Daily Papers

Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood. Despite recent advances in deep-learning genomic approaches, accurately predicting and prioritizing clinically relevant mutations in gene regulatory regions remains a major challenge. Here we introduce Deep VRegulome, a deep-learning method for prediction and interpretation of functionally disruptive variants in the human regulome, which combines 700 DNABERT fine-tuned models, trained on vast amounts of ENCODE gene regulatory regions, with variant scoring, motif analysis, attention-based visualization, and survival analysis. We showcase its application on TCGA glioblastoma WGS dataset in prioritizing survival-associated mutations and regulatory regions. The analysis identified 572 splice-disrupting and 9,837 transcription-factor binding site altering mutations occurring in greater than 10% of glioblastoma samples. Survival analysis linked 1352 mutations and 563 disrupted regulatory regions to patient outcomes, enabling stratification via non-coding mutation signatures. All the code, fine-tuned models, and an interactive data portal are publicly available.

Image quality scoring and interpreting are two fundamental components of Image Quality Assessment (IQA). The former quantifies image quality, while the latter enables descriptive question answering about image quality. Traditionally, these two tasks have been addressed independently. However, from the perspective of the Human Visual System (HVS) and the Perception-Decision Integration Model, they are inherently interconnected: interpreting serves as the foundation for scoring, while scoring provides an abstract summary of interpreting. Thus, unifying these capabilities within a single model is both intuitive and logically coherent. In this paper, we propose Q-SiT (Quality Scoring and Interpreting joint Teaching), a unified framework that enables large multimodal models (LMMs) to learn both image quality scoring and interpreting simultaneously. We achieve this by transforming conventional IQA datasets into learnable question-answering datasets and incorporating human-annotated quality interpreting data for training. Furthermore, we introduce an efficient scoring & interpreting balance strategy, which first determines the optimal data mix ratio on lightweight LMMs and then maps this ratio to primary LMMs for fine-tuning adjustment. This strategy not only mitigates task interference and enhances cross-task knowledge transfer but also significantly reduces computational costs compared to direct optimization on full-scale LMMs. With this joint learning framework and corresponding training strategy, we develop Q-SiT, the first model capable of simultaneously performing image quality scoring and interpreting tasks, along with its lightweight variant, Q-SiT-mini. Experimental results demonstrate that Q-SiT achieves strong performance in both tasks with superior generalization IQA abilities.Project page at https://github.com/Q-Future/Q-SiT.

Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization tool. Compared to its predecessors, tmVar 3.0 is able to recognize a wide spectrum of variant related entities (e.g., allele and copy number variants), and to group different variant mentions belonging to the same concept in an article for improved accuracy. Moreover, tmVar3 provides additional variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar3 exhibits a state-of-the-art performance with over 90% accuracy in F-measure in variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar3 is freely available for download. We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP. Availability: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of variant effects from Deep Mutational Scanning (DMS) assays using a Normalised Log-odds Ratio (NLR) head. We find consistent improvements in a held-out protein test set, and on independent DMS and clinical variant annotation benchmarks from ProteinGym and ClinVar. These findings demonstrate that DMS is a promising source of sequence diversity and supervised training data for improving the performance of PLMs for variant effect prediction.

Elucidating the functional effect of missense variants is of crucial importance, yet challenging. To understand the impact of such variants, we fine-tuned the ESM2 protein language model to classify 20 protein features at amino acid resolution. We used the resulting models to: 1) identify protein features that are enriched in either pathogenic or benign missense variants, 2) compare the characteristics of proteins with reference or alternate alleles to understand how missense variants affect protein functionality. We show that our model can be used to reclassify some variants of unknown significance. We also demonstrate the usage of our models for understanding the potential effect of variants on protein features.

In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden of labor for genetic diagnostics and research from the gathering of data to its interpretation. Helix presents a state of the art platform for the prediction of pathogenicity in human missense variants. In addition to offering best-in-class predictive performance, Helix offers a platform that allows researchers to analyze and interpret variants in depth that can be accessed at helixlabs.ai.

Moral stories are a time-tested vehicle for transmitting values, yet modern NLP lacks a large, structured corpus that couples coherent narratives with explicit ethical lessons. We close this gap with TF1-EN-3M, the first open dataset of three million English-language fables generated exclusively by instruction-tuned models no larger than 8B parameters. Each story follows a six-slot scaffold (character -> trait -> setting -> conflict -> resolution -> moral), produced through a combinatorial prompt engine that guarantees genre fidelity while covering a broad thematic space. A hybrid evaluation pipeline blends (i) a GPT-based critic that scores grammar, creativity, moral clarity, and template adherence with (ii) reference-free diversity and readability metrics. Among ten open-weight candidates, an 8B-parameter Llama-3 variant delivers the best quality-speed trade-off, producing high-scoring fables on a single consumer GPU (<24 GB VRAM) at approximately 13.5 cents per 1,000 fables. We release the dataset, generation code, evaluation scripts, and full metadata under a permissive license, enabling exact reproducibility and cost benchmarking. TF1-EN-3M opens avenues for research in instruction following, narrative intelligence, value alignment, and child-friendly educational AI, demonstrating that large-scale moral storytelling no longer requires proprietary giant models.

While Large Language Models (LLMs) excel on standardized medical exams, high scores often fail to translate to high-quality responses for real-world medical queries. Current evaluations rely heavily on multiple-choice questions, failing to capture the unstructured, ambiguous, and long-tail complexities inherent in genuine user inquiries. To bridge this gap, we introduce QuarkMedBench, an ecologically valid benchmark tailored for real-world medical LLM assessment. We compiled a massive dataset spanning Clinical Care, Wellness Health, and Professional Inquiry, comprising 20,821 single-turn queries and 3,853 multi-turn sessions. To objectively evaluate open-ended answers, we propose an automated scoring framework that integrates multi-model consensus with evidence-based retrieval to dynamically generate 220,617 fine-grained scoring rubrics (~9.8 per query). During evaluation, hierarchical weighting and safety constraints structurally quantify medical accuracy, key-point coverage, and risk interception, effectively mitigating the high costs and subjectivity of human grading. Experimental results demonstrate that the generated rubrics achieve a 91.8% concordance rate with clinical expert blind audits, establishing highly dependable medical reliability. Crucially, baseline evaluations on this benchmark reveal significant performance disparities among state-of-the-art models when navigating real-world clinical nuances, highlighting the limitations of conventional exam-based metrics. Ultimately, QuarkMedBench establishes a rigorous, reproducible yardstick for measuring LLM performance on complex health issues, while its framework inherently supports dynamic knowledge updates to prevent benchmark obsolescence.

Adapting vision-language models to remote sensing imagery presents a fundamental challenge: both the visual and linguistic distributions of satellite data lie far outside natural image pretraining corpora. Despite this, prompting remains the dominant deployment paradigm, driven by the assumption that domain-specific language can guide frozen model representations toward specialized tasks. We test this assumption directly on a domain where the mismatch is prominent: cloud segmentation for satellite imagery. Using CLIPSeg on the CloudSEN12+ cloud segmentation benchmark, we evaluate 60 prompt variants spanning simple labels, domain terminology, appearance descriptors, and contextual cues, finding that every variant underperforms the zero-shot baseline (0.255 mIoU), with engineered prompts scoring as low as 0.07 mIoU. No amount of linguistic refinement bridges the gap between CLIP's natural image representations and satellite spectral imagery. In contrast, supervised fine-tuning with just 0.1% labeled data (~8 images) surpasses zero-shot performance overall, and 5-10% data recovers ~85% of maximum achievable mIoU. Full fine-tuning consistently outperforms low-rank adaptation by 0.03-0.09 mIoU, with the largest gaps for spectrally ambiguous classes, and at 0.5 to 1% labeled data, fine-tuning temporarily degrades performance on these classes before recovering, a supervision dip that aggregate mIoU can mask. For practitioners adapting vision-language models to specialized imagery, our results deliver a clear message: labeled data is not the expensive alternative to prompting; it is the worthwhile path.

Fine-tuning of pre-trained transformer models has become the standard approach for solving common NLP tasks. Most of the existing approaches rely on a randomly initialized classifier on top of such networks. We argue that this fine-tuning procedure is sub-optimal as the pre-trained model has no prior on the specific classifier labels, while it might have already learned an intrinsic textual representation of the task. In this paper, we introduce a new scoring method that casts a plausibility ranking task in a full-text format and leverages the masked language modeling head tuned during the pre-training phase. We study commonsense reasoning tasks where the model must rank a set of hypotheses given a premise, focusing on the COPA, Swag, HellaSwag and CommonsenseQA datasets. By exploiting our scoring method without fine-tuning, we are able to produce strong baselines (e.g. 80% test accuracy on COPA) that are comparable to supervised approaches. Moreover, when fine-tuning directly on the proposed scoring function, we show that our method provides a much more stable training phase across random restarts (e.g times 10 standard deviation reduction on COPA test accuracy) and requires less annotated data than the standard classifier approach to reach equivalent performances.

We introduce BM25S, an efficient Python-based implementation of BM25 that only depends on Numpy and Scipy. BM25S achieves up to a 500x speedup compared to the most popular Python-based framework by eagerly computing BM25 scores during indexing and storing them into sparse matrices. It also achieves considerable speedups compared to highly optimized Java-based implementations, which are used by popular commercial products. Finally, BM25S reproduces the exact implementation of five BM25 variants based on Kamphuis et al. (2020) by extending eager scoring to non-sparse variants using a novel score shifting method. The code can be found at https://github.com/xhluca/bm25s

This paper presents the RMIT--ADM+S participation in the SIGIR 2025 LiveRAG Challenge. Our Generation-Retrieval-Augmented Generation (GRAG) approach relies on generating a hypothetical answer that is used in the retrieval phase, alongside the original question. GRAG also incorporates a pointwise large language model (LLM)-based re-ranking step prior to final answer generation. We describe the system architecture and the rationale behind our design choices. In particular, a systematic evaluation using the Grid of Points (GoP) framework and N-way ANOVA enabled comparison across multiple configurations, including query variant generation, question decomposition, rank fusion strategies, and prompting techniques for answer generation. Our system achieved a Relevance score of 1.199 and a Faithfulness score of 0.477 on the private leaderboard, placing among the top four finalists in the LiveRAG 2025 Challenge.

Current research on generative language models (GLMs) for automated text scoring (ATS) has focused almost exclusively on querying proprietary models via Application Programming Interfaces (APIs). Yet such practices raise issues around transparency and security, and these methods offer little in the way of efficiency or customizability. With the recent proliferation of smaller, open-source models, there is the option to explore GLMs with computers equipped with modest, consumer-grade hardware, that is, for the "GPU poor." In this study, we analyze the performance and efficiency of open-source, small-scale GLMs for ATS. Results show that GLMs can be fine-tuned to achieve adequate, though not state-of-the-art, performance. In addition to ATS, we take small steps towards analyzing models' capacity for generating feedback by prompting GLMs to explain their scores. Model-generated feedback shows promise, but requires more rigorous evaluation focused on targeted use cases.

We consider whether off-policy experience from a smaller, weaker model can elicit capability in a stronger learner that on-policy RL fine-tuning (e.g., GRPO) does not reach. We find that injecting mathematically wrong drafts from a smaller but more domain-trained model -- mismatched to the current problem -- into a stronger learner's GRPO context consistently outperforms standard on-policy GRPO on held-out MATH-500 and out-of-distribution AIME 2025/2026. Concretely, we use Mathstral-7B as the learner, Qwen2.5-Math-1.5B as the draft model, 8.8K Level 3--5 MATH problems (with MATH-500 held out), and train with Dr. GRPO. Mismatch is an active ingredient: shuffling drafts to mismatched problems while holding everything else constant yields +1.62pp on MATH-500 (greedy pass@1) over the matched-wrong variant (n=10 seeds, p=0.0015, Welch's t). In fact, the mismatched-wrong variant leads all other variants we tested on MATH-500 across both greedy pass@1 and sampling pass@k. On out-of-distribution AIME 2025 and 2026, the mismatched-wrong variant uniquely lifts pass@k above both Mathstral-7B (in its native [INST] format) and the Qwen2.5-Math-1.5B draft model at every sample budget from k=1 to k=1024 across 2 seeds (+14.2pp on 2025 and +9.0pp on 2026 at pass@1024 over Mathstral-7B), and at pass@1024 also leads no-draft, matched-wrong, and mismatched-correct variants on both years. All variants use the same prompt with no draft injection at test time. The recipe -- trained on a single GPU with no SFT, no reward models, no synthesized data, and no produce-critique-revise inner loop -- reaches 71.98% MATH-500 on Mathstral-7B-v0.1, the highest published result on this model to our knowledge, surpassing the heavier WizardMath pipeline at 70.9% on full MATH (SFT + PPO with process/instruction reward models).

Passage ranking involves two stages: passage retrieval and passage re-ranking, which are important and challenging topics for both academics and industries in the area of Information Retrieval (IR). However, the commonly-used datasets for passage ranking usually focus on the English language. For non-English scenarios, such as Chinese, the existing datasets are limited in terms of data scale, fine-grained relevance annotation and false negative issues. To address this problem, we introduce T2Ranking, a large-scale Chinese benchmark for passage ranking. T2Ranking comprises more than 300K queries and over 2M unique passages from real-world search engines. Expert annotators are recruited to provide 4-level graded relevance scores (fine-grained) for query-passage pairs instead of binary relevance judgments (coarse-grained). To ease the false negative issues, more passages with higher diversities are considered when performing relevance annotations, especially in the test set, to ensure a more accurate evaluation. Apart from the textual query and passage data, other auxiliary resources are also provided, such as query types and XML files of documents which passages are generated from, to facilitate further studies. To evaluate the dataset, commonly used ranking models are implemented and tested on T2Ranking as baselines. The experimental results show that T2Ranking is challenging and there is still scope for improvement. The full data and all codes are available at https://github.com/THUIR/T2Ranking/

Recent advances in large language model (LLM) embeddings have enabled powerful representations for biological data, but most applications to date focus only on gene-level information. We present one of the first systematic frameworks to generate variant-level embeddings across the entire human genome. Using curated annotations from FAVOR, ClinVar, and the GWAS Catalog, we constructed semantic text descriptions for 8.9 billion possible variants and generated embeddings at three scales: 1.5 million HapMap3+MEGA variants, ~90 million imputed UK Biobank variants, and ~9 billion all possible variants. Embeddings were produced with both OpenAI's text-embedding-3-large and the open-source Qwen3-Embedding-0.6B models. Baseline experiments demonstrate high predictive accuracy for variant properties, validating the embeddings as structured representations of genomic variation. We outline two downstream applications: embedding-informed hypothesis testing by extending the Frequentist And Bayesian framework to genome-wide association studies, and embedding-augmented genetic risk prediction that enhances standard polygenic risk scores. These resources, publicly available on Hugging Face, provide a foundation for advancing large-scale genomic discovery and precision medicine.

