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Rahul Thapa

Publications and source records attributed to Rahul Thapa.

At least 19 recordsLinked to original sources

Learning transferable human physiology from two million hours of sleep with SleepFM-2

Sleep provides a nightly window into health by capturing coordinated activity across the brain, heart, muscles and respiratory system. We introduce SleepFM-2, a sleep foundation model developed and evaluated on 282,511 polysomnography recordings from 26 cohorts, including 235,865 used for pretraining. These data span more than two million hours of multimodal physiology. Compared with SleepFM, SleepFM-2 improves disease prediction and sleep scoring, supports arousal, limb movement and respiratory event detection, and transfers to wearable sensing and subjective sleep phenotypes. A model combining its PSG representation with age, sex and BMI met a prespecified discrimination and significance criterion for 215 subsequently recorded EHR phenotypes in two held-out cohorts, including one health system unseen during pretraining. For 155 phenotypes, the PSG representation added reproducible information beyond demographics. SleepFM-2 also outperformed a 480-feature baseline derived from the same recordings. Its disease scores revealed a reproducible principal component associated with reduced sigma-band spatial coupling and increased hypnodensity entropy. The frozen encoder performed within the observed range of expert scorers for sleep events and transferred to wakeful EEG, headband and in-ear EEG, wrist PPG and wrist accelerometry. It improved sleep staging across six accelerometry cohorts and achieved disease-prediction performance in UK Biobank similar to models pretrained directly on accelerometry. Finally, SleepFM-2 captured aspects of subjective sleep not recovered by conventional PSG summaries, particularly reports of the recorded night. These results show that multimodal sleep physiology can provide a transferable representation of human health across diseases, clinical tasks, sensors and subjective experience.

cs.AI

Reconstruction: A Blind Benchmark for Recovering Research Ideas from Pre-Publication Bibliographies

Can a language model recover the true research idea of a published paper when given only that paper's pre-publication bibliography? We introduce Reconstruction, a blind idea-recovery benchmark that withholds the seed paper and all contemporaneous or future literature, and asks models to propose hypotheses that an independent large language model judge matches against the held-out ground-truth idea. A strict anti-leakage protocol-temporal citation cutoff, anonymous reference IDs, and frozen per-paper bibliographies, which prevents prompt-time leakage of the seed idea. Across six scientific domains and 643 evaluated papers, seven frontier models achieve only modest Match rates (approx. 3-15%). We then evaluate a reference-only multi-agent (top 4) pipeline that combines cross-model review with a Swiss tournament over aligned hypothesis slots, without external web search. Cross-model review plus tournament selection raises Match rates to approx. 23-42% across all six domains, which is an observed approx. 2.4x lift over the best single-model baseline. This draft reports the protocol, anti-leakage design, and current results as an arXiv timestamp.

cs.AI

How Do Agents Fail on AutoResearch: End-to-End Diagnostic Evaluation on 100 Real-World Frontier Research Tasks

AI has long assisted scientific research, but the rapid advance of LLMs and agentic scaffolds is reshaping the landscape; a single system can now carry whole-stage research from an initial hypothesis all the way to final published paper, which is a paradigm now referred to as AutoResearch. Existing evaluations reveal little about how these agents operate or where they break down. Tasks are narrowly-scoped, evaluation measures performance but not process, and failure diagnoses lack systematic coverage or artifact-level visibility. To address this gap, we introduce AutoResearchEval, featuring 100 tasks grounded in published frontier science across 7 scientific domains and the full research lifecycle, including ideation, retrieval, execution, analysis, writing, and review. Evaluating 8 harness-model combinations yields 800 autoresearch agent trajectories, with process-level annotation. We organize these insights into AutoResearch Failure Taxonomy or ARFT, a framework of 45 empirically-grounded failure patterns. To enable scalable fine-grained attribution, we leverage a human-calibrated agent-as-a-judge pipeline to inspect complete trajectories and intermediate artifacts. Failure patterns converge on a single overarching limitation, namely that current agents lack a metacognitive loop, which entails the ability to check what they produced against what they found, revise when it does not hold up, and question whether the path they took was sound. The same patterns recur across all 8 harness-model combinations, including the strongest models tested, locating the deficit at the model level rather than in any particular scaffold; whether orchestration-level interventions can close it is an open question this work does not test. We publicly release AutoResearchEval and ARFT to facilitate continued research and development in autonomous scientific discovery.

