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Aug 5

MATRIX: Multi-Agent simulaTion fRamework for safe Interactions and conteXtual clinical conversational evaluation

Despite the growing use of large language models (LLMs) in clinical dialogue systems, existing evaluations focus on task completion or fluency, offering little insight into the behavioral and risk management requirements essential for safety-critical systems. This paper presents MATRIX (Multi-Agent simulaTion fRamework for safe Interactions and conteXtual clinical conversational evaluation), a structured, extensible framework for safety-oriented evaluation of clinical dialogue agents. MATRIX integrates three components: (1) a safety-aligned taxonomy of clinical scenarios, expected system behaviors and failure modes derived through structured safety engineering methods; (2) BehvJudge, an LLM-based evaluator for detecting safety-relevant dialogue failures, validated against expert clinician annotations; and (3) PatBot, a simulated patient agent capable of producing diverse, scenario-conditioned responses, evaluated for realism and behavioral fidelity with human factors expertise, and a patient-preference study. Across three experiments, we show that MATRIX enables systematic, scalable safety evaluation. BehvJudge with Gemini 2.5-Pro achieves expert-level hazard detection (F1 0.96, sensitivity 0.999), outperforming clinicians in a blinded assessment of 240 dialogues. We also conducted one of the first realism analyses of LLM-based patient simulation, showing that PatBot reliably simulates realistic patient behavior in quantitative and qualitative evaluations. Using MATRIX, we demonstrate its effectiveness in benchmarking five LLM agents across 2,100 simulated dialogues spanning 14 hazard scenarios and 10 clinical domains. MATRIX is the first framework to unify structured safety engineering with scalable, validated conversational AI evaluation, enabling regulator-aligned safety auditing. We release all evaluation tools, prompts, structured scenarios, and datasets.

  • 12 authors
·
Aug 25, 2025

PEEM: Prompt Engineering Evaluation Metrics for Interpretable Joint Evaluation of Prompts and Responses

Prompt design is a primary control interface for large language models (LLMs), yet standard evaluations largely reduce performance to answer correctness, obscuring why a prompt succeeds or fails and providing little actionable guidance. We propose PEEM (Prompt Engineering Evaluation Metrics), a unified framework for joint and interpretable evaluation of both prompts and responses. PEEM defines a structured rubric with 9 axes: 3 prompt criteria (clarity/structure, linguistic quality, fairness) and 6 response criteria (accuracy, coherence, relevance, objectivity, clarity, conciseness), and uses an LLM-based evaluator to output (i) scalar scores on a 1-5 Likert scale and (ii) criterion-specific natural-language rationales grounded in the rubric. Across 7 benchmarks and 5 task models, PEEM's accuracy axis strongly aligns with conventional accuracy while preserving model rankings (aggregate Spearman rho about 0.97, Pearson r about 0.94, p < 0.001). A multi-evaluator study with four models shows consistent relative judgments (pairwise rho = 0.68-0.85), supporting evaluator-agnostic deployment. Beyond alignment, PEEM captures complementary linguistic failure modes and remains informative under prompt perturbations: prompt-quality trends track downstream accuracy under iterative rewrites, semantic adversarial manipulations induce clear score degradation, and meaning-preserving paraphrases yield high stability (robustness rate about 76.7-80.6%). Finally, using only PEEM scores and rationales as feedback, a zero-shot prompt rewriting loop improves downstream accuracy by up to 11.7 points, outperforming supervised and RL-based prompt-optimization baselines. Overall, PEEM provides a reproducible, criterion-driven protocol that links prompt formulation to response behavior and enables systematic diagnosis and optimization of LLM interactions.

  • 4 authors
·
Mar 11

HREF: Human Response-Guided Evaluation of Instruction Following in Language Models

Evaluating the capability of Large Language Models (LLMs) in following instructions has heavily relied on a powerful LLM as the judge, introducing unresolved biases that deviate the judgments from human judges. In this work, we reevaluate various choices for automatic evaluation on a wide range of instruction-following tasks. We experiment with methods that leverage human-written responses and observe that they enhance the reliability of automatic evaluations across a wide range of tasks, resulting in up to a 3.2% improvement in agreement with human judges. We also discovered that human-written responses offer an orthogonal perspective to model-generated responses in following instructions and should be used as an additional context when comparing model responses. Based on these observations, we develop a new evaluation benchmark, Human Response-Guided Evaluation of Instruction Following (HREF), comprising 4,258 samples across 11 task categories with a composite evaluation setup, employing a composite evaluation setup that selects the most reliable method for each category. In addition to providing reliable evaluation, HREF emphasizes individual task performance and is free from contamination. Finally, we study the impact of key design choices in HREF, including the size of the evaluation set, the judge model, the baseline model, and the prompt template. We host a live leaderboard that evaluates LLMs on the private evaluation set of HREF.

  • 4 authors
·
Dec 19, 2024

Language Models Improve When Pretraining Data Matches Target Tasks

Every data selection method inherently has a target. In practice, these targets often emerge implicitly through benchmark-driven iteration: researchers develop selection strategies, train models, measure benchmark performance, then refine accordingly. This raises a natural question: what happens when we make this optimization explicit? To explore this, we propose benchmark-targeted ranking (BETR), a simple method that selects pretraining documents based on similarity to benchmark training examples. BETR embeds benchmark examples and a sample of pretraining documents in a shared space, scores this sample by similarity to benchmarks, then trains a lightweight classifier to predict these scores for the full corpus. We compare data selection methods by training over 500 models spanning 10^{19} to 10^{22} FLOPs and fitting scaling laws to them. From this, we find that simply aligning pretraining data to evaluation benchmarks using BETR achieves a 2.1x compute multiplier over DCLM-Baseline (4.7x over unfiltered data) and improves performance on 9 out of 10 tasks across all scales. BETR also generalizes well: when targeting a diverse set of benchmarks disjoint from our evaluation suite, it still matches or outperforms baselines. Our scaling analysis further reveals a clear trend: larger models require less aggressive filtering. Overall, our findings show that directly matching pretraining data to target tasks precisely shapes model capabilities and highlight that optimal selection strategies must adapt to model scale.

  • 10 authors
·
Jul 16, 2025

Omni-DuplexEval: Evaluating Real-time Duplex Omni-modal Interaction

Real-time duplex interaction is essential for multimodal AI systems operating in real-world scenarios, where models must continuously process streaming inputs and respond at appropriate moments. However, most existing multimodal large language models (MLLMs) are evaluated in offline settings, where the entire video input is processed before any response is generated. While recent work has started to explore real-time duplex MLLMs, there is still no comprehensive benchmark or automatic evaluation method for this setting. To address this gap, we propose Omni-DuplexEval, a benchmark for systematically evaluating real-time duplex interaction. The benchmark consists of two complementary scenarios: (1) Real-Time Description, which evaluates the ability to generate continuous, time-aligned responses that track evolving multimodal inputs, and (2) Proactive Reminder, which evaluates the ability to identify salient events and respond at appropriate moments. Omni-DuplexEval contains 660 videos with fine-grained, human-annotated labels and precise temporal metadata, spanning 9 tasks grounded in real-world scenarios, where all questions are formulated as open-ended queries. We further introduce an automatic evaluation framework based on LLM-as-a-Judge, which enables systematic assessment by jointly evaluating response-content alignment and response timing through timestamp-aware and sequential reasoning, achieving strong alignment with human judgments. Experiments on state-of-the-art duplex MLLMs reveal substantial limitations. The best-performing model achieves only 39.6% overall, while scoring only 20.0% on Proactive Reminder. Our analysis identifies two key challenges: models struggle to balance timely responses with coherent, holistic content generation, and they often fail to determine both when to respond and what to produce. We hope our work facilitates further progress in MLLMs.

