arXiv:2601.04577v1 Announce Type: new Abstract: While AI innovation accelerates rapidly, the intellectual process behind breakthroughs -- how researchers identify gaps, synthesize prior work, and generate insights -- remains poorly understood. The lack of structured data on scientific reasoning hinders systematic analysis and development of AI research agents. We introduce Sci-Reasoning, the first dataset capturing the intellectual synthesis behind high-quality AI research. Using community-validated quality signals and an LLM-accelerated, human-verified pipeline, we trace Oral and Spotlight papers across NeurIPS, ICML, and ICLR (2023-2025) to its key predecessors, articulating specific reasoning links in a structured format. Our analysis identifies 15 distinct thinking patterns, with three dominant strategies accounting for 52.7%: Gap-Driven Reframing (24.2%), Cross-Domain Synthesis (18.0%), and Representation Shift (10.5%). The most powerful innovation recipes combine multiple patterns: Gap-Driven Reframing + Representation Shift, Cross-Domain Synthesis + Representation Shift, and Gap-Driven Reframing + Cross-Domain Synthesis. This dataset enables quantitative studies of scientific progress and provides structured reasoning trajectories for training the next generation AI research agents.

arXiv:2601.04531v1 Announce Type: cross Abstract: Large Language Models (LLMs) have demonstrated significant potential in medical Question Answering (QA), yet they remain prone to hallucinations and ungrounded reasoning, limiting their reliability in high-stakes clinical scenarios. While Retrieval-Augmented Generation (RAG) mitigates these issues by incorporating external knowledge, conventional single-shot retrieval often fails to resolve complex biomedical queries requiring multi-step inference. To address this, we propose Self-MedRAG, a self-reflective hybrid framework designed to mimic the iterative hypothesis-verification process of clinical reasoning. Self-MedRAG integrates a hybrid retrieval strategy, combining sparse (BM25) and dense (Contriever) retrievers via Reciprocal Rank Fusion (RRF) to maximize evidence coverage. It employs a generator to produce answers with supporting rationales, which are then assessed by a lightweight self-reflection module using Natural Language Inference (NLI) or LLM-based verification. If the rationale lacks sufficient evidentiary support, the system autonomously reformulates the query and iterates to refine the context. We evaluated Self-MedRAG on the MedQA and PubMedQA benchmarks. The results demonstrate that our hybrid retrieval approach significantly outperforms single-retriever baselines. Furthermore, the inclusion of the self-reflective loop yielded substantial gains, increasing accuracy on MedQA from 80.00% to 83.33% and on PubMedQA from 69.10% to 79.82%. These findings confirm that integrating hybrid retrieval with iterative, evidence-based self-reflection effectively reduces unsupported claims and enhances the clinical reliability of LLM-based systems.

arXiv:2601.05148v1 Announce Type: cross Abstract: Pathology foundation models substantially advanced the possibilities in computational pathology -- yet tradeoffs in terms of performance, robustness, and computational requirements remained, which limited their clinical deployment. In this report, we present Atlas 2, Atlas 2-B, and Atlas 2-S, three pathology vision foundation models which bridge these shortcomings by showing state-of-the-art performance in prediction performance, robustness, and resource efficiency in a comprehensive evaluation across eighty public benchmarks. Our models were trained on the largest pathology foundation model dataset to date comprising 5.5 million histopathology whole slide images, collected from three medical institutions Charit\'e - Universt\"atsmedizin Berlin, LMU Munich, and Mayo Clinic.

arXiv:2512.00949v2 Announce Type: replace-cross Abstract: For patients undergoing systemic cancer therapy, the time between clinic visits is full of uncertainties and risks of unmonitored side effects. To bridge this gap in care, we developed and prospectively trialed a multi-modal AI framework for remote patient monitoring (RPM). This system integrates multi-modal data from the HALO-X platform, such as demographics, wearable sensors, daily surveys, and clinical events. Our observational trial is one of the largest of its kind and has collected over 2.1 million data points (6,080 patient-days) of monitoring from 84 patients. We developed and adapted a multi-modal AI model to handle the asynchronous and incomplete nature of real-world RPM data, forecasting a continuous risk of future adverse events. The model achieved an accuracy of 83.9% (AUROC=0.70). Notably, the model identified previous treatments, wellness check-ins, and daily maximum heart rate as key predictive features. A case study demonstrated the model's ability to provide early warnings by outputting escalating risk profiles prior to the event. This work establishes the feasibility of multi-modal AI RPM for cancer care and offers a path toward more proactive patient support.(Accepted at Europe NeurIPS 2025 Multimodal Representation Learning for Healthcare Workshop. Best Paper Poster Award.)

