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Aug 31

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.

  • 9 authors
·
Nov 21, 2023

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 Many sources are historical documents and are the result of Optical Character Recognition (OCR).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.

  • 4 authors
·
Oct 29, 2024 2

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

  • 4 authors
·
Feb 25, 2022

Redefining Experts: Interpretable Decomposition of Language Models for Toxicity Mitigation

Large Language Models have demonstrated impressive fluency across diverse tasks, yet their tendency to produce toxic content remains a critical challenge for AI safety and public trust. Existing toxicity mitigation approaches primarily manipulate individual neuron activations, but these methods suffer from instability, context dependence, and often compromise the model's core language abilities. To address these shortcomings, we investigate three key questions: the stability of neuron-level toxicity indicators, the advantages of structural (layer-wise) representations, and the interpretability of mechanisms driving toxic generation. Through extensive experiments on Jigsaw and ToxiCN datasets, we show that aggregated layer-wise features provide more robust signals than single neurons. Moreover, we observe conceptual limitations in prior works that conflate toxicity detection experts and generation experts within neuron-based interventions. To mitigate this, we propose a novel principled intervention technique, EigenShift, based on eigen-decomposition of the language model's final output layer. This method selectively targets generation-aligned components, enabling precise toxicity suppression without impairing linguistic competence. Our method requires no additional training or fine-tuning, incurs minimal computational cost, and is grounded in rigorous theoretical analysis.

  • 4 authors
·
Sep 20, 2025

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.

  • 12 authors
·
Mar 10, 2024

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.

  • 10 authors
·
Nov 29, 2023

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.

  • 4 authors
·
Jun 23, 2025

Chinese Toxic Language Mitigation via Sentiment Polarity Consistent Rewrites

Detoxifying offensive language while preserving the speaker's original intent is a challenging yet critical goal for improving the quality of online interactions. Although large language models (LLMs) show promise in rewriting toxic content, they often default to overly polite rewrites, distorting the emotional tone and communicative intent. This problem is especially acute in Chinese, where toxicity often arises implicitly through emojis, homophones, or discourse context. We present ToxiRewriteCN, the first Chinese detoxification dataset explicitly designed to preserve sentiment polarity. The dataset comprises 1,556 carefully annotated triplets, each containing a toxic sentence, a sentiment-aligned non-toxic rewrite, and labeled toxic spans. It covers five real-world scenarios: standard expressions, emoji-induced and homophonic toxicity, as well as single-turn and multi-turn dialogues. We evaluate 17 LLMs, including commercial and open-source models with variant architectures, across four dimensions: detoxification accuracy, fluency, content preservation, and sentiment polarity. Results show that while commercial and MoE models perform best overall, all models struggle to balance safety with emotional fidelity in more subtle or context-heavy settings such as emoji, homophone, and dialogue-based inputs. We release ToxiRewriteCN to support future research on controllable, sentiment-aware detoxification for Chinese.

  • 6 authors
·
May 21, 2025

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.

  • 5 authors
·
Sep 23, 2020

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.

  • 6 authors
·
Mar 17, 2022

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.

  • 8 authors
·
Jun 12, 2025

MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to understand and modify molecular structures is critical for optimizing drug properties such as efficacy and toxicity. However, existing models and benchmarks often overlook toxicity-related challenges, focusing primarily on general property optimization without adequately addressing safety concerns. In addition, even existing toxicity repair benchmarks suffer from limited data diversity, low structural validity of generated molecules, and heavy reliance on proxy models for toxicity assessment. To address these limitations, we propose MolDeTox, a novel benchmark for molecular detoxification, designed to enable fine-grained and reliable evaluation of toxicity-aware molecular optimization across stepwise tasks. We evaluate a wide range of general-purpose LLMs and VLMs under diverse settings, and demonstrate that understanding and generating molecules at the fragment-level improves structural validity and enhances the quality of generated molecules. Moreover, through detailed task-level performance analysis, MolDeTox provides an interpretable benchmark that enables a deeper understanding of the detoxification process. Our dataset is available at : https://huggingface.co/datasets/MolDeTox/MolDeTox

  • 5 authors
·
May 11

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.

