arXiv:2601.13122v1 Announce Type: new Abstract: Modern general-purpose AI systems made using large language and vision models, are capable of performing a range of tasks like writing text articles, generating and debugging codes, querying databases, and translating from one language to another, which has made them quite popular across industries. However, there are risks like hallucinations, toxicity, and stereotypes in their output that make them untrustworthy. We review various risks and vulnerabilities of modern general-purpose AI along eight widely accepted responsible AI (RAI) principles (fairness, privacy, explainability, robustness, safety, truthfulness, governance, and sustainability) and compare how they are non-existent or less severe and easily mitigable in traditional task-specific counterparts. We argue that this is due to the non-deterministically high Degree of Freedom in output (DoFo) of general-purpose AI (unlike the deterministically constant or low DoFo of traditional task-specific AI systems), and there is a need to rethink our approach to RAI for general-purpose AI. Following this, we derive C2V2 (Control, Consistency, Value, Veracity) desiderata to meet the RAI requirements for future general-purpose AI systems, and discuss how recent efforts in AI alignment, retrieval-augmented generation, reasoning enhancements, etc. fare along one or more of the desiderata. We believe that the goal of developing responsible general-purpose AI can be achieved by formally modeling application- or domain-dependent RAI requirements along C2V2 dimensions, and taking a system design approach to suitably combine various techniques to meet the desiderata.

arXiv:2601.11560v1 Announce Type: cross Abstract: Biomedical knowledge graphs (KGs) encode vast, heterogeneous information spanning literature, genes, pathways, drugs, diseases, and clinical trials, but leveraging them collectively for scientific discovery remains difficult. Their structural differences, continual evolution, and limited cross-resource alignment require substantial manual integration, limiting the depth and scale of knowledge exploration. We introduce DeepEvidence, an AI-agent framework designed to perform Deep Research across various heterogeneous biomedical KGs. Unlike generic Deep Research systems that rely primarily on internet-scale text, DeepEvidence incorporates specialized knowledge-graph tooling and coordinated exploration strategies to systematically bridge heterogeneous resources. At its core is an orchestrator that directs two complementary agents: Breadth-First ReSearch (BFRS) for broad, multi-graph entity search, and Depth-First ReSearch (DFRS) for multi-hop, evidence-focused reasoning. An internal, incrementally built evidence graph provides a structured record of retrieved entities, relations, and supporting evidence. To operate at scale, DeepEvidence includes unified interfaces for querying diverse biomedical APIs and an execution sandbox that enables programmatic data retrieval, extraction, and analysis. Across established deep-reasoning benchmarks and four key stages of the biomedical discovery lifecycle: drug discovery, pre-clinical experimentation, clinical trial development, and evidence-based medicine, DeepEvidence demonstrates substantial gains in systematic exploration and evidence synthesis. These results highlight the potential of knowledge-graph-driven Deep Research to accelerate biomedical discovery.

arXiv:2601.12471v1 Announce Type: cross Abstract: Current evaluation of large language models (LLMs) overwhelmingly prioritizes accuracy; however, in real-world and safety-critical applications, the ability to abstain when uncertain is equally vital for trustworthy deployment. We introduce MedAbstain, a unified benchmark and evaluation protocol for abstention in medical multiple-choice question answering (MCQA) -- a discrete-choice setting that generalizes to agentic action selection -- integrating conformal prediction, adversarial question perturbations, and explicit abstention options. Our systematic evaluation of both open- and closed-source LLMs reveals that even state-of-the-art, high-accuracy models often fail to abstain with uncertain. Notably, providing explicit abstention options consistently increases model uncertainty and safer abstention, far more than input perturbations, while scaling model size or advanced prompting brings little improvement. These findings highlight the central role of abstention mechanisms for trustworthy LLM deployment and offer practical guidance for improving safety in high-stakes applications.