Background: Structured medication reviews (SMRs) are an essential component of medication optimization, especially for patients with multimorbidity and polypharmacy. However, the process remains challenging due to the complexities of patient data, time constraints, and the need for coordination among health care professionals (HCPs). This study explores HCPs’ perspectives on the integration of artificial intelligence (AI)–assisted tools to enhance the SMR process, with a focus on the potential benefits of and barriers to adoption. Objective: This study aims to identify the key user requirements for AI-assisted tools to improve the efficiency and effectiveness of SMRs, specifically for patients with multimorbidity, complex polypharmacy, and frailty. Methods: A qualitative study was conducted involving focus groups and semistructured interviews with HCPs and patients in the United Kingdom. Participants included physicians, pharmacists, clinical pharmacologists, psychiatrists from primary and secondary care, a policy maker, and patients with multimorbidity. Data were analyzed using a hybrid inductive and deductive thematic analysis approach to identify themes related to AI-assisted tool functionality, workflow integration, user-interface visualization, and usability in the SMR process. Results: Four major themes emerged from the analysis: innovative AI potential, optimizing electronic patient record visualization, functionality of the AI tool for SMRs, and facilitators of and barriers to AI tool implementation. HCPs identified the potential of AI to support patient identification and prioritizing those at risk of medication-related harm. AI-assisted tools were viewed as essential in detecting prescribing gaps, drug interactions, and patient risk trajectories over time. Participants emphasized the importance of presenting patient data in an intuitive format, with a patient interface for shared decision-making. Suggestions included color-coding blood results, highlighting critical medication reviews, and providing timelines of patient medical histories. HCPs stressed the need for AI tools to integrate seamlessly with existing electronic patient record systems and provide actionable insights without overwhelming users with excessive notifications or “pop-up” alerts. Factors influencing the uptake of AI-assisted tools included the need for user-friendly design, evidence of tool effectiveness (though some were skeptical about the predictive accuracy of AI models), and addressing concerns around digital exclusion. Conclusions: The findings highlight the potential for AI-assisted tools to streamline and optimize the SMR process, particularly for patients with multimorbidity and complex polypharmacy. However, successful implementation depends on addressing concerns related to workflow integration, user acceptance, and evidence of effectiveness. User-centered design is crucial to ensure that AI-assisted tools support HCPs in delivering high-quality, patient-centered care while minimizing cognitive overload and alert fatigue.