  • 7 authors
·
Aug 5, 2025 2

ToxiShield: Promoting Inclusive Developer Communication through Real-Time Toxicity Filtering

Toxic interactions during code reviews can undermine teamwork and hinder productivity in software engineering (SE) teams. While prior studies explore toxicity detection and empirical investigation, they lack real-time detoxification tools to support the SE community. To address this gap, we present ToxiShield, a browser extension for GitHub pull requests that is built using three modules: i) Toxicity Filter -- to identify whether a text is toxic, ii) Communication coach -- to facilitate just-in-time fine-grained toxicity categorization with explanations, and iii) The Reframer -- that generates a revised, constructive alternative of a toxic text. For each module, we trained and evaluated multiple deep learning and Large Language Models (LLMs) to identify the best choice. A BERT-based binary detection model, trained on 38,761 code review samples, achieves 98% accuracy and an F1-score of 97% and is the selected one for the Toxicity Filter module. For the Communication Coach, prompt-tuned Claude 3.5 Sonnet achieved the best performance with 39% MCC and 42% F1 in multiclass toxicity classification with detailed reasoning. For Reframer, we evaluated five LLMs using a fine-tuning strategy on a dataset of 10,120 code review comments. The fine-tuned Llama 3.2 model achieves 95.27% style transfer accuracy, 97.03% fluency, 67.07% content preservation, and an 84% J-score. We further validated ToxiShield through a human evaluation using the Technology Acceptance Model with 10 participants, confirming its perceived usefulness and ease of adoption. ToxiShield sets a benchmark for advancing constructive communication in software engineering, driving inclusivity and healthier collaboration in open-source communities.

  • 5 authors
·
Apr 14

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.

  • 4 authors
·
Sep 29, 2024

HODDI: A Dataset of High-Order Drug-Drug Interactions for Computational Pharmacovigilance

Drug-side effect research is vital for understanding adverse reactions arising in complex multi-drug therapies. However, the scarcity of higher-order datasets that capture the combinatorial effects of multiple drugs severely limits progress in this field. Existing resources such as TWOSIDES primarily focus on pairwise interactions. To fill this critical gap, we introduce HODDI, the first Higher-Order Drug-Drug Interaction Dataset, constructed from U.S. Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) records spanning the past decade, to advance computational pharmacovigilance. HODDI contains 109,744 records involving 2,506 unique drugs and 4,569 unique side effects, specifically curated to capture multi-drug interactions and their collective impact on adverse effects. Comprehensive statistical analyses demonstrate HODDI's extensive coverage and robust analytical metrics, making it a valuable resource for studying higher-order drug relationships. Evaluating HODDI with multiple models, we found that simple Multi-Layer Perceptron (MLP) can outperform graph models, while hypergraph models demonstrate superior performance in capturing complex multi-drug interactions, further validating HODDI's effectiveness. Our findings highlight the inherent value of higher-order information in drug-side effect prediction and position HODDI as a benchmark dataset for advancing research in pharmacovigilance, drug safety, and personalized medicine. The dataset and codes are available at https://github.com/TIML-Group/HODDI.

  • 6 authors
·
Feb 10, 2025

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.

  • 2 authors
·
Apr 19, 2024

CoGate-LSTM: Prototype-Guided Feature-Space Gating for Mitigating Gradient Dilution in Imbalanced Toxic Comment Classification