cs.CL

Agentic AI-enabled discovery across large-scale sleep physiology

Sleep occupies roughly one-third of human life, yet many aspects of its physiology remain poorly understood. Large polysomnography (PSG) datasets offer new opportunities to study sleep and its links to disease, but extracting insight from these recordings requires substantial expert effort and remains difficult for general-purpose AI systems. We developed AI Sleep Co-Scientist, an expert-guided environment in which human scientists direct specialist agents for hypothesis development, signal preprocessing, and statistical analysis, reviewing intermediate outputs. Each reported result is linked to the executable code that produced it. Across four cohorts of approximately 124,000 PSG recordings and more than 50 TB of raw signals, we conducted five case studies spanning how sleep physiology relates to future disease, how it distinguishes clinical phenotypes, and how sleep is organized and regulated. Diminished network-level physiological coupling during sleep was associated with incident Parkinson's disease (HR 1.48) and Alzheimer's disease (HR 1.38). A physiologically structured late-fusion sleep-age model outperformed an unconstrained early-fusion approach, and its age residual was associated with incident disease across multiple organ systems. Arousal dynamics characterized comorbid insomnia and sleep apnoea as an intermediate phenotype skewed towards obstructive sleep apnoea, distinguished by prolonged post-arousal wakefulness. Rapid eye movement (REM) bout duration tracked preceding non-REM sleep more closely than intervening wakefulness. Transient-oscillation analysis identified a fast-sigma deficit and excess centrofrontal theta activity in narcolepsy type 1. Together, these findings connect sleep to disease risk, clinical classification, and its own regulation, and show how agentic AI can support large-scale, multimodal discovery.

cs.MA

Mechanistic Interpretability of EEG Foundation Models via Sparse Autoencoders

EEG foundation models achieve state-of-the-art clinical performance, yet the internal computations driving their predictions remain opaque: a barrier to clinical trust. We apply TopK Sparse Autoencoders (SAEs) across three architecturally distinct EEG transformers: SleepFM, REVE, and LaBraM to extract sparse feature dictionaries from their embeddings. By grounding these features in a clinical taxonomy (abnormality, age, sex, and medication), we benchmark monosemanticity and entanglement across architectures. A single hyperparameter procedure, driven by an intrinsic dictionary health audit, transfers robustly across all three architectures. Via concept steering, we introduce a "target vs. off-target" probe area metric to quantify steering selectivity and reveal three operational regimes: selectively steerable, encoded but entangled, and non-encoded. This framework exposes critical representational failures: "wrecking-ball" interventions that collapse global model performance, and clinical entanglements, such as age-pathology confounding, where it is impossible to suppress one concept without corrupting the other. Finally, a spectral decoder maps these interventions back to the amplitude spectrum, translating latent manipulations into physiologically interpretable frequency signatures, such as pathological slow-wave suppression and $\alpha$-band restoration.

cs.LG

Pretraining on Sleep Data Improves non-Sleep Biosignal Tasks

Sleep foundation models have recently demonstrated strong performance on in-domain polysomnography tasks, including sleep staging, apnea detection, and disease risk prediction. In this work, we investigate whether sleep biosignals can serve as an effective pretraining distribution for learning representations that transfer beyond sleep to adjacent domains. Following sleep foundation models, we perform sleep-only multimodal contrastive pretraining (with a leave-one-out objective) and evaluate transfer to non-sleep EEG and ECG, two well-benchmarked biosignal modalities with heterogeneous datasets and clinically meaningful downstream tasks. Across eight downstream tasks spanning multiple EEG and ECG datasets, sleep pretraining consistently improves performance relative to training from scratch. Moreover, on several tasks, we achieve performance competitive with or surpassing prior specialized state-of-the-art and foundation models.