arXiv:2601.12607v1 Announce Type: cross Abstract: As Large Language Models (LLMs) become ubiquitous across various scientific domains, their lack of ability to perform complex tasks like running simulations or to make complex decisions limits their utility. LLM-based agents bridge this gap due to their ability to call external resources and tools and thus are now rapidly gaining popularity. However, coming up with a workflow that can balance the models, cloud providers, and external resources is very challenging, making implementing an agentic system more of a hindrance than a help. In this work, we present a domain-agnostic, model-independent workflow for an agentic framework that can act as a scientific assistant while being run entirely on cloud. Built with a supervisor agent marshaling an array of agents with individual capabilities, our framework brings together straightforward tasks like literature review and data analysis with more complex ones like simulation runs. We describe the framework here in full, including a proof-of-concept system we built to accelerate the study of Catalysts, which is highly important in the field of Chemistry and Material Science. We report the cost to operate and use this framework, including the breakdown of the cost by services use. We also evaluate our system on a custom-curated synthetic benchmark and a popular Chemistry benchmark, and also perform expert validation of the system. The results show that our system is able to route the task to the correct agent 90% of the time and successfully complete the assigned task 97.5% of the time for the synthetic tasks and 91% of the time for real-world tasks, while still achieving better or comparable accuracy to most frontier models, showing that this is a viable framework for other scientific domains to replicate.

arXiv:2601.12805v1 Announce Type: cross Abstract: Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, However, their ability to reliably reason from gene-level knowledge to functional understanding, a core requirement for knowledge-enhanced cell atlas interpretation, remains largely underexplored. To address this gap, we introduce SciHorizon-GENE, a large-scale gene-centric benchmark constructed from authoritative biological databases. The benchmark integrates curated knowledge for over 190K human genes and comprises more than 540K questions covering diverse gene-to-function reasoning scenarios relevant to cell type annotation, functional interpretation, and mechanism-oriented analysis. Motivated by behavioral patterns observed in preliminary examinations, SciHorizon-GENE evaluates LLMs along four biologically critical perspectives: research attention sensitivity, hallucination tendency, answer completeness, and literature influence, explicitly targeting failure modes that limit the safe adoption of LLMs in biological interpretation pipelines. We systematically evaluate a wide range of state-of-the-art general-purpose and biomedical LLMs, revealing substantial heterogeneity in gene-level reasoning capabilities and persistent challenges in generating faithful, complete, and literature-grounded functional interpretations. Our benchmark establishes a systematic foundation for analyzing LLM behavior at the gene scale and offers insights for model selection and development, with direct relevance to knowledge-enhanced biological interpretation.

arXiv:2601.12910v1 Announce Type: cross Abstract: We present SciCoQA, a dataset for detecting discrepancies between scientific publications and their codebases to ensure faithful implementations. We construct SciCoQA from GitHub issues and reproducibility papers, and to scale our dataset, we propose a synthetic data generation method for constructing paper-code discrepancies. We analyze the paper-code discrepancies in detail and propose discrepancy types and categories to better understand the occurring mismatches. In total, our dataset consists of 611 paper-code discrepancies (81 real, 530 synthetic), spanning diverse computational science disciplines, including AI, Physics, Quantitative Biology, and others. Our evaluation of 21 LLMs highlights the difficulty of SciCoQA, particularly for instances involving omitted paper details, long-context inputs, and data outside the models' pre-training corpus. The best performing model in our evaluation, GPT-5, can only detect 45.7\% of real-world paper-code discrepancies.

arXiv:2601.12946v1 Announce Type: cross Abstract: Generative artificial intelligence (AI) is rapidly populating medical records with synthetic content, creating a feedback loop where future models are increasingly at risk of training on uncurated AI-generated data. However, the clinical consequences of this AI-generated data contamination remain unexplored. Here, we show that in the absence of mandatory human verification, this self-referential cycle drives a rapid erosion of pathological variability and diagnostic reliability. By analysing more than 800,000 synthetic data points across clinical text generation, vision-language reporting, and medical image synthesis, we find that models progressively converge toward generic phenotypes regardless of the model architecture. Specifically, rare but critical findings, including pneumothorax and effusions, vanish from the synthetic content generated by AI models, while demographic representations skew heavily toward middle-aged male phenotypes. Crucially, this degradation is masked by false diagnostic confidence; models continue to issue reassuring reports while failing to detect life-threatening pathology, with false reassurance rates tripling to 40%. Blinded physician evaluation confirms that this decoupling of confidence and accuracy renders AI-generated documentation clinically useless after just two generations. We systematically evaluate three mitigation strategies, finding that while synthetic volume scaling fails to prevent collapse, mixing real data with quality-aware filtering effectively preserves diversity. Ultimately, our results suggest that without policy-mandated human oversight, the deployment of generative AI threatens to degrade the very healthcare data ecosystems it relies upon.

