levels of complexity, including solid-state impurity doping, metal-organic framework (MOF) chemical formula, and property relations. Our results demonstrate that our zero-shot agent, with the appropriate tools, is capable of attaining performance that is either superior or comparable to the state-of-the-art fine-tuned materials information extraction methods. This approach simplifies compilation of machine learning-ready datasets for various materials discovery applications, and significantly ease the accessibility of advanced natural language processing tools for novice users in natural language. The methodology in this work is developed as an open-source software on https://github.com/AI4ChemS/Eunomia.

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

Evidence Inference 2.0: More Data, Better Models

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/.

GemNet-OC: Developing Graph Neural Networks for Large and Diverse Molecular Simulation Datasets

Recent years have seen the advent of molecular simulation datasets that are orders of magnitude larger and more diverse. These new datasets differ substantially in four aspects of complexity: 1. Chemical diversity (number of different elements), 2. system size (number of atoms per sample), 3. dataset size (number of data samples), and 4. domain shift (similarity of the training and test set). Despite these large differences, benchmarks on small and narrow datasets remain the predominant method of demonstrating progress in graph neural networks (GNNs) for molecular simulation, likely due to cheaper training compute requirements. This raises the question -- does GNN progress on small and narrow datasets translate to these more complex datasets? This work investigates this question by first developing the GemNet-OC model based on the large Open Catalyst 2020 (OC20) dataset. GemNet-OC outperforms the previous state-of-the-art on OC20 by 16% while reducing training time by a factor of 10. We then compare the impact of 18 model components and hyperparameter choices on performance in multiple datasets. We find that the resulting model would be drastically different depending on the dataset used for making model choices. To isolate the source of this discrepancy we study six subsets of the OC20 dataset that individually test each of the above-mentioned four dataset aspects. We find that results on the OC-2M subset correlate well with the full OC20 dataset while being substantially cheaper to train on. Our findings challenge the common practice of developing GNNs solely on small datasets, but highlight ways of achieving fast development cycles and generalizable results via moderately-sized, representative datasets such as OC-2M and efficient models such as GemNet-OC. Our code and pretrained model weights are open-sourced.

Automatic Dataset Construction (ADC): Sample Collection, Data Curation, and Beyond

Large-scale data collection is essential for developing personalized training data, mitigating the shortage of training data, and fine-tuning specialized models. However, creating high-quality datasets quickly and accurately remains a challenge due to annotation errors, the substantial time and costs associated with human labor. To address these issues, we propose Automatic Dataset Construction (ADC), an innovative methodology that automates dataset creation with negligible cost and high efficiency. Taking the image classification task as a starting point, ADC leverages LLMs for the detailed class design and code generation to collect relevant samples via search engines, significantly reducing the need for manual annotation and speeding up the data generation process. Despite these advantages, ADC also encounters real-world challenges such as label errors (label noise) and imbalanced data distributions (label bias). We provide open-source software that incorporates existing methods for label error detection, robust learning under noisy and biased data, ensuring a higher-quality training data and more robust model training procedure. Furthermore, we design three benchmark datasets focused on label noise detection, label noise learning, and class-imbalanced learning. These datasets are vital because there are few existing datasets specifically for label noise detection, despite its importance. Finally, we evaluate the performance of existing popular methods on these datasets, thereby facilitating further research in the field.

ATOM3D: Tasks On Molecules in Three Dimensions

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of either systematic performance benchmarks or a unified toolkit for interacting with molecular data. To address this, we present ATOM3D, a collection of both novel and existing benchmark datasets spanning several key classes of biomolecules. We implement several classes of three-dimensional molecular learning methods for each of these tasks and show that they consistently improve performance relative to methods based on one- and two-dimensional representations. The specific choice of architecture proves to be critical for performance, with three-dimensional convolutional networks excelling at tasks involving complex geometries, graph networks performing well on systems requiring detailed positional information, and the more recently developed equivariant networks showing significant promise. Our results indicate that many molecular problems stand to gain from three-dimensional molecular learning, and that there is potential for improvement on many tasks which remain underexplored. To lower the barrier to entry and facilitate further developments in the field, we also provide a comprehensive suite of tools for dataset processing, model training, and evaluation in our open-source atom3d Python package. All datasets are available for download from https://www.atom3d.ai .