cs.LG

Structured Scaling of AI Discovery Across Diverse Scientific Domains

Scientific discovery often requires many cycles of proposing, testing, and refining candidate solutions. Language models can increasingly participate in these loops, but simply generating more attempts does not ensure progress: parallel searches may duplicate one another and iterative refinement may become trapped in poor directions. The central challenge is therefore not only to scale AI-driven discovery, but to structure that scaling so that evaluation signals compound over time. Here we introduce SimpleTES (Simple Test-time Evaluation-driven Scaling), a framework that focuses on the structured scaling of AI discovery loops, organizing evaluator queries across independent trajectories, iterative refinement, local candidate selection, and the selective reuse of evaluated histories. Drawing on structural features of scientific communities, SimpleTES uses a single open-source GPT-OSS model to establish new state-of-the-art solutions across 28 open-ended problems in diverse scientific domains ranging from quantum physics and astronomy to biology, AI, and mathematics. These include a 24.5% reduction in quantum circuit compilation overhead, up to 23% lower propulsive cost for deep-space trajectories, a 2.17x faster lasso-path solver, an 8.5% lower-error whole-brain neural-activity predictor, the fastest reported TriMul kernel, and new mathematical constructions beyond prior human or AI records. We further post-train the model for long-horizon discovery by assigning each attempt the final outcome of the trajectory it helped produce. This improves performance on both training and held-out mathematics problems, further advancing the frontier. Together, these results establish structured scaling as a general mechanism for advancing AI scientific discovery.

cs.LG

MedGemma 1.5 Technical Report

We introduce MedGemma 1.5 4B, the latest model in the MedGemma collection. MedGemma 1.5 expands on MedGemma 1 by integrating additional capabilities: high-dimensional medical imaging (CT/MRI volumes and histopathology whole slide images), anatomical localization via bounding boxes, multi-timepoint chest X-ray analysis, and improved medical document understanding (lab reports, electronic health records). We detail the innovations required to enable these modalities within a single architecture, including new training data, long-context 3D volume slicing, and whole-slide pathology sampling. Compared to MedGemma 1 4B, MedGemma 1.5 4B demonstrates significant gains in these new areas, improving 3D MRI condition classification accuracy by 11% and 3D CT condition classification by 3% (absolute improvements). In whole slide pathology imaging, MedGemma 1.5 4B achieves a 47% macro F1 gain. Additionally, it improves anatomical localization with a 35% increase in Intersection over Union on chest X-rays and achieves a 4% macro accuracy for longitudinal (multi-timepoint) chest x-ray analysis. Beyond its improved multimodal performance over MedGemma 1, MedGemma 1.5 improves on text-based clinical knowledge and reasoning, improving by 5% on MedQA accuracy and 22% on EHRQA accuracy. It also achieves an average of 18% macro F1 on 4 different lab report information extraction datasets (EHR Datasets 2, 3, 4, and Mendeley Clinical Laboratory Test Reports). Taken together, MedGemma 1.5 serves as a robust, open resource for the community, designed as an improved foundation on which developers can create the next generation of medical AI systems. Resources and tutorials for building upon MedGemma 1.5 can be found at https://goo.gle/medgemma.

cs.AI

Stanford Sleep Bench: Evaluating Polysomnography Pre-training Methods for Sleep Foundation Models

Polysomnography (PSG), the gold standard test for sleep analysis, generates vast amounts of multimodal clinical data, presenting an opportunity to leverage self-supervised representation learning (SSRL) for pre-training foundation models to enhance sleep analysis. However, progress in sleep foundation models is hindered by two key limitations: (1) the lack of a shared dataset and benchmark with diverse tasks for training and evaluation, and (2) the absence of a systematic evaluation of SSRL approaches across sleep-related tasks. To address these gaps, we introduce Stanford Sleep Bench, a large-scale PSG dataset comprising 17,467 recordings totaling over 163,000 hours from a major sleep clinic, including 13 clinical disease prediction tasks alongside canonical sleep-related tasks such as sleep staging, apnea diagnosis, and age estimation. We systematically evaluate SSRL pre-training methods on Stanford Sleep Bench, assessing downstream performance across four tasks: sleep staging, apnea diagnosis, age estimation, and disease and mortality prediction. Our results show that multiple pretraining methods achieve comparable performance for sleep staging, apnea diagnosis, and age estimation. However, for mortality and disease prediction, contrastive learning significantly outperforms other approaches while also converging faster during pretraining. To facilitate reproducibility and advance sleep research, we will release Stanford Sleep Bench along with pretrained model weights, training pipelines, and evaluation code.