  • 8 authors
·
May 16 1

Efficient Response Generation Method Selection for Fine-Tuning Large Language Models

The training data for fine-tuning large language models (LLMs) is typically structured as input-output pairs. However, for many tasks, there can be multiple equally valid output variations for the same input. Recent studies have observed that the choice of output variation used in training can affect the model's performance. This raises an important question: how can we generate the most effective output from the many possible response generation strategy options? Rather than relying on the traditional but resource-intensive train-and-evaluate approach, this paper proposes a scalable, approximate method for estimating the quality of a small subset of generated training data derived from the same input. We then evaluate how well this small subset of generated output fits the target model we are trying to train. We present a large-scale benchmark covering diverse reasoning-based datasets to support our study. The central idea is that a good output should closely resemble the output generated by the target LLM. We formalize this 'closeness' as the expected alignment score between a candidate output and the output sampled from the target LLM. We connect this measurement to the perplexity metric used in previous literature and demonstrate that leveraging an alignment-based metric can provide better predictions of model performance. Using this strategy, we can evaluate a small subset of the generated output from each response generation strategy option, then select the most effective strategy. We show that an LLM trained on data generated by the selected strategy could lead to a significant performance gain in many cases.

  • 3 authors
·
Feb 17, 2025

Between Help and Harm: An Evaluation of Mental Health Crisis Handling by LLMs

Large language model-powered chatbots have transformed how people seek information, especially in high-stakes contexts like mental health. Despite their support capabilities, safe detection and response to crises such as suicidal ideation and self-harm are still unclear, hindered by the lack of unified crisis taxonomies and clinical evaluation standards. We address this by creating: (1) a taxonomy of six crisis categories; (2) a dataset of over 2,000 inputs from 12 mental health datasets, classified into these categories; and (3) a clinical response assessment protocol. We also use LLMs to identify crisis inputs and audit five models for response safety and appropriateness. First, we built a clinical-informed crisis taxonomy and evaluation protocol. Next, we curated 2,252 relevant examples from over 239,000 user inputs, then tested three LLMs for automatic classification. In addition, we evaluated five models for the appropriateness of their responses to a user's crisis, graded on a 5-point Likert scale from harmful (1) to appropriate (5). While some models respond reliably to explicit crises, risks still exist. Many outputs, especially in self-harm and suicidal categories, are inappropriate or unsafe. Different models perform variably; some, like gpt-5-nano and deepseek-v3.2-exp, have low harm rates, but others, such as gpt-4o-mini and grok-4-fast, generate more unsafe responses. All models struggle with indirect signals, default replies, and context misalignment. These results highlight the urgent need for better safeguards, crisis detection, and context-aware responses in LLMs. They also show that alignment and safety practices, beyond scale, are crucial for reliable crisis support. Our taxonomy, datasets, and evaluation methods support ongoing AI mental health research, aiming to reduce harm and protect vulnerable users.

  • 8 authors
·
Apr 7

Constructing interval variables via faceted Rasch measurement and multitask deep learning: a hate speech application

We propose a general method for measuring complex variables on a continuous, interval spectrum by combining supervised deep learning with the Constructing Measures approach to faceted Rasch item response theory (IRT). We decompose the target construct, hate speech in our case, into multiple constituent components that are labeled as ordinal survey items. Those survey responses are transformed via IRT into a debiased, continuous outcome measure. Our method estimates the survey interpretation bias of the human labelers and eliminates that influence on the generated continuous measure. We further estimate the response quality of each labeler using faceted IRT, allowing responses from low-quality labelers to be removed. Our faceted Rasch scaling procedure integrates naturally with a multitask deep learning architecture for automated prediction on new data. The ratings on the theorized components of the target outcome are used as supervised, ordinal variables for the neural networks' internal concept learning. We test the use of an activation function (ordinal softmax) and loss function (ordinal cross-entropy) designed to exploit the structure of ordinal outcome variables. Our multitask architecture leads to a new form of model interpretation because each continuous prediction can be directly explained by the constituent components in the penultimate layer. We demonstrate this new method on a dataset of 50,000 social media comments sourced from YouTube, Twitter, and Reddit and labeled by 11,000 U.S.-based Amazon Mechanical Turk workers to measure a continuous spectrum from hate speech to counterspeech. We evaluate Universal Sentence Encoders, BERT, and RoBERTa as language representation models for the comment text, and compare our predictive accuracy to Google Jigsaw's Perspective API models, showing significant improvement over this standard benchmark.

  • 4 authors
·
Sep 21, 2020

A Scalable Framework for Evaluating Health Language Models

Large language models (LLMs) have emerged as powerful tools for analyzing complex datasets. Recent studies demonstrate their potential to generate useful, personalized responses when provided with patient-specific health information that encompasses lifestyle, biomarkers, and context. As LLM-driven health applications are increasingly adopted, rigorous and efficient one-sided evaluation methodologies are crucial to ensure response quality across multiple dimensions, including accuracy, personalization and safety. Current evaluation practices for open-ended text responses heavily rely on human experts. This approach introduces human factors and is often cost-prohibitive, labor-intensive, and hinders scalability, especially in complex domains like healthcare where response assessment necessitates domain expertise and considers multifaceted patient data. In this work, we introduce Adaptive Precise Boolean rubrics: an evaluation framework that streamlines human and automated evaluation of open-ended questions by identifying gaps in model responses using a minimal set of targeted rubrics questions. Our approach is based on recent work in more general evaluation settings that contrasts a smaller set of complex evaluation targets with a larger set of more precise, granular targets answerable with simple boolean responses. We validate this approach in metabolic health, a domain encompassing diabetes, cardiovascular disease, and obesity. Our results demonstrate that Adaptive Precise Boolean rubrics yield higher inter-rater agreement among expert and non-expert human evaluators, and in automated assessments, compared to traditional Likert scales, while requiring approximately half the evaluation time of Likert-based methods. This enhanced efficiency, particularly in automated evaluation and non-expert contributions, paves the way for more extensive and cost-effective evaluation of LLMs in health.

  • 13 authors
·
Mar 30, 2025

Beyond Overall Accuracy: A Psychometric Deep Dive into the Topic-Specific Medical Capabilities of 80 Large Language Models

As Large Language Models (LLMs) are increasingly proposed for high-stakes medical applications, there has emerged a critical need for reliable and accurate evaluation methodologies. Traditional accuracy metrics fail inadequately as they neither capture question characteristics nor offer topic-specific insights. To address this gap, we introduce MedIRT, a rigorous evaluation framework grounded in Item Response Theory (IRT), the gold standard in high-stakes educational testing. Unlike previous research relying on archival data, we prospectively gathered fresh responses from 80 diverse LLMs on a balanced, 1,100-question USMLE-aligned benchmark. Using one unidimensional two-parameter logistic IRT model per topic, we estimate LLM's latent model ability jointly with question difficulty and discrimination, yielding more stable and nuanced performance rankings than accuracy alone. Notably, we identify distinctive ``spiky'' ability profiles, where overall rankings can be misleading due to highly specialized model abilities. While GPT-5 was the top performer in a majority of domains (8 of 11), it was outperformed in Social Science and Communication by Claude-3-opus, demonstrating that even an overall 23rd-ranked model can hold the top spot for specific competencies. Furthermore, we demonstrate IRT's utility in auditing benchmarks by identifying flawed questions. We synthesize these findings into a practical decision-support framework that integrates our multi-factor competency profiles with operational metrics. This work establishes a robust, psychometrically grounded methodology essential for the safe, effective, and trustworthy deployment of LLMs in healthcare.

  • 4 authors
·
Sep 28, 2025

Quality Is Not a Safety Proxy Under Quantization

Quantized checkpoints are often screened first with quality metrics and only later, if at all, with direct safety tests. This paper audits that shortcut on a matched 51-row matrix spanning 6 models, 4 families, a 7-level GGUF ladder, and AWQ/GPTQ INT4 checkpoints. In this matrix the shortcut fails: all 36 quality-safety pairings split direction across models, and 9 hidden-danger rows plus 1 near-hidden-danger row show quality stable or improved while refusal falls by 12-68 percentage points. Seven of the 11 AWQ/GPTQ rows are hidden-danger. A four-probe mechanistic follow-up over the 17 Hugging Face-backed FP16/AWQ/GPTQ cells does not rescue it: entropy, refusal-direction, and calibration probes are weak or null separators of dangerous rows, and although probe-identified safety-associated neurons absorb 1.39times more quantization error overall (p < 5 times 10^{-7}), the effect is not regime-specific. Claude Sonnet 4 relabels 11,470 items in a predefined stratified set, agrees with the primary gemma3:12b judge on 89.9\% of rows (κ= 0.873, 95\% CI [0.866, 0.881]), and changes 0/10 hidden-danger cells. A calibrated study-internal behavioral screen -- the Refusal Template Stability Index (RTSI), built from four refusal-template drift features and calibrated on this matrix -- routes 10/10 hidden- or near-hidden-danger rows to direct safety testing (Wilson 95\% CI lower bound 0.72) while leaving 23 of 45 non-baseline rows in a low-risk bucket under both in-sample scoring and row-level leave-one-out validation; on the same matrix, the best single-feature baselines (unique-prefix-rate-delta, raw refusal-rate delta) recover 9/10 and 8/10 respectively at matched bucket size, and cross-stack transfer requires recalibration. For the quantized checkpoints, model families, and safety outcomes studied here, retained quality cannot waive direct safety evaluation.