Toxic text classification for online moderation remains challenging under extreme class imbalance, where rare but high-risk labels such as threat and severe_toxic are consistently underdetected by conventional models. We propose CoGate-LSTM, a parameter-efficient recurrent architecture built around a novel cosine-similarity feature gating mechanism that adaptively rescales token embeddings by their directional similarity to a learned toxicity prototype. Unlike token-position attention, the gate emphasizes feature directions most informative for minority toxic classes. The model combines frozen multi-source embeddings (GloVe, FastText, and BERT-CLS), a character-level BiLSTM, embedding-space SMOTE, and weighted focal loss. On the Jigsaw Toxic Comment benchmark, CoGate-LSTM achieves 0.881 macro-F1 (95% CI: [0.873, 0.889]) and 96.0% accuracy, outperforming fine-tuned BERT by 6.9 macro-F1 points (p < 0.001) and XGBoost by 4.7, while using only 7.3M parameters (about 15times fewer than BERT) and 48 ms CPU inference latency. Gains are strongest on minority labels, with F1 improvements of +71% for severe_toxic, +33% for threat, and +28% for identity_hate relative to fine-tuned BERT. Ablations identify cosine gating as the primary driver of performance (-4.8 macro-F1 when removed), with additional benefits from character-level fusion (-2.4) and multi-head attention (-2.9). CoGate-LSTM also transfers reasonably across datasets, reaching a 0.71 macro-F1 zero-shot on the Contextual Abuse Dataset and 0.73 with lightweight threshold adaptation. These results show that direction-aware feature gating offers an effective and efficient alternative to large, fully fine-tuned transformers for classifying imbalanced toxic comments.

google Google
·
Apr 6

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.

  • 5 authors
·
Nov 8, 2023 1

On the Limits of LLM Adaptability: Impact of Model-Internalized Priors on Annotation Task Performance

Large Language Models (LLMs) are increasingly used for zero-shot annotation and LLM-as-a-judge tasks, yet their reliability hinges on how model-internalized priors interact with user-provided instructions. We investigate three dimensions of this interaction: (1) how an LLM's familiarity with data and task definitions affects performance, (2) the extent to which additional information in prompts can correct zero-shot errors ("decision stickiness"), and (3) model susceptibility to misaligned task definitions. Through experiments on toxicity detection across diverse datasets (spanning social media, gaming, news, and forums) using both dense and mixture-of-experts models, we find that nearly two-thirds of zero-shot errors are resistant to correction, with an overall rescue rate (fraction of initial errors corrected by prompting) of only 34.8%. High-confidence errors prove especially resistant to correction. When given misaligned definitions, LLMs follow them while maintaining confidence levels unchanged from the aligned condition. Crucially, we introduce Definition-Specific Familiarity (DSF), which measures alignment between a model's internal concept and the task definition. After controlling for dataset-level confounds, DSF shows a positive association with model performance (partial r = +0.41), while three distinct memorization metrics (ROUGE-L, BERTScore, and embedding cosine similarity) all fail to show a positive association. These findings show the limitations of prompt-based correction in annotation tasks, highlighting the importance of definition alignment over text-level memorization.

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.

  • 12 authors
·
Aug 14, 2025

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.

  • 7 authors
·
Jun 27, 2024

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

  • 8 authors
·
Nov 29, 2024

LinEAS: End-to-end Learning of Activation Steering with a Distributional Loss

The growing use of generative models in daily life calls for efficient mechanisms to control their generation, to e.g., produce safe content or provide users with tools to explore style changes. Ideally, such mechanisms should require low volume of unpaired data (i.e., without explicit preference), and should be cheap, both at train and inference time, while preserving output quality. Recent research has shown that such mechanisms can be obtained by intervening exclusively on model activations, with the goal of correcting distributional differences between activations seen when using prompts from a source vs. a target set (e.g., toxic and non-toxic sentences). While cheap, these fast methods are inherently crude: their maps are tuned locally, not accounting for their impact on downstream layers, resulting in interventions that cause unintended shifts when used out-of-sample. We propose in this work linear end-to-end activation steering (LinEAS), an approach trained with a global loss that accounts simultaneously for all layer-wise distributional shifts. In addition to being more robust, the loss used to train LinEAS can be regularized with sparsifying norms, which can automatically carry out neuron selection. LinEAS only requires a handful of unpaired samples to be effective, and beats similar baselines on toxicity mitigation in language models, becoming competitive with oracle-dependent methods that have access to strong supervision. LinEAS is modality-agnostic and we empirically find that it outperforms existing activation steering methods at mitigating and including new concepts at the output of single-step text-to-image generation models.

apple Apple
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Mar 11, 2025 1

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.