arXiv:2601.13564v1 Announce Type: cross Abstract: Designing fluorescent small molecules with tailored optical and physicochemical properties requires navigating vast, underexplored chemical space while satisfying multiple objectives and constraints. Conventional generate-score-screen approaches become impractical under such realistic design specifications, owing to their low search efficiency, unreliable generalizability of machine-learning prediction, and the prohibitive cost of quantum chemical calculation. Here we present LUMOS, a data-and-physics driven framework for inverse design of fluorescent molecules. LUMOS couples generator and predictor within a shared latent representation, enabling direct specification-to-molecule design and efficient exploration. Moreover, LUMOS combines neural networks with a fast time-dependent density functional theory (TD-DFT) calculation workflow to build a suite of complementary predictors spanning different trade-offs in speed, accuracy, and generalizability, enabling reliable property prediction across diverse scenarios. Finally, LUMOS employs a property-guided diffusion model integrated with multi-objective evolutionary algorithms, enabling de novo design and molecular optimization under multiple objectives and constraints. Across comprehensive benchmarks, LUMOS consistently outperforms baseline models in terms of accuracy, generalizability and physical plausibility for fluorescence property prediction, and demonstrates superior performance in multi-objective scaffold- and fragment-level molecular optimization. Further validation using TD-DFT and molecular dynamics (MD) simulations demonstrates that LUMOS can generate valid fluorophores that meet various target specifications. Overall, these results establish LUMOS as a data-physics dual-driven framework for general fluorophore inverse design.

arXiv:2601.13659v1 Announce Type: cross Abstract: Multimodal Sentiment Analysis integrates Linguistic, Visual, and Acoustic. Mainstream approaches based on modality-invariant and modality-specific factorization or on complex fusion still rely on spatiotemporal mixed modeling. This ignores spatiotemporal heterogeneity, leading to spatiotemporal information asymmetry and thus limited performance. Hence, we propose TSDA, Temporal-Spatial Decouple before Act, which explicitly decouples each modality into temporal dynamics and spatial structural context before any interaction. For every modality, a temporal encoder and a spatial encoder project signals into separate temporal and spatial body. Factor-Consistent Cross-Modal Alignment then aligns temporal features only with their temporal counterparts across modalities, and spatial features only with their spatial counterparts. Factor specific supervision and decorrelation regularization reduce cross factor leakage while preserving complementarity. A Gated Recouple module subsequently recouples the aligned streams for task. Extensive experiments show that TSDA outperforms baselines. Ablation analysis studies confirm the necessity and interpretability of the design.

arXiv:2601.13710v1 Announce Type: cross Abstract: Artificial intelligence has reshaped medical imaging, yet the use of AI on clinical data for prospective decision support remains limited. We study pre-operative prediction of clinically meaningful improvement in chronic rhinosinusitis (CRS), defining success as a more than 8.9-point reduction in SNOT-22 at 6 months (MCID). In a prospectively collected cohort where all patients underwent surgery, we ask whether models using only pre-operative clinical data could have identified those who would have poor outcomes, i.e. those who should have avoided surgery. We benchmark supervised ML (logistic regression, tree ensembles, and an in-house MLP) against generative AI (ChatGPT, Claude, Gemini, Perplexity), giving each the same structured inputs and constraining outputs to binary recommendations with confidence. Our best ML model (MLP) achieves 85 % accuracy with superior calibration and decision-curve net benefit. GenAI models underperform on discrimination and calibration across zero-shot setting. Notably, GenAI justifications align with clinician heuristics and the MLP's feature importance, repeatedly highlighting baseline SNOT-22, CT/endoscopy severity, polyp phenotype, and physchology/pain comorbidities. We provide a reproducible tabular-to-GenAI evaluation protocol and subgroup analyses. Findings support an ML-first, GenAI- augmented workflow: deploy calibrated ML for primary triage of surgical candidacy, with GenAI as an explainer to enhance transparency and shared decision-making.