Background: The rapid growth of social media as an information channel has enabled the swift spread of inaccurate or false health information, significantly impacting public health. This widespread dissemination of misinformation has caused confusion, eroded trust in health authorities, led to noncompliance with health guidelines, and encouraged risky health behaviors. Understanding the dynamics of misinformation on social media is essential for devising effective public health communication strategies. Objective: This study aims to present a comprehensive and automated approach that leverages Large Language Models (LLMs) and Machine Learning (ML) techniques to detect misinformation on social media, uncover the underlying causes and themes, and generate refutation arguments, facilitating control of its spread and promoting public health outcomes by inoculating people against health misinformation. Methods: We use two datasets to train three LLMs, namely BERT, T5, and GPT-2, to classify documents into two categories: misinformation and non-misinformation. Additionally, we employ a separate dataset to identify misinformation topics. To analyze these topics, we applied three topic modeling algorithms—Latent Dirichlet Allocation (LDA), Top2Vec, and BERTopic—and selected the optimal model based on performance evaluated across three metrics. Using a prompting approach, we extract sentence-level representations for the topics to uncover their underlying themes. Finally, we design a prompt text capable of identifying misinformation themes effectively. Codes are available at https://github.com/SamiraMalek/MDIP-MDIS. Results: The trained BERT model demonstrated exceptional performance, achieving 98% accuracy in classifying misinformation and non-misinformation, with a 44% reduction in false positive rates for AI-generated misinformation. Among the three topic modeling approaches employed, BERTopic outperformed the others, achieving the highest metrics with a Coherence Value (CV) of 0.41, Normalized Pointwise Mutual Information (NPMI) of -0.086, and Inverted RBO (IRBO) of 0.99. To address the issue of unclassified documents, we developed an algorithm to assign each document to its closest topic. Additionally, we proposed a novel method using prompt engineering to generate sentence-level representations for each topic, achieving a 99.6% approval rate as "appropriate" or "somewhat appropriate" by three independent raters. We further designed a prompt text to identify themes of misinformation topics and developed another prompt capable of detecting misinformation themes with 82% accuracy. Conclusions: This study presents a comprehensive and automated approach to addressing health misinformation on social media using advanced machine learning and natural language processing techniques. By leveraging large language models (LLMs) and prompt engineering, the system effectively detects misinformation, identifies underlying themes, and provides explanatory responses to combat its spread. The proposed method was tested on an English-language COVID-19–related dataset and has not been evaluated on real-world online social media data; the experiments were conducted offline.

npj Digital Medicine, Published online: 07 January 2026; doi:10.1038/s41746-025-02324-4

An autonomous agentic workflow for clinical detection of cognitive concerns using large language models

arXiv:2601.01321v1 Announce Type: new Abstract: Digital twins, as precise digital representations of physical systems, have evolved from passive simulation tools into intelligent and autonomous entities through the integration of artificial intelligence technologies. This paper presents a unified four-stage framework that systematically characterizes AI integration across the digital twin lifecycle, spanning modeling, mirroring, intervention, and autonomous management. By synthesizing existing technologies and practices, we distill a unified four-stage framework that systematically characterizes how AI methodologies are embedded across the digital twin lifecycle: (1) modeling the physical twin through physics-based and physics-informed AI approaches, (2) mirroring the physical system into a digital twin with real-time synchronization, (3) intervening in the physical twin through predictive modeling, anomaly detection, and optimization strategies, and (4) achieving autonomous management through large language models, foundation models, and intelligent agents. We analyze the synergy between physics-based modeling and data-driven learning, highlighting the shift from traditional numerical solvers to physics-informed and foundation models for physical systems. Furthermore, we examine how generative AI technologies, including large language models and generative world models, transform digital twins into proactive and self-improving cognitive systems capable of reasoning, communication, and creative scenario generation. Through a cross-domain review spanning eleven application domains, including healthcare, aerospace, smart manufacturing, robotics, and smart cities, we identify common challenges related to scalability, explainability, and trustworthiness, and outline directions for responsible AI-driven digital twin systems.

arXiv:2601.01718v1 Announce Type: new Abstract: We introduce Yuan3.0 Flash, an open-source Mixture-of-Experts (MoE) MultiModal Large Language Model featuring 3.7B activated parameters and 40B total parameters, specifically designed to enhance performance on enterprise-oriented tasks while maintaining competitive capabilities on general-purpose tasks. To address the overthinking phenomenon commonly observed in Large Reasoning Models (LRMs), we propose Reflection-aware Adaptive Policy Optimization (RAPO), a novel RL training algorithm that effectively regulates overthinking behaviors. In enterprise-oriented tasks such as retrieval-augmented generation (RAG), complex table understanding, and summarization, Yuan3.0 Flash consistently achieves superior performance. Moreover, it also demonstrates strong reasoning capabilities in domains such as mathematics, science, etc., attaining accuracy comparable to frontier model while requiring only approximately 1/4 to 1/2 of the average tokens. Yuan3.0 Flash has been fully open-sourced to facilitate further research and real-world deployment: https://github.com/Yuan-lab-LLM/Yuan3.0.