  • 11 authors
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May 22, 2023

Forbidden Science: Dual-Use AI Challenge Benchmark and Scientific Refusal Tests

The development of robust safety benchmarks for large language models requires open, reproducible datasets that can measure both appropriate refusal of harmful content and potential over-restriction of legitimate scientific discourse. We present an open-source dataset and testing framework for evaluating LLM safety mechanisms across mainly controlled substance queries, analyzing four major models' responses to systematically varied prompts. Our results reveal distinct safety profiles: Claude-3.5-sonnet demonstrated the most conservative approach with 73% refusals and 27% allowances, while Mistral attempted to answer 100% of queries. GPT-3.5-turbo showed moderate restriction with 10% refusals and 90% allowances, and Grok-2 registered 20% refusals and 80% allowances. Testing prompt variation strategies revealed decreasing response consistency, from 85% with single prompts to 65% with five variations. This publicly available benchmark enables systematic evaluation of the critical balance between necessary safety restrictions and potential over-censorship of legitimate scientific inquiry, while providing a foundation for measuring progress in AI safety implementation. Chain-of-thought analysis reveals potential vulnerabilities in safety mechanisms, highlighting the complexity of implementing robust safeguards without unduly restricting desirable and valid scientific discourse.

  • 2 authors
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Feb 7, 2025 2

PCB-Vision: A Multiscene RGB-Hyperspectral Benchmark Dataset of Printed Circuit Boards

Addressing the critical theme of recycling electronic waste (E-waste), this contribution is dedicated to developing advanced automated data processing pipelines as a basis for decision-making and process control. Aligning with the broader goals of the circular economy and the United Nations (UN) Sustainable Development Goals (SDG), our work leverages non-invasive analysis methods utilizing RGB and hyperspectral imaging data to provide both quantitative and qualitative insights into the E-waste stream composition for optimizing recycling efficiency. In this paper, we introduce 'PCB-Vision'; a pioneering RGB-hyperspectral printed circuit board (PCB) benchmark dataset, comprising 53 RGB images of high spatial resolution paired with their corresponding high spectral resolution hyperspectral data cubes in the visible and near-infrared (VNIR) range. Grounded in open science principles, our dataset provides a comprehensive resource for researchers through high-quality ground truths, focusing on three primary PCB components: integrated circuits (IC), capacitors, and connectors. We provide extensive statistical investigations on the proposed dataset together with the performance of several state-of-the-art (SOTA) models, including U-Net, Attention U-Net, Residual U-Net, LinkNet, and DeepLabv3+. By openly sharing this multi-scene benchmark dataset along with the baseline codes, we hope to foster transparent, traceable, and comparable developments of advanced data processing across various scientific communities, including, but not limited to, computer vision and remote sensing. Emphasizing our commitment to supporting a collaborative and inclusive scientific community, all materials, including code, data, ground truth, and masks, will be accessible at https://github.com/hifexplo/PCBVision.

  • 6 authors
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Jan 12, 2024

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.

  • 20 authors
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Feb 28, 2024

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.

  • 17 authors
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Oct 19, 2020

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.

  • 7 authors
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Aug 21, 2024 4

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/.