MegaScience: Pushing the Frontiers of Post-Training Datasets for Science Reasoning

Scientific reasoning is critical for developing AI scientists and supporting human researchers in advancing the frontiers of natural science discovery. However, the open-source community has primarily focused on mathematics and coding while neglecting the scientific domain, largely due to the absence of open, large-scale, high-quality, verifiable scientific reasoning datasets. To bridge this gap, we first present TextbookReasoning, an open dataset featuring truthful reference answers extracted from 12k university-level scientific textbooks, comprising 650k reasoning questions spanning 7 scientific disciplines. We further introduce MegaScience, a large-scale mixture of high-quality open-source datasets totaling 1.25 million instances, developed through systematic ablation studies that evaluate various data selection methodologies to identify the optimal subset for each publicly available scientific dataset. Meanwhile, we build a comprehensive evaluation system covering diverse subjects and question types across 15 benchmarks, incorporating comprehensive answer extraction strategies to ensure accurate evaluation metrics. Our experiments demonstrate that our datasets achieve superior performance and training efficiency with more concise response lengths compared to existing open-source scientific datasets. Furthermore, we train Llama3.1, Qwen2.5, and Qwen3 series base models on MegaScience, which significantly outperform the corresponding official instruct models in average performance. In addition, MegaScience exhibits greater effectiveness for larger and stronger models, suggesting a scaling benefit for scientific tuning. We release our data curation pipeline, evaluation system, datasets, and seven trained models to the community to advance scientific reasoning research.

Assessing Language Model Deployment with Risk Cards

This paper introduces RiskCards, a framework for structured assessment and documentation of risks associated with an application of language models. As with all language, text generated by language models can be harmful, or used to bring about harm. Automating language generation adds both an element of scale and also more subtle or emergent undesirable tendencies to the generated text. Prior work establishes a wide variety of language model harms to many different actors: existing taxonomies identify categories of harms posed by language models; benchmarks establish automated tests of these harms; and documentation standards for models, tasks and datasets encourage transparent reporting. However, there is no risk-centric framework for documenting the complexity of a landscape in which some risks are shared across models and contexts, while others are specific, and where certain conditions may be required for risks to manifest as harms. RiskCards address this methodological gap by providing a generic framework for assessing the use of a given language model in a given scenario. Each RiskCard makes clear the routes for the risk to manifest harm, their placement in harm taxonomies, and example prompt-output pairs. While RiskCards are designed to be open-source, dynamic and participatory, we present a "starter set" of RiskCards taken from a broad literature survey, each of which details a concrete risk presentation. Language model RiskCards initiate a community knowledge base which permits the mapping of risks and harms to a specific model or its application scenario, ultimately contributing to a better, safer and shared understanding of the risk landscape.

Evaluation data contamination in LLMs: how do we measure it and (when) does it matter?

Hampering the interpretation of benchmark scores, evaluation data contamination has become a growing concern in the evaluation of LLMs, and an active area of research studies its effects. While evaluation data contamination is easily understood intuitively, it is surprisingly difficult to define precisely which samples should be considered contaminated and, consequently, how it impacts benchmark scores. We propose that these questions should be addressed together and that contamination metrics can be assessed based on whether models benefit from the examples they mark contaminated. We propose a novel analysis method called ConTAM, and show with a large scale survey of existing and novel n-gram based contamination metrics across 13 benchmarks and 7 models from 2 different families that ConTAM can be used to better understand evaluation data contamination and its effects. We find that contamination may have a much larger effect than reported in recent LLM releases and benefits models differently at different scales. We also find that considering only the longest contaminated substring provides a better signal than considering a union of all contaminated substrings, and that doing model and benchmark specific threshold analysis greatly increases the specificity of the results. Lastly, we investigate the impact of hyperparameter choices, finding that, among other things, both using larger values of n and disregarding matches that are infrequent in the pre-training data lead to many false negatives. With ConTAM, we provide a method to empirically ground evaluation data contamination metrics in downstream effects. With our exploration, we shed light on how evaluation data contamination can impact LLMs and provide insight into the considerations important when doing contamination analysis. We end our paper by discussing these in more detail and providing concrete suggestions for future work.