arXiv:2510.23045v5 Announce Type: replace Abstract: Artificial intelligence is undergoing a profound transition from a computational instrument to an autonomous originator of scientific knowledge. This emerging paradigm, the AI scientist, is architected to emulate the complete scientific workflow-from initial hypothesis generation to the final synthesis of publishable findings-thereby promising to fundamentally reshape the pace and scale of discovery. However, the rapid and unstructured proliferation of these systems has created a fragmented research landscape, obscuring overarching methodological principles and developmental trends. This survey provides a systematic and comprehensive synthesis of this domain by introducing a unified, six-stage methodological framework that deconstructs the end-to-end scientific process into: Literature Review, Idea Generation, Experimental Preparation, Experimental Execution, Scientific Writing, and Paper Generation. Through this analytical lens, we chart the field's evolution from early Foundational Modules (2022-2023) to integrated Closed-Loop Systems (2024), and finally to the current frontier of Scalability, Impact, and Human-AI Collaboration (2025-present). By rigorously synthesizing these developments, this survey not only clarifies the current state of autonomous science but also provides a critical roadmap for overcoming remaining challenges in robustness and governance, ultimately guiding the next generation of systems toward becoming trustworthy and indispensable partners in human scientific inquiry.

arXiv:2410.00475v5 Announce Type: replace-cross Abstract: This paper presents a probabilistic approach to analyzing copyright infringement disputes. Evidentiary principles shaped by case law are formalized in probabilistic terms, and the ``inverse ratio rule'' -- a controversial legal doctrine adopted by some courts -- is examined. Although this rule has faced significant criticism, a formal proof demonstrates its validity, provided it is properly defined. The probabilistic approach is further employed to study the copyright safety of generative AI. Specifically, the Near Access-Free (NAF) condition, previously proposed as a strategy for mitigating the heightened copyright infringement risks of generative AI, is evaluated. The analysis reveals limitations in its justifiability and efficacy.

arXiv:2511.21755v2 Announce Type: replace-cross Abstract: The integration of generative artificial intelligence (GenAI) and large language models (LLMs) into scientific research and higher education presents a paradigm shift, offering revolutionizing opportunities while simultaneously raising profound ethical, legal, and regulatory questions. This study examines the complex intersection of AI and science, with a specific focus on the challenges posed to copyright law and the principles of open science. The author argues that current regulatory frameworks in key jurisdictions like the United States, China, the European Union, and the United Kingdom, while aiming to foster innovation, contain significant gaps, particularly concerning the use of copyrighted works and open science outputs for AI training. Widely adopted licensing mechanisms, such as Creative Commons, fail to adequately address the nuances of AI training, and the pervasive lack of attribution within AI systems fundamentally challenges established notions of originality. While current doctrine treats AI training as potentially fair use, this paper argues such mechanisms are inadequate and that copyright holders should retain explicit opt-out rights regardless of fair use doctrine. Instead, the author advocates for upholding authors' rights to refuse the use of their works for AI training and proposes that universities assume a leading role in shaping responsible AI governance. The conclusion is that a harmonized international legislative effort is urgently needed to ensure transparency, protect intellectual property, and prevent the emergence of an oligopolistic market structure that could prioritize commercial profit over scientific integrity and equitable knowledge production. This is a substantially expanded and revised version of a work originally presented at the 20th International Conference on Scientometrics & Informetrics (Kochetkov, 2025).