Distinct-n scoreLi2016 is a widely used automatic metric for evaluating diversity in language generation tasks. However, we observed that the original approach for calculating distinct scores has evident biases that tend to assign higher penalties to longer sequences. We refine the calculation of distinct scores by scaling the number of distinct tokens based on their expectations. We provide both empirical and theoretical evidence to show that our method effectively removes the biases existing in the original distinct score. Our experiments show that our proposed metric, Expectation-Adjusted Distinct (EAD), correlates better with human judgment in evaluating response diversity. To foster future research, we provide an example implementation at https://github.com/lsy641/Expectation-Adjusted-Distinct.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

Zero-shot LLMs are now also used for textual classification tasks, e.g., sentiment/emotion detection of a given input as a sentence/article. However, their performance can be suboptimal in such data annotation tasks. We introduce a novel technique Perceived Confidence Scoring (PCS) that evaluates LLM's confidence for its classification of an input by leveraging Metamorphic Relations (MRs). The MRs generate semantically equivalent yet textually mutated versions of the input. Following the principles of Metamorphic Testing (MT), the mutated versions are expected to have annotation labels similar to the input. By analyzing the consistency of LLM responses across these variations, PCS computes a confidence score based on the frequency of predicted labels. PCS can be used both for single LLM and multiple LLM settings (e.g., majority voting). We introduce an algorithm Perceived Differential Evolution (PDE) that determines the optimal weights assigned to the MRs and the LLMs for a classification task. Empirical evaluation shows PCS significantly improves zero-shot accuracy for Llama-3-8B-Instruct (4.96%) and Mistral-7B-Instruct-v0.3 (10.52%), with Gemma-2-9b-it showing a 9.39% gain. When combining all three models, PCS significantly outperforms majority voting by 7.75%.

Automated Short Answer Scoring (ASAS) is a critical component in educational assessment. While traditional ASAS systems relied on rule-based algorithms or complex deep learning methods, recent advancements in Generative Language Models (GLMs) offer new opportunities for improvement. This study explores the application of GLMs to ASAS, leveraging their off-the-shelf capabilities and performance in various domains. We propose a novel pipeline that combines vector databases, transformer-based encoders, and GLMs to enhance short answer scoring accuracy. Our approach stores training responses in a vector database, retrieves semantically similar responses during inference, and employs a GLM to analyze these responses and determine appropriate scores. We further optimize the system through fine-tuned retrieval processes and prompt engineering. Evaluation on the SemEval 2013 dataset demonstrates a significant improvement on the SCIENTSBANK 3-way and 2-way tasks compared to existing methods, highlighting the potential of GLMs in advancing ASAS technology.

Multi-modal generative document parsing systems challenge traditional evaluation: unlike deterministic OCR or layout models, they often produce semantically correct yet structurally divergent outputs. Conventional metrics-CER, WER, IoU, or TEDS-misclassify such diversity as error, penalizing valid interpretations and obscuring system behavior. We introduce SCORE (Structural and COntent Robust Evaluation), an interpretation-agnostic framework that integrates (i) adjusted edit distance for robust content fidelity, (ii) token-level diagnostics to distinguish hallucinations from omissions, (iii) table evaluation with spatial tolerance and semantic alignment, and (iv) hierarchy-aware consistency checks. Together, these dimensions enable evaluation that embraces representational diversity while enforcing semantic rigor. Across 1,114 pages spanning a holistic benchmark and a field dataset, SCORE consistently revealed cross-dataset performance patterns missed by standard metrics. In 2-5% of pages with ambiguous table structures, traditional metrics penalized systems by 12-25% on average, leading to distorted rankings. SCORE corrected these cases, recovering equivalence between alternative but valid interpretations. Moreover, by normalizing generative outputs into a format-agnostic representation, SCORE reproduces traditional scores (e.g., table F1 up to 0.93) without requiring object-detection pipelines, demonstrating that generative parsing alone suffices for comprehensive evaluation. By exposing how interpretive diversity impacts evaluation outcomes and providing multi-dimensional, interpretable diagnostics, SCORE establishes foundational principles for semantically grounded, fair, and practical benchmarking of modern document parsing systems.

In this paper, we critically evaluate the capabilities of the state-of-the-art multimodal large language model, i.e., GPT-4 with Vision (GPT-4V), on Visual Question Answering (VQA) task. Our experiments thoroughly assess GPT-4V's proficiency in answering questions paired with images using both pathology and radiology datasets from 11 modalities (e.g. Microscopy, Dermoscopy, X-ray, CT, etc.) and fifteen objects of interests (brain, liver, lung, etc.). Our datasets encompass a comprehensive range of medical inquiries, including sixteen distinct question types. Throughout our evaluations, we devised textual prompts for GPT-4V, directing it to synergize visual and textual information. The experiments with accuracy score conclude that the current version of GPT-4V is not recommended for real-world diagnostics due to its unreliable and suboptimal accuracy in responding to diagnostic medical questions. In addition, we delineate seven unique facets of GPT-4V's behavior in medical VQA, highlighting its constraints within this complex arena. The complete details of our evaluation cases are accessible at https://github.com/ZhilingYan/GPT4V-Medical-Report.

Retrieval Augmented Generation (RAG) has become one of the most popular paradigms for enabling LLMs to access external data, and also as a mechanism for grounding to mitigate against hallucinations. When implementing RAG you can face several challenges like effective integration of retrieval models, efficient representation learning, data diversity, computational efficiency optimization, evaluation, and quality of text generation. Given all these challenges, every day a new technique to improve RAG appears, making it unfeasible to experiment with all combinations for your problem. In this context, this paper presents good practices to implement, optimize, and evaluate RAG for the Brazilian Portuguese language, focusing on the establishment of a simple pipeline for inference and experiments. We explored a diverse set of methods to answer questions about the first Harry Potter book. To generate the answers we used the OpenAI's gpt-4, gpt-4-1106-preview, gpt-3.5-turbo-1106, and Google's Gemini Pro. Focusing on the quality of the retriever, our approach achieved an improvement of MRR@10 by 35.4% compared to the baseline. When optimizing the input size in the application, we observed that it is possible to further enhance it by 2.4%. Finally, we present the complete architecture of the RAG with our recommendations. As result, we moved from a baseline of 57.88% to a maximum relative score of 98.61%.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

We introduce CAT, a framework designed to evaluate and visualize the interplay of accuracy and response consistency of Large Language Models (LLMs) under controllable input variations, using multiple-choice (MC) benchmarks as a case study. Current evaluation practices primarily focus on model capabilities such as accuracy or benchmark scores and, more recently, measuring consistency is being considered an essential property for deploying LLMs in high-stake, real-world applications. We argue in this paper that although both dimensions should still be evaluated independently, their inter-dependency also need to be considered for a more nuanced evaluation of LLMs. At the core of CAT are the Consistency-Accuracy Relation (CAR) curves, which visualize how model accuracy varies with increasing consistency requirements, as defined by the Minimum-Consistency Accuracy (MCA) metric. We further propose the Consistency-Oriented Robustness Estimate (CORE) index, a global metric that combines the area and shape of the CAR curve to quantify the trade-off between accuracy and consistency. We present a practical demonstration of our framework across a diverse set of generalist and domain-specific LLMs, evaluated on multiple MC benchmarks. We also outline how CAT can be extended beyond MC tasks to support long-form, open-ended evaluations through adaptable scoring functions.

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.

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

Patient recruitment is challenging for clinical trials. We introduce TrialGPT, an end-to-end framework for zero-shot patient-to-trial matching with large language models. TrialGPT comprises three modules: it first performs large-scale filtering to retrieve candidate trials (TrialGPT-Retrieval); then predicts criterion-level patient eligibility (TrialGPT-Matching); and finally generates trial-level scores (TrialGPT-Ranking). We evaluate TrialGPT on three cohorts of 183 synthetic patients with over 75,000 trial annotations. TrialGPT-Retrieval can recall over 90% of relevant trials using less than 6% of the initial collection. Manual evaluations on 1,015 patient-criterion pairs show that TrialGPT-Matching achieves an accuracy of 87.3% with faithful explanations, close to the expert performance. The TrialGPT-Ranking scores are highly correlated with human judgments and outperform the best-competing models by 43.8% in ranking and excluding trials. Furthermore, our user study reveals that TrialGPT can reduce the screening time by 42.6% in patient recruitment. Overall, these results have demonstrated promising opportunities for patient-to-trial matching with TrialGPT.

We present our winning system for Task~B (generation with reference passages) in SemEval-2026 Task~8: MTRAGEval. Our method is a heterogeneous ensemble of seven LLMs with two prompting variants, where a GPT-4o-mini judge selects the best candidate per instance. We ranked 1st out of 26 teams, achieving a conditioned harmonic mean of 0.7827 and outperforming the strongest baseline (gpt-oss-120b, 0.6390). Ablations show that diversity in model families, scales, and prompting strategies is essential, with the ensemble consistently beating any single model. We also introduce Meno-Lite-0.1, a 7B domain-adapted model with a strong cost--performance trade-off, and analyse MTRAGEval, highlighting annotation limitations and directions for improvement. Our code is publicly available: https://github.com/RaguTeam/ragu_mtrag_semeval

The approval success rate of drug candidates is very low with the majority of failure due to safety and efficacy. Increasingly available high dimensional information on targets, drug molecules and indications provides an opportunity for ML methods to integrate multiple data modalities and better predict clinically promising drug targets. Notably, drug targets with human genetics evidence are shown to have better odds to succeed. However, a recent tensor factorization-based approach found that additional information on targets and indications might not necessarily improve the predictive accuracy. Here we revisit this approach by integrating different types of human genetics evidence collated from publicly available sources to support each target-indication pair. We use Bayesian tensor factorization to show that models incorporating all available human genetics evidence (rare disease, gene burden, common disease) modestly improves the clinical outcome prediction over models using single line of genetics evidence. We provide additional insight into the relative predictive power of different types of human genetics evidence for predicting the success of clinical outcomes.

Unstructured clinical notes contain essential patient information but are challenging for physicians to search and interpret efficiently. Although large language models (LLMs) have shown promise in question answering (QA), most existing systems lack transparency, usability, and alignment with clinical workflows. This work introduces an interactive QA system that enables physicians to query clinical notes via text or voice and receive extractive answers highlighted directly in the note for traceability. The system was built using OpenAI models with zero-shot prompting and evaluated across multiple metrics, including exact string match, word overlap, SentenceTransformer similarity, and BERTScore. Results show that while exact match scores ranged from 47 to 62 percent, semantic similarity scores exceeded 87 percent, indicating strong contextual alignment even when wording varied. To assess usability, the system was also evaluated using simulated clinical personas. Seven diverse physician and nurse personas interacted with the system across scenario-based tasks and provided structured feedback. The evaluations highlighted strengths in intuitive design and answer accessibility, alongside opportunities for enhancing explanation clarity.

Generations from large language models (LLMs) can be improved by sampling and scoring multiple solutions to select a final answer. Current "sample and select" methods such as self-consistency (SC) rely on majority voting to score answers. However, when tasks have many distinct and valid answers, selection by voting requires a large number of samples. This makes SC prohibitively expensive for interactive tasks that involve generating multiple actions (answers) sequentially. After establishing that majority voting fails to provide consistent gains on such tasks, we demonstrate how to increase success rates by softening the scoring criterion. We introduce Soft Self-Consistency (SOFT-SC), which replaces SC's discontinuous scoring with a continuous score computed from model likelihoods, allowing for selection even when actions are sparsely distributed. SOFT-SC improves both performance and efficiency on long-horizon interactive tasks, requiring half as many samples as SC for comparable or better performance. For a fixed number of samples, SOFT-SC leads to a 1.3% increase over SC in absolute success rate on writing bash programs, a 6.6% increase on online shopping (WebShop), and a 4.7% increase for an interactive household game (ALFWorld). Finally, we show that SOFT-SC can be applied to both open-source and black-box models.

With the rapid advancement of large language models (LLMs), there is a pressing need for a comprehensive evaluation suite to assess their capabilities and limitations. Existing LLM leaderboards often reference scores reported in other papers without consistent settings and prompts, which may inadvertently encourage cherry-picking favored settings and prompts for better results. In this work, we introduce GPT-Fathom, an open-source and reproducible LLM evaluation suite built on top of OpenAI Evals. We systematically evaluate 10+ leading LLMs as well as OpenAI's legacy models on 20+ curated benchmarks across 7 capability categories, all under aligned settings. Our retrospective study on OpenAI's earlier models offers valuable insights into the evolutionary path from GPT-3 to GPT-4. Currently, the community is eager to know how GPT-3 progressively improves to GPT-4, including technical details like whether adding code data improves LLM's reasoning capability, which aspects of LLM capability can be improved by SFT and RLHF, how much is the alignment tax, etc. Our analysis sheds light on many of these questions, aiming to improve the transparency of advanced LLMs.

