Daily Papers

This paper presents AI Wizards' participation in the CLEF 2025 CheckThat! Lab Task 1: Subjectivity Detection in News Articles, classifying sentences as subjective/objective in monolingual, multilingual, and zero-shot settings. Training/development datasets were provided for Arabic, German, English, Italian, and Bulgarian; final evaluation included additional unseen languages (e.g., Greek, Romanian, Polish, Ukrainian) to assess generalization. Our primary strategy enhanced transformer-based classifiers by integrating sentiment scores, derived from an auxiliary model, with sentence representations, aiming to improve upon standard fine-tuning. We explored this sentiment-augmented architecture with mDeBERTaV3-base, ModernBERT-base (English), and Llama3.2-1B. To address class imbalance, prevalent across languages, we employed decision threshold calibration optimized on the development set. Our experiments show sentiment feature integration significantly boosts performance, especially subjective F1 score. This framework led to high rankings, notably 1st for Greek (Macro F1 = 0.51).

Tracking how data is mentioned and used in research papers provides critical insights for improving data discoverability, quality, and production. However, manually identifying and classifying dataset mentions across vast academic literature is resource-intensive and not scalable. This paper presents a machine learning framework that automates dataset mention detection across research domains by leveraging large language models (LLMs), synthetic data, and a two-stage fine-tuning process. We employ zero-shot extraction from research papers, an LLM-as-a-Judge for quality assessment, and a reasoning agent for refinement to generate a weakly supervised synthetic dataset. The Phi-3.5-mini instruct model is pre-fine-tuned on this dataset, followed by fine-tuning on a manually annotated subset. At inference, a ModernBERT-based classifier efficiently filters dataset mentions, reducing computational overhead while maintaining high recall. Evaluated on a held-out manually annotated sample, our fine-tuned model outperforms NuExtract-v1.5 and GLiNER-large-v2.1 in dataset extraction accuracy. Our results highlight how LLM-generated synthetic data can effectively address training data scarcity, improving generalization in low-resource settings. This framework offers a pathway toward scalable monitoring of dataset usage, enhancing transparency, and supporting researchers, funders, and policymakers in identifying data gaps and strengthening data accessibility for informed decision-making.

Extracting tables and key-value pairs from financial documents is essential for business workflows such as auditing, data analytics, and automated invoice processing. In this work, we introduce Spatial ModernBERT-a transformer-based model augmented with spatial embeddings-to accurately detect and extract tabular data and key-value fields from complex financial documents. We cast the extraction task as token classification across three heads: (1) Label Head, classifying each token as a label (e.g., PO Number, PO Date, Item Description, Quantity, Base Cost, MRP, etc.); (2) Column Head, predicting column indices; (3) Row Head, distinguishing the start of item rows and header rows. The model is pretrained on the PubTables-1M dataset, then fine-tuned on a financial document dataset, achieving robust performance through cross-entropy loss on each classification head. We propose a post-processing method to merge tokens using B-I-IB tagging, reconstruct the tabular layout, and extract key-value pairs. Empirical evaluation shows that Spatial ModernBERT effectively leverages both textual and spatial cues, facilitating highly accurate table and key-value extraction in real-world financial documents.

Large Language Models (LLMs) are increasingly powerful but remain vulnerable to prompt injection attacks, where malicious inputs cause the model to deviate from its intended instructions. This paper introduces Sentinel, a novel detection model, qualifire/prompt-injection-sentinel, based on the \answerdotai/ModernBERT-large architecture. By leveraging ModernBERT's advanced features and fine-tuning on an extensive and diverse dataset comprising a few open-source and private collections, Sentinel achieves state-of-the-art performance. This dataset amalgamates varied attack types, from role-playing and instruction hijacking to attempts to generate biased content, alongside a broad spectrum of benign instructions, with private datasets specifically targeting nuanced error correction and real-world misclassifications. On a comprehensive, unseen internal test set, Sentinel demonstrates an average accuracy of 0.987 and an F1-score of 0.980. Furthermore, when evaluated on public benchmarks, it consistently outperforms strong baselines like protectai/deberta-v3-base-prompt-injection-v2. This work details Sentinel's architecture, its meticulous dataset curation, its training methodology, and a thorough evaluation, highlighting its superior detection capabilities.

Encoder-based transformer models are central to biomedical and clinical Natural Language Processing (NLP), as their bidirectional self-attention makes them well-suited for efficiently extracting structured information from unstructured text through discriminative tasks. However, encoders have seen slower development compared to decoder models, leading to limited domain adaptation in biomedical and clinical settings. We introduce BioClinical ModernBERT, a domain-adapted encoder that builds on the recent ModernBERT release, incorporating long-context processing and substantial improvements in speed and performance for biomedical and clinical NLP. BioClinical ModernBERT is developed through continued pretraining on the largest biomedical and clinical corpus to date, with over 53.5 billion tokens, and addresses a key limitation of prior clinical encoders by leveraging 20 datasets from diverse institutions, domains, and geographic regions, rather than relying on data from a single source. It outperforms existing biomedical and clinical encoders on four downstream tasks spanning a broad range of use cases. We release both base (150M parameters) and large (396M parameters) versions of BioClinical ModernBERT, along with training checkpoints to support further research.