  • 1 authors
·
Jun 7

Large Language Model Evaluation via Matrix Nuclear-Norm

As large language models (LLMs) continue to evolve, efficient evaluation metrics are vital for assessing their ability to compress information and reduce redundancy. While traditional metrics like Matrix Entropy offer valuable insights, they are computationally intensive for large-scale models due to their \( O(n^3) \) time complexity with Singular Value Decomposition (SVD). To mitigate this issue, we introduce the Matrix Nuclear-Norm, which not only serves as a metric to quantify the data compression proficiency of LLM but also provides a convex approximation of matrix rank to capture both predictive discriminability and diversity. By employing the \( L_{1,2}-norm \) to further approximate the nuclear norm, we can effectively assess the model's information compression capabilities. This approach reduces the time complexity to \( O(n^2) \) and eliminates the need for SVD computation. Consequently, the Matrix Nuclear-Norm achieves speeds 8 to 24 times faster than Matrix Entropy for the CEREBRAS-GPT model as sizes increase from 111M to 6.7B. This performance gap becomes more pronounced with larger models, as validated in tests with other models like Pythia. Additionally, evaluations on benchmarks and model responses confirm that our proposed Matrix Nuclear-Norm is a reliable, scalable, and efficient tool for assessing LLMs' performance, striking a balance between accuracy and computational efficiency. The code is available at https://github.com/MLGroupJLU/MatrixNuclearNorm.

  • 4 authors
·
Oct 14, 2024 2

Transfer Learning for Meta-analysis Under Covariate Shift

Randomized controlled trials often do not represent the populations where decisions are made, and covariate shift across studies can invalidate standard IPD meta-analysis and transport estimators. We propose a placebo-anchored transport framework that treats source-trial outcomes as abundant proxy signals and target-trial placebo outcomes as scarce, high-fidelity gold labels to calibrate baseline risk. A low-complexity (sparse) correction anchors proxy outcome models to the target population, and the anchored models are embedded in a cross-fitted doubly robust learner, yielding a Neyman-orthogonal, target-site doubly robust estimator for patient-level heterogeneous treatment effects when target treated outcomes are available. We distinguish two regimes: in connected targets (with a treated arm), the method yields target-identified effect estimates; in disconnected targets (placebo-only), it reduces to a principled screen--then--transport procedure under explicit working-model transport assumptions. Experiments on synthetic data and a semi-synthetic IHDP benchmark evaluate pointwise CATE accuracy, ATE error, ranking quality for targeting, decision-theoretic policy regret, and calibration. Across connected settings, the proposed method is best or near-best and improves substantially over proxy-only, target-only, and transport baselines at small target sample sizes; in disconnected settings, it retains strong ranking performance for targeting while pointwise accuracy depends on the strength of the working transport condition.

  • 3 authors
·
Apr 5

CONFLARE: CONFormal LArge language model REtrieval

Retrieval-augmented generation (RAG) frameworks enable large language models (LLMs) to retrieve relevant information from a knowledge base and incorporate it into the context for generating responses. This mitigates hallucinations and allows for the updating of knowledge without retraining the LLM. However, RAG does not guarantee valid responses if retrieval fails to identify the necessary information as the context for response generation. Also, if there is contradictory content, the RAG response will likely reflect only one of the two possible responses. Therefore, quantifying uncertainty in the retrieval process is crucial for ensuring RAG trustworthiness. In this report, we introduce a four-step framework for applying conformal prediction to quantify retrieval uncertainty in RAG frameworks. First, a calibration set of questions answerable from the knowledge base is constructed. Each question's embedding is compared against document embeddings to identify the most relevant document chunks containing the answer and record their similarity scores. Given a user-specified error rate ({\alpha}), these similarity scores are then analyzed to determine a similarity score cutoff threshold. During inference, all chunks with similarity exceeding this threshold are retrieved to provide context to the LLM, ensuring the true answer is captured in the context with a (1-{\alpha}) confidence level. We provide a Python package that enables users to implement the entire workflow proposed in our work, only using LLMs and without human intervention.

  • 5 authors
·
Apr 3, 2024

Self-Judge: Selective Instruction Following with Alignment Self-Evaluation

Pre-trained large language models (LLMs) can be tailored to adhere to human instructions through instruction tuning. However, due to shifts in the distribution of test-time data, they may not always execute instructions accurately, potentially generating factual errors or misaligned content when acting as chat assistants. To enhance the reliability of LLMs in following instructions, we propose the study of selective instruction following, whereby the system declines to execute instructions if the anticipated response quality is low. We train judge models that can predict numerical quality scores for model responses. To address data scarcity, we introduce Self-J, a novel self-training framework for developing judge models without needing human-annotated quality scores. Our method leverages the model's inherent self-evaluation capability to extract information about response quality from labeled instruction-tuning data. It incorporates a gold reference answer to facilitate self-evaluation and recalibrates by assessing the semantic similarity between the response sample and the gold reference. During the training phase, we implement self-distillation as a regularization technique to enhance the capability of reference-free estimation. To validate alignment evaluation on general instruction-following tasks, we collect large-scale high-quality instructions from Hugging Face for model training and evaluation. Extensive experiments on five open-source models show that our method correlates much more with GPT-4 than strong baselines, e.g., supervised models distilled from GPT-4 and GPT-3.5-turbo. Our analysis shows our model's strong generalization across domains. Additionally, our judge models serve as good reward models, e.g., boosting WizardLM-13B-V1.2 from 89.17 to 92.48 and from 12.03 to 15.90 in version v1 and v2 of AlpacaEval respectively using best-of-32 sampling with our judge models.

  • 2 authors
·
Sep 2, 2024

GIST: Targeted Data Selection for Instruction Tuning via Coupled Optimization Geometry

Targeted data selection has emerged as a crucial paradigm for efficient instruction tuning, aiming to identify a small yet influential subset of training examples for a specific target task. In practice, influence is often measured through the effect of an example on parameter updates. To make selection scalable, many approaches leverage optimizer statistics (e.g., Adam states) as an axis-aligned surrogate for update geometry (i.e., diagonal precondition), implicitly treating parameters as coordinate-wise independent. We show that this assumption breaks down in parameter-efficient fine-tuning (PEFT) methods such as LoRA. In this setting, the induced optimization geometry exhibits strong cross-parameter coupling with non-trivial off-diagonal interactions, while the task-relevant update directions are confined to a low-dimensional subspace. Motivated by this mismatch, we propose GIST (Gradient Isometric Subspace Transformation), a simple yet principled alternative that replaces axis-aligned scaling with robust subspace alignment. GIST recovers a task-specific subspace from validation gradients via spectral filtering (SVD), projects training gradients into this coupled subspace, and scores examples by their alignment with target directions.Extensive experiments have demonstrated that GIST matches or outperforms the state-of-the-art baseline with only 0.29% of the storage and 25% of the computational time under the same selection budget.