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and generation across various domains, including medicine. We present a comprehensive evaluation of GPT-4, a state-of-the-art LLM, on medical competency examinations and benchmark datasets. GPT-4 is a general-purpose model that is not specialized for medical problems through training or engineered to solve clinical tasks. Our analysis covers two sets of official practice materials for the USMLE, a three-step examination program used to assess clinical competency and grant licensure in the United States. We also evaluate performance on the MultiMedQA suite of benchmark datasets. Beyond measuring model performance, experiments were conducted to investigate the influence of test questions containing both text and images on model performance, probe for memorization of content during training, and study probability calibration, which is of critical importance in high-stakes applications like medicine. Our results show that GPT-4, without any specialized prompt crafting, exceeds the passing score on USMLE by over 20 points and outperforms earlier general-purpose models (GPT-3.5) as well as models specifically fine-tuned on medical knowledge (Med-PaLM, a prompt-tuned version of Flan-PaLM 540B). In addition, GPT-4 is significantly better calibrated than GPT-3.5, demonstrating a much-improved ability to predict the likelihood that its answers are correct. We also explore the behavior of the model qualitatively through a case study that shows the ability of GPT-4 to explain medical reasoning, personalize explanations to students, and interactively craft new counterfactual scenarios around a medical case. Implications of the findings are discussed for potential uses of GPT-4 in medical education, assessment, and clinical practice, with appropriate attention to challenges of accuracy and safety.

We present **vstash**, a local-first document memory system that combines vector similarity search with full-text keyword matching via Reciprocal Rank Fusion (RRF) and adaptive per-query IDF weighting. All data resides in a single SQLite file using sqlite-vec for approximate nearest neighbor search and FTS5 for keyword matching. We make four primary contributions. **(1)** Self-supervised embedding refinement via hybrid retrieval disagreement: across 753 BEIR queries on SciFact, NFCorpus, and FiQA, 74.5% produce top-10 disagreement between vector-heavy (vec=0.95, fts=0.05) and FTS-heavy (vec=0.05, fts=0.95) search (per-dataset rates 63.4% / 73.4% / 86.7%, Section 5.2), providing a free training signal without human labels. Fine-tuning BGE-small (33M params) with MultipleNegativesRankingLoss on 76K disagreement triples improves NDCG@10 on all 5 BEIR datasets (up to +19.5% on NFCorpus vs. BGE-small base RRF, Table 6). On 3 of 5 datasets, under different preprocessing, the tuned 33M-parameter pipeline matches or exceeds published ColBERTv2 results (110M params) and an untrained BGE-base (110M); on FiQA and ArguAna it underperforms ColBERTv2 (Section 5.5). **(2)** Adaptive RRF with per-query IDF weighting improves NDCG@10 on all 5 BEIR datasets versus fixed weights (up to +21.4% on ArguAna), achieving 0.7263 on SciFact with BGE-small. **(3)** A negative result on post-RRF scoring: frequency+decay, history-augmented recall, and cross-encoder reranking all failed to improve NDCG. **(4)** A production-grade substrate with integrity checking, schema versioning, ranking diagnostics, and a distance-based relevance signal validated on 50,425 relevance-judged queries across the 5 BEIR datasets. Search latency remains 20.9 ms median at 50K chunks with stable NDCG. The fine-tuned model is published as `Stffens/bge-small-rrf-v2` on HuggingFace. All code, data, and experiments are open-source.

Automated scoring engines are increasingly being used to score the free-form text responses that students give to questions. Such engines are not designed to appropriately deal with responses that a human reader would find alarming such as those that indicate an intention to self-harm or harm others, responses that allude to drug abuse or sexual abuse or any response that would elicit concern for the student writing the response. Our neural network models have been designed to help identify these anomalous responses from a large collection of typical responses that students give. The responses identified by the neural network can be assessed for urgency, severity, and validity more quickly by a team of reviewers than otherwise possible. Given the anomalous nature of these types of responses, our goal is to maximize the chance of flagging these responses for review given the constraint that only a fixed percentage of responses can viably be assessed by a team of reviewers.

Large language models (LLMs) hold great promise in summarizing medical evidence. Most recent studies focus on the application of proprietary LLMs. Using proprietary LLMs introduces multiple risk factors, including a lack of transparency and vendor dependency. While open-source LLMs allow better transparency and customization, their performance falls short compared to proprietary ones. In this study, we investigated to what extent fine-tuning open-source LLMs can further improve their performance in summarizing medical evidence. Utilizing a benchmark dataset, MedReview, consisting of 8,161 pairs of systematic reviews and summaries, we fine-tuned three broadly-used, open-sourced LLMs, namely PRIMERA, LongT5, and Llama-2. Overall, the fine-tuned LLMs obtained an increase of 9.89 in ROUGE-L (95% confidence interval: 8.94-10.81), 13.21 in METEOR score (95% confidence interval: 12.05-14.37), and 15.82 in CHRF score (95% confidence interval: 13.89-16.44). The performance of fine-tuned LongT5 is close to GPT-3.5 with zero-shot settings. Furthermore, smaller fine-tuned models sometimes even demonstrated superior performance compared to larger zero-shot models. The above trends of improvement were also manifested in both human and GPT4-simulated evaluations. Our results can be applied to guide model selection for tasks demanding particular domain knowledge, such as medical evidence summarization.

Measuring diversity accurately is important for many scientific fields, including machine learning (ML), ecology, and chemistry. The Vendi Score was introduced as a generic similarity-based diversity metric that extends the Hill number of order q=1 by leveraging ideas from quantum statistical mechanics. Contrary to many diversity metrics in ecology, the Vendi Score accounts for similarity and does not require knowledge of the prevalence of the categories in the collection to be evaluated for diversity. However, the Vendi Score treats each item in a given collection with a level of sensitivity proportional to the item's prevalence. This is undesirable in settings where there is a significant imbalance in item prevalence. In this paper, we extend the other Hill numbers using similarity to provide flexibility in allocating sensitivity to rare or common items. This leads to a family of diversity metrics -- Vendi scores with different levels of sensitivity -- that can be used in a variety of applications. We study the properties of the scores in a synthetic controlled setting where the ground truth diversity is known. We then test their utility in improving molecular simulations via Vendi Sampling. Finally, we use the Vendi scores to better understand the behavior of image generative models in terms of memorization, duplication, diversity, and sample quality.

This research investigates prompt designs of evaluating generated texts using large language models (LLMs). While LLMs are increasingly used for scoring various inputs, creating effective prompts for open-ended text evaluation remains challenging due to model sensitivity and subjectivity in evaluation of text generation. Our study experimented with different prompt structures, altering the sequence of output instructions and including explanatory reasons. We found that the order of presenting reasons and scores significantly influences LLMs' scoring, with a different level of rule understanding in the prompt. An additional optimization may enhance scoring alignment if sufficient data is available. This insight is crucial for improving the accuracy and consistency of LLM-based evaluations.

Identifying disease phenotypes from electronic health records (EHRs) is critical for numerous secondary uses. Manually encoding physician knowledge into rules is particularly challenging for rare diseases due to inadequate EHR coding, necessitating review of clinical notes. Large language models (LLMs) offer promise in text understanding but may not efficiently handle real-world clinical documentation. We propose a zero-shot LLM-based method enriched by retrieval-augmented generation and MapReduce, which pre-identifies disease-related text snippets to be used in parallel as queries for the LLM to establish diagnosis. We show that this method as applied to pulmonary hypertension (PH), a rare disease characterized by elevated arterial pressures in the lungs, significantly outperforms physician logic rules (F_1 score of 0.62 vs. 0.75). This method has the potential to enhance rare disease cohort identification, expanding the scope of robust clinical research and care gap identification.

Many modern AI question-answering systems convert text into vectors and retrieve the closest matches to a user question. While effective for topical similarity, similarity scores alone do not explain why some retrieved text can serve as evidence while other equally similar text cannot. When many candidates receive similar scores, systems may select sentences that are redundant, incomplete, or address different conditions than the question requires. This paper presents a deterministic evidence selection framework for retrieval-augmented question answering. The approach introduces Meaning-Utility Estimation (MUE) and Diversity-Utility Estimation (DUE), fixed scoring and redundancy-control procedures that determine evidence admissibility prior to answer generation. Each sentence or record is evaluated independently using explicit signals for semantic relatedness, term coverage, conceptual distinctiveness, and redundancy. No training or fine-tuning is required. In the prototype, a unit is accepted only if it explicitly states the fact, rule, or condition required by the task. Units are not merged or expanded. If no unit independently satisfies the requirement, the system returns no answer. This deterministic gating produces compact, auditable evidence sets and establishes a clear boundary between relevant text and usable evidence.

We conduct a systematic audit of three widely used reasoning benchmarks, SocialIQa, FauxPas-EAI, and ToMi, and uncover pervasive flaws in both benchmark items and evaluation methodology. Using five LLMs (GPT-{3, 3.5, 4, o1}, and LLaMA 3.1) as diagnostic tools, we identify structural, semantic, and pragmatic issues in benchmark design (e.g., duplicated items, ambiguous wording, and implausible answers), as well as scoring procedures that prioritize output form over reasoning process. Through systematic human annotation and re-evaluation on cleaned benchmark subsets, we find that model scores often improve not due to due to erratic surface wording variations and not to improved reasoning. Infact, further analyses show that model performance is highly sensitive to minor input variations such as context availability and phrasing, revealing that high scores may reflect alignment with format-specific cues rather than consistent inference based on the input. These findings challenge the validity of current benchmark-based claims about reasoning in LLMs, and highlight the need for evaluation protocols that assess reasoning as a process of drawing inference from available information, rather than as static output selection. We release audited data and evaluation tools to support more interpretable and diagnostic assessments of model reasoning.

Medical coding translates clinical documentation into standardized codes for billing, research, and public health, but manual coding is time-consuming and error-prone. Existing automation efforts rely on small datasets that poorly represent real-world patient heterogeneity. We trained a language model on 5.8 million electronic health records from 1.8 million patients across nearly all specialties in Eastern Denmark (2006--2016) to predict ICD-10 codes from clinical notes, medications, and laboratory results. Evaluated on 270,000 held-out patients, the model achieved a micro F1 of 71.8% and a top-10 recall of 95.5%. Performance varied by specialty (F1: 53--91%), with higher scores in specialties with well-defined diagnostic criteria. Codes appearing predominantly as secondary diagnoses had markedly lower F1 scores. For three such codes (suicide-related behaviors, weight disorders, and hypertension), the model identified thousands of uncoded cases, of which 76-86% were confirmed valid upon manual review, suggesting systematic under-coding rather than model error. These findings suggest under-coding of secondary diagnoses in Eastern Denmark during this period, with potential implications for epidemiological research, public health surveillance, and understanding of multimorbidity. Similar time constraints and reimbursement structures in other healthcare systems suggest this may not be isolated to this dataset. The model can automate coding for approximately 50% of cases and provide accurate suggestions for most others, and may offer a practical solution to help capture missed secondary conditions.

The growing awareness of safety concerns in large language models (LLMs) has sparked considerable interest in the evaluation of safety within current research endeavors. This study investigates an interesting issue pertaining to the evaluation of LLMs, namely the substantial discrepancy in performance between multiple-choice questions and open-ended questions. Inspired by research on jailbreak attack patterns, we argue this is caused by mismatched generalization. That is, the LLM does not have a comprehensive understanding of the complex concept of safety. Instead, it only remembers what to answer for open-ended safety questions, which makes it unable to solve other forms of safety tests. We refer to this phenomenon as fake alignment and construct a comparative benchmark to empirically verify its existence in LLMs. Such fake alignment renders previous evaluation protocols unreliable. To address this, we introduce the Fake alIgNment Evaluation (FINE) framework and two novel metrics--Consistency Score (CS) and Consistent Safety Score (CSS), which jointly assess two complementary forms of evaluation to quantify fake alignment and obtain corrected performance estimates. Applying FINE to 14 widely-used LLMs reveals several models with purported safety are poorly aligned in practice. Our work highlights potential limitations in prevailing alignment methodologies.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

Medical reasoning models (MRMs) achieve superior performance on medical benchmarks compared to medical LLMs; however, high accuracy alone is insufficient for practical deployment. One of such requirements for real-world application is robustness to varying output constraints. Specifically, posing the same medical question while requesting different answer formats should not affect the underlying correctness of the response. We investigate this phenomenon in this paper, focusing on MRMs. To quantify this behavior, we propose the metric answer-format robustness: the ability to reliably generate correct outputs across varying specified formats. We examine three representative formats: multiple-choice, open-ended question-answering, and ranked lists. Across 15 proprietary and open-weight models, we observe substantial variation in format robustness (35-100%). Furthermore, we conduct controlled fine-tuning experiments on a shared backbone with matched training data to isolate the effects of the fine-tuning paradigm. We find that supervised fine-tuning yields more stable behavior across formats, whereas reinforcement fine-tuning often exhibits higher cross-format brittleness, with the degree of instability strongly dependent on reward design. Overall, answer-format robustness in MRMs is trainable yet brittle and requires careful evaluation for practical medical use.

Accurate interpretation of lab results is crucial in clinical medicine, yet most patient portals use universal normal ranges, ignoring conditional factors like age and gender. This study introduces Lab-AI, an interactive system that offers personalized normal ranges using retrieval-augmented generation (RAG) from credible health sources. Lab-AI has two modules: factor retrieval and normal range retrieval. We tested these on 122 lab tests: 40 with conditional factors and 82 without. For tests with factors, normal ranges depend on patient-specific information. Our results show GPT-4-turbo with RAG achieved a 0.948 F1 score for factor retrieval and 0.995 accuracy for normal range retrieval. GPT-4-turbo with RAG outperformed the best non-RAG system by 33.5% in factor retrieval and showed 132% and 100% improvements in question-level and lab-level performance, respectively, for normal range retrieval. These findings highlight Lab-AI's potential to enhance patient understanding of lab results.