arXiv:2601.02008v1 Announce Type: new Abstract: Explainability domain generalization and rare class reliability are critical challenges in medical AI where deep models often fail under real world distribution shifts and exhibit bias against infrequent clinical conditions This paper introduces XAIMeD an explainable medical AI framework that integrates clinically accurate expert knowledge into deep learning through a unified neuro symbolic architecture XAIMeD is designed to improve robustness under distribution shift enhance rare class sensitivity and deliver transparent clinically aligned interpretations The framework encodes clinical expertise as logical connectives over atomic medical propositions transforming them into machine checkable class specific rules Their diagnostic utility is quantified through weighted feature satisfaction scores enabling a symbolic reasoning branch that complements neural predictions A confidence weighted fusion integrates symbolic and deep outputs while a Hunt inspired adaptive routing mechanism guided by Entropy Imbalance Gain EIG and Rare Class Gini mitigates class imbalance high intra class variability and uncertainty We evaluate XAIMeD across diverse modalities on four challenging tasks i Seizure Onset Zone SOZ localization from rs fMRI ii Diabetic Retinopathy grading across 6 multicenter datasets demonstrate substantial performance improvements including 6 percent gains in cross domain generalization and a 10 percent improved rare class F1 score far outperforming state of the art deep learning baselines Ablation studies confirm that the clinically grounded symbolic components act as effective regularizers ensuring robustness to distribution shifts XAIMeD thus provides a principled clinically faithful and interpretable approach to multimodal medical AI.

arXiv:2601.00926v1 Announce Type: cross Abstract: Modern enterprise retrieval systems must handle short, underspecified queries such as ``foreign transaction fee refund'' and ``recent check status''. In these cases, semantic nuance and metadata matter but per-query large language model (LLM) re-ranking and manual labeling are costly. We present Metadata-Aware Cross-Model Alignment (MACA), which distills a calibrated metadata aware LLM re-ranker into a compact student retriever, avoiding online LLM calls. A metadata-aware prompt verifies the teacher's trustworthiness by checking consistency under permutations and robustness to paraphrases, then supplies listwise scores, hard negatives, and calibrated relevance margins. The student trains with MACA's MetaFusion objective, which combines a metadata conditioned ranking loss with a cross model margin loss so it learns to push the correct answer above semantically similar candidates with mismatched topic, sub-topic, or entity. On a proprietary consumer banking FAQ corpus and BankFAQs, the MACA teacher surpasses a MAFA baseline at Accuracy@1 by five points on the proprietary set and three points on BankFAQs. MACA students substantially outperform pretrained encoders; e.g., on the proprietary corpus MiniLM Accuracy@1 improves from 0.23 to 0.48, while keeping inference free of LLM calls and supporting retrieval-augmented generation.

arXiv:2601.01701v1 Announce Type: cross Abstract: Anomaly detection is increasingly becoming crucial for maintaining the safety, reliability, and efficiency of industrial systems. Recently, with the advent of digital twins and data-driven decision-making, several statistical and machine-learning methods have been proposed. However, these methods face several challenges, such as dependence on only real sensor datasets, limited labeled data, high false alarm rates, and privacy concerns. To address these problems, we propose a suite of digital twin-integrated federated learning (DTFL) methods that enhance global model performance while preserving data privacy and communication efficiency. Specifically, we present five novel approaches: Digital Twin-Based Meta-Learning (DTML), Federated Parameter Fusion (FPF), Layer-wise Parameter Exchange (LPE), Cyclic Weight Adaptation (CWA), and Digital Twin Knowledge Distillation (DTKD). Each method introduces a unique mechanism to combine synthetic and real-world knowledge, balancing generalization with communication overhead. We conduct an extensive experiment using a publicly available cyber-physical anomaly detection dataset. For a target accuracy of 80%, CWA reaches the target in 33 rounds, FPF in 41 rounds, LPE in 48 rounds, and DTML in 87 rounds, whereas the standard FedAvg baseline and DTKD do not reach the target within 100 rounds. These results highlight substantial communication-efficiency gains (up to 62% fewer rounds than DTML and 31% fewer than LPE) and demonstrate that integrating DT knowledge into FL accelerates convergence to operationally meaningful accuracy thresholds for IIoT anomaly detection.

