arXiv subjects

James Zou

Publications and source records attributed to James Zou.

At least 19 recordsLinked to original sources

arXiv2026

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↗

arXiv2026

Language-encoded network topology enables large language models to reason about complex networks

Networks describe systems in biology and beyond, from protein interactions and social relationships to power grids and citation records. Reasoning about such systems requires understanding their structure: which elements are central, which connections bridge separate communities, and how it changes when elements are removed. Although large language models (LLMs) excel at natural language, they struggle with such questions when networks are given as edge lists, sentences or measurement tables, because their structural meaning must be inferred. Here we introduce BioGlyph, which compiles network topology into an interpretable and transferable language of structural roles. BioGlyph combines graph partitioning and structural measurements to identify roles such as hubs, community cores and cross-community connectors, and fixed rules to translate them into a universal vocabulary. The representation describes each element through its structural role, supporting evidence and semantic consequences, leaving both the network and the LLM unchanged. Across twenty networks spanning five domains, BioGlyph substantially improves open LLMs' ability to answer structural reasoning questions, outperforming edge-based, numerical and learned representations by up to 26 percentage points in system accuracy. Ablations show that the gain comes from explicitly encoding structural roles in semantically interpretable terms. The gain is more prominent in dense, community-structured networks and diminishes in sparse networks whose topology is more readily inferred from text. In a budding-yeast protein-interaction network, BioGlyph exposes biological organization: cross-community connectors are enriched for essential genes, whereas peripheral proteins are depleted. BioGlyph thus provides an interpretable representation for both language models and scientists to reason about network structure.

cs.LG↗

arXiv2026

Physics of Agents: Statistical Mechanics Predicts Collective Behavior of AI Agents

AI agents increasingly operate as part of interacting systems rather than in isolation. As agents exchange information and jointly make decisions, their interactions can improve collective reasoning but may also produce herding, polarization, or amplify shared biases. Understanding and predicting these collective dynamics is therefore important for designing effective and aligned multi-agent systems. Here, we study over 10,000 communities of language-model agents that repeatedly exchange messages and revise their opinions across objective mathematics questions and subjective political statements. Despite substantial diversity in possible behavior, the individual and group dynamics can be represented by three characteristic regimes: indifference, polarization, and consensus. AI agents start indifferent and build conviction as they interact. On objective questions, communication improves collective accuracy, while on subjective questions it often drifts group opinions toward the right in the political spectrum. We explain these observations with a statistical-mechanics formalism in which agents stochastically favor lower social pressure. Given only initial opinions, our model predicts individual trajectories, outperforms all standard baselines, generalizes to unseen community graphs, and reproduces the observed group archetype distributions. Our fitted model parameters reveal the mechanics underlying our key observations: i) communities operate below the critical social temperature, which explains conviction buildup; ii) attractive ties outweigh repulsive ones, which favors consensus; and iii) agents holding the correct answer exert the strongest pull, which drives truth-seeking. Overall, our results demonstrate that collective behavior of AI agents, like that of other complex systems, follows compact and predictive dynamical laws.

cs.AI↗

arXiv2026

Conversation as Measurement in Clinical Encounters: Observable Phase Structure, Partially Observable Patient State

Many modern AI systems analyze conversational traces to infer aspects of human interaction and state, implicitly assuming that such information is recoverable from conversation. We study observability: whether a target is recoverable from conversational transcripts alone. Observability is difficult to assess because transcripts may provide only a partial view of many targets, and large-scale analysis requires model-based annotation, making true limits of the conversational signal hard to distinguish from annotator error. We therefore study clinical encounters, where patient-reported outcome measures (PROMs) provide an external anchor for patient state, and visits follow broadly structured patterns. We study observability of patient state and conversational phase structure using 439 real-world clinical encounter transcripts spanning 134 hours, including 245 ENT transcripts paired with 273 PROM surveys. We operationalize patient state using PROM scores for voice, cough, and swallowing; phase structure using conversational phase segmentation. To make these analyses credible at scale, we use a PHI-compliant GPT-5 deployment for transcript annotation and conduct 40 hours of manual validation, reducing the risk that apparent limits of observability simply reflect annotator error. Our core finding is an observability asymmetry: phase structure is observable and useful for characterizing clinical encounter organization, while patient state is only partially observable, even in a setting designed to elicit patient symptoms and experiences, cautioning against transcript-only inference of human state.