cs.LG

Disentangling Reasoning and Knowledge in Medical Large Language Models

Medical reasoning in large language models (LLMs) aims to emulate clinicians' diagnostic thinking, but current benchmarks such as MedQA-USMLE, MedMCQA, and PubMedQA often mix reasoning with factual recall. We address this by separating 11 biomedical QA benchmarks into reasoning- and knowledge-focused subsets using a PubMedBERT classifier that reaches 81 percent accuracy, comparable to human performance. Our analysis shows that only 32.8 percent of questions require complex reasoning. We evaluate biomedical models (HuatuoGPT-o1, MedReason, m1) and general-domain models (DeepSeek-R1, o4-mini, Qwen3), finding consistent gaps between knowledge and reasoning performance. For example, HuatuoGPT-o1 scores 56.9 on knowledge but only 44.8 on reasoning. In adversarial tests where models are misled with incorrect initial reasoning, biomedical models degrade sharply, while larger or RL-trained general models show more robustness. To address this, we train BioMed-R1 using fine-tuning and reinforcement learning on reasoning-heavy examples. It achieves the strongest performance among similarly sized models. Further gains may come from incorporating clinical case reports and training with adversarial and backtracking scenarios.

cs.CL

MedCaseReasoning: Evaluating and learning diagnostic reasoning from clinical case reports

Doctors and patients alike increasingly use Large Language Models (LLMs) to diagnose clinical cases. However, unlike domains such as math or coding, where correctness can be objectively defined by the final answer, medical diagnosis requires both the outcome and the reasoning process to be accurate. Currently, widely used medical benchmarks like MedQA and MMLU assess only accuracy in the final answer, overlooking the quality and faithfulness of the clinical reasoning process. To address this limitation, we introduce MedCaseReasoning, the first open-access dataset for evaluating LLMs on their ability to align with clinician-authored diagnostic reasoning. The dataset includes 14,489 diagnostic question-and-answer cases, each paired with detailed reasoning statements derived from open-access medical case reports. We evaluate state-of-the-art reasoning LLMs on MedCaseReasoning and find significant shortcomings in their diagnoses and reasoning: for instance, the top-performing open-source model, DeepSeek-R1, achieves only 48% 10-shot diagnostic accuracy and mentions only 64% of the clinician reasoning statements (recall). However, we demonstrate that fine-tuning LLMs on the reasoning traces derived from MedCaseReasoning significantly improves diagnostic accuracy and clinical reasoning recall by an average relative gain of 29% and 41%, respectively. The open-source dataset, code, and models are available at https://github.com/kevinwu23/Stanford-MedCaseReasoning.

cs.CL

How Well Can General Vision-Language Models Learn Medicine By Watching Public Educational Videos?

Publicly available biomedical videos, such as those on YouTube, serve as valuable educational resources for medical students. Unlike standard machine learning datasets, these videos are designed for human learners, often mixing medical imagery with narration, explanatory diagrams, and contextual framing. In this work, we investigate whether such pedagogically rich, yet non-standardized and heterogeneous videos can effectively teach general-domain vision-language models biomedical knowledge. To this end, we introduce OpenBiomedVi, a biomedical video instruction tuning dataset comprising 1031 hours of video-caption and Q/A pairs, curated through a multi-step human-in-the-loop pipeline. Diverse biomedical video datasets are rare, and OpenBiomedVid fills an important gap by providing instruction-style supervision grounded in real-world educational content. Surprisingly, despite the informal and heterogeneous nature of these videos, the fine-tuned Qwen-2-VL models exhibit substantial performance improvements across most benchmarks. The 2B model achieves gains of 98.7% on video tasks, 71.2% on image tasks, and 0.2% on text tasks. The 7B model shows improvements of 37.09% on video and 11.2% on image tasks, with a slight degradation of 2.7% on text tasks compared to their respective base models. To address the lack of standardized biomedical video evaluation datasets, we also introduce two new expert curated benchmarks, MIMICEchoQA and SurgeryVideoQA. On these benchmarks, the 2B model achieves gains of 99.1% and 98.1%, while the 7B model shows gains of 22.5% and 52.1%, respectively, demonstrating the models' ability to generalize and perform biomedical video understanding on cleaner and more standardized datasets than those seen during training. These results suggest that educational videos created for human learning offer a surprisingly effective training signal for biomedical VLMs.