Objective: This study aims to evaluate and compare the performance of two Japanese language models-conventional Bidirectional Encoder Representations from Transformers (BERT) and the newer ModernBERT-in classifying findings from chest CT reports, with a focus on tokenization efficiency, processing time, and classification performance. Methods: We conducted a retrospective study using the CT-RATE-JPN dataset containing 22,778 training reports and 150 test reports. Both models were fine-tuned for multi-label classification of 18 common chest CT conditions. The training data was split in 18,222:4,556 for training and validation. Performance was evaluated using F1 scores for each condition and exact match accuracy across all 18 labels. Results: ModernBERT demonstrated superior tokenization efficiency, requiring 24.0% fewer tokens per document (258.1 vs. 339.6) compared to BERT Base. This translated to significant performance improvements, with ModernBERT completing training in 1877.67 seconds versus BERT's 3090.54 seconds (39% reduction). ModernBERT processed 38.82 samples per second during training (1.65x faster) and 139.90 samples per second during inference (1.66x faster). Despite these efficiency gains, classification performance remained comparable, with ModernBERT achieving superior F1 scores in 8 conditions, while BERT performed better in 4 conditions. Overall exact match accuracy was slightly higher for ModernBERT (74.67% vs. 72.67%), though this difference was not statistically significant (p=0.6291). Conclusion: ModernBERT offers substantial improvements in tokenization efficiency and training speed without sacrificing classification performance. These results suggest that ModernBERT is a promising candidate for clinical applications in Japanese radiology reports analysis.

We introduce Clinical ModernBERT, a transformer based encoder pretrained on large scale biomedical literature, clinical notes, and medical ontologies, incorporating PubMed abstracts, MIMIC IV clinical data, and medical codes with their textual descriptions. Building on ModernBERT the current state of the art natural language text encoder featuring architectural upgrades such as rotary positional embeddings (RoPE), Flash Attention, and extended context length up to 8,192 tokens our model adapts these innovations specifically for biomedical and clinical domains. Clinical ModernBERT excels at producing semantically rich representations tailored for long context tasks. We validate this both by analyzing its pretrained weights and through empirical evaluation on a comprehensive suite of clinical NLP benchmarks.

Encoder-only transformer models like BERT are widely adopted as a pre-trained backbone for tasks like sentence classification and retrieval. However, pretraining of encoder models with large-scale corpora and long contexts has been relatively underexplored compared to decoder-only transformers. In this work, we present llm-jp-modernbert, a ModernBERT model trained on a publicly available, massive Japanese corpus with a context length of 8192 tokens. While our model does not surpass existing baselines on downstream tasks, it achieves good results on fill-mask test evaluations. We also analyze the effect of context length expansion through pseudo-perplexity experiments. Furthermore, we investigate sentence embeddings in detail, analyzing their transitions during training and comparing them with those from other existing models, confirming similar trends with models sharing the same architecture. To support reproducibility and foster the development of long-context BERT, we release our model, along with the training and evaluation code.

While encoder-only models such as BERT and ModernBERT are ubiquitous in real-world NLP applications, their conventional reliance on task-specific classification heads can limit their applicability compared to decoder-based large language models (LLMs). In this work, we introduce ModernBERT-Large-Instruct, a 0.4B-parameter encoder model that leverages its masked language modelling (MLM) head for generative classification. Our approach employs an intentionally simple training loop and inference mechanism that requires no heavy pre-processing, heavily engineered prompting, or architectural modifications. ModernBERT-Large-Instruct exhibits strong zero-shot performance on both classification and knowledge-based tasks, outperforming similarly sized LLMs on MMLU and achieving 93% of Llama3-1B's MMLU performance with 60% less parameters. We also demonstrate that, when fine-tuned, the generative approach using the MLM head matches or even surpasses traditional classification-head methods across diverse NLU tasks.This capability emerges specifically in models trained on contemporary, diverse data mixes, with models trained on lower volume, less-diverse data yielding considerably weaker performance. Although preliminary, these results demonstrate the potential of using the original generative masked language modelling head over traditional task-specific heads for downstream tasks. Our work suggests that further exploration into this area is warranted, highlighting many avenues for future improvements.

Retrieval Augmented Generation (RAG) systems remain vulnerable to hallucinated answers despite incorporating external knowledge sources. We present LettuceDetect a framework that addresses two critical limitations in existing hallucination detection methods: (1) the context window constraints of traditional encoder-based methods, and (2) the computational inefficiency of LLM based approaches. Building on ModernBERT's extended context capabilities (up to 8k tokens) and trained on the RAGTruth benchmark dataset, our approach outperforms all previous encoder-based models and most prompt-based models, while being approximately 30 times smaller than the best models. LettuceDetect is a token-classification model that processes context-question-answer triples, allowing for the identification of unsupported claims at the token level. Evaluations on the RAGTruth corpus demonstrate an F1 score of 79.22% for example-level detection, which is a 14.8% improvement over Luna, the previous state-of-the-art encoder-based architecture. Additionally, the system can process 30 to 60 examples per second on a single GPU, making it more practical for real-world RAG applications.