LiPO: Listwise Preference Optimization through Learning-to-Rank

Aligning language models (LMs) with curated human feedback is critical to control their behaviors in real-world applications. Several recent policy optimization methods, such as DPO and SLiC, serve as promising alternatives to the traditional Reinforcement Learning from Human Feedback (RLHF) approach. In practice, human feedback often comes in a format of a ranked list over multiple responses to amortize the cost of reading prompt. Multiple responses can also be ranked by reward models or AI feedback. There lacks such a study on directly fitting upon a list of responses. In this work, we formulate the LM alignment as a listwise ranking problem and describe the Listwise Preference Optimization (LiPO) framework, where the policy can potentially learn more effectively from a ranked list of plausible responses given the prompt. This view draws an explicit connection to Learning-to-Rank (LTR), where most existing preference optimization work can be mapped to existing ranking objectives, especially pairwise ones. Following this connection, we provide an examination of ranking objectives that are not well studied for LM alignment withDPO and SLiC as special cases when list size is two. In particular, we highlight a specific method, LiPO-{\lambda}, which leverages a state-of-the-art listwise ranking objective and weights each preference pair in a more advanced manner. We show that LiPO-{\lambda} can outperform DPO and SLiC by a clear margin on two preference alignment tasks.

  • 12 authors
·
Feb 2, 2024 6

EvalAgent: Discovering Implicit Evaluation Criteria from the Web

Evaluation of language model outputs on structured writing tasks is typically conducted with a number of desirable criteria presented to human evaluators or large language models (LLMs). For instance, on a prompt like "Help me draft an academic talk on coffee intake vs research productivity", a model response may be evaluated for criteria like accuracy and coherence. However, high-quality responses should do more than just satisfy basic task requirements. An effective response to this query should include quintessential features of an academic talk, such as a compelling opening, clear research questions, and a takeaway. To help identify these implicit criteria, we introduce EvalAgent, a novel framework designed to automatically uncover nuanced and task-specific criteria. EvalAgent first mines expert-authored online guidance. It then uses this evidence to propose diverse, long-tail evaluation criteria that are grounded in reliable external sources. Our experiments demonstrate that the grounded criteria produced by EvalAgent are often implicit (not directly stated in the user's prompt), yet specific (high degree of lexical precision). Further, EvalAgent criteria are often not satisfied by initial responses but they are actionable, such that responses can be refined to satisfy them. Finally, we show that combining LLM-generated and EvalAgent criteria uncovers more human-valued criteria than using LLMs alone.

  • 6 authors
·
Apr 21, 2025

ArxivBench: Can LLMs Assist Researchers in Conducting Research?

Large language models (LLMs) have demonstrated remarkable effectiveness in completing various tasks such as reasoning, translation, and question answering. However the issue of factual incorrect content in LLM-generated responses remains a persistent challenge. In this study, we evaluate both proprietary and open-source LLMs on their ability to respond with relevant research papers and accurate links to articles hosted on the arXiv platform, based on high level prompts. To facilitate this evaluation, we introduce arXivBench, a benchmark specifically designed to assess LLM performance across eight major subject categories on arXiv and five subfields within computer science, one of the most popular categories among them. Our findings reveal a concerning accuracy of LLM-generated responses depending on the subject, with some subjects experiencing significantly lower accuracy than others. Notably, Claude-3.5-Sonnet exhibits a substantial advantage in generating both relevant and accurate responses. And interestingly, most LLMs achieve a much higher accuracy in the Artificial Intelligence sub-field than other sub-fields. This benchmark provides a standardized tool for evaluating the reliability of LLM-generated scientific responses, promoting more dependable use of LLMs in academic and research environments. Our code is open-sourced at https://github.com/arxivBenchLLM/arXivBench and our dataset is available on huggingface at https://huggingface.co/datasets/arXivBenchLLM/arXivBench.

  • 3 authors
·
Apr 6, 2025

Large Language Models Encode Clinical Knowledge

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but the quality bar for medical and clinical applications is high. Today, attempts to assess models' clinical knowledge typically rely on automated evaluations on limited benchmarks. There is no standard to evaluate model predictions and reasoning across a breadth of tasks. To address this, we present MultiMedQA, a benchmark combining six existing open question answering datasets spanning professional medical exams, research, and consumer queries; and HealthSearchQA, a new free-response dataset of medical questions searched online. We propose a framework for human evaluation of model answers along multiple axes including factuality, precision, possible harm, and bias. In addition, we evaluate PaLM (a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM, on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA, MedMCQA, PubMedQA, MMLU clinical topics), including 67.6% accuracy on MedQA (US Medical License Exam questions), surpassing prior state-of-the-art by over 17%. However, human evaluation reveals key gaps in Flan-PaLM responses. To resolve this we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, recall of knowledge, and medical reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal important limitations of today's models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLM models for clinical applications.

  • 30 authors
·
Dec 26, 2022

Cost-Efficient Estimation of General Abilities Across Benchmarks

Thousands of diverse benchmarks have been developed to measure the quality of large language models (LLMs). Yet prior work has demonstrated that LLM performance is often sufficiently explained by a small set of latent factors, or abilities. This suggests the potential for more efficient and principled benchmarking, but it remains difficult to compare the quality of different methods. Motivated by predictive validity, we argue that the quality of a benchmarking framework should be grounded in how efficiently it enables the prediction of model performance on unseen tasks. To analyze this objective, we collect the "Wide-scale Item Level Dataset" (WILD), a dataset of item-model response pairs, comprising evaluations of 65 models on 109,564 unique items spanning 163 tasks drawn from 27 datasets. This dataset enables the first analysis of how different techniques can predict a model's performance on a large, diverse collection of unseen tasks under different budget constraints. We demonstrate that combining a modified multidimensional item response theory (IRT) model with adaptive item selection driven by optimal experimental design can predict performance on 112 held-out benchmark tasks with a mean absolute error (MAE) of less than 7%, and can do so after observing only 16 items. We further demonstrate that incorporating cost-aware discount factors into our selection criteria can reduce the total tokens needed to reach 7% MAE from 141,000 tokens to only 22,000, an 85% reduction in evaluation cost.

  • 5 authors
·
Mar 31

SimpleSafetyTests: a Test Suite for Identifying Critical Safety Risks in Large Language Models

The past year has seen rapid acceleration in the development of large language models (LLMs). However, without proper steering and safeguards, LLMs will readily follow malicious instructions, provide unsafe advice, and generate toxic content. We introduce SimpleSafetyTests (SST) as a new test suite for rapidly and systematically identifying such critical safety risks. The test suite comprises 100 test prompts across five harm areas that LLMs, for the vast majority of applications, should refuse to comply with. We test 11 open-access and open-source LLMs and four closed-source LLMs, and find critical safety weaknesses. While some of the models do not give a single unsafe response, most give unsafe responses to more than 20% of the prompts, with over 50% unsafe responses in the extreme. Prepending a safety-emphasising system prompt substantially reduces the occurrence of unsafe responses, but does not completely stop them from happening. Trained annotators labelled every model response to SST (n = 3,000). We use these annotations to evaluate five AI safety filters (which assess whether a models' response is unsafe given a prompt) as a way of automatically evaluating models' performance on SST. The filters' performance varies considerably. There are also differences across the five harm areas, and on the unsafe versus safe responses. The widely-used Perspective API has 72% accuracy and a newly-created zero-shot prompt to OpenAI's GPT-4 performs best with 89% accuracy. Content Warning: This paper contains prompts and responses that relate to child abuse, suicide, self-harm and eating disorders, scams and fraud, illegal items, and physical harm.

  • 7 authors
·
Nov 14, 2023

Rephrase and Respond: Let Large Language Models Ask Better Questions for Themselves

Misunderstandings arise not only in interpersonal communication but also between humans and Large Language Models (LLMs). Such discrepancies can make LLMs interpret seemingly unambiguous questions in unexpected ways, yielding incorrect responses. While it is widely acknowledged that the quality of a prompt, such as a question, significantly impacts the quality of the response provided by LLMs, a systematic method for crafting questions that LLMs can better comprehend is still underdeveloped. In this paper, we present a method named `Rephrase and Respond' (RaR), which allows LLMs to rephrase and expand questions posed by humans and provide responses in a single prompt. This approach serves as a simple yet effective prompting method for improving performance. We also introduce a two-step variant of RaR, where a rephrasing LLM first rephrases the question and then passes the original and rephrased questions together to a different responding LLM. This facilitates the effective utilization of rephrased questions generated by one LLM with another. Our experiments demonstrate that our methods significantly improve the performance of different models across a wide range to tasks. We further provide a comprehensive comparison between RaR and the popular Chain-of-Thought (CoT) methods, both theoretically and empirically. We show that RaR is complementary to CoT and can be combined with CoT to achieve even better performance. Our work not only contributes to enhancing LLM performance efficiently and effectively but also sheds light on a fair evaluation of LLM capabilities. Data and codes are available at https://github.com/uclaml/Rephrase-and-Respond.