cs.CV

OctoTools: An Agentic Framework with Extensible Tools for Complex Reasoning

Solving complex reasoning tasks may involve visual understanding, domain knowledge retrieval, numerical calculation, and multi-step reasoning. Existing methods augment large language models (LLMs) with external tools but are restricted to specialized domains, limited tool types, or require additional training data. In this paper, we introduce OctoTools, a training-free, user-friendly, and easily extensible multi-agent framework designed to tackle complex reasoning across diverse domains. OctoTools introduces standardized tool cards to encapsulate tool functionality, a planner for both high-level and low-level planning, and an executor to carry out tool usage. We validate OctoTools' generality across 16 diverse tasks (including MathVista, MMLU-Pro, MedQA, and GAIA-Text), achieving substantial average accuracy gains of 9.3% over GPT-4o. Furthermore, OctoTools also outperforms AutoGen, GPT-Functions, and LangChain by up to 10.6% when given the same set of tools. Through comprehensive analysi, ablations, and robustness tests with compact backbones and noisy tool environments, OctoTools demonstrates advantages in task planning, effective tool usage, and multi-step problem solving. Code, demos, and visualization are publicly available at https://octotools.github.io/.

cs.LG

SMIR: Efficient Synthetic Data Pipeline To Improve Multi-Image Reasoning

Vision-Language Models (VLMs) excel at understanding single images, aided by high-quality instruction datasets. However, multi-image reasoning remains underexplored in the open-source community due to two key challenges: (1) scaling datasets with correlated images and complex reasoning instructions is resource-intensive, and (2) robust evaluation benchmarks for multi-image tasks are lacking. To address this, we introduce SMiR, a synthetic data-generation pipeline for multi-image reasoning, along with a high-quality dataset generated using this pipeline. SMiR efficiently extracts correlated images via multimodal embeddings, integrates visual and descriptive information, and leverages open-source LLMs to generate quality instructions. Using this approach, we produce 160K synthetic training samples, offering a cost-effective alternative to closed-source solutions. Additionally, we present SMiR-Bench, a multi-image reasoning benchmark comprising 200 diverse examples across seven complex reasoning tasks. SMiR-Bench is multi-turn and employs a VLM judge to evaluate free-form responses, providing a comprehensive assessment of model expressiveness and reasoning capability across modalities. We demonstrate the effectiveness of SMiR by fine-tuning open-source VLMs and evaluating them on SMiR-Bench.

cs.CV

Dragonfly: Multi-Resolution Zoom-In Encoding Enhances Vision-Language Models

Recent advances in vision-language models (VLMs) have demonstrated the advantages of processing images at higher resolutions and utilizing multi-crop features to preserve native resolution details. However, despite these improvements, existing vision transformers (ViTs) still struggle to capture fine-grained details from less prominent objects, charts, and embedded text, limiting their effectiveness in certain tasks. In this paper, we extend recent high-resolution and multi-crop techniques by not only preserving the native resolution, but zooming in beyond it and extracting features from a large number of image sub-crops. This enhancement allows our model to better capture fine-grained details, overcoming the limitations of current ViTs. To manage the increased token count and computational complexity, we demonstrate that a simple mean-pooling aggregation over tokens is effective. Our model, Dragonfly, achieves competitive performance on general-domain tasks such as ScienceQA and AI2D, and excels in tasks requiring fine-grained image understanding, including TextVQA and ChartQA. Among models in the 7-8B parameter range, Dragonfly consistently ranks at the top across ten general-domain benchmarks, achieving the highest or second-highest scores in most cases, outperforming models that are significantly larger or trained on larger datasets. Our biomedical model, Dragonfly-Med, sets new benchmarks on several medical tasks, achieving 91.6% accuracy on SLAKE (compared to 84.8% for Med-Gemini), a 67.1% token F1 score on Path-VQA (compared to 62.7% for Med-PaLM M), and state-of-the-art results across the majority of image captioning tasks. Overall, our work highlights the persistent challenge of engineering visual representations with fixed-resolution ViTs, and proposes a simple yet effective solution to address this issue and boost performance in both general and specialized domains.

cs.CV

SleepFM: Multi-modal Representation Learning for Sleep Across Brain Activity, ECG and Respiratory Signals