  • 5 authors
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May 8, 2020

Model Surgery: Modulating LLM's Behavior Via Simple Parameter Editing

Large Language Models (LLMs) have demonstrated great potential as generalist assistants, showcasing powerful task understanding and problem-solving capabilities. To deploy LLMs as AI assistants, it is crucial that these models exhibit desirable behavioral traits, such as non-toxicity and resilience against jailbreak attempts. Current methods for detoxification or preventing jailbreaking usually involve Supervised Fine-Tuning (SFT) or Reinforcement Learning from Human Feedback (RLHF), which requires finetuning billions of parameters through gradient descent with substantial computation cost. Furthermore, models modified through SFT and RLHF may deviate from the pretrained models, potentially leading to a degradation in foundational LLM capabilities. In this paper, we observe that surprisingly, directly editing a small subset of parameters can effectively modulate specific behaviors of LLMs, such as detoxification and resistance to jailbreaking. Specifically, for a behavior that we aim to avoid, we employ a linear classifier, which we term the behavior probe, to classify binary behavior labels within the hidden state space of the LLM. Using this probe, we introduce an algorithm to identify a critical subset of LLM parameters that significantly influence this targeted behavior. Then we directly edit these selected parameters by shifting them towards the behavior probe. Such a direct parameter editing method necessitates only inference-level computational resources. Experiments demonstrate that in the representative detoxification task, our approach achieves reductions of up to 90.0\% in toxicity on the RealToxicityPrompts dataset and 49.2\% on ToxiGen, while maintaining the LLM's general capabilities in areas such as common sense, question answering, and mathematics. Our code is available at https://github.com/lucywang720/model-surgery.

  • 8 authors
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Jul 11, 2024 4

The Dataset Nutrition Label: A Framework To Drive Higher Data Quality Standards

Artificial intelligence (AI) systems built on incomplete or biased data will often exhibit problematic outcomes. Current methods of data analysis, particularly before model development, are costly and not standardized. The Dataset Nutrition Label (the Label) is a diagnostic framework that lowers the barrier to standardized data analysis by providing a distilled yet comprehensive overview of dataset "ingredients" before AI model development. Building a Label that can be applied across domains and data types requires that the framework itself be flexible and adaptable; as such, the Label is comprised of diverse qualitative and quantitative modules generated through multiple statistical and probabilistic modelling backends, but displayed in a standardized format. To demonstrate and advance this concept, we generated and published an open source prototype with seven sample modules on the ProPublica Dollars for Docs dataset. The benefits of the Label are manyfold. For data specialists, the Label will drive more robust data analysis practices, provide an efficient way to select the best dataset for their purposes, and increase the overall quality of AI models as a result of more robust training datasets and the ability to check for issues at the time of model development. For those building and publishing datasets, the Label creates an expectation of explanation, which will drive better data collection practices. We also explore the limitations of the Label, including the challenges of generalizing across diverse datasets, and the risk of using "ground truth" data as a comparison dataset. We discuss ways to move forward given the limitations identified. Lastly, we lay out future directions for the Dataset Nutrition Label project, including research and public policy agendas to further advance consideration of the concept.

  • 5 authors
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May 9, 2018

IRepair: An Intent-Aware Approach to Repair Data-Driven Errors in Large Language Models

Not a day goes by without hearing about the impressive feats of large language models (LLMs), and equally, not a day passes without hearing about their challenges. LLMs are notoriously vulnerable to biases in their dataset, leading to issues such as toxicity. While domain-adaptive training has been employed to mitigate these issues, these techniques often address all model parameters indiscriminately during the repair process, resulting in poor repair quality and reduced model versatility. In this paper, we introduce a novel dynamic slicing-based intent-aware LLM repair strategy, IRepair. This approach selectively targets the most error-prone sections of the model for repair. Specifically, we propose dynamically slicing the model's most sensitive layers that require immediate attention, concentrating repair efforts on those areas. This method enables more effective repairs with potentially less impact on the model's overall performance by altering a smaller portion of the model. We evaluated our technique on three models from the GPT2 and GPT-Neo families, with parameters ranging from 800M to 1.6B, in a toxicity mitigation setup. Our results show that IRepair repairs errors 43.6% more effectively while causing 46% less disruption to general performance compared to the closest baseline, direct preference optimization. Our empirical analysis also reveals that errors are more concentrated in a smaller section of the model, with the top 20% of layers exhibiting 773% more error density than the remaining 80\%. This highlights the need for selective repair. Additionally, we demonstrate that a dynamic selection approach is essential for addressing errors dispersed throughout the model, ensuring a robust and efficient repair.