  • 4 authors
·
Nov 7, 2023

LLMs Can Generate a Better Answer by Aggregating Their Own Responses

Large Language Models (LLMs) have shown remarkable capabilities across tasks, yet they often require additional prompting techniques when facing complex problems. While approaches like self-correction and response selection have emerged as popular solutions, recent studies have shown these methods perform poorly when relying on the LLM itself to provide feedback or selection criteria. We argue this limitation stems from the fact that common LLM post-training procedures lack explicit supervision for discriminative judgment tasks. In this paper, we propose Generative Self-Aggregation (GSA), a novel prompting method that improves answer quality without requiring the model's discriminative capabilities. GSA first samples multiple diverse responses from the LLM, then aggregates them to obtain an improved solution. Unlike previous approaches, our method does not require the LLM to correct errors or compare response quality; instead, it leverages the model's generative abilities to synthesize a new response based on the context of multiple samples. While GSA shares similarities with the self-consistency (SC) approach for response aggregation, SC requires specific verifiable tokens to enable majority voting. In contrast, our approach is more general and can be applied to open-ended tasks. Empirical evaluation demonstrates that GSA effectively improves response quality across various tasks, including mathematical reasoning, knowledge-based problems, and open-ended generation tasks such as code synthesis and conversational responses.

  • 9 authors
·
Mar 6, 2025

Compared to What? Baselines and Metrics for Counterfactual Prompting

Counterfactual prompting (i.e., perturbing a single factor and measuring output change) is widely used to evaluate things like LLM bias and CoT faithfulness. But in this work we argue that observed effects cannot be attributed to the targeted factor without accounting for baseline ``meaning-preserving'' modifications to text that establish general model sensitivity. This is because every counterfactual edit is a compound treatment that bundles the variable of interest with incidental surface-form variation; this violates treatment variation irrelevance. We observe prediction flip rates on MedQA of 14.9% when we surgically change patient gender. However, this is statistically indistinguishable from the flip rates induced by simply paraphrasing inputs (14.1%). In this case, it would therefore be unwarranted to conclude that the LLM is especially sensitive to patient gender. To account for this and robustly measure the effects of targeted interventions, we propose a framework in which we compare (via statistical testing) differences observed under target interventions to those induced by paraphrasing inputs. We then use this framework to revisit a analysis done on the MedPerturb dataset, which reported evidence of model sensitivity to patient demographics and stylistic cues. We find that these effects largely dissipate when we account for general model sensitivity, with only 5 of 120 tests reaching statistical significance. Applying the same framework to occupational biography classification, we detect clearly significant directional gender bias, showing that the framework identifies real directional effects even when they are small. We evaluate a range of metrics -- aggregate, per-sample distributional, and regression -- and find that per-sample metrics are dramatically more powerful than aggregate metrics and regression powerfully and uniquely characterizes effect direction and magnitude.

  • 4 authors
·
Apr 30

Automated Rubrics for Reliable Evaluation of Medical Dialogue Systems

Large Language Models (LLMs) are increasingly used for clinical decision support, where hallucinations and unsafe suggestions may pose direct risks to patient safety. These risks are particularly challenging as they often manifest as subtle clinical errors that evade detection by generic metrics, while expert-authored fine-grained rubrics remain costly to construct and difficult to scale. In this paper, we propose a retrieval-augmented multi-agent framework designed to automate the generation of instance-specific evaluation rubrics. Our approach grounds evaluation in authoritative medical evidence by decomposing retrieved content into atomic facts and synthesizing them with user interaction constraints to form verifiable, fine-grained evaluation criteria. Evaluated on HealthBench, our framework achieves a Clinical Intent Alignment (CIA) score of 60.12%, a statistically significant improvement over the GPT-4o baseline (55.16%). In discriminative tests, our rubrics yield a mean score delta (μ_Δ = 8.658) and an AUROC of 0.977, nearly doubling the quality separation achieved by GPT-4o baseline (4.972). Beyond evaluation, our rubrics effectively guide response refinement, improving quality by 9.2% (from 59.0% to 68.2%). This provides a scalable and transparent foundation for both evaluating and improving medical LLMs. The code is available at https://anonymous.4open.science/r/Automated-Rubric-Generation-AF3C/.

  • 4 authors
·
Jan 21

Ruler: A Model-Agnostic Method to Control Generated Length for Large Language Models

The instruction-following ability of large language models enables humans to interact with AI agents in a natural way. However, when required to generate responses of a specific length, large language models often struggle to meet users' needs due to their inherent difficulty in accurately perceiving numerical constraints. To explore the ability of large language models to control the length of generated responses, we propose the Target Length Generation Task (TLG) and design two metrics, Precise Match (PM) and Flexible Match (FM) to evaluate the model's performance in adhering to specified response lengths. Furthermore, we introduce a novel, model-agnostic approach called Ruler, which employs Meta Length Tokens (MLTs) to enhance the instruction-following ability of large language models under length-constrained instructions. Specifically, Ruler equips LLMs with the ability to generate responses of a specified length based on length constraints within the instructions. Moreover, Ruler can automatically generate appropriate MLT when length constraints are not explicitly provided, demonstrating excellent versatility and generalization. Comprehensive experiments show the effectiveness of Ruler across different LLMs on Target Length Generation Task, e.g., at All Level 27.97 average gain on PM, 29.57 average gain on FM. In addition, we conduct extensive ablation experiments to further substantiate the efficacy and generalization of Ruler. Our code and data is available at https://github.com/Geaming2002/Ruler.

  • 8 authors
·
Sep 27, 2024 2

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

  • 9 authors
·
Jun 20, 2022

Answer Matching Outperforms Multiple Choice for Language Model Evaluation

Multiple choice benchmarks have long been the workhorse of language model evaluation because grading multiple choice is objective and easy to automate. However, we show multiple choice questions from popular benchmarks can often be answered without even seeing the question. These shortcuts arise from a fundamental limitation of discriminative evaluation not shared by evaluations of the model's free-form, generative answers. Until recently, there appeared to be no viable, scalable alternative to multiple choice--but, we show that this has changed. We consider generative evaluation via what we call answer matching: Give the candidate model the question without the options, have it generate a free-form response, then use a modern language model with the reference answer to determine if the response matches the reference. To compare the validity of different evaluation strategies, we annotate MMLU-Pro and GPQA-Diamond to obtain human grading data, and measure the agreement of each evaluation approach. We find answer matching using recent models--even small ones--achieves near-perfect agreement, in the range of inter-annotator agreement. In contrast, both multiple choice evaluation and using LLM-as-a-judge without reference answers aligns poorly with human grading. Improving evaluations via answer matching is not merely a conceptual concern: the rankings of several models change significantly when evaluating their free-form responses with answer matching. In light of these findings, we discuss how to move the evaluation ecosystem from multiple choice to answer matching.

  • 5 authors
·
Jul 3, 2025 2

Do LLMs Know When to NOT Answer? Investigating Abstention Abilities of Large Language Models

Abstention Ability (AA) is a critical aspect of Large Language Model (LLM) reliability, referring to an LLM's capability to withhold responses when uncertain or lacking a definitive answer, without compromising performance. Although previous studies have attempted to improve AA, they lack a standardised evaluation method and remain unsuitable for black-box models where token prediction probabilities are inaccessible. This makes comparative analysis challenging, especially for state-of-the-art closed-source commercial LLMs. This paper bridges this gap by introducing a black-box evaluation approach and a new dataset, Abstain-QA, crafted to rigorously assess AA across varied question types (answerable and unanswerable), domains (well-represented and under-represented), and task types (fact centric and reasoning). We also propose a new confusion matrix, the ''Answerable-Unanswerable Confusion Matrix'' (AUCM) which serves as the basis for evaluating AA, by offering a structured and precise approach for assessment. Finally, we explore the impact of three prompting strategies-Strict Prompting, Verbal Confidence Thresholding, and Chain-of-Thought (CoT)-on improving AA. Our results indicate that even powerful models like GPT-4, Mixtral 8x22b encounter difficulties with abstention; however, strategic approaches such as Strict prompting and CoT can enhance this capability.