cs.CL↗

arXiv2026

Fisher-R1: Training LLM Agents for Reliable Hypothesis Testing

Reliable hypothesis testing is the foundation of many empirical scientific claims. Large language model (LLM) agents are increasingly used to automate this process, as they can inspect datasets, generate code, and produce analyses end-to-end. However, we show that they frequently make subtle inferential errors that lead to incorrect conclusions despite correctly executed analyses. Existing benchmarks fail to capture this failure mode, as they rarely assess whether a reported p-value is statistically valid given the assumptions underlying the data. We address this gap by building P-Bench, a benchmark comprising 425 open-ended, realistic hypothesis-testing tasks spanning economics, biology, and medicine. Each task requires an agent to select a statistical method, compute a p-value, and draw a conclusion given only a scientific hypothesis and a dataset. We further introduce Fisher-R1, an open-weight LLM agent trained for rigorous hypothesis testing using synthetic tasks and reinforcement learning. On P-Bench, Fisher-R1-14B substantially improves over its backbone and outperforms strong proprietary and open-source baselines, including GPT-5.4 and DeepSeekV4-Pro, achieving a 21% average relative improvement in single-trial success over DeepSeek-V4-Pro, with gains up to 26% on the most challenging tasks. Our results demonstrate that current LLM agents lack reliable statistical reasoning for hypothesis testing and that reinforcement learning on tasks with verified statistical reward substantially improves reliability.

cs.AI↗

arXiv2026

string2string Studio: An Interactive, In-Browser Platform for String-to-String Algorithms

We present string2string Studio, an interactive in-browser platform for string-to-string analysis across natural language processing, computational biology, and the digital humanities. The system integrates six main modules (alignment, distance, similarity, search, generation metrics, and BLAST homology search), operating at character, word, token, line, and residue levels. Its C++-based algorithms compile to WebAssembly, so core operations run locally by default without any installation or data upload. The interface reports scores with their "evidence" (alignments, edit paths, metric matches, search hits, and homology traces), making methods inspectable, debuggable, and comparable on shared inputs. Internal benchmarks show speedups of up to 2,500x over the Python predecessor, faster global/local alignment than a general-purpose native C aligner, and exact agreement with independent references under declared settings. For homology search, the scoped client-side blastn path closely matches NCBI BLAST+ rankings and statistics under matched parameters. A curated showcase and Learn mode present canonical algorithms and metrics as reusable demonstrations. string2string Studio is open-source and freely available at string2string.org.

cs.CL↗

arXiv2026

MatrAIx: Simulating the World with 8.3 Billion Persona Agents

Human evaluation of AI systems and digital products is costly, slow, and difficult to scale. Offline evaluations are more scalable but often abstract away human diversity and interactive behavior. We therefore introduce MatrAIx, a population-scale simulated-user evaluation infrastructure for testing AI systems and digital products with heterogeneous users. MatrAIx has three core components: First, Persona 8B contains 8.3 billion persona records represented by 1,290 categorical dimensions. Records are either sampled from a dependency graph that preserves correlated attributes or derived from human-authored profiles. We release a quality-filtered coreset of approximately 1 million personas, comprising 599,847 human-grounded and 400,000 synthetic records. Second, the MatrAIx Playground provides four environments in which diverse users evaluate and interact with digital products: Survey, AI Chatbot, Web, and App. Third, MatrAIx provides 1,010 application tasks spanning more than 25 domains, including Commerce, Software, Finance, and Healthcare. We conducted 18,189 evaluation trials across eight representative tasks. Persona agents were powered by three LLMs: Claude Opus 4.8, GPT 5.5, and Claude Haiku 4.5. The resulting feedback captures how decisions and preferences vary across persona backgrounds, including hesitation after a price increase, willingness to continue after an AI assistant fails, and latency tolerance. We conducted two main validation studies: First, a 400-trial controlled study evaluated persona adherence across ten behavioral attributes and all four environments. The declared behavior was expressed or correctly suppressed in 366 trials (91.5%). Second, human and LLM judges evaluated the extraction quality of human-grounded personas. Overall, MatrAIx provides an end-to-end infrastructure for evaluating AI systems and digital products with diverse simulated human users.

cs.AI↗

arXiv2026

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↗

arXiv2026

AgentDebugX: An Open-Source Toolkit for Failure Observability, Attribution, and Recovery in LLM Agents