  • 4 authors
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Feb 10, 2025

DCA-Bench: A Benchmark for Dataset Curation Agents

The quality of datasets plays an increasingly crucial role in the research and development of modern artificial intelligence (AI). Despite the proliferation of open dataset platforms nowadays, data quality issues, such as insufficient documentation, inaccurate annotations, and ethical concerns, remain common in datasets widely used in AI. Furthermore, these issues are often subtle and difficult to be detected by rule-based scripts, requiring expensive manual identification and verification by dataset users or maintainers. With the increasing capability of large language models (LLMs), it is promising to streamline the curation of datasets with LLM agents. In this work, as the initial step towards this goal, we propose a dataset curation agent benchmark, DCA-Bench, to measure LLM agents' capability of detecting hidden dataset quality issues. Specifically, we collect diverse real-world dataset quality issues from eight open dataset platforms as a testbed. Additionally, to establish an automatic pipeline for evaluating the success of LLM agents, which requires a nuanced understanding of the agent outputs, we implement a dedicated Evaluator using another LLM agent. We demonstrate that the LLM-based Evaluator empirically aligns well with human evaluation, allowing reliable automatic evaluation on the proposed benchmark. We further conduct experiments on several baseline LLM agents on the proposed benchmark and demonstrate the complexity of the task, indicating that applying LLMs to real-world dataset curation still requires further in-depth exploration and innovation. Finally, the proposed benchmark can also serve as a testbed for measuring the capability of LLMs in problem discovery rather than just problem-solving. The benchmark suite is available at https://github.com/TRAIS-Lab/dca-bench.

  • 5 authors
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Jun 11, 2024

Harm in AI-Driven Societies: An Audit of Toxicity Adoption on Chirper.ai

Large Language Models (LLMs) are increasingly embedded in autonomous agents that engage, converse, and co-evolve in online social platforms. While prior work has documented the generation of toxic content by LLMs, far less is known about how exposure to harmful content shapes agent behavior over time, particularly in environments composed entirely of interacting AI agents. In this work, we study toxicity adoption of LLM-driven agents on Chirper.ai, a fully AI-driven social platform. Specifically, we model interactions in terms of stimuli (posts) and responses (comments). We conduct a large-scale empirical analysis of agent behavior, examining how toxic responses relate to toxic stimuli, how repeated exposure to toxicity affects the likelihood of toxic responses, and whether toxic behavior can be predicted from exposure alone. Our findings show that toxic responses are more likely following toxic stimuli, and, at the same time, cumulative toxic exposure (repeated over time) significantly increases the probability of toxic responding. We further introduce two influence metrics, revealing a strong negative correlation between induced and spontaneous toxicity. Finally, we show that the number of toxic stimuli alone enables accurate prediction of whether an agent will eventually produce toxic content. These results highlight exposure as a critical risk factor in the deployment of LLM agents, particularly as such agents operate in online environments where they may engage not only with other AI chatbots, but also with human counterparts. This could trigger unwanted and pernicious phenomena, such as hate-speech propagation and cyberbullying. In an effort to reduce such risks, monitoring exposure to toxic content may provide a lightweight yet effective mechanism for auditing and mitigating harmful behavior in the wild.

  • 3 authors
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Jan 3

Learning Diagnostic Reasoning for Decision Support in Toxicology

Acute poly-substance intoxication requires rapid, life-saving decisions under substantial uncertainty, as clinicians must rely on incomplete ingestion details and nonspecific symptoms. Effective diagnostic reasoning in this chaotic environment requires fusing unstructured, non-medical narratives (e.g. paramedic scene descriptions and unreliable patient self-reports or known histories), with structured medical data like vital signs. While Large Language Models (LLMs) show potential for processing such heterogeneous inputs, they struggle in this setting, often underperforming simple baselines that rely solely on patient histories. To address this, we present DeToxR (Decision-support for Toxicology with Reasoning), the first adaptation of Reinforcement Learning (RL) to emergency toxicology. We design a robust data-fusion engine for multi-label prediction across 14 substance classes based on an LLM finetuned with Group Relative Policy Optimization (GRPO). We optimize the model's reasoning directly using a clinical performance reward. By formulating a multi-label agreement metric as the reward signal, the model is explicitly penalized for missing co-ingested substances and hallucinating absent poisons. Our model significantly outperforms its unadapted base LLM counterpart and supervised baselines. Furthermore, in a clinical validation study, the model indicates a clinical advantage by outperforming an expert toxicologist in identifying the correct poisons (Micro-F1: 0.644 vs. 0.473). These results demonstrate the potential of RL-aligned LLMs to synthesize unstructured pre-clinical narratives and structured medical data for decision support in high-stakes environments.