  • 4 authors
·
Jul 23, 2024

Peering Through Preferences: Unraveling Feedback Acquisition for Aligning Large Language Models

Aligning large language models (LLMs) with human values and intents critically involves the use of human or AI feedback. While dense feedback annotations are expensive to acquire and integrate, sparse feedback presents a structural design choice between ratings (e.g., score Response A on a scale of 1-7) and rankings (e.g., is Response A better than Response B?). In this work, we analyze the effect of this design choice for the alignment and evaluation of LLMs. We uncover an inconsistency problem wherein the preferences inferred from ratings and rankings significantly disagree 60% for both human and AI annotators. Our subsequent analysis identifies various facets of annotator biases that explain this phenomena, such as human annotators would rate denser responses higher while preferring accuracy during pairwise judgments. To our surprise, we also observe that the choice of feedback protocol also has a significant effect on the evaluation of aligned LLMs. In particular, we find that LLMs that leverage rankings data for alignment (say model X) are preferred over those that leverage ratings data (say model Y), with a rank-based evaluation protocol (is X/Y's response better than reference response?) but not with a rating-based evaluation protocol (score Rank X/Y's response on a scale of 1-7). Our findings thus shed light on critical gaps in methods for evaluating the real-world utility of language models and their strong dependence on the feedback protocol used for alignment. Our code and data are available at https://github.com/Hritikbansal/sparse_feedback.

  • 3 authors
·
Aug 30, 2023

Self-Instructed Derived Prompt Generation Meets In-Context Learning: Unlocking New Potential of Black-Box LLMs

Large language models (LLMs) have shown success in generating high-quality responses. In order to achieve better alignment with LLMs with human preference, various works are proposed based on specific optimization process, which, however, is not suitable to Black-Box LLMs like GPT-4, due to inaccessible parameters. In Black-Box LLMs case, their performance is highly dependent on the quality of the provided prompts. Existing methods to enhance response quality often involve a prompt refinement model, yet these approaches potentially suffer from semantic inconsistencies between the refined and original prompts, and typically overlook the relationship between them. To address these challenges, we introduce a self-instructed in-context learning framework that empowers LLMs to deliver more effective responses by generating reliable derived prompts to construct informative contextual environments. Our approach incorporates a self-instructed reinforcement learning mechanism, enabling direct interaction with the response model during derived prompt generation for better alignment. We then formulate querying as an in-context learning task, using responses from LLMs combined with the derived prompts to establish a contextual demonstration for the original prompt. This strategy ensures alignment with the original query, reduces discrepancies from refined prompts, and maximizes the LLMs' in-context learning capability. Extensive experiments demonstrate that the proposed method not only generates more reliable derived prompts but also significantly enhances LLMs' ability to deliver more effective responses, including Black-Box models such as GPT-4.

  • 5 authors
·
Sep 2, 2024

Reaching Beyond the Mode: RL for Distributional Reasoning in Language Models

Given a question, a language model (LM) implicitly encodes a distribution over possible answers. In practice, post-training procedures for LMs often collapse this distribution onto a single dominant mode. While this is generally not a problem for benchmark-style evaluations that assume one correct answer, many real-world tasks inherently involve multiple valid answers or irreducible uncertainty. Examples include medical diagnosis, ambiguous question answering, and settings with incomplete information. In these cases, we would like LMs to generate multiple plausible hypotheses, ideally with confidence estimates for each one, and without computationally intensive repeated sampling to generate non-modal answers. This paper describes a multi-answer reinforcement learning approach for training LMs to perform distributional reasoning over multiple answers during inference. We modify the RL objective to enable models to explicitly generate multiple candidate answers in a single forward pass, internalizing aspects of inference-time search into the model's generative process. Across question-answering, medical diagnostic, and coding benchmarks, we observe improved diversity, coverage, and set-level calibration scores compared to single answer trained baselines. Models trained with our approach require fewer tokens to generate multiple answers than competing approaches. On coding tasks, they are also substantially more accurate. These results position multi-answer RL as a principled and compute-efficient alternative to inference-time scaling procedures such as best-of-k. Code and more information can be found at https://multi-answer-rl.github.io/.

New combinational therapies for cancer using modern statistical mechanics

We investigate a new dynamical system that describes tumor-host interaction. The equation that describes the untreated tumor growth is based on non-extensive statistical mechanics. Recently, this model has been shown to fit successfully exponential, Gompertz, logistic, and power-law tumor growths. We have been able to include as many hallmarks of cancer as possible. We study also the dynamic response of cancer under therapy. Using our model, we can make predictions about the different outcomes when we change the parameters, and/or the initial conditions. We can determine the importance of different factors to influence tumor growth. We discover synergistic therapeutic effects of different treatments and drugs. Cancer is generally untreatable using conventional monotherapy. We consider conventional therapies, oncogene-targeted therapies, tumor-suppressors gene-targeted therapies, immunotherapies, anti-angiogenesis therapies, virotherapy, among others. We need therapies with the potential to target both tumor cells and the tumors' microenvironment. Drugs that target oncogenes and tumor-suppressor genes can be effective in the treatment of some cancers. However, most tumors do reoccur. We have found that the success of the new therapeutic agents can be seen when used in combination with other cancer-cell-killing therapies. Our results have allowed us to design a combinational therapy that can lead to the complete eradication of cancer.

  • 19 authors
·
Feb 2, 2019

Beyond No: Quantifying AI Over-Refusal and Emotional Attachment Boundaries

We present an open-source benchmark and evaluation framework for assessing emotional boundary handling in Large Language Models (LLMs). Using a dataset of 1156 prompts across six languages, we evaluated three leading LLMs (GPT-4o, Claude-3.5 Sonnet, and Mistral-large) on their ability to maintain appropriate emotional boundaries through pattern-matched response analysis. Our framework quantifies responses across seven key patterns: direct refusal, apology, explanation, deflection, acknowledgment, boundary setting, and emotional awareness. Results demonstrate significant variation in boundary-handling approaches, with Claude-3.5 achieving the highest overall score (8.69/10) and producing longer, more nuanced responses (86.51 words on average). We identified a substantial performance gap between English (average score 25.62) and non-English interactions (< 0.22), with English responses showing markedly higher refusal rates (43.20% vs. < 1% for non-English). Pattern analysis revealed model-specific strategies, such as Mistral's preference for deflection (4.2%) and consistently low empathy scores across all models (< 0.06). Limitations include potential oversimplification through pattern matching, lack of contextual understanding in response analysis, and binary classification of complex emotional responses. Future work should explore more nuanced scoring methods, expand language coverage, and investigate cultural variations in emotional boundary expectations. Our benchmark and methodology provide a foundation for systematic evaluation of LLM emotional intelligence and boundary-setting capabilities.

  • 2 authors
·
Feb 20, 2025 3

EVA: Towards a universal model of the immune system

The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell resolution and are evaluated on technical metrics often disconnected from actual drug development tasks and challenges. Here, we introduce EVA, the first cross-species, multimodal foundation model of immunology and inflammation, a therapeutic area where shared pathogenic mechanisms create unique opportunities for transfer learning. EVA harmonizes transcriptomics data across species, platforms, and resolutions, and integrates histology data to produce rich, unified patient representations. We establish clear scaling laws, demonstrating that increasing model size and compute translates to improvements in both pretraining and downstream tasks performance. We introduce a comprehensive evaluation suite of 39 tasks spanning the drug development pipeline: zero-shot target efficacy and gene function prediction for discovery, cross-species or cross-diseases molecular perturbations for preclinical development, and patient stratification with treatment response prediction or disease activity prediction for clinical trials applications. We benchmark EVA against several state-of-the-art biological foundation models and baselines on these tasks, and demonstrate state-of-the-art results on each task category. Using mechanistic interpretability, we further identify biological meaningful features, revealing intertwined representations across species and technologies. We release an open version of EVA for transcriptomics to accelerate research on immune-mediated diseases.