MALADE: Orchestration of LLM-powered Agents with Retrieval Augmented Generation for Pharmacovigilance

In the era of Large Language Models (LLMs), given their remarkable text understanding and generation abilities, there is an unprecedented opportunity to develop new, LLM-based methods for trustworthy medical knowledge synthesis, extraction and summarization. This paper focuses on the problem of Pharmacovigilance (PhV), where the significance and challenges lie in identifying Adverse Drug Events (ADEs) from diverse text sources, such as medical literature, clinical notes, and drug labels. Unfortunately, this task is hindered by factors including variations in the terminologies of drugs and outcomes, and ADE descriptions often being buried in large amounts of narrative text. We present MALADE, the first effective collaborative multi-agent system powered by LLM with Retrieval Augmented Generation for ADE extraction from drug label data. This technique involves augmenting a query to an LLM with relevant information extracted from text resources, and instructing the LLM to compose a response consistent with the augmented data. MALADE is a general LLM-agnostic architecture, and its unique capabilities are: (1) leveraging a variety of external sources, such as medical literature, drug labels, and FDA tools (e.g., OpenFDA drug information API), (2) extracting drug-outcome association in a structured format along with the strength of the association, and (3) providing explanations for established associations. Instantiated with GPT-4 Turbo or GPT-4o, and FDA drug label data, MALADE demonstrates its efficacy with an Area Under ROC Curve of 0.90 against the OMOP Ground Truth table of ADEs. Our implementation leverages the Langroid multi-agent LLM framework and can be found at https://github.com/jihyechoi77/malade.

Modeling PROTAC Degradation Activity with Machine Learning

PROTACs are a promising therapeutic modality that harnesses the cell's built-in degradation machinery to degrade specific proteins. Despite their potential, developing new PROTACs is challenging and requires significant domain expertise, time, and cost. Meanwhile, machine learning has transformed drug design and development. In this work, we present a strategy for curating open-source PROTAC data and an open-source deep learning tool for predicting the degradation activity of novel PROTAC molecules. The curated dataset incorporates important information such as pDC_{50}, D_{max}, E3 ligase type, POI amino acid sequence, and experimental cell type. Our model architecture leverages learned embeddings from pretrained machine learning models, in particular for encoding protein sequences and cell type information. We assessed the quality of the curated data and the generalization ability of our model architecture against new PROTACs and targets via three tailored studies, which we recommend other researchers to use in evaluating their degradation activity models. In each study, three models predict protein degradation in a majority vote setting, reaching a top test accuracy of 82.6% and 0.848 ROC AUC, and a test accuracy of 61% and 0.615 ROC AUC when generalizing to novel protein targets. Our results are not only comparable to state-of-the-art models for protein degradation prediction, but also part of an open-source implementation which is easily reproducible and less computationally complex than existing approaches.

Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

Machine Learning for Shipwreck Segmentation from Side Scan Sonar Imagery: Dataset and Benchmark

Open-source benchmark datasets have been a critical component for advancing machine learning for robot perception in terrestrial applications. Benchmark datasets enable the widespread development of state-of-the-art machine learning methods, which require large datasets for training, validation, and thorough comparison to competing approaches. Underwater environments impose several operational challenges that hinder efforts to collect large benchmark datasets for marine robot perception. Furthermore, a low abundance of targets of interest relative to the size of the search space leads to increased time and cost required to collect useful datasets for a specific task. As a result, there is limited availability of labeled benchmark datasets for underwater applications. We present the AI4Shipwrecks dataset, which consists of 24 distinct shipwreck sites totaling 286 high-resolution labeled side scan sonar images to advance the state-of-the-art in autonomous sonar image understanding. We leverage the unique abundance of targets in Thunder Bay National Marine Sanctuary in Lake Huron, MI, to collect and compile a sonar imagery benchmark dataset through surveys with an autonomous underwater vehicle (AUV). We consulted with expert marine archaeologists for the labeling of robotically gathered data. We then leverage this dataset to perform benchmark experiments for comparison of state-of-the-art supervised segmentation methods, and we present insights on opportunities and open challenges for the field. The dataset and benchmarking tools will be released as an open-source benchmark dataset to spur innovation in machine learning for Great Lakes and ocean exploration. The dataset and accompanying software are available at https://umfieldrobotics.github.io/ai4shipwrecks/.