In passage retrieval system, the initial passage retrieval results may be unsatisfactory, which can be refined by a reranking scheme. Existing solutions to passage reranking focus on enriching the interaction between query and each passage separately, neglecting the context among the top-ranked passages in the initial retrieval list. To tackle this problem, we propose a Hybrid and Collaborative Passage Reranking (HybRank) method, which leverages the substantial similarity measurements of upstream retrievers for passage collaboration and incorporates the lexical and semantic properties of sparse and dense retrievers for reranking. Besides, built on off-the-shelf retriever features, HybRank is a plug-in reranker capable of enhancing arbitrary passage lists including previously reranked ones. Extensive experiments demonstrate the stable improvements of performance over prevalent retrieval and reranking methods, and verify the effectiveness of the core components of HybRank.

Aspect sentiment quadruple prediction (ASQP) facilitates a detailed understanding of opinions expressed in a text by identifying the opinion term, aspect term, aspect category and sentiment polarity for each opinion. However, annotating a full set of training examples to fine-tune models for ASQP is a resource-intensive process. In this study, we explore the capabilities of large language models (LLMs) for zero- and few-shot learning on the ASQP task across five diverse datasets. We report F1 scores slightly below those obtained with state-of-the-art fine-tuned models but exceeding previously reported zero- and few-shot performance. In the 40-shot setting on the Rest16 restaurant domain dataset, LLMs achieved an F1 score of 52.46, compared to 60.39 by the best-performing fine-tuned method MVP. Additionally, we report the performance of LLMs in target aspect sentiment detection (TASD), where the F1 scores were also close to fine-tuned models, achieving 66.03 on Rest16 in the 40-shot setting, compared to 72.76 with MVP. While human annotators remain essential for achieving optimal performance, LLMs can reduce the need for extensive manual annotation in ASQP tasks.

Many tasks revolve around editing a document, whether code or text. We formulate the revision similarity problem to unify a wide range of machine learning evaluation problems whose goal is to assess a revision to an existing document. We observe that revisions usually change only a small portion of an existing document, so the existing document and its immediate revisions share a majority of their content. We formulate five adequacy criteria for revision similarity measures, designed to align them with human judgement. We show that popular pairwise measures, like BLEU, fail to meet these criteria, because their scores are dominated by the shared content. They report high similarity between two revisions when humans would assess them as quite different. This is a fundamental flaw we address. We propose a novel static measure, Excision Score (ES), which computes longest common subsequence (LCS) to remove content shared by an existing document with the ground truth and predicted revisions, before comparing only the remaining divergent regions. This is analogous to a surgeon creating a sterile field to focus on the work area. We use approximation to speed the standard cubic LCS computation to quadratic. In code-editing evaluation, where static measures are often used as a cheap proxy for passing tests, we demonstrate that ES surpasses existing measures. When aligned with test execution on HumanEvalFix, ES improves over its nearest competitor, SARI, by 12% Pearson correlation and by >21% over standard measures like BLEU. The key criterion is invariance to shared context; when we perturb HumanEvalFix with increased shared context, ES' improvement over SARI increases to 20% and >30% over standard measures. ES also handles other corner cases that other measures do not, such as correctly aligning moved code blocks, and appropriately rewarding matching insertions or deletions.

We develop new conformal inference methods for obtaining validity guarantees on the output of large language models (LLMs). Prior work in conformal language modeling identifies a subset of the text that satisfies a high-probability guarantee of correctness. These methods work by filtering claims from the LLM's original response if a scoring function evaluated on the claim fails to exceed a threshold calibrated via split conformal prediction. Existing methods in this area suffer from two deficiencies. First, the guarantee stated is not conditionally valid. The trustworthiness of the filtering step may vary based on the topic of the response. Second, because the scoring function is imperfect, the filtering step can remove many valuable and accurate claims. We address both of these challenges via two new conformal methods. First, we generalize the conditional conformal procedure of Gibbs et al. (2023) in order to adaptively issue weaker guarantees when they are required to preserve the utility of the output. Second, we show how to systematically improve the quality of the scoring function via a novel algorithm for differentiating through the conditional conformal procedure. We demonstrate the efficacy of our approach on biography and medical question-answering datasets.

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise--the disagreement between model and metric defined candidate rankings--minimized. Code to create, select, and optimize calibration sets is available at https://github.com/griff4692/calibrating-summaries

Medical vision-language datasets are often limited in size and biased toward negative findings, as clinicians report abnormalities mostly but might omit some positive/neutral findings because they might be considered as irrelevant to the patient's condition. We propose a self-supervised data enrichment method that leverages semantic clustering of report sentences. Then we enrich the findings in the medical reports in the training set by adding positive/neutral observations from different clusters in a self-supervised manner. Our approach yields consistent gains in supervised fine-tuning (5.63%, 3.04%, 7.40%, 5.30%, 7.47% average gains on COMET score, Bert score, Sentence Bleu, CheXbert-F1 and RadGraph-F1 scores respectively). Ablation studies confirm that improvements stem from semantic clustering rather than random augmentation. Furthermore, we introduce a way to incorporate semantic cluster information into the reward design for GRPO training, which leads to further performance gains (2.78%, 3.14%, 12.80% average gains on COMET score, Bert score and Sentence Bleu scores respectively). We share our code at https://anonymous.4open.science/r/SemEnrich-75CF

While recent preference alignment algorithms for language models have demonstrated promising results, supervised fine-tuning (SFT) remains imperative for achieving successful convergence. In this paper, we study the crucial role of SFT within the context of preference alignment, emphasizing that a minor penalty for the disfavored generation style is sufficient for preference-aligned SFT. Building on this foundation, we introduce a straightforward and innovative reference model-free monolithic odds ratio preference optimization algorithm, ORPO, eliminating the necessity for an additional preference alignment phase. We demonstrate, both empirically and theoretically, that the odds ratio is a sensible choice for contrasting favored and disfavored styles during SFT across the diverse sizes from 125M to 7B. Specifically, fine-tuning Phi-2 (2.7B), Llama-2 (7B), and Mistral (7B) with ORPO on the UltraFeedback alone surpasses the performance of state-of-the-art language models with more than 7B and 13B parameters: achieving up to 12.20% on AlpacaEval_{2.0} (Figure 1), 66.19% on IFEval (instruction-level loose, Table 6), and 7.32 in MT-Bench (Figure 12). We release code and model checkpoints for Mistral-ORPO-alpha (7B) and Mistral-ORPO-beta (7B).

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

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

Automated essay scoring (AES) involves predicting a score that reflects the writing quality of an essay. Most existing AES systems produce only a single overall score. However, users and L2 learners expect scores across different dimensions (e.g., vocabulary, grammar, coherence) for English essays in real-world applications. To address this need, we have developed two models that automatically score English essays across multiple dimensions by employing fine-tuning and other strategies on two large datasets. The results demonstrate that our systems achieve impressive performance in evaluation using three criteria: precision, F1 score, and Quadratic Weighted Kappa. Furthermore, our system outperforms existing methods in overall scoring.

In this work we design an end-to-end deep learning architecture for predicting, on Chest X-rays images (CXR), a multi-regional score conveying the degree of lung compromise in COVID-19 patients. Such semi-quantitative scoring system, namely Brixia~score, is applied in serial monitoring of such patients, showing significant prognostic value, in one of the hospitals that experienced one of the highest pandemic peaks in Italy. To solve such a challenging visual task, we adopt a weakly supervised learning strategy structured to handle different tasks (segmentation, spatial alignment, and score estimation) trained with a "from-the-part-to-the-whole" procedure involving different datasets. In particular, we exploit a clinical dataset of almost 5,000 CXR annotated images collected in the same hospital. Our BS-Net demonstrates self-attentive behavior and a high degree of accuracy in all processing stages. Through inter-rater agreement tests and a gold standard comparison, we show that our solution outperforms single human annotators in rating accuracy and consistency, thus supporting the possibility of using this tool in contexts of computer-assisted monitoring. Highly resolved (super-pixel level) explainability maps are also generated, with an original technique, to visually help the understanding of the network activity on the lung areas. We also consider other scores proposed in literature and provide a comparison with a recently proposed non-specific approach. We eventually test the performance robustness of our model on an assorted public COVID-19 dataset, for which we also provide Brixia~score annotations, observing good direct generalization and fine-tuning capabilities that highlight the portability of BS-Net in other clinical settings. The CXR dataset along with the source code and the trained model are publicly released for research purposes.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

Large language models are increasingly used as personal assistants, yet most lack a persistent user model, forcing users to repeatedly restate preferences across sessions. We propose Vector-Adapted Retrieval Scoring (VARS), a pipeline-agnostic, frozen-backbone framework that represents each user with long-term and short-term vectors in a shared preference space and uses these vectors to bias retrieval scoring over structured preference memory. The vectors are updated online from weak scalar rewards from users' feedback, enabling personalization without per-user fine-tuning. We evaluate on MultiSessionCollab, an online multi-session collaboration benchmark with rich user preference profiles, across math and code tasks. Under frozen backbones, the main benefit of user-aware retrieval is improved interaction efficiency rather than large gains in raw task accuracy: our full VARS agent achieves the strongest overall performance, matches a strong Reflection baseline in task success, and reduces timeout rate and user effort. The learned long-term vectors also align with cross-user preference overlap, while short-term vectors capture session-specific adaptation, supporting the interpretability of the dual-vector design. Code, model, and data are available at https://github.com/YurenHao0426/VARS.

U.S. immigration law spans thousands of pages of official policy, federal regulations, and procedural guidance that change frequently and carry high stakes for petitioners who lack legal representation. We describe the construction of ImmigrationQA, a source-grounded question-answering dataset of 17,058 pairs across 13 immigration subdomains, and the fine-tuning of a Llama 3.2 3B Instruct model on that dataset using parameter-efficient LoRA. The corpus was assembled from 11 primary and secondary sources -- including the USCIS Policy Manual, 8 CFR, BIA precedent decisions, and community Q&A -- yielding 10,056 validated canonical documents and 18,308 text chunks. Structured QA pairs were generated from these chunks using Claude Sonnet 4.6 via five mode-specific prompts, with 22 pairs rejected for insufficient source-span overlap. The fine-tuned model was evaluated against a held-out split of 993 pairs using LLM-as-judge scoring on a 101-example stratified sample. The fine-tuned model scored a mean of 1.08/3.0 (16.8% fully correct; 101-example stratified eval) versus the Llama 3 8B base model at 0.85/3.0 (4% fully correct), a relative improvement of 27% in mean score; a zero-shot Claude Sonnet baseline scored 1.52/3.0 (25% fully correct). The fine-tuned model shows concentrated improvement in procedural subdomains (travel documents, adjustment of status, nonimmigrant visas) while remaining weak on complex legal reasoning and time-sensitive statistics. The full pipeline ran for approximately $29 in cloud compute. All artifacts -- dataset, model, code, and prompt templates -- are publicly released. The system is not a substitute for legal counsel and does not reflect regulatory changes after the corpus crawl date.

The hypothesis that pretrained large language models (LLMs) necessitate only minimal supervision during the fine-tuning (SFT) stage (Zhou et al., 2024) has been substantiated by recent advancements in data curation and selection research. However, their stability and generalizability are compromised due to the vulnerability to experimental setups and validation protocols, falling short of surpassing random sampling (Diddee & Ippolito, 2024; Xia et al., 2024b). Built upon LLMs, multi-modal LLMs (MLLMs), combined with the sheer token volume and heightened heterogeneity of data sources, amplify both the significance and complexity of data selection. To harvest multi-modal instructional data in a robust and efficient manner, we re-define the granularity of the quality metric by decomposing it into 14 vision-language-related capabilities, and introduce multi-modal rich scorers to evaluate the capabilities of each data candidate. To promote diversity, in light of the inherent objective of the alignment stage, we take interaction style as diversity indicator and use a multi-modal rich styler to identify data instruction patterns. In doing so, our multi-modal rich scorers and styler (mmSSR) guarantee that high-scoring information is conveyed to users in diversified forms. Free from embedding-based clustering or greedy sampling, mmSSR efficiently scales to millions of data with varying budget constraints, supports customization for general or specific capability acquisition, and facilitates training-free generalization to new domains for curation. Across 10+ experimental settings, validated by 14 multi-modal benchmarks, we demonstrate consistent improvements over random sampling, baseline strategies and state-of-the-art selection methods, achieving 99.1% of full performance with only 30% of the 2.6M data.

Estimating the performance difficulty of a musical score is crucial in music education for adequately designing the learning curriculum of the students. Although the Music Information Retrieval community has recently shown interest in this task, existing approaches mainly use machine-readable scores, leaving the broader case of sheet music images unaddressed. Based on previous works involving sheet music images, we use a mid-level representation, bootleg score, describing notehead positions relative to staff lines coupled with a transformer model. This architecture is adapted to our task by introducing an encoding scheme that reduces the encoded sequence length to one-eighth of the original size. In terms of evaluation, we consider five datasets -- more than 7500 scores with up to 9 difficulty levels -- , two of them particularly compiled for this work. The results obtained when pretraining the scheme on the IMSLP corpus and fine-tuning it on the considered datasets prove the proposal's validity, achieving the best-performing model with a balanced accuracy of 40.34\% and a mean square error of 1.33. Finally, we provide access to our code, data, and models for transparency and reproducibility.

Multimodal large language models (LLMs) are increasingly explored as automated evaluators in clinical settings, yet their scoring behavior on ordinal clinical scales remains poorly understood. We benchmark three frontier LLM families against supervised deep learning models for scoring Clock Drawing Test (CDT) images on two public datasets using the Shulman rubric. While fully fine-tuned Vision Transformers achieve the best calibration (MAE 0.52, within-1 accuracy 91%), zero-shot LLMs remain competitive on tolerance-based agreement (GPT-5 MAE 0.67, within-1 accuracy 92%) despite higher absolute error. However, per-score analysis reveals that all three LLM families exhibit a pronounced central tendency effect (systematic endpoint compression): predictions are systematically compressed toward the middle of the scale, with over-prediction at the low end (score 0 to 1) and under-prediction at the high end (score 5 to 4). This effect disproportionately affects the clinically critical extremes where accurate scoring most impacts screening decisions for cognitive impairment. Targeted ablations show that neither few-shot exemplars spanning the full score range nor removing clinical terminology from the prompt eliminates the effect. Our findings extend the LLM-as-a-judge bias literature from NLP evaluation to clinical assessment, and highlight the need for calibration-aware evaluation and post-hoc calibration before deploying LLM-based raters in high-stakes screening workflows.