  • 11 authors
·
Feb 10

RTI-Bench: A Structured Dataset for Indian Right-to-Information Decision Analysis

India's Right to Information Act, 2005 gives every citizen the right to demand information from public authorities, yet in practice most people cannot make sense of the dense administrative language used in Central Information Commission (CIC) decisions, let alone predict whether an appeal is worth filing. This paper introduces RTI-Bench, a structured dataset of CIC decisions with outcome labels, exemption citations, IRAC-style reasoning components, and procedural timelines. To the best of our knowledge it is the first publicly released structured dataset for Indian RTI administrative decisions. The dataset draws from two sources: 1,218 cases from a publicly available instruction-response corpus (with structured fields added through rule-based extraction), and 298 CIC decision PDFs collected directly from the Commission portal, spanning five commissioners and three document format generations from 2023 to 2026. Label coverage reaches 89% on the instruction-response corpus. For the PDF subset of 239 primary decisions, coverage is 51% in this first release. A random sample of 50 labelled cases was manually reviewed, yielding a label precision of 95.3%. A zero-shot Mistral 7B baseline on 100 cases gives 57.3% accuracy and 37.0% macro-F1 on outcome prediction, well above the majority-class baseline of 14.3% macro-F1. RTI-Bench is available at https://huggingface.co/datasets/joyboseroy/rti-bench

  • 1 authors
·
May 15

Large Language Models are not Fair Evaluators

In this paper, we uncover a systematic bias in the evaluation paradigm of adopting large language models~(LLMs), e.g., GPT-4, as a referee to score and compare the quality of responses generated by candidate models. We find that the quality ranking of candidate responses can be easily hacked by simply altering their order of appearance in the context. This manipulation allows us to skew the evaluation result, making one model appear considerably superior to the other, e.g., Vicuna-13B could beat ChatGPT on 66 over 80 tested queries with ChatGPT as an evaluator. To address this issue, we propose a calibration framework with three simple yet effective strategies: 1) Multiple Evidence Calibration, which requires the evaluator model to generate multiple evaluation evidence before assigning ratings; 2) Balanced Position Calibration, which aggregates results across various orders to determine the final score; 3) Human-in-the-Loop Calibration, which introduces a balanced position diversity entropy to measure the difficulty of each example and seeks human assistance when needed. We also manually annotate the "win/tie/lose" outcomes of responses from ChatGPT and Vicuna-13B in the Vicuna Benchmark's question prompt, and extensive experiments demonstrate that our approach successfully mitigates evaluation bias, resulting in closer alignment with human judgments. We release our code and human annotation at https://github.com/i-Eval/FairEval to facilitate future research.

  • 10 authors
·
May 29, 2023

Exploring Response Uncertainty in MLLMs: An Empirical Evaluation under Misleading Scenarios

Multimodal large language models (MLLMs) have recently achieved state-of-the-art performance on tasks ranging from visual question answering to video understanding. However, existing studies have concentrated mainly on visual-textual misalignment, leaving largely unexplored the MLLMs' ability to preserve an originally correct answer when confronted with misleading information. We reveal a response uncertainty phenomenon: across nine standard datasets, twelve state-of-the-art open-source MLLMs overturn a previously correct answer in 65% of cases after receiving a single deceptive cue. To systematically quantify this vulnerability, we propose a two-stage evaluation pipeline: (1) elicit each model's original response on unperturbed inputs; (2) inject explicit (false-answer hints) and implicit (contextual contradictions) misleading instructions, and compute the misleading rate - the fraction of correct-to-incorrect flips. Leveraging the most susceptible examples, we curate the Multimodal Uncertainty Benchmark (MUB), a collection of image-question pairs stratified into low, medium, and high difficulty based on how many of twelve state-of-the-art MLLMs they mislead. Extensive evaluation on twelve open-source and five closed-source models reveals a high uncertainty: average misleading rates exceed 86%, with explicit cues over 67.19% and implicit cues over 80.67%. To reduce the misleading rate, we then fine-tune all open-source MLLMs on a compact 2000-sample mixed-instruction dataset, reducing misleading rates to 6.97% (explicit) and 32.77% (implicit), boosting consistency by nearly 29.37% on highly deceptive inputs, and slightly improving accuracy on standard benchmarks. Our code is available at https://github.com/Yunkaidang/uncertainty

  • 11 authors
·
Nov 4, 2024

Multiple Choice Questions: Reasoning Makes Large Language Models (LLMs) More Self-Confident Even When They Are Wrong

One of the most widely used methods to evaluate LLMs are Multiple Choice Question (MCQ) tests. MCQ benchmarks enable the testing of LLM knowledge on almost any topic at scale as the results can be processed automatically. To help the LLM answer, a few examples called few shots can be included in the prompt. Moreover, the LLM can be asked to answer the question directly with the selected option or to first provide the reasoning and then the selected answer, which is known as chain of thought. In addition to checking whether the selected answer is correct, the evaluation can look at the LLM-estimated probability of its response as an indication of the confidence of the LLM in the response. In this paper, we study how the LLM confidence in its answer depends on whether the model has been asked to answer directly or to provide the reasoning before answering. The results of the evaluation of questions on a wide range of topics in seven different models show that LLMs are more confident in their answers when they provide reasoning before the answer. This occurs regardless of whether the selected answer is correct. Our hypothesis is that this behavior is due to the reasoning that modifies the probability of the selected answer, as the LLM predicts the answer based on the input question and the reasoning that supports the selection made. Therefore, LLM estimated probabilities seem to have intrinsic limitations that should be understood in order to use them in evaluation procedures. Interestingly, the same behavior has been observed in humans, for whom explaining an answer increases confidence in its correctness.

  • 5 authors
·
Jan 16, 2025 2

CUE-R: Beyond the Final Answer in Retrieval-Augmented Generation

As language models shift from single-shot answer generation toward multi-step reasoning that retrieves and consumes evidence mid-inference, evaluating the role of individual retrieved items becomes more important. Existing RAG evaluation typically targets final-answer quality, citation faithfulness, or answer-level attribution, but none of these directly targets the intervention-based, per-evidence-item utility view we study here. We introduce CUE-R, a lightweight intervention-based framework for measuring per-evidence-item operational utility in single-shot RAG using shallow observable retrieval-use traces. CUE-R perturbs individual evidence items via REMOVE, REPLACE, and DUPLICATE operators, then measures changes along three utility axes (correctness, proxy-based grounding faithfulness, and confidence error) plus a trace-divergence signal. We also outline an operational evidence-role taxonomy for interpreting intervention outcomes. Experiments on HotpotQA and 2WikiMultihopQA with Qwen-3 8B and GPT-5.2 reveal a consistent pattern: REMOVE and REPLACE substantially harm correctness and grounding while producing large trace shifts, whereas DUPLICATE is often answer-redundant yet not fully behaviorally neutral. A zero-retrieval control confirms that these effects arise from degradation of meaningful retrieval. A two-support ablation further shows that multi-hop evidence items can interact non-additively: removing both supports harms performance far more than either single removal. Our results suggest that answer-only evaluation misses important evidence effects and that intervention-based utility analysis is a practical complement for RAG evaluation.

intuit Intuit
·
Apr 6 2

Sparse Linear Regression is Easy on Random Supports

Sparse linear regression is one of the most basic questions in machine learning and statistics. Here, we are given as input a design matrix X in R^{N times d} and measurements or labels {y} in R^N where {y} = {X} {w}^* + {xi}, and {xi} is the noise in the measurements. Importantly, we have the additional constraint that the unknown signal vector {w}^* is sparse: it has k non-zero entries where k is much smaller than the ambient dimension. Our goal is to output a prediction vector {w} that has small prediction error: 1{N}cdot |{X} {w}^* - {X} {w}|^2_2. Information-theoretically, we know what is best possible in terms of measurements: under most natural noise distributions, we can get prediction error at most epsilon with roughly N = O(k log d/epsilon) samples. Computationally, this currently needs d^{Omega(k)} run-time. Alternately, with N = O(d), we can get polynomial-time. Thus, there is an exponential gap (in the dependence on d) between the two and we do not know if it is possible to get d^{o(k)} run-time and o(d) samples. We give the first generic positive result for worst-case design matrices {X}: For any {X}, we show that if the support of {w}^* is chosen at random, we can get prediction error epsilon with N = poly(k, log d, 1/epsilon) samples and run-time poly(d,N). This run-time holds for any design matrix {X} with condition number up to 2^{poly(d)}. Previously, such results were known for worst-case {w}^*, but only for random design matrices from well-behaved families, matrices that have a very low condition number (poly(log d); e.g., as studied in compressed sensing), or those with special structural properties.