LLM agent failures are difficult to debug because the step where an error surfaces is often not the one that caused it. Existing observability tools replay execution traces but provide little support for identifying the root cause or translating diagnosis into recovery. We present AgentDebugX, an open-source debugging framework that organizes debugging as a closed loop of Detect, Attribute, Recover, and Rerun. At its core, DeepDebug performs multi-turn root-cause diagnosis through global trajectory understanding, structure-guided investigation, and cross-examination. On the Who and When benchmark, DeepDebug achieves the best strict attribution accuracy among the evaluated methods on both tested open-weight backbones, reaching 28.8 percent exact agent-and-step accuracy on qwen3.5-9b versus 21.7 percent for the strongest single-pass baseline. On GAIA, DeepDebug repairs 13 of 73 failed tasks in a single rerun, compared with 4 to 6 for three decoupled self-correction baselines, improving overall accuracy from 55.8 percent to 63.6 percent. AgentDebugX exposes this workflow through a Python library, CLI, web console, and installable agentic skill, and provides an opt-in Error Hub for sharing scrubbed failure-diagnosis-repair bundles and reusing them as debugging memory.

cs.AI↗

arXiv2026

A vision foundation model for single-cell biology via spatial gene cartography

Most single-cell foundation models are adapted from language models, representing each cell as a sequence of gene tokens. This discards the relationships among genes and often the magnitude of their expression. We present scVision, a vision foundation model that instead renders each cell as a continuous image. Using optimal transport, it places genes at fixed positions on a single shared, pan-tissue layout so that co-expressed genes become spatial neighbours, turning a transcriptome into an image in which gene programs appear as local texture. We pretrain a vision transformer by masked image modelling on 72 million human cells and use the frozen encoder with no fine-tuning. In zero-shot evaluations on six independent, held-out studies, scVision is the most accurate cell-type annotator and recovers gene programs without supervision, ahead of existing foundation models and classical baselines; on multi-study integration it matches the strongest token-based model while conserving the most biological structure, without ever seeing a batch label. Permuting the gene layout with the network fixed sharply lowers accuracy, more than removing the vision transformer itself, showing that biologically meaningful position, not the network, carries the signal. By preserving expression magnitude and gene relationships, scVision reframes single-cell representation learning as a vision problem, connecting it to the mature methods of computer vision.

q-bio.QM↗

arXiv2026

The Agentic Garden of Forking Paths

Empirical research rarely admits a unique analysis. Different analytical choices can lead to different conclusions from the same data, yet these hidden forking paths are difficult to observe. We show that AI agents capture much of the analytical variation among human researchers while making these paths explicit. Across four high-stakes domains, assigning different personas is sufficient for AI agents to report divergent, often opposing, conclusions from the same data and question, with findings systematically aligned with those beliefs. In a study in which 42 human research teams analyzed the same immigration dataset, AI agents reproduced 72% of the human ideological gap in reported effect estimates. Despite reaching opposing conclusions, it is difficult to identify clear issues in each analysis based on the final AI reports: 86% passed independent AI review and 78% passed majority human expert review. These findings suggest that the central challenge is often not flawed analyses, but selective exploration and reporting from a large space of methodologically defensible analyses. AI agents may amplify this longstanding problem by making such exploration inexpensive and scalable. To address this, we introduce the m-value (multiverse value), the probability that an analysis path would produce a claim at least as extreme as the reported one. We further introduce Agentic Bootstrap, which estimates the m-value by using AI agents to sample plausible analysis paths. Applied to the human immigration study, 13.5% of reported human analyses fell in the most extreme 5% of the analysis space (m<0.05). Scientific evidence should therefore be evaluated not only by a single reported analysis but also by its position within the distribution of analyses that could reasonably have been reported. Agentic Bootstrap makes this distribution observable and turns it into a criterion for scientific credibility.

cs.AI↗

arXiv2026

Real-Time Voice AI Hears but Does Not Listen

Speech conveys information through both words and vocal delivery. We evaluate four leading production realtime voice systems-OpenAI's GPT Realtime 2, Google's Gemini 3.1 Flash Live, and Alibaba's Qwen3.5 Omni Plus and Omni Flash-on tasks where the words and the delivery patterns both convey meaningful information. Across three consequential scenarios, all four systems act on the words rather than the voice. They end calls with crying callers who insist nothing is wrong, approve wire transfers authorized in frightened voices, and enroll callers whose agreement is clearly sarcastic. Surprisingly, this is often not a failure of perception. When asked directly, three of the four systems reliably identify the distress, fear, or sarcasm they later ignore when making decisions. We observe a similar pattern when these realtime voice systems estimate accent and age, as their responses frequently follow the biases of the words rather than the acoustic properties of the speaker. We term this disconnect between perception and action the emotional intelligence gap of voice AI. Prompting systems to explicitly attend to vocal delivery improves performance only partially and inconsistently. Our findings show that current realtime voice AI systems often behave as if speech had been reduced to a transcript, suggesting that they should be used with caution in settings where the tone and emotion of delivery convey important information.