  • 6 authors
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Mar 30

Open Catalyst Experiments 2024 (OCx24): Bridging Experiments and Computational Models

The search for low-cost, durable, and effective catalysts is essential for green hydrogen production and carbon dioxide upcycling to help in the mitigation of climate change. Discovery of new catalysts is currently limited by the gap between what AI-accelerated computational models predict and what experimental studies produce. To make progress, large and diverse experimental datasets are needed that are reproducible and tested at industrially-relevant conditions. We address these needs by utilizing a comprehensive high-throughput characterization and experimental pipeline to create the Open Catalyst Experiments 2024 (OCX24) dataset. The dataset contains 572 samples synthesized using both wet and dry methods with X-ray fluorescence and X-ray diffraction characterization. We prepared 441 gas diffusion electrodes, including replicates, and evaluated them using zero-gap electrolysis for carbon dioxide reduction (CO_2RR) and hydrogen evolution reactions (HER) at current densities up to 300 mA/cm^2. To find correlations with experimental outcomes and to perform computational screens, DFT-verified adsorption energies for six adsorbates were calculated on sim20,000 inorganic materials requiring 685 million AI-accelerated relaxations. Remarkably from this large set of materials, a data driven Sabatier volcano independently identified Pt as being a top candidate for HER without having any experimental measurements on Pt or Pt-alloy samples. We anticipate the availability of experimental data generated specifically for AI training, such as OCX24, will significantly improve the utility of computational models in selecting materials for experimental screening.

  • 20 authors
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Nov 17, 2024

DataComp: In search of the next generation of multimodal datasets

Large multimodal datasets have been instrumental in recent breakthroughs such as CLIP, Stable Diffusion, and GPT-4. At the same time, datasets rarely receive the same research attention as model architectures or training algorithms. To address this shortcoming in the machine learning ecosystem, we introduce DataComp, a benchmark where the training code is fixed and researchers innovate by proposing new training sets. We provide a testbed for dataset experiments centered around a new candidate pool of 12.8B image-text pairs from Common Crawl. Participants in our benchmark design new filtering techniques or curate new data sources and then evaluate their new dataset by running our standardized CLIP training code and testing on 38 downstream test sets. Our benchmark consists of multiple scales, with four candidate pool sizes and associated compute budgets ranging from 12.8M to 12.8B samples seen during training. This multi-scale design facilitates the study of scaling trends and makes the benchmark accessible to researchers with varying resources. Our baseline experiments show that the DataComp workflow is a promising way of improving multimodal datasets. We introduce DataComp-1B, a dataset created by applying a simple filtering algorithm to the 12.8B candidate pool. The resulting 1.4B subset enables training a CLIP ViT-L/14 from scratch to 79.2% zero-shot accuracy on ImageNet. Our new ViT-L/14 model outperforms a larger ViT-g/14 trained on LAION-2B by 0.7 percentage points while requiring 9x less training compute. We also outperform OpenAI's CLIP ViT-L/14 by 3.7 percentage points, which is trained with the same compute budget as our model. These gains highlight the potential for improving model performance by carefully curating training sets. We view DataComp-1B as only the first step and hope that DataComp paves the way toward the next generation of multimodal datasets.

  • 34 authors
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Apr 27, 2023

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.

  • 4 authors
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Jun 4, 2024

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.

microsoft Microsoft
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Jun 17, 2025

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.

  • 5 authors
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May 24, 2024