Retrieval-Augmented Generation (RAG) enriches Large Language Models (LLMs) by combining their internal, parametric knowledge with external, non-parametric sources, with the goal of improving factual correctness and minimizing hallucinations. The LiveRAG 2025 challenge explores RAG solutions to maximize accuracy on DataMorgana's QA pairs, which are composed of single-hop and multi-hop questions. The challenge provides access to sparse OpenSearch and dense Pinecone indices of the Fineweb 10BT dataset. It restricts model use to LLMs with up to 10B parameters and final answer generation with Falcon-3-10B. A judge-LLM assesses the submitted answers along with human evaluators. By exploring distinct retriever combinations and RAG solutions under the challenge conditions, our final solution emerged using InstructRAG in combination with a Pinecone retriever and a BGE reranker. Our solution achieved a correctness score of 1.13 and a faithfulness score of 0.55, placing fourth in the SIGIR 2025 LiveRAG Challenge.

The development of large language models (LLMs) has achieved superior performance in a range of downstream tasks, including LLM-based retrieval-augmented generation (RAG). The quality of generated content heavily relies on the usefulness of the retrieved information and the capacity of LLMs' internal information processing mechanism to incorporate it in answer generation. It is generally assumed that the retrieved information is relevant to the question. However, the retrieved information may have a variable degree of relevance and usefulness, depending on the question and the document collection. It is important to take into account the relevance of the retrieved information in answer generation. In this paper, we propose OpenDecoder, a new approach that leverages explicit evaluation of the retrieved information as quality indicator features for generation. We aim to build a RAG model that is more robust to varying levels of noisy context. Three types of explicit evaluation information are considered: relevance score, ranking score, and QPP (query performance prediction) score. The experimental results on five benchmark datasets demonstrate the effectiveness and better robustness of OpenDecoder by outperforming various baseline methods. Importantly, this paradigm is flexible to be integrated with the post-training of LLMs for any purposes and incorporated with any type of external indicators.

As Large Language Models (LLMs) are increasingly integrated into healthcare to address complex inquiries, ensuring their reliability remains a critical challenge. Recent studies have highlighted that generic LLMs often struggle in clinical contexts, occasionally producing misleading guidance. To mitigate these risks, this research focuses on the domain-specific adaptation of Llama-2-7B using the Low-Rank Adaptation (LoRA) technique. By injecting trainable low-rank matrices into the Transformer layers, we efficiently adapted the model using authentic patient-physician transcripts while preserving the foundational knowledge of the base model. Our objective was to enhance precision and contextual relevance in responding to medical queries by capturing the specialized nuances of clinical discourse. Due to the resource-intensive nature of large-scale human validation, the model's performance was evaluated through a dual-track framework: Track A utilized traditional lexical similarity metrics (e.g., BLEU, ROUGE), while Track B employed an "LLM-as-a-Judge" paradigm using GPT-4 for semantic assessment. Our results demonstrate that while the LoRA-enhanced model achieved significant improvements across all quantitative lexical dimensions, a profound disagreement surfaced in the GPT-4 evaluation, which marginally favored the baseline model's conversational flow. This metric divergence underscores a pivotal finding: traditional automated scores may not fully reflect clinical utility. Consequently, we propose that while automated metrics and LLM judges serve as valuable developmental proxies, rigorous validation by human medical experts remains an indispensable requirement for the safe deployment of LLMs in healthcare settings.

Recent works have revealed the great potential of speculative decoding in accelerating the autoregressive generation process of large language models. The success of these methods relies on the alignment between draft candidates and the sampled outputs of the target model. Existing methods mainly achieve draft-target alignment with training-based methods, e.g., EAGLE, Medusa, involving considerable training costs. In this paper, we present a training-free alignment-augmented speculative decoding algorithm. We propose alignment sampling, which leverages output distribution obtained in the prefilling phase to provide more aligned draft candidates. To further benefit from high-quality but non-aligned draft candidates, we also introduce a simple yet effective flexible verification strategy. Through an adaptive probability threshold, our approach can improve generation accuracy while further improving inference efficiency. Experiments on 8 datasets (including question answering, summarization and code completion tasks) show that our approach increases the average generation score by 3.3 points for the LLaMA3 model. Our method achieves a mean acceptance length up to 2.39 and speed up generation by 2.23.

Aligning large language models with human objectives is paramount, yet common approaches including RLHF suffer from unstable and resource-intensive training. In response to this challenge, we introduce ARGS, Alignment as Reward-Guided Search, a novel framework that integrates alignment into the decoding process, eliminating the need for expensive RL training. By adjusting the model's probabilistic predictions using a reward signal, ARGS generates texts with semantic diversity while being aligned with human preferences, offering a promising and flexible solution for aligning language models. Notably, ARGS demonstrates consistent enhancements in average reward compared to baselines across diverse alignment tasks and various model dimensions. For example, under the same greedy-based decoding strategy, our method improves the average reward by 19.56% relative to the baseline and secures a preference or tie score of 64.33% in GPT-4 evaluation. We believe that our framework, emphasizing decoding-time alignment, paves the way for more responsive language models in the future. Code is publicly available at: https://github.com/deeplearning-wisc/args.

Given the dominance of dense retrievers that do not generalize well beyond their training dataset distributions, domain-specific test sets are essential in evaluating retrieval. There are few test datasets for retrieval systems intended for use by healthcare providers in a point-of-care setting. To fill this gap we have collaborated with medical professionals to create CURE, an ad-hoc retrieval test dataset for passage ranking with 2000 queries spanning 10 medical domains with a monolingual (English) and two cross-lingual (French/Spanish -> English) conditions. In this paper, we describe how CURE was constructed and provide baseline results to showcase its effectiveness as an evaluation tool. CURE is published with a Creative Commons Attribution Non Commercial 4.0 license and can be accessed on Hugging Face.

Recent advances such as Chain-of-Thought prompting have significantly improved large language models (LLMs) in zero-shot medical reasoning. However, prompting-based methods often remain shallow and unstable, while fine-tuned medical LLMs suffer from poor generalization under distribution shifts and limited adaptability to unseen clinical scenarios. To address these limitations, we present TAGS, a test-time framework that combines a broadly capable generalist with a domain-specific specialist to offer complementary perspectives without any model fine-tuning or parameter updates. To support this generalist-specialist reasoning process, we introduce two auxiliary modules: a hierarchical retrieval mechanism that provides multi-scale exemplars by selecting examples based on both semantic and rationale-level similarity, and a reliability scorer that evaluates reasoning consistency to guide final answer aggregation. TAGS achieves strong performance across nine MedQA benchmarks, boosting GPT-4o accuracy by 13.8%, DeepSeek-R1 by 16.8%, and improving a vanilla 7B model from 14.1% to 23.9%. These results surpass several fine-tuned medical LLMs, without any parameter updates. The code will be available at https://github.com/JianghaoWu/TAGS.

A standard way to evaluate the abilities of LLM involves presenting a multiple-choice question and selecting the option with the highest logit as the model's predicted answer. However, such a format for evaluating LLMs has limitations, since even if the model knows the correct answer, it may struggle to select the corresponding letter simply due to difficulties in following this rigid format. To address this, we introduce new scores that better capture and reveal model's underlying knowledge: the Query-Key Score (QK-score), derived from the interaction between query and key representations in attention heads, and the Attention Score, based on attention weights. These scores are extracted from specific select-and-copy heads, which show consistent performance across popular Multi-Choice Question Answering (MCQA) datasets. Based on these scores, our method improves knowledge extraction, yielding up to 16\% gain for LLaMA2-7B and up to 10\% for larger models on popular MCQA benchmarks. At the same time, the accuracy on a simple synthetic dataset, where the model explicitly knows the right answer, increases by almost 60\%, achieving nearly perfect accuracy, therefore demonstrating the method's efficiency in mitigating MCQA format limitations. To support our claims, we conduct experiments on models ranging from 7 billion to 70 billion parameters in both zero- and few-shot setups.

Many existing conditional score-based data generation methods utilize Bayes' theorem to decompose the gradients of a log posterior density into a mixture of scores. These methods facilitate the training procedure of conditional score models, as a mixture of scores can be separately estimated using a score model and a classifier. However, our analysis indicates that the training objectives for the classifier in these methods may lead to a serious score mismatch issue, which corresponds to the situation that the estimated scores deviate from the true ones. Such an issue causes the samples to be misled by the deviated scores during the diffusion process, resulting in a degraded sampling quality. To resolve it, we formulate a novel training objective, called Denoising Likelihood Score Matching (DLSM) loss, for the classifier to match the gradients of the true log likelihood density. Our experimental evidence shows that the proposed method outperforms the previous methods on both Cifar-10 and Cifar-100 benchmarks noticeably in terms of several key evaluation metrics. We thus conclude that, by adopting DLSM, the conditional scores can be accurately modeled, and the effect of the score mismatch issue is alleviated.

Despite notable advancements in Multimodal Large Language Models (MLLMs), most state-of-the-art models have not undergone thorough alignment with human preferences. This gap exists because current alignment research has primarily achieved progress in specific areas (e.g., hallucination reduction), while the broader question of whether aligning models with human preferences can systematically enhance MLLM capability remains largely unexplored. To this end, we introduce MM-RLHF, a dataset containing 120k fine-grained, human-annotated preference comparison pairs. This dataset represents a substantial advancement over existing resources, offering superior size, diversity, annotation granularity, and quality. Leveraging this dataset, we propose several key innovations to improve both the quality of reward models and the efficiency of alignment algorithms. Notably, we introduce a Critique-Based Reward Model, which generates critiques of model outputs before assigning scores, offering enhanced interpretability and more informative feedback compared to traditional scalar reward mechanisms. Additionally, we propose Dynamic Reward Scaling, a method that adjusts the loss weight of each sample according to the reward signal, thereby optimizing the use of high-quality comparison pairs. Our approach is rigorously evaluated across 10 distinct dimensions and 27 benchmarks, with results demonstrating significant and consistent improvements in model performance. Specifically, fine-tuning LLaVA-ov-7B with MM-RLHF and our alignment algorithm leads to a 19.5% increase in conversational abilities and a 60% improvement in safety. We have open-sourced the preference dataset, reward model, training and evaluation code, as well as reward modeling and safety benchmarks. For more details, please visit our project page: https://mm-rlhf.github.io.

While text-to-visual models now produce photo-realistic images and videos, they struggle with compositional text prompts involving attributes, relationships, and higher-order reasoning such as logic and comparison. In this work, we conduct an extensive human study on GenAI-Bench to evaluate the performance of leading image and video generation models in various aspects of compositional text-to-visual generation. We also compare automated evaluation metrics against our collected human ratings and find that VQAScore -- a metric measuring the likelihood that a VQA model views an image as accurately depicting the prompt -- significantly outperforms previous metrics such as CLIPScore. In addition, VQAScore can improve generation in a black-box manner (without finetuning) via simply ranking a few (3 to 9) candidate images. Ranking by VQAScore is 2x to 3x more effective than other scoring methods like PickScore, HPSv2, and ImageReward at improving human alignment ratings for DALL-E 3 and Stable Diffusion, especially on compositional prompts that require advanced visio-linguistic reasoning. We will release a new GenAI-Rank benchmark with over 40,000 human ratings to evaluate scoring metrics on ranking images generated from the same prompt. Lastly, we discuss promising areas for improvement in VQAScore, such as addressing fine-grained visual details. We will release all human ratings (over 80,000) to facilitate scientific benchmarking of both generative models and automated metrics.

Current benchmarks for AI clinician systems, often based on multiple-choice exams or manual rubrics, fail to capture the depth, robustness, and safety required for real-world clinical practice. To address this, we introduce the GAPS framework, a multidimensional paradigm for evaluating Grounding (cognitive depth), Adequacy (answer completeness), Perturbation (robustness), and Safety. Critically, we developed a fully automated, guideline-anchored pipeline to construct a GAPS-aligned benchmark end-to-end, overcoming the scalability and subjectivity limitations of prior work. Our pipeline assembles an evidence neighborhood, creates dual graph and tree representations, and automatically generates questions across G-levels. Rubrics are synthesized by a DeepResearch agent that mimics GRADE-consistent, PICO-driven evidence review in a ReAct loop. Scoring is performed by an ensemble of large language model (LLM) judges. Validation confirmed our automated questions are high-quality and align with clinician judgment. Evaluating state-of-the-art models on the benchmark revealed key failure modes: performance degrades sharply with increased reasoning depth (G-axis), models struggle with answer completeness (A-axis), and they are highly vulnerable to adversarial perturbations (P-axis) as well as certain safety issues (S-axis). This automated, clinically-grounded approach provides a reproducible and scalable method for rigorously evaluating AI clinician systems and guiding their development toward safer, more reliable clinical practice.

Large language models (LLMs) are increasingly used to assist ideation in research, but evaluating the quality of LLM-generated research proposals remains difficult: novelty and soundness are hard to measure automatically, and large-scale human evaluation is costly. We propose a verifiable alternative by reframing proposal generation as a time-sliced scientific forecasting problem. Given a research question and inspiring papers available before a cutoff time, the model generates a structured proposal and is evaluated by whether it anticipates research directions that appear in papers published after the time. We operationalize this objective with the Future Alignment Score (FAS), computed via retrieval and LLM-based semantic scoring against a held-out future corpus. To train models, we build a time-consistent dataset of 17,771 papers from targets and their pre-cutoff citations, and synthesize reasoning traces that teach gap identification and inspiration borrowing. Across Llama-3.1 and Qwen2.5 models, future-aligned tuning improves future alignment over unaligned baselines (up to +10.6% overall FAS), and domain-expert human evaluation corroborates improved proposal quality. Finally, we demonstrate practical impact by implementing two model-generated proposals with a code agent, obtaining 4.17% accuracy gain on MATH from a new prompting strategy and consistent improvements for a novel model-merging method.