arXiv:2601.01576v2 Announce Type: replace-cross Abstract: Evaluating novelty is critical yet challenging in peer review, as reviewers must assess submissions against a vast, rapidly evolving literature. This report presents OpenNovelty, an LLM-powered agentic system for transparent, evidence-based novelty analysis. The system operates through four phases: (1) extracting the core task and contribution claims to generate retrieval queries; (2) retrieving relevant prior work based on extracted queries via semantic search engine; (3) constructing a hierarchical taxonomy of core-task-related work and performing contribution-level full-text comparisons against each contribution; and (4) synthesizing all analyses into a structured novelty report with explicit citations and evidence snippets. Unlike naive LLM-based approaches, \textsc{OpenNovelty} grounds all assessments in retrieved real papers, ensuring verifiable judgments. We deploy our system on 500+ ICLR 2026 submissions with all reports publicly available on our website, and preliminary analysis suggests it can identify relevant prior work, including closely related papers that authors may overlook. OpenNovelty aims to empower the research community with a scalable tool that promotes fair, consistent, and evidence-backed peer review.

arXiv:2601.02123v2 Announce Type: replace-cross Abstract: Large language models (LLMs) exhibit strong medical knowledge and can generate factually accurate responses. However, existing models often fail to account for individual patient contexts, producing answers that are clinically correct yet poorly aligned with patients' needs. In this work, we introduce DeCode, a training-free, model-agnostic framework that adapts existing LLMs to produce contextualized answers in clinical settings. We evaluate DeCode on OpenAI HealthBench, a comprehensive and challenging benchmark designed to assess clinical relevance and validity of LLM responses. DeCode improves the previous state of the art from $28.4\%$ to $49.8\%$, corresponding to a $75\%$ relative improvement. Experimental results suggest the effectiveness of DeCode in improving clinical question answering of LLMs.

Background: Given the global demographic shifts and rapid digitalization, digital engagement has emerged as a critical determinant of healthy aging. While previous research has linked digital engagement to cognitive outcomes, the underlying mechanisms remain underexplored among Chinese older adults. Objective: This study aimed to analyze the relationships between digital engagement and cognitive function among older adults in China through a moderated mediation model guided by the technological reserve hypothesis, with digital health literacy (DHL) and social support as mediators and living arrangements as a moderator. Methods: We conducted a cross-sectional questionnaire survey using stratified multistage sampling from June to November 2024, including 8123 participants aged 55 years and older. Digital engagement, defined as older adults’ use of contemporary digital technologies to support routine daily activities, autonomy, independence, and social inclusion, was assessed using a multidimensional questionnaire. The Chinese eHealth Literacy Scale, the 3-item short version of the Perceived Social Support Scale, and the Mini-Cog test were used to assess DHL, social support, and cognitive function. Guided by a directed acyclic graph based on the technological reserve hypothesis, mediation and moderated mediation analyses were performed using the PROCESS macro in SPSS (IBM Corp) with 5000 bootstrap resamples. Results: Digital engagement was positively associated with cognitive function among older adults (β=0.241, 95% CI 0.216-0.265). This association was partially mediated by DHL (β=0.059, 95% CI 0.049-0.069) and social support (β=0.012, 95% CI 0.008-0.016), with the combined indirect effects accounting for 29.5% of the total effect (β=0.071, 95% CI 0.061-0.082). Additionally, living arrangements significantly moderated the associations between digital engagement and cognitive function (β=0.109, 95% CI 0.052-0.166), digital engagement and DHL (β=0.063, 95% CI 0.014-0.112), and digital engagement and social support (β=0.151, 95% CI 0.089-0.212). These effects were stronger among older adults living alone. Conclusions: This study contributes to the understanding of cognitive aging in the digital environment from the perspective of the technological reserve hypothesis and digital engagement. Digital engagement influenced cognitive function via DHL and social support, and these associations of digital engagement with cognitive function, DHL, and social support were stronger among older adults living alone. Digital health interventions and public health policies should target both DHL and social support among older populations and prioritize older adults living alone.

npj Digital Medicine, Published online: 20 January 2026; doi:10.1038/s41746-025-02180-2

An artificial intelligence-powered learning health system to improve sepsis detection and quality of care: a before-and-after study

npj Digital Medicine, Published online: 20 January 2026; doi:10.1038/s41746-026-02337-7

Clinically-guided models or foundation models? predicting cervical spondylotic myelopathy from electronic health records