  • 3 authors
·
Nov 8, 2025

Evaluating Commercial AI Chatbots as News Intermediaries

AI chatbots are rapidly shaping how people encounter the news, yet no prior study has systematically measured how accurately these systems, with their proprietary search integrations and retrieval-synthesis pipelines, handle emerging facts across languages and regions. We present a 14-day (February 9-22, 2026) evaluation of six AI chatbots (Gemini 3 Flash and Pro, Grok 4, Claude 4.5 Sonnet, GPT-5 and GPT-4o mini) on 2,100 factual questions derived from same-day BBC News reporting across six regional services (US & Canada, Arabic, Afrique, Hindi, Russian, Turkish). The best systems achieve over 90% multiple-choice accuracy on questions about events reported hours earlier. The same systems, however, lose 11-13% under free-response evaluation, and 16-17% across the cohort. We further characterize three failure patterns. First, every model achieves its lowest accuracy on Hindi (79% vs. 89-91% elsewhere) and citations indicate an Anglophone retrieval bias (e.g., models answering Hindi queries cite English Wikipedia more than any Hindi outlet). Second, retrieval, not reasoning, failures drive over 70% of all errors. When models retrieve a correct source, they often extract the correct answer; the problem is to land on the right source in the first place. Third, models achieving 88-96% accuracy on well-formed questions drop to 19-70% when questions contain subtle false premises, with the most vulnerable model accepting fabricated facts 64% of the time. We also identify a detection-accuracy paradox: the best false-premise detector ranks second in adversarial accuracy (abstention rate), while a weaker detector ranks first, showing that premise detection and answer recovery are partially independent capabilities. Overall, these suggest that high accuracy can mask systematic regional inequity, near-total dependence on retrieval infrastructure, and vulnerability to imperfect queries real users pose.

  • 8 authors
·
May 20

The Fellowship of the LLMs: Multi-Agent Workflows for Synthetic Preference Optimization Dataset Generation

This paper presents synthetic Preference Optimization (PO) datasets generated using multi-agent workflows and evaluates the effectiveness and potential of these workflows in the dataset generation process. PO dataset generation requires two modules: (1) response evaluation, and (2) response generation. In the response evaluation module, the responses from Large Language Models (LLMs) are evaluated and ranked - a task typically carried out by human annotators that we automate using LLMs. We assess the response evaluation module in a 2 step process. In step 1, we assess LLMs as evaluators using three distinct prompting strategies. In step 2, we apply the winning prompting strategy to compare the performance of LLM-as-a-Judge, LLMs-as-a-Jury, and LLM Debate. In each step, we use inter-rater agreement using Cohen's Kappa between human annotators and LLMs. For the response generation module, we compare different configurations for the LLM Feedback Loop using the identified LLM evaluator configuration. We use the win rate (the fraction of times a generation framework is selected as the best by an LLM evaluator) to determine the best multi-agent configuration for generation. After identifying the best configurations for both modules, we use models from the GPT, Gemma, and Llama families to generate our PO datasets using the above pipeline. We generate two types of PO datasets, one to improve the generation capabilities of individual LLM and the other to improve the multi-agent workflow. Our evaluation shows that GPT-4o-as-a-Judge is more consistent across datasets when the candidate responses do not include responses from the GPT family. Additionally, we find that the LLM Feedback Loop, with Llama as the generator and Gemma as the reviewer, achieves a notable 71.8% and 73.8% win rate over single-agent Llama and Gemma, respectively.

  • 5 authors
·
Aug 16, 2024

Towards a deep learning approach for classifying treatment response in glioblastomas

Glioblastomas are the most aggressive type of glioma, having a 5-year survival rate of 6.9%. Treatment typically involves surgery, followed by radiotherapy and chemotherapy, and frequent magnetic resonance imaging (MRI) scans to monitor disease progression. To assess treatment response, radiologists use the Response Assessment in Neuro-Oncology (RANO) criteria to categorize the tumor into one of four labels based on imaging and clinical features: complete response, partial response, stable disease, and progressive disease. This assessment is very complex and time-consuming. Since deep learning (DL) has been widely used to tackle classification problems, this work aimed to implement the first DL pipeline for the classification of RANO criteria based on two consecutive MRI acquisitions. The models were trained and tested on the open dataset LUMIERE. Five approaches were tested: 1) subtraction of input images, 2) different combinations of modalities, 3) different model architectures, 4) different pretraining tasks, and 5) adding clinical data. The pipeline that achieved the best performance used a Densenet264 considering only T1-weighted, T2-weighted, and Fluid Attenuated Inversion Recovery (FLAIR) images as input without any pretraining. A median Balanced Accuracy of 50.96% was achieved. Additionally, explainability methods were applied. Using Saliency Maps, the tumor region was often successfully highlighted. In contrast, Grad-CAM typically failed to highlight the tumor region, with some exceptions observed in the Complete Response and Progressive Disease classes, where it effectively identified the tumor region. These results set a benchmark for future studies on glioblastoma treatment response assessment based on the RANO criteria while emphasizing the heterogeneity of factors that might play a role when assessing the tumor's response to treatment.

  • 6 authors
·
Apr 25, 2025

HumanLM: Simulating Users with State Alignment Beats Response Imitation

Large Language Models (LLMs) are increasingly used to simulate how specific users respond to a given context, enabling more user-centric applications that rely on user feedback. However, existing user simulators mostly imitate surface-level patterns and language styles, which fail to reflect the underlying states of real users (e.g., beliefs and emotions). To address these limitations, we propose a novel training framework, HumanLM, which builds user simulators that accurately reflect real users. Our key insight is that, in addition to generating responses, the model should generate natural-language latent states that align with ground-truth responses through reinforcement learning. These latent states correspond to a set of psychologically grounded state dimensions that drive how real users respond. HumanLM further synthesizes these aligned latent states into responses that accurately represent real users. For extensive evaluation, we develop Humanual, a comprehensive benchmark for simulating real users based on public data. Humanual consists of six large-scale datasets with 26k users and 216k responses in total, spanning diverse tasks such as generating user responses to daily life issues, political blogs, and chat sessions with LLM assistants. Across datasets, HumanLM significantly outperforms alternative approaches, achieving an average relative improvement of 16.3% in alignment scores from an LLM judge. In a real-time simulation study with 111 participants, HumanLM achieves the highest similarity to real user responses and competitive human-likeness scores.

  • 10 authors
·
Feb 7

Who's Asking? Simulating Role-Based Questions for Conversational AI Evaluation

Language model users often embed personal and social context in their questions. The asker's role -- implicit in how the question is framed -- creates specific needs for an appropriate response. However, most evaluations, while capturing the model's capability to respond, often ignore who is asking. This gap is especially critical in stigmatized domains such as opioid use disorder (OUD), where accounting for users' contexts is essential to provide accessible, stigma-free responses. We propose CoRUS (COmmunity-driven Roles for User-centric Question Simulation), a framework for simulating role-based questions. Drawing on role theory and posts from an online OUD recovery community (r/OpiatesRecovery), we first build a taxonomy of asker roles -- patients, caregivers, practitioners. Next, we use it to simulate 15,321 questions that embed each role's goals, behaviors, and experiences. Our evaluations show that these questions are both highly believable and comparable to real-world data. When used to evaluate five LLMs, for the same question but differing roles, we find systematic differences: vulnerable roles, such as patients and caregivers, elicit more supportive responses (+17%) and reduced knowledge content (-19%) in comparison to practitioners. Our work demonstrates how implicitly signaling a user's role shapes model responses, and provides a methodology for role-informed evaluation of conversational AI.

  • 6 authors
·
Oct 19, 2025