Recent advances in large language models (LLMs) have shown impressive performance in passage reranking tasks. Despite their success, LLM-based methods still face challenges in efficiency and sensitivity to external biases. (1) Existing models rely mostly on autoregressive generation and sliding window strategies to rank passages, which incur heavy computational overhead as the number of passages increases. (2) External biases, such as position or selection bias, hinder the model's ability to accurately represent passages and increase input-order sensitivity. To address these limitations, we introduce a novel passage reranking model, called Multi-View-guided Passage Reranking (MVP). MVP is a non-generative LLM-based reranking method that encodes query-passage information into diverse view embeddings without being influenced by external biases. For each view, it combines query-aware passage embeddings to produce a distinct anchor vector, which is then used to directly compute relevance scores in a single decoding step. In addition, it employs an orthogonal loss to make the views more distinctive. Extensive experiments demonstrate that MVP, with just 220M parameters, matches the performance of much larger 7B-scale fine-tuned models while achieving a 100x reduction in inference latency. Notably, the 3B-parameter variant of MVP achieves state-of-the-art performance on both in-domain and out-of-domain benchmarks. The source code is available at: https://github.com/bulbna/MVP

Ensembling Vision-Language Models (VLMs) from different providers maximizes benchmark accuracy, yet models from the same architectural family share correlated errors that standard voting ignores. We study this structure across 17 VLMs from 8 families on VQAv2, TextVQA, and GQA. Family-correlated errors reduce effective ensemble dimensionality to 2.5-3.6 independent voters and create a Misleading tier (1.5-6.5% of questions) where correlated majority errors destroy accuracy to 0% despite the best model being correct. We propose three family-aware methods. Hierarchical Family Voting (HFV) aggregates within families before voting across them, recovering +18-26 pp on the Misleading tier. QualRCCV, a training-free method weighting models by calibration, family quality, and inverse family size, is the first to beat calibrated voting on all three benchmarks (p<0.05). Learned Candidate Scoring (LCS) trains a cross-validated classifier to re-rank candidate answers using support breadth, family diversity, and model quality, achieving the largest gains: +0.68% VQAv2, +0.61% TextVQA, +2.45% GQA -- all significant -- and is the only learned method that never degrades any benchmark. On VQAv2 test-standard (EvalAI), LCS reaches 87.83% with 12 models, confirming generalization.

Modern ML systems ingest data aggregated from diverse sources, such as synthetic, human-annotated, and live customer traffic. Understanding which examples are important to the performance of a learning algorithm is crucial for efficient model training. Recently, a growing body of literature has given rise to various "influence scores," which use training artifacts such as model confidence or checkpointed gradients to identify important subsets of data. However, these methods have primarily been developed in computer vision settings, and it remains unclear how well they generalize to language-based tasks using pretrained models. In this paper, we explore the applicability of influence scores in language classification tasks. We evaluate a diverse subset of these scores on the SNLI dataset by quantifying accuracy changes in response to pruning training data through random and influence-score-based sampling. We then stress-test one of the scores -- "variance of gradients" (VoG) from Agarwal et al. (2022) -- in an NLU model stack that was exposed to dynamic user speech patterns in a voice assistant type of setting. Our experiments demonstrate that in many cases, encoder-based language models can be finetuned on roughly 50% of the original data without degradation in performance metrics. Along the way, we summarize lessons learned from applying out-of-the-box implementations of influence scores, quantify the effects of noisy and class-imbalanced data, and offer recommendations on score-based sampling for better accuracy and training efficiency.

This research introduces ScoreRAG, an approach to enhance the quality of automated news generation. Despite advancements in Natural Language Processing and large language models, current news generation methods often struggle with hallucinations, factual inconsistencies, and lack of domain-specific expertise when producing news articles. ScoreRAG addresses these challenges through a multi-stage framework combining retrieval-augmented generation, consistency relevance evaluation, and structured summarization. The system first retrieves relevant news documents from a vector database, maps them to complete news items, and assigns consistency relevance scores based on large language model evaluations. These documents are then reranked according to relevance, with low-quality items filtered out. The framework proceeds to generate graded summaries based on relevance scores, which guide the large language model in producing complete news articles following professional journalistic standards. Through this methodical approach, ScoreRAG aims to significantly improve the accuracy, coherence, informativeness, and professionalism of generated news articles while maintaining stability and consistency throughout the generation process. The code and demo are available at: https://github.com/peiyun2260/ScoreRAG.

Recently, using a powerful proprietary Large Language Model (LLM) (e.g., GPT-4) as an evaluator for long-form responses has become the de facto standard. However, for practitioners with large-scale evaluation tasks and custom criteria in consideration (e.g., child-readability), using proprietary LLMs as an evaluator is unreliable due to the closed-source nature, uncontrolled versioning, and prohibitive costs. In this work, we propose Prometheus, a fully open-source LLM that is on par with GPT-4's evaluation capabilities when the appropriate reference materials (reference answer, score rubric) are accompanied. We first construct the Feedback Collection, a new dataset that consists of 1K fine-grained score rubrics, 20K instructions, and 100K responses and language feedback generated by GPT-4. Using the Feedback Collection, we train Prometheus, a 13B evaluator LLM that can assess any given long-form text based on customized score rubric provided by the user. Experimental results show that Prometheus scores a Pearson correlation of 0.897 with human evaluators when evaluating with 45 customized score rubrics, which is on par with GPT-4 (0.882), and greatly outperforms ChatGPT (0.392). Furthermore, measuring correlation with GPT-4 with 1222 customized score rubrics across four benchmarks (MT Bench, Vicuna Bench, Feedback Bench, Flask Eval) shows similar trends, bolstering Prometheus's capability as an evaluator LLM. Lastly, Prometheus achieves the highest accuracy on two human preference benchmarks (HHH Alignment & MT Bench Human Judgment) compared to open-sourced reward models explicitly trained on human preference datasets, highlighting its potential as an universal reward model. We open-source our code, dataset, and model at https://github.com/kaistAI/Prometheus.

The widespread applicability and increasing omnipresence of LLMs have instigated a need to align LLM responses to user and stakeholder preferences. Many preference optimization approaches have been proposed that fine-tune LLM parameters to achieve good alignment. However, such parameter tuning is known to interfere with model performance on many tasks. Moreover, keeping up with shifting user preferences is tricky in such a situation. Decoding-time alignment with reward model guidance solves these issues at the cost of increased inference time. However, most of such methods fail to strike the right balance between exploration and exploitation of reward -- often due to the conflated formulation of these two aspects - to give well-aligned responses. To remedy this we decouple these two aspects and implement them in an evolutionary fashion: exploration is enforced by decoding from mutated instructions and exploitation is represented as the periodic replacement of poorly-rewarded generations with well-rewarded ones. Empirical evidences indicate that this strategy outperforms many preference optimization and decode-time alignment approaches on two widely accepted alignment benchmarks AlpacaEval 2 and MT-Bench. Our implementation will be available at: https://darwin-alignment.github.io.

Personalized treatment effect estimates are often of interest in high-stakes applications -- thus, before deploying a model estimating such effects in practice, one needs to be sure that the best candidate from the ever-growing machine learning toolbox for this task was chosen. Unfortunately, due to the absence of counterfactual information in practice, it is usually not possible to rely on standard validation metrics for doing so, leading to a well-known model selection dilemma in the treatment effect estimation literature. While some solutions have recently been investigated, systematic understanding of the strengths and weaknesses of different model selection criteria is still lacking. In this paper, instead of attempting to declare a global `winner', we therefore empirically investigate success- and failure modes of different selection criteria. We highlight that there is a complex interplay between selection strategies, candidate estimators and the data used for comparing them, and provide interesting insights into the relative (dis)advantages of different criteria alongside desiderata for the design of further illuminating empirical studies in this context.

This paper is aimed at evaluating state-of-the-art models for Multi-document Summarization (MDS) on different types of datasets in various domains and investigating the limitations of existing models to determine future research directions. To address this gap, we conducted an extensive literature review to identify state-of-the-art models and datasets. We analyzed the performance of PRIMERA and PEGASUS models on BigSurvey-MDS and MS^2 datasets, which posed unique challenges due to their varied domains. Our findings show that the General-Purpose Pre-trained Model LED outperforms PRIMERA and PEGASUS on the MS^2 dataset. We used the ROUGE score as a performance metric to evaluate the identified models on different datasets. Our study provides valuable insights into the models' strengths and weaknesses, as well as their applicability in different domains. This work serves as a reference for future MDS research and contributes to the development of accurate and robust models which can be utilized on demanding datasets with academically and/or scientifically complex data as well as generalized, relatively simple datasets.

This study investigates retrieval-augmented summarization by specifically examining the impact of exemplar summary lengths under length constraints, not covered by previous work. We propose a Diverse Length-aware Maximal Marginal Relevance (DL-MMR) algorithm to better control summary lengths. This algorithm combines the query relevance with diverse target lengths in retrieval-augmented summarization. Unlike previous methods that necessitate exhaustive exemplar exemplar relevance comparisons using MMR, DL-MMR considers the exemplar target length as well and avoids comparing exemplars to each other, thereby reducing computational cost and conserving memory during the construction of an exemplar pool. Experimental results showed the effectiveness of DL-MMR, which considers length diversity, compared to the original MMR algorithm. DL-MMR additionally showed the effectiveness in memory saving of 781,513 times and computational cost reduction of 500,092 times, while maintaining the same level of informativeness.

Current question-answering benchmarks predominantly focus on accuracy in realizable prediction tasks. Conditioned on a question and answer-key, does the most likely token match the ground truth? Such benchmarks necessarily fail to evaluate LLMs' ability to quantify ground-truth outcome uncertainty. In this work, we focus on the use of LLMs as risk scores for unrealizable prediction tasks. We introduce folktexts, a software package to systematically generate risk scores using LLMs, and evaluate them against US Census data products. A flexible API enables the use of different prompting schemes, local or web-hosted models, and diverse census columns that can be used to compose custom prediction tasks. We evaluate 17 recent LLMs across five proposed benchmark tasks. We find that zero-shot risk scores produced by multiple-choice question-answering have high predictive signal but are widely miscalibrated. Base models consistently overestimate outcome uncertainty, while instruction-tuned models underestimate uncertainty and produce over-confident risk scores. In fact, instruction-tuning polarizes answer distribution regardless of true underlying data uncertainty. This reveals a general inability of instruction-tuned LLMs to express data uncertainty using multiple-choice answers. A separate experiment using verbalized chat-style risk queries yields substantially improved calibration across instruction-tuned models. These differences in ability to quantify data uncertainty cannot be revealed in realizable settings, and highlight a blind-spot in the current evaluation ecosystem that folktexts covers.

In recent years, the rapid increase in scientific papers has overwhelmed traditional review mechanisms, resulting in varying quality of publications. Although existing methods have explored the capabilities of Large Language Models (LLMs) for automated scientific reviewing, their generated contents are often generic or partial. To address the issues above, we introduce an automated paper reviewing framework SEA. It comprises of three modules: Standardization, Evaluation, and Analysis, which are represented by models SEA-S, SEA-E, and SEA-A, respectively. Initially, SEA-S distills data standardization capabilities of GPT-4 for integrating multiple reviews for a paper. Then, SEA-E utilizes standardized data for fine-tuning, enabling it to generate constructive reviews. Finally, SEA-A introduces a new evaluation metric called mismatch score to assess the consistency between paper contents and reviews. Moreover, we design a self-correction strategy to enhance the consistency. Extensive experimental results on datasets collected from eight venues show that SEA can generate valuable insights for authors to improve their papers.

Recent advances in instruction-guided image editing underscore the need for effective automated evaluation. While Vision-Language Models (VLMs) have been explored as judges, open-source models struggle with alignment, and proprietary models lack transparency and cost efficiency. Additionally, no public training datasets exist to fine-tune open-source VLMs, only small benchmarks with diverse evaluation schemes. To address this, we introduce ADIEE, an automated dataset creation approach which is then used to train a scoring model for instruction-guided image editing evaluation. We generate a large-scale dataset with over 100K samples and use it to fine-tune a LLaVA-NeXT-8B model modified to decode a numeric score from a custom token. The resulting scorer outperforms all open-source VLMs and Gemini-Pro 1.5 across all benchmarks, achieving a 0.0696 (+17.24%) gain in score correlation with human ratings on AURORA-Bench, and improving pair-wise comparison accuracy by 4.03% (+7.21%) on GenAI-Bench and 4.75% (+9.35%) on AURORA-Bench, respectively, compared to the state-of-the-art. The scorer can act as a reward model, enabling automated best edit selection and model fine-tuning. Notably, the proposed scorer can boost MagicBrush model's average evaluation score on ImagenHub from 5.90 to 6.43 (+8.98%). Our code and models are available at https://github.com/SherryXTChen/ADIEE.git.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

Current preference learning methods achieve high accuracy on standard benchmarks but exhibit significant performance degradation when objective quality signals are removed. We introduce WritingPreferenceBench, a dataset of 1,800 human-annotated preference pairs (1,200 English, 600 Chinese) across 8 creative writing genres, where responses are matched for objective correctness, factual accuracy, and length. On this benchmark, sequence-based reward models--the standard architecture for RLHF--achieve only 52.7% mean accuracy, while zero-shot language model judges perform at 53.9%. In contrast, generative reward models that produce explicit reasoning chains achieve 81.8% accuracy. We observe high within-model variance across genres: individual models range from 18.2% to 81.8% accuracy across different writing categories, with standard deviations averaging 10.1%. This variance persists regardless of model scale, with 27B parameter models showing no consistent improvement over 8B variants. Our results suggest that current RLHF methods primarily learn to detect objective errors rather than capture subjective quality preferences (e.g., creativity, stylistic flair, and emotional resonance), and that successful preference modeling may require intermediate reasoning representations rather than direct classification.