Sleep is a complex physiological process evaluated through various modalities recording electrical brain, cardiac, and respiratory activities. We curate a large polysomnography dataset from over 14,000 participants comprising over 100,000 hours of multi-modal sleep recordings. Leveraging this extensive dataset, we developed SleepFM, the first multi-modal foundation model for sleep analysis. We show that a novel leave-one-out approach for contrastive learning significantly improves downstream task performance compared to representations from standard pairwise contrastive learning. A logistic regression model trained on SleepFM's learned embeddings outperforms an end-to-end trained convolutional neural network (CNN) on sleep stage classification (macro AUROC 0.88 vs 0.72 and macro AUPRC 0.72 vs 0.48) and sleep disordered breathing detection (AUROC 0.85 vs 0.69 and AUPRC 0.77 vs 0.61). Notably, the learned embeddings achieve 48% top-1 average accuracy in retrieving the corresponding recording clips of other modalities from 90,000 candidates. This work demonstrates the value of holistic multi-modal sleep modeling to fully capture the richness of sleep recordings. SleepFM is open source and available at https://github.com/rthapa84/sleepfm-codebase.

cs.LG

Standing on FURM ground -- A framework for evaluating Fair, Useful, and Reliable AI Models in healthcare systems

The impact of using artificial intelligence (AI) to guide patient care or operational processes is an interplay of the AI model's output, the decision-making protocol based on that output, and the capacity of the stakeholders involved to take the necessary subsequent action. Estimating the effects of this interplay before deployment, and studying it in real time afterwards, are essential to bridge the chasm between AI model development and achievable benefit. To accomplish this, the Data Science team at Stanford Health Care has developed a Testing and Evaluation (T&E) mechanism to identify fair, useful and reliable AI models (FURM) by conducting an ethical review to identify potential value mismatches, simulations to estimate usefulness, financial projections to assess sustainability, as well as analyses to determine IT feasibility, design a deployment strategy, and recommend a prospective monitoring and evaluation plan. We report on FURM assessments done to evaluate six AI guided solutions for potential adoption, spanning clinical and operational settings, each with the potential to impact from several dozen to tens of thousands of patients each year. We describe the assessment process, summarize the six assessments, and share our framework to enable others to conduct similar assessments. Of the six solutions we assessed, two have moved into a planning and implementation phase. Our novel contributions - usefulness estimates by simulation, financial projections to quantify sustainability, and a process to do ethical assessments - as well as their underlying methods and open source tools, are available for other healthcare systems to conduct actionable evaluations of candidate AI solutions.

cs.CY

OpenMedLM: Prompt engineering can out-perform fine-tuning in medical question-answering with open-source large language models

LLMs have become increasingly capable at accomplishing a range of specialized-tasks and can be utilized to expand equitable access to medical knowledge. Most medical LLMs have involved extensive fine-tuning, leveraging specialized medical data and significant, thus costly, amounts of computational power. Many of the top performing LLMs are proprietary and their access is limited to very few research groups. However, open-source (OS) models represent a key area of growth for medical LLMs due to significant improvements in performance and an inherent ability to provide the transparency and compliance required in healthcare. We present OpenMedLM, a prompting platform which delivers state-of-the-art (SOTA) performance for OS LLMs on medical benchmarks. We evaluated a range of OS foundation LLMs (7B-70B) on four medical benchmarks (MedQA, MedMCQA, PubMedQA, MMLU medical-subset). We employed a series of prompting strategies, including zero-shot, few-shot, chain-of-thought (random selection and kNN selection), and ensemble/self-consistency voting. We found that OpenMedLM delivers OS SOTA results on three common medical LLM benchmarks, surpassing the previous best performing OS models that leveraged computationally costly extensive fine-tuning. The model delivers a 72.6% accuracy on the MedQA benchmark, outperforming the previous SOTA by 2.4%, and achieves 81.7% accuracy on the MMLU medical-subset, establishing itself as the first OS LLM to surpass 80% accuracy on this benchmark. Our results highlight medical-specific emergent properties in OS LLMs which have not yet been documented to date elsewhere, and showcase the benefits of further leveraging prompt engineering to improve the performance of accessible LLMs for medical applications.

cs.CL