This study explores strategies for efficiently classifying scientific full texts using both small, BERT-based models and local large language models like Llama-3.1 8B. We focus on developing methods for selecting subsets of input sentences to reduce input size while simultaneously enhancing classification performance. To this end, we compile a novel dataset consisting of full-text scientific papers from the field of invasion biology, specifically addressing the impacts of invasive species. These papers are aligned with publicly available impact assessments created by researchers for the International Union for Conservation of Nature (IUCN). Through extensive experimentation, we demonstrate that various sources like human evidence annotations, LLM-generated annotations or explainability scores can be used to train sentence selection models that improve the performance of both encoder- and decoder-based language models while optimizing efficiency through the reduction in input length, leading to improved results even if compared to models like ModernBERT that are able to handle the complete text as input. Additionally, we find that repeated sampling of shorter inputs proves to be a very effective strategy that, at a slightly increased cost, can further improve classification performance.

Encoder-only transformer models such as BERT offer a great performance-size tradeoff for retrieval and classification tasks with respect to larger decoder-only models. Despite being the workhorse of numerous production pipelines, there have been limited Pareto improvements to BERT since its release. In this paper, we introduce ModernBERT, bringing modern model optimizations to encoder-only models and representing a major Pareto improvement over older encoders. Trained on 2 trillion tokens with a native 8192 sequence length, ModernBERT models exhibit state-of-the-art results on a large pool of evaluations encompassing diverse classification tasks and both single and multi-vector retrieval on different domains (including code). In addition to strong downstream performance, ModernBERT is also the most speed and memory efficient encoder and is designed for inference on common GPUs.

Pretrained transformer-encoder models like DeBERTaV3 and ModernBERT introduce architectural advancements aimed at improving efficiency and performance. Although the authors of ModernBERT report improved performance over DeBERTaV3 on several benchmarks, the lack of disclosed training data and the absence of comparisons using a shared dataset make it difficult to determine whether these gains are due to architectural improvements or differences in training data. In this work, we conduct a controlled study by pretraining ModernBERT on the same dataset as CamemBERTaV2, a DeBERTaV3 French model, isolating the effect of model design. Our results show that the previous model generation remains superior in sample efficiency and overall benchmark performance, with ModernBERT's primary advantage being faster training and inference speed. However, the new proposed model still provides meaningful architectural improvements compared to earlier models such as BERT and RoBERTa. Additionally, we observe that high-quality pre-training data accelerates convergence but does not significantly improve final performance, suggesting potential benchmark saturation. These findings show the importance of disentangling pretraining data from architectural innovations when evaluating transformer models.

Modern information retrieval systems often employ a two-stage pipeline: an efficient initial retrieval stage followed by a computationally intensive reranking stage. Cross-encoders have shown strong effectiveness for reranking due to their deep analysis of query-document pairs. This paper studies the impact of the Lion optimizer, a recent alternative to AdamW, during fine-tuning of cross-encoder rerankers. We fine-tune three transformer models-MiniLM, GTE, and ModernBERT-on the MS MARCO passage ranking dataset using both optimizers. GTE and ModernBERT support extended context lengths (up to 8192 tokens). We evaluate effectiveness using TREC 2019 Deep Learning Track and MS MARCO dev set (MRR@10). Experiments, run on the Modal cloud platform, reveal that ModernBERT with Lion achieves the best NDCG@10 (0.7225) and MAP (0.5121) on TREC DL 2019, while MiniLM with Lion ties ModernBERT for MRR@10 (0.5988) on MS MARCO dev. Lion also provides superior GPU efficiency, improving utilization by 2.67% to 10.33% across models. We analyze performance trends using standard IR metrics and discuss the optimizer's impact on training dynamics across architectures.

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

In this technical report, we present Falcon Mamba 7B, a new base large language model based on the novel Mamba architecture. Falcon Mamba 7B is trained on 5.8 trillion tokens with carefully selected data mixtures. As a pure Mamba-based model, Falcon Mamba 7B surpasses leading open-weight models based on Transformers, such as Mistral 7B, Llama3.1 8B, and Falcon2 11B. It is on par with Gemma 7B and outperforms models with different architecture designs, such as RecurrentGemma 9B and RWKV-v6 Finch 7B/14B. Currently, Falcon Mamba 7B is the best-performing Mamba model in the literature at this scale, surpassing both existing Mamba and hybrid Mamba-Transformer models, according to the Open LLM Leaderboard. Due to its architecture, Falcon Mamba 7B is significantly faster at inference and requires substantially less memory for long sequence generation. Despite recent studies suggesting that hybrid Mamba-Transformer models outperform pure architecture designs, we demonstrate that even the pure Mamba design can achieve similar, or even superior results compared to the Transformer and hybrid designs. We make the weights of our implementation of Falcon Mamba 7B publicly available on https://huggingface.co/tiiuae/falcon-mamba-7b, under a permissive license.