Recent advancements in large language model(LLM) performance on medical multiple choice question (MCQ) benchmarks have stimulated interest from healthcare providers and patients globally. Particularly in low-and middle-income countries (LMICs) facing acute physician shortages and lack of specialists, LLMs offer a potentially scalable pathway to enhance healthcare access and reduce costs. However, their effectiveness in the Global South, especially across the African continent, remains to be established. In this work, we introduce AfriMed-QA, the first large scale Pan-African English multi-specialty medical Question-Answering (QA) dataset, 15,000 questions (open and closed-ended) sourced from over 60 medical schools across 16 countries, covering 32 medical specialties. We further evaluate 30 LLMs across multiple axes including correctness and demographic bias. Our findings show significant performance variation across specialties and geographies, MCQ performance clearly lags USMLE (MedQA). We find that biomedical LLMs underperform general models and smaller edge-friendly LLMs struggle to achieve a passing score. Interestingly, human evaluations show a consistent consumer preference for LLM answers and explanations when compared with clinician answers.

This paper describes a system designed to distinguish between AI-generated and human-written scientific excerpts in the DAGPap24 competition hosted within the Fourth Workshop on Scientific Document Processing. In this competition the task is to find artificially generated token-level text fragments in documents of a scientific domain. Our work focuses on the use of a multi-task learning architecture with two heads. The application of this approach is justified by the specificity of the task, where class spans are continuous over several hundred characters. We considered different encoder variations to obtain a state vector for each token in the sequence, as well as a variation in splitting fragments into tokens to further feed into the input of a transform-based encoder. This approach allows us to achieve a 9% quality improvement relative to the baseline solution score on the development set (from 0.86 to 0.95) using the average macro F1-score, as well as a score of 0.96 on a closed test part of the dataset from the competition.

Pretrained transformer models, such as BERT and T5, have shown to be highly effective at ad-hoc passage and document ranking. Due to inherent sequence length limits of these models, they need to be run over a document's passages, rather than processing the entire document sequence at once. Although several approaches for aggregating passage-level signals have been proposed, there has yet to be an extensive comparison of these techniques. In this work, we explore strategies for aggregating relevance signals from a document's passages into a final ranking score. We find that passage representation aggregation techniques can significantly improve over techniques proposed in prior work, such as taking the maximum passage score. We call this new approach PARADE. In particular, PARADE can significantly improve results on collections with broad information needs where relevance signals can be spread throughout the document (such as TREC Robust04 and GOV2). Meanwhile, less complex aggregation techniques may work better on collections with an information need that can often be pinpointed to a single passage (such as TREC DL and TREC Genomics). We also conduct efficiency analyses, and highlight several strategies for improving transformer-based aggregation.

This paper introduces InstUPR, an unsupervised passage reranking method based on large language models (LLMs). Different from existing approaches that rely on extensive training with query-document pairs or retrieval-specific instructions, our method leverages the instruction-following capabilities of instruction-tuned LLMs for passage reranking without any additional fine-tuning. To achieve this, we introduce a soft score aggregation technique and employ pairwise reranking for unsupervised passage reranking. Experiments on the BEIR benchmark demonstrate that InstUPR outperforms unsupervised baselines as well as an instruction-tuned reranker, highlighting its effectiveness and superiority. Source code to reproduce all experiments is open-sourced at https://github.com/MiuLab/InstUPR

The rapid release of both language models and benchmarks makes it increasingly costly to evaluate every model on every dataset. In practice, models are often evaluated on different samples, making scores difficult to compare across studies. To address this, we propose a framework based on multidimensional Item Response Theory (IRT) that uses anchor items to calibrate new benchmarks to the evaluation suite while holding previously calibrated item parameters fixed. Our approach supports a realistic evaluation setting in which datasets are introduced over time and models are evaluated only on the datasets available at the time of evaluation, while a fixed anchor set for each dataset is used so that results from different evaluation periods can be compared directly. In large-scale experiments on more than 400 models, our framework predicts full-evaluation performance within 2-3 percentage points using only 100 anchor questions per dataset, with Spearman ρgeq 0.9 for ranking preservation, showing that it is possible to extend benchmark suites over time while preserving score comparability, at a constant evaluation cost per new dataset. Code available at https://github.com/eliyahabba/growing-pains

High-quality pre-training data is crutial for large language models, where quality captures factual reliability and semantic value, and diversity ensures broad coverage and distributional heterogeneity. Existing approaches typically rely on single or multiple-dimensional score-based selection. However, directly selecting top-scored data often degrades performance, and sampling from a broader range is required to recover results. The above non-monotonicity between dataset scores and downstream benchmark results reveals a fundamental bias: score-based methods collapse correlated dimensions, causing top-scored data to appear high-quality while systematically overlooking diversity. We argue that ensuring diversity requires decomposing correlated metrics into orthogonal feature dimensions, from which the top-scored data can be directly selected. Therefore, we proposed the Orthogonal Diversity-Aware Selection (ODiS) algorithm, which preserves both quality and diversity during data selection. First, ODiS evaluates data from multiple dimensions, covering language quality, knowledge quality, and comprehension difficulty. The multi-dimensional scores are then decorrelated via Principal Component Analysis (PCA), yielding orthogonal evaluation dimensions. For each dimension, a Roberta-based scorer is trained to regress the data onto PCA-projected scores, enabling scalable inference on large corpora. Finally, ODiS constructs the training dataset by selecting top-scored data within each orthogonal dimension, thereby ensuring both quality and diversity. Empirical results show that ODiS-selected data exhibit less than 2\% inter-dimension overlap, confirming orthogonality between dimensions. More importantly, models trained with ODiS-selected data significantly outperform other baselines on downstream benchmarks, highlighting the necessity of orthogonal, diversity-aware data selection for LLMs.

Large language models (LLMs) are currently applied to scientific paper evaluation by assigning an absolute score to each paper independently. However, since score scales vary across conferences, time periods, and evaluation criteria, models trained on absolute scores are prone to fitting narrow, context-specific rules rather than developing robust scholarly judgment. To overcome this limitation, we propose shifting paper evaluation from isolated scoring to collaborative ranking. In particular, we design Comparison-Native framework for Paper Evaluation (CNPE), integrating comparison into both data construction and model learning. We first propose a graph-based similarity ranking algorithm to facilitate the sampling of more informative and discriminative paper pairs from a collection. We then enhance relative quality judgment through supervised fine-tuning and reinforcement learning with comparison-based rewards. At inference, the model performs pairwise comparisons over sampled paper pairs and aggregates these preference signals into a global relative quality ranking. Experimental results demonstrate that our framework achieves an average relative improvement of 21.8\% over the strong baseline DeepReview-14B, while exhibiting robust generalization to five previously unseen datasets. https://github.com/ECNU-Text-Computing/ComparisonReview{Code}.

Despite significant progress in generative AI, comprehensive evaluation remains challenging because of the lack of effective metrics and standardized benchmarks. For instance, the widely-used CLIPScore measures the alignment between a (generated) image and text prompt, but it fails to produce reliable scores for complex prompts involving compositions of objects, attributes, and relations. One reason is that text encoders of CLIP can notoriously act as a "bag of words", conflating prompts such as "the horse is eating the grass" with "the grass is eating the horse". To address this, we introduce the VQAScore, which uses a visual-question-answering (VQA) model to produce an alignment score by computing the probability of a "Yes" answer to a simple "Does this figure show '{text}'?" question. Though simpler than prior art, VQAScore computed with off-the-shelf models produces state-of-the-art results across many (8) image-text alignment benchmarks. We also compute VQAScore with an in-house model that follows best practices in the literature. For example, we use a bidirectional image-question encoder that allows image embeddings to depend on the question being asked (and vice versa). Our in-house model, CLIP-FlanT5, outperforms even the strongest baselines that make use of the proprietary GPT-4V. Interestingly, although we train with only images, VQAScore can also align text with video and 3D models. VQAScore allows researchers to benchmark text-to-visual generation using complex texts that capture the compositional structure of real-world prompts. We introduce GenAI-Bench, a more challenging benchmark with 1,600 compositional text prompts that require parsing scenes, objects, attributes, relationships, and high-order reasoning like comparison and logic. GenAI-Bench also offers over 15,000 human ratings for leading image and video generation models such as Stable Diffusion, DALL-E 3, and Gen2.

Instruction tuning is critical for adapting large language models (LLMs) to downstream tasks, and recent studies have demonstrated that small amounts of human-curated data can outperform larger datasets, challenging traditional data scaling laws. While LLM-based data quality rating systems offer a cost-effective alternative to human annotation, they often suffer from inaccuracies and biases, even in powerful models like GPT-4. In this work, we introduce DS2, a Diversity-aware Score curation method for Data Selection. By systematically modeling error patterns through a score transition matrix, DS2 corrects LLM-based scores and promotes diversity in the selected data samples. Our approach shows that a curated subset (just 3.3% of the original dataset) outperforms full-scale datasets (300k samples) across various machine-alignment benchmarks, and matches or surpasses human-aligned datasets such as LIMA with the same sample size (1k samples). These findings challenge conventional data scaling assumptions, highlighting that redundant, low-quality samples can degrade performance and reaffirming that "more can be less."

Recent progress in large language models (LLMs) has showcased impressive proficiency in numerous Arabic natural language processing (NLP) applications. Nevertheless, their effectiveness in Arabic medical NLP domains has received limited investigation. This research examines the degree to which state-of-the-art LLMs demonstrate and articulate healthcare knowledge in Arabic, assessing their capabilities across a varied array of Arabic medical tasks. We benchmark several LLMs using a medical dataset proposed in the Arabic NLP AraHealthQA challenge in MedArabiQ2025 track. Various base LLMs were assessed on their ability to accurately provide correct answers from existing choices in multiple-choice questions (MCQs) and fill-in-the-blank scenarios. Additionally, we evaluated the capacity of LLMs in answering open-ended questions aligned with expert answers. Our results reveal significant variations in correct answer prediction accuracy and low variations in semantic alignment of generated answers, highlighting both the potential and limitations of current LLMs in Arabic clinical contexts. Our analysis shows that for MCQs task, the proposed majority voting solution, leveraging three base models (Gemini Flash 2.5, Gemini Pro 2.5, and GPT o3), outperforms others, achieving up to 77% accuracy and securing first place overall in the Arahealthqa 2025 shared task-track 2 (sub-task 1) challenge. Moreover, for the open-ended questions task, several LLMs were able to demonstrate excellent performance in terms of semantic alignment and achieve a maximum BERTScore of 86.44%.

Recent work pairs LLMs with evolutionary search to iteratively generate, modify, and select code using task-specific feedback. These systems have produced strong results in mathematical discovery and algorithm design, yet a fundamental question remains: what do they actually evolve? Progress is typically summarized by the best score a run reaches under a task-specific evaluator, but that score can reflect several different mechanisms: new algorithmic structure, re-tuning an existing strategy, recombining ideas already in the model's internal knowledge, or overfitting to the evaluator. Distinguishing these mechanisms requires inspecting the search process itself, not only its final outcome. We introduce EvoTrace, a dataset of evolutionary coding traces spanning four evolutionary frameworks, reasoning and non-reasoning models, and 16 tasks across mathematics and algorithm design. To analyze these traces, we develop EvoReplay, a replay-based methodology that reconstructs the local search states behind high-scoring solutions and tests controlled interventions, including adjusting constants, removing program components and substituting models or prompting contexts. We annotate every code edit in EvoTrace with one of nine recurring edit types using an LLM-as-judge pipeline validated against blind human re-annotation. Across EvoTrace, most score gains come from a small subset of these edit types. We further find a deterministic cycling pattern: about 30% of code lines added during search are byte-identical re-introductions of previously-deleted lines, present throughout nearly every run. These results show that benchmark gains in evolutionary coding agents can arise from qualitatively different mechanisms, only some of which correspond to new algorithmic structure. EvoTrace enables more diagnostic evaluation of evolutionary coding agents beyond final benchmark scores.

As of September 2023, ChatGPT correctly answers "what is 7+8" with 15, but when asked "7+8=15, True or False" it responds with "False". This inconsistency between generating and validating an answer is prevalent in language models (LMs) and erodes trust. In this paper, we propose a framework for measuring the consistency between generation and validation (which we call generator-validator consistency, or GV-consistency), finding that even GPT-4, a state-of-the-art LM, is GV-consistent only 76% of the time. To improve the consistency of LMs, we propose to finetune on the filtered generator and validator responses that are GV-consistent, and call this approach consistency fine-tuning. We find that this approach improves GV-consistency of Alpaca-30B from 60% to 93%, and the improvement extrapolates to unseen tasks and domains (e.g., GV-consistency for positive style transfers extrapolates to unseen styles like humor). In addition to improving consistency, consistency fine-tuning improves both generator quality and validator accuracy without using any labeled data. Evaluated across 6 tasks, including math questions, knowledge-intensive QA, and instruction following, our method improves the generator quality by 16% and the validator accuracy by 6.3% across all tasks.

The integration of large language models (LLMs) into medical practice holds transformative potential, yet their real-world clinical utility remains limited by critical alignment challenges: (1) a disconnect between static evaluation benchmarks and dynamic clinical cognitive needs, (2) difficulties in adapting to evolving, multi-source medical standards, and (3) the inability of conventional reward models to capture nuanced, multi-dimensional medical quality criteria. To address these gaps, we propose MR-RML (Multidimensional Rubric-oriented Reward Model Learning) via GPRC (Geometric Projection Reference Constraints), a novel alignment framework that integrates medical standards into a structured "Dimensions-Scenarios-Disciplines" matrix to guide data generation and model optimization. MR-RML introduces three core innovations: (1) a "Dimensions-Scenarios-Disciplines" medical standard system that embeds domain standards into the full training pipeline; (2) an independent multi-dimensional reward model that decomposes evaluation criteria, shifting from real-time rubric-based scoring to internalized reward modeling for improved consistency and cost-efficiency; (3) geometric projection reference constraints that transform medical cognitive logic into mathematical regularization, aligning scoring gradients with clinical reasoning and enabling synthetic data-driven training. Through extensive evaluations on the authoritative medical benchmark Healthbench, our method yields substantial performance gains over the base LLM Qwen-32B (45% on the full subset and 85% on Hard subset, respectively). It achieves a SOTA among open-source LLMs with scores of 62.7 (full subset) and 44.7 (hard subset), while also outperforming the majority of closed-source models.