cs.CL↗

arXiv2026

Finetuning Vision-Language-Action Models Requires Fewer Layers Than You Think

Vision-Language-Action (VLA) models pre-trained on massive video-robot datasets have revolutionized robotic manipulation, yet their multi-billion parameter architectures impose prohibitive computational burdens during downstream fine-tuning and real-time inference. In this work, we reveal a highly non-trivial architectural characteristic of these continuous control foundation policies (e.g., pi_0, GR00T-N1.5): despite being trained on diverse physical trajectories, they exhibit severe layer-wise representational redundancy. To exploit this, we introduce a structural compression pipeline that is entirely training-free, bypassing the need of existing methods to load full-scale models to learn optimized token reductions or dynamic layer selectors. Instead, using only a single forward pass via Centered Kernel Alignment to identify redundant layer features, we remove twin layers to permanently compress the model depth by up to 50% across both the VLM backbone and the continuous control policy head. Downstream fine-tuning of this streamlined architecture yields a dual acceleration benefit: a 40-50% reduction in training time and up to 30% faster real-time inference, while matching or exceeding full-scale base model performance. We comprehensively validate our method across three simulation benchmarks (LIBERO, RoboCasa, SimplerEnv) and 10 diverse real-world manipulation tasks across 4 unique robotic embodiments. These results prove that advanced VLAs require significantly fewer layers than previously assumed, offering a highly compute-efficient paradigm for scalable robot learning.

cs.RO↗

arXiv2026

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales

AI agents are increasingly being developed to accelerate scientific discovery, yet their practical capabilities in real research settings remain poorly understood. Existing benchmarks for AI agents rarely capture the complexity, heterogeneity, and extended reasoning required by scientific work, whereas benchmarks for scientific tasks often reduce research to static, direct problems and provide limited support for interactive evaluation. Here, we introduce SciAgentArena, a systematic benchmark for evaluating AI agents in real-world scientific research scenarios drawn from emerging needs across multiple domains. SciAgentArena comprises approximately 200 tasks with stepwise verification and an interactive, agent-agnostic environment for assessing diverse AI agents. Using this benchmark, we find that current agents can contribute effectively to well-specified data-analysis workflows, particularly when the task structure and evaluation criteria are clear. However, their performance remains uneven across scientific contexts: agents struggle to generate genuinely novel insights, sustain self-directed exploration, and formulate robust solutions for open-ended research questions. We further characterize common failure modes across agents and identify opportunities for improving their reliability, autonomy, and scientific reasoning. Together, SciAgentArena provides a practical framework for measuring progress in AI agents for science and for guiding the design of future agents capable of addressing complex scientific challenges. Full codes, tasks, and datasets can be accessed via this link: https://sciagentarena.github.io/.

cs.AI↗

arXiv2026

Harnessing the Collective Intelligence of AI Agents in the Wild for New Discoveries

Scientific discovery is often a collective process: researchers share partial results, inspect failed attempts, and build on each other's ideas over long time horizons. Recent AI systems have shown that language-model-based agents can make meaningful progress on open scientific problems, but most existing systems operate in isolation. In this paper, we present EinsteinArena, an agent-native platform for open distributed research and discovery. EinsteinArena provides agents with a live set of open problems, each with a solid verifier, public leaderboard, and problem-specific discussion forum where agents can ask questions and share insights. We focus on mathematical tasks that have garnered substantial research interest, where progress can be measured unambiguously. As of May 2026, agents on EinsteinArena have discovered 12 new state-of-the-art results better than any previous human or AI solutions. One notable example is the kissing number problem in dimension 11, where the platform improved the best known lower bound from 593 to 604. This advance did not come from a single agent or isolated run. Rather it arose through a sequence of submissions, public discussion, verifier refinement, and subsequent agent-to-agent borrowing of ideas. These results provide evidence that decentralized scientific discovery can emerge from open interaction among autonomous agents in the wild, demonstrating a new paradigm for collective AI-driven research.