Toxicity in ChatGPT: Analyzing Persona-assigned Language Models

Large language models (LLMs) have shown incredible capabilities and transcended the natural language processing (NLP) community, with adoption throughout many services like healthcare, therapy, education, and customer service. Since users include people with critical information needs like students or patients engaging with chatbots, the safety of these systems is of prime importance. Therefore, a clear understanding of the capabilities and limitations of LLMs is necessary. To this end, we systematically evaluate toxicity in over half a million generations of ChatGPT, a popular dialogue-based LLM. We find that setting the system parameter of ChatGPT by assigning it a persona, say that of the boxer Muhammad Ali, significantly increases the toxicity of generations. Depending on the persona assigned to ChatGPT, its toxicity can increase up to 6x, with outputs engaging in incorrect stereotypes, harmful dialogue, and hurtful opinions. This may be potentially defamatory to the persona and harmful to an unsuspecting user. Furthermore, we find concerning patterns where specific entities (e.g., certain races) are targeted more than others (3x more) irrespective of the assigned persona, that reflect inherent discriminatory biases in the model. We hope that our findings inspire the broader AI community to rethink the efficacy of current safety guardrails and develop better techniques that lead to robust, safe, and trustworthy AI systems.

Rethinking Symbolic Regression Datasets and Benchmarks for Scientific Discovery

This paper revisits datasets and evaluation criteria for Symbolic Regression, a task of expressing given data using mathematical equations, specifically focused on its potential for scientific discovery. Focused on a set of formulas used in the existing datasets based on Feynman Lectures on Physics, we recreate 120 datasets to discuss the performance of symbolic regression for scientific discovery (SRSD). For each of the 120 SRSD datasets, we carefully review the properties of the formula and its variables to design reasonably realistic sampling range of values so that our new SRSD datasets can be used for evaluating the potential of SRSD such as whether or not an SR method can (re)discover physical laws from such datasets. As an evaluation metric, we also propose to use normalized edit distances between a predicted equation and the ground-truth equation trees. While existing metrics are either binary or errors between the target values and an SR model's predicted values for a given input, normalized edit distances evaluate a sort of similarity between the ground-truth and predicted equation trees. We have conducted experiments on our new SRSD datasets using five state-of-the-art SR methods in SRBench and a simple baseline based on a recent Transformer architecture. The results show that we provide a more realistic performance evaluation and open up a new machine learning-based approach for scientific discovery. Our datasets and code repository are publicly available.

Arboretum: A Large Multimodal Dataset Enabling AI for Biodiversity

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.

Ethical and social risks of harm from Language Models

This paper aims to help structure the risk landscape associated with large-scale Language Models (LMs). In order to foster advances in responsible innovation, an in-depth understanding of the potential risks posed by these models is needed. A wide range of established and anticipated risks are analysed in detail, drawing on multidisciplinary expertise and literature from computer science, linguistics, and social sciences. We outline six specific risk areas: I. Discrimination, Exclusion and Toxicity, II. Information Hazards, III. Misinformation Harms, V. Malicious Uses, V. Human-Computer Interaction Harms, VI. Automation, Access, and Environmental Harms. The first area concerns the perpetuation of stereotypes, unfair discrimination, exclusionary norms, toxic language, and lower performance by social group for LMs. The second focuses on risks from private data leaks or LMs correctly inferring sensitive information. The third addresses risks arising from poor, false or misleading information including in sensitive domains, and knock-on risks such as the erosion of trust in shared information. The fourth considers risks from actors who try to use LMs to cause harm. The fifth focuses on risks specific to LLMs used to underpin conversational agents that interact with human users, including unsafe use, manipulation or deception. The sixth discusses the risk of environmental harm, job automation, and other challenges that may have a disparate effect on different social groups or communities. In total, we review 21 risks in-depth. We discuss the points of origin of different risks and point to potential mitigation approaches. Lastly, we discuss organisational responsibilities in implementing mitigations, and the role of collaboration and participation. We highlight directions for further research, particularly on expanding the toolkit for assessing and evaluating the outlined risks in LMs.

EcoVerse: An Annotated Twitter Dataset for Eco-Relevance Classification, Environmental Impact Analysis, and Stance Detection

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.