Large language models (LLMs) have recently become the leading source of answers for users' questions online. Despite their ability to offer eloquent answers, their accuracy and reliability can pose a significant challenge. This is especially true for sensitive domains such as biomedicine, where there is a higher need for factually correct answers. This paper introduces a biomedical retrieval-augmented generation (RAG) system designed to enhance the reliability of generated responses. The system is based on a fine-tuned LLM for the referenced question-answering, where retrieved relevant abstracts from PubMed are passed to LLM's context as input through a prompt. Its output is an answer based on PubMed abstracts, where each statement is referenced accordingly, allowing the users to verify the answer. Our retrieval system achieves an absolute improvement of 23% compared to the PubMed search engine. Based on the manual evaluation on a small sample, our fine-tuned LLM component achieves comparable results to GPT-4 Turbo in referencing relevant abstracts. We make the dataset used to fine-tune the models and the fine-tuned models based on Mistral-7B-instruct-v0.1 and v0.2 publicly available.

This study investigates GPT-4's assessment of its performance in healthcare applications. A simple prompting technique was used to prompt the LLM with questions taken from the United States Medical Licensing Examination (USMLE) questionnaire and it was tasked to evaluate its confidence score before posing the question and after asking the question. The questionnaire was categorized into two groups-questions with feedback (WF) and questions with no feedback(NF) post-question. The model was asked to provide absolute and relative confidence scores before and after each question. The experimental findings were analyzed using statistical tools to study the variability of confidence in WF and NF groups. Additionally, a sequential analysis was conducted to observe the performance variation for the WF and NF groups. Results indicate that feedback influences relative confidence but doesn't consistently increase or decrease it. Understanding the performance of LLM is paramount in exploring its utility in sensitive areas like healthcare. This study contributes to the ongoing discourse on the reliability of AI, particularly of LLMs like GPT-4, within healthcare, offering insights into how feedback mechanisms might be optimized to enhance AI-assisted medical education and decision support.

Recent research has leveraged large language model multi-agent systems for complex problem-solving while trying to reduce the manual effort required to build them, driving the development of automated agent workflow optimization methods. However, existing methods remain inflexible due to representational limitations, a lack of adaptability, and poor scalability when relying on discrete optimization techniques. We address these challenges with ScoreFlow, a simple yet high-performance framework that leverages efficient gradient-based optimization in a continuous space. ScoreFlow incorporates Score-DPO, a novel variant of the direct preference optimization method that accounts for quantitative feedback. Across six benchmarks spanning question answering, coding, and mathematical reasoning, ScoreFlow achieves an 8.2% improvement over existing baselines. Moreover, it empowers smaller models to outperform larger ones with lower inference costs. Project: https://github.com/Gen-Verse/ScoreFlow

Large language models (LLMs) have made significant advancements in various natural language processing tasks, including question answering (QA) tasks. While incorporating new information with the retrieval of relevant passages is a promising way to improve QA with LLMs, the existing methods often require additional fine-tuning which becomes infeasible with recent LLMs. Augmenting retrieved passages via prompting has the potential to address this limitation, but this direction has been limitedly explored. To this end, we design a simple yet effective framework to enhance open-domain QA (ODQA) with LLMs, based on the summarized retrieval (SuRe). SuRe helps LLMs predict more accurate answers for a given question, which are well-supported by the summarized retrieval that could be viewed as an explicit rationale extracted from the retrieved passages. Specifically, SuRe first constructs summaries of the retrieved passages for each of the multiple answer candidates. Then, SuRe confirms the most plausible answer from the candidate set by evaluating the validity and ranking of the generated summaries. Experimental results on diverse ODQA benchmarks demonstrate the superiority of SuRe, with improvements of up to 4.6% in exact match (EM) and 4.0% in F1 score over standard prompting approaches. SuRe also can be integrated with a broad range of retrieval methods and LLMs. Finally, the generated summaries from SuRe show additional advantages to measure the importance of retrieved passages and serve as more preferred rationales by models and humans.

Researchers and developers increasingly rely on toxicity scoring to moderate generative language model outputs, in settings such as customer service, information retrieval, and content generation. However, toxicity scoring may render pertinent information inaccessible, rigidify or "value-lock" cultural norms, and prevent language reclamation processes, particularly for marginalized people. In this work, we extend the concept of algorithmic recourse to generative language models: we provide users a novel mechanism to achieve their desired prediction by dynamically setting thresholds for toxicity filtering. Users thereby exercise increased agency relative to interactions with the baseline system. A pilot study (n = 30) supports the potential of our proposed recourse mechanism, indicating improvements in usability compared to fixed-threshold toxicity-filtering of model outputs. Future work should explore the intersection of toxicity scoring, model controllability, user agency, and language reclamation processes -- particularly with regard to the bias that many communities encounter when interacting with generative language models.

Deep-learning based Automatic Essay Scoring (AES) systems are being actively used by states and language testing agencies alike to evaluate millions of candidates for life-changing decisions ranging from college applications to visa approvals. However, little research has been put to understand and interpret the black-box nature of deep-learning based scoring algorithms. Previous studies indicate that scoring models can be easily fooled. In this paper, we explore the reason behind their surprising adversarial brittleness. We utilize recent advances in interpretability to find the extent to which features such as coherence, content, vocabulary, and relevance are important for automated scoring mechanisms. We use this to investigate the oversensitivity i.e., large change in output score with a little change in input essay content) and overstability i.e., little change in output scores with large changes in input essay content) of AES. Our results indicate that autoscoring models, despite getting trained as "end-to-end" models with rich contextual embeddings such as BERT, behave like bag-of-words models. A few words determine the essay score without the requirement of any context making the model largely overstable. This is in stark contrast to recent probing studies on pre-trained representation learning models, which show that rich linguistic features such as parts-of-speech and morphology are encoded by them. Further, we also find that the models have learnt dataset biases, making them oversensitive. To deal with these issues, we propose detection-based protection models that can detect oversensitivity and overstability causing samples with high accuracies. We find that our proposed models are able to detect unusual attribution patterns and flag adversarial samples successfully.

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.

Social determinants of health (SDoH) have an important impact on patient outcomes but are incompletely collected from the electronic health records (EHR). This study researched the ability of large language models to extract SDoH from free text in EHRs, where they are most commonly documented, and explored the role of synthetic clinical text for improving the extraction of these scarcely documented, yet extremely valuable, clinical data. 800 patient notes were annotated for SDoH categories, and several transformer-based models were evaluated. The study also experimented with synthetic data generation and assessed for algorithmic bias. Our best-performing models were fine-tuned Flan-T5 XL (macro-F1 0.71) for any SDoH, and Flan-T5 XXL (macro-F1 0.70). The benefit of augmenting fine-tuning with synthetic data varied across model architecture and size, with smaller Flan-T5 models (base and large) showing the greatest improvements in performance (delta F1 +0.12 to +0.23). Model performance was similar on the in-hospital system dataset but worse on the MIMIC-III dataset. Our best-performing fine-tuned models outperformed zero- and few-shot performance of ChatGPT-family models for both tasks. These fine-tuned models were less likely than ChatGPT to change their prediction when race/ethnicity and gender descriptors were added to the text, suggesting less algorithmic bias (p<0.05). At the patient-level, our models identified 93.8% of patients with adverse SDoH, while ICD-10 codes captured 2.0%. Our method can effectively extracted SDoH information from clinic notes, performing better compare to GPT zero- and few-shot settings. These models could enhance real-world evidence on SDoH and aid in identifying patients needing social support.

Score-based generative models (SGMs) sample from a target distribution by iteratively transforming noise using the score function of the perturbed target. For any finite training set, this score function can be evaluated in closed form, but the resulting SGM memorizes its training data and does not generate novel samples. In practice, one approximates the score by training a neural network via score-matching. The error in this approximation promotes generalization, but neural SGMs are costly to train and sample, and the effective regularization this error provides is not well-understood theoretically. In this work, we instead explicitly smooth the closed-form score to obtain an SGM that generates novel samples without training. We analyze our model and propose an efficient nearest-neighbor-based estimator of its score function. Using this estimator, our method achieves competitive sampling times while running on consumer-grade CPUs.

There is a long history, as well as a recent explosion of interest, in statistical and generative modeling approaches based on score functions -- derivatives of the log-likelihood of a distribution. In seminal works, Hyv\"arinen proposed vanilla score matching as a way to learn distributions from data by computing an estimate of the score function of the underlying ground truth, and established connections between this method and established techniques like Contrastive Divergence and Pseudolikelihood estimation. It is by now well-known that vanilla score matching has significant difficulties learning multimodal distributions. Although there are various ways to overcome this difficulty, the following question has remained unanswered -- is there a natural way to sample multimodal distributions using just the vanilla score? Inspired by a long line of related experimental works, we prove that the Langevin diffusion with early stopping, initialized at the empirical distribution, and run on a score function estimated from data successfully generates natural multimodal distributions (mixtures of log-concave distributions).

Foundation models rely on large-scale web-crawled datasets, which frequently contain noisy data, biases, and irrelevant content. Existing data selection techniques typically use human heuristics, downstream evaluation datasets, or specialized scoring models, and can overlook samples' utility in the training process. Instead, we propose a new approach, Mimic Score, a data quality metric that uses a pretrained reference model as a guide to assess the usefulness of data samples for training a new model. It relies on the alignment between the gradient of the new model parameters and the vector pointing toward the reference model in weight space. Samples that misalign with this direction are considered low-value and can be filtered out. Motivated by the Mimic score, we develop Grad-Mimic, a data selection framework that identifies and prioritizes useful samples, automating the selection process to create effective filters. Empirically, using Mimic scores to guide model training results in consistent performance gains across six image datasets and enhances the performance of CLIP models. Moreover, Mimic scores and their associated filters improve upon existing filtering methods and offer accurate estimation of dataset quality.

Large Language Models (LLMs) rely on Human Preference Alignment (HPA) to ensure the generation of safe content. Due to the heavy cost associated with fine-tuning, fine-tuning-free methods have emerged, typically modifying LLM decoding with external auxiliary methods. However, these methods do not essentially enhance the LLM itself. In this paper, we rethink the derivation procedures of DPO, based on which we conversely build an instant scorer using the states of the LLM before and after In-context Learning (ICL). Accordingly, we propose a novel approach called In-Context Direct Preference Optimization (ICDPO). It enables LLMs to borrow the HPA capabilities from superior LLMs with ICL, generating well-aligned responses as estimated by the aforementioned instant scorer, thereby enhancing the final performance. ICDPO can be further enhanced with a two-stage retriever and an upgraded scorer, both offering benefits. Extensive experiments show its effectiveness, particularly in outperforming two fine-tuning-free baselines, and it exhibits competitiveness with SFT + LoRA. We also conduct detailed analyses to offer comprehensive insights into ICDPO.

Intelligent drug recommendation based on Electronic Health Records (EHRs) is critical for improving the quality and efficiency of clinical decision-making. By leveraging large-scale patient data, drug recommendation systems can assist physicians in selecting the most appropriate medications according to a patient's medical history, diagnoses, laboratory results, and comorbidities. Recent advances in large language models (LLMs) have shown remarkable capabilities in complex reasoning and medical text understanding, making them promising tools for drug recommendation tasks. However, the application of LLMs for Chinese clinical medication recommendation remains largely unexplored. In this work, we conduct a systematic investigation of LLM-based methodologies for Chinese discharge medication recommendation. We evaluate several representative LLM families (GLM, Llama, Qwen) under a unified methodological framework including zero-shot prompting, in-context learning, chain-of-thought prompting, and supervised fine-tuning using LoRA. We analyze model behavior across reasoning styles, error patterns, domain adaptation mechanisms, and robustness. Experimental results show that while supervised fine-tuning improves model performance, there remains substantial room for improvement, with the best model achieving the F1 score of 0.5648 and Jaccard score of 0.4477. Our findings highlight both the potential and limitations of LLMs for Chinese drug recommendation.

Common evaluation paradigms for language models focus on scoring single responses through accuracy metrics or proper scoring rules, failing to capture the full richness of a model's belief state. Recent work illustrates that language models hallucinate in-part because they are optimised to be good test-takers under binary scoring schemes that reward any answer over abstention. While this insight naturally leads to penalty-based approaches, they ignore crucial distinctions in how models distribute uncertainty, for example between hedging toward incorrect answers versus hedging toward "I don't know" responses. A novel evaluation metric, the Distributional Correctness Score (DCS), is introduced to solve this problem, i.e., of not considering a model's entire probability distribution over answer choices. DCS naturally distinguishes between harmful overconfidence in wrong answers and uncertainty expressed through abstention, providing scores in an interpretable default range. Through theoretical analysis and illustrative examples, DCS is demonstrated to offer a more nuanced and aligned evaluation paradigm that incentivises models to express genuine uncertainty rather than guessing. Adapting 12 existing evaluation benchmarks to DCS's variants and measuring performance on six language models reveals that for half of the tested benchmarks scores are negative across all tested models, indicating significant tendencies towards hallucination.

In the expanding field of language model applications, medical knowledge representation remains a significant challenge due to the specialized nature of the domain. Large language models, such as GPT-4, obtain reasonable scores on medical question answering tasks, but smaller models are far behind. In this work, we introduce a method to improve the proficiency of a small language model in the medical domain by employing a two-fold approach. We first fine-tune the model on a corpus of medical textbooks. Then, we use GPT-4 to generate questions similar to the downstream task, prompted with textbook knowledge, and use them to fine-tune the model. Additionally, we introduce ECN-QA, a novel medical question answering dataset containing ``progressive questions'' composed of related sequential questions. We show the benefits of our training strategy on this dataset. The study's findings highlight the potential of small language models in the medical domain when appropriately fine-tuned. The code and weights are available at https://github.com/raidium-med/MQG.