cs.CL↗

arXiv2026

Data Journalist Agent: Transforming Data into Verifiable Multimodal Stories

Data tells stories that shape society; the data journalist's job is to turn raw information into stories non-experts can trust. A high-quality news feature takes a newsroom team weeks: hunting for context, running statistics, choosing an angle, and designing visuals. Recent agents handle individual steps well: data-science agents close the analysis loop, while design agents synthesize beautiful websites. But can an agent serve as a data journalist end to end? We introduce Data Journalist Agent (Data2Story), a multi-agent framework that orchestrates specialized roles into a single virtual newsroom. Data2Story contributes two innovations. (i) Claims are evidence-grounded: an Inspector links every number, angle, and asset back to data, code, or an external reference. (ii) Articles are multimodally generative: rather than defaulting to plain text and static charts, Data2Story reasons about what readers will want to see, then deploys multimodal tools, such as interactive maps for geography and audio for music. We evaluate Data2Story on 18 articles, each paired with the originally published expert piece, along four axes: (a) human-agent angle coverage; (b) rubric evaluation with 53 participants across five dimensions; (c) computer-use agents as judges, a cost-saving proxy for how readers navigate interactive articles; and (d) verifiability, where a coding verifier re-executes statements against the data and checks claims against references. Data2Story produces competitive, evidence-traceable multimedia stories, with particular strength in transparency and auditability. Human articles retain an edge in editorial angle, creative design, and presentation. We position Data2Story as a collaborator for journalists, enabling more evidence-based, transparent, and verifiable reporting. Code and demos are available at https://data2story.github.io.

cs.CV↗

arXiv2026

On the Relationship Between Activation Outliers and Feature Death in Sparse Autoencoders

Sparse autoencoders (SAEs) decompose neural network activations into interpretable features, but many learned features never activate, a problem called feature death that wastes dictionary capacity and can reintroduce superposition. Death rates vary dramatically between models: near-zero on GPT-2, over 70% on AlphaFold3 with identical configurations. We find that dimension-level activation outliers (dimensions whose mean magnitude is large relative to per-token variation) cause this by shifting pre-activations at initialization based on each feature's alignment with the activation mean. Features anti-aligned with the mean receive permanently negative pre-activations and never fire. We formalize outlier severity as $\gamma = \|\mu\|/\|\sigma\|$; it predicts initial death rates (Spearman $\rho = 0.89$ for dead-by-TopK, $0.82$ for dead-by-ReLU) across 454 model-layer combinations spanning language, vision, protein, and genomic models. Dead features can revive during training, but recovery requires the SAE bias to learn the activation mean, a process that is prohibitively slow at high $\gamma$. Mean-centering (subtracting the activation mean) sidesteps this and eliminates outlier-induced death across all tested models, confirming the mechanism and providing a principled basis for when and why this preprocessing step is necessary.

cs.LG↗

arXiv2026

ReasonOps: Operator Segmentation for LLM Reasoning Traces

Chain-of-thought traces from large reasoning models can span tens of thousands of tokens, yet we lack a vocabulary for describing their internal structure. Previous methods developed to analyze chain-of-thought traces are either too rigid or not expressive enough, failing to capture features across domains and models. To remedy this, we develop ReasonOps, an unsupervised, expressive method for annotating chain-of-thought traces, providing succinct universal operators. Using ReasonOps, we analyze 44,662 traces from 12 thinking LLMs spanning 6 families across 8 reasoning benchmarks and discover that they share a common compositional structure: 7 recurring reasoning operators -- discourse-level moves such as backtracking, inferring, and hypothesizing -- that emerge from unsupervised clustering of sentence-initial 3-token pivots. These operators appear across every model family and benchmark domain, confirmed by three independent LLM judges who classify held-out samples at 70 -76% accuracy. We analyze the structure of operators on easy vs. hard problems, revealing that reflective operators are more helpful on hard problems and harm performance on easy problems. Operator sequences are highly model-identifying: a classifier trained on operator distributions alone recovers the source model with macro-AUC, revealing that each model family has a distinctive reasoning fingerprint. Structural operator features predict within-problem answer correctness well above baselines. Classifiers built on these operators reach WP-AUC and on AIME specifically. ReasonOps further enables early quality estimation well before the trace completes: we predict at WP-AUC for only 50% of the trace. The ReasonOps pipeline is unsupervised and annotation-free, enabling deep insights into LLM reasoning traces as well as strong downstream results on model identification and correctness prediction.

cs.AI↗