arXiv:2508.17215v2 Announce Type: replace-cross Abstract: Large Vision-Language Models (LVLMs) augmented with Retrieval-Augmented Generation (RAG) are increasingly employed in medical AI to enhance factual grounding through external clinical image-text retrieval. However, this reliance creates a significant attack surface. We propose MedThreatRAG, a novel multimodal poisoning framework that systematically probes vulnerabilities in medical RAG systems by injecting adversarial image-text pairs. A key innovation of our approach is the construction of a simulated semi-open attack environment, mimicking real-world medical systems that permit periodic knowledge base updates via user or pipeline contributions. Within this setting, we introduce and emphasize Cross-Modal Conflict Injection (CMCI), which embeds subtle semantic contradictions between medical images and their paired reports. These mismatches degrade retrieval and generation by disrupting cross-modal alignment while remaining sufficiently plausible to evade conventional filters. While basic textual and visual attacks are included for completeness, CMCI demonstrates the most severe degradation. Evaluations on IU-Xray and MIMIC-CXR QA tasks show that MedThreatRAG reduces answer F1 scores by up to 27.66% and lowers LLaVA-Med-1.5 F1 rates to as low as 51.36%. Our findings expose fundamental security gaps in clinical RAG systems and highlight the urgent need for threat-aware design and robust multimodal consistency checks. Finally, we conclude with a concise set of guidelines to inform the safe development of future multimodal medical RAG systems.

arXiv:2512.14329v2 Announce Type: replace-cross Abstract: Dynamic prediction of locomotor capacity after stroke could enable more individualized rehabilitation, yet current assessments largely provide static impairment scores and do not indicate whether patients can perform specific tasks such as slope walking or stair climbing. Here, we present a wearable-informed data-physics hybrid generative framework that reconstructs a stroke survivor's locomotor control from wearable inertial sensing and predicts task-conditioned post-stroke locomotion in new environments. From a single 20 m level-ground walking trial recorded by five IMUs, the framework personalizes a physics-based digital avatar using a healthy-motion prior and hybrid imitation learning, generating dynamically feasible, patient-specific movements for inclined walking and stair negotiation. Across 11 stroke inpatients, predicted postures reached 82.2% similarity for slopes and 69.9% for stairs, substantially exceeding a physics-only baseline. In a multicentre pilot randomized study (n = 21; 28 days), access to scenario-specific locomotion predictions to support task selection and difficulty titration was associated with larger gains in Fugl-Meyer lower-extremity scores than standard care (mean change 6.0 vs 3.7 points; $p

Nature Medicine, Published online: 05 January 2026; doi:10.1038/s41591-025-04080-0

This multicenter study demonstrates use of dried and capillary blood as a minimally invasive, scalable approach for Alzheimer’s biomarker testing in research, with potential as a widely scalable population-based research approach, especially in resource-limited settings.

arXiv:2511.00094v2 Announce Type: replace-cross Abstract: Robotic systems have become integral to smart environments, enabling applications ranging from urban surveillance and automated agriculture to industrial automation. However, their effective operation in dynamic settings - such as smart cities and precision farming - is challenged by continuously evolving topographies and environmental conditions. Traditional control systems often struggle to adapt quickly, leading to inefficiencies or operational failures. To address this limitation, we propose a novel framework for autonomous and dynamic reconfiguration of robotic controllers using Digital Twin technology. Our approach leverages a virtual replica of the robot's operational environment to simulate and optimize movement trajectories in response to real-world changes. By recalculating paths and control parameters in the Digital Twin and deploying the updated code to the physical robot, our method ensures rapid and reliable adaptation without manual intervention. This work advances the integration of Digital Twins in robotics, offering a scalable solution for enhancing autonomy in smart, dynamic environments.

Nature Medicine, Published online: 02 January 2026; doi:10.1038/s41591-025-04043-5

Results of the phase 1/2 TACTOPS trial show that autologous T cell therapy targeting PRAME, SSX2, MAGEA4, Survivin and NY-ESO-1 in patients with pancreatic ductal adenocarcinoma is feasible and safe, and leads to encouraging clinical responses and evidence of antigen spreading in responders.

arXiv:2512.22470v1 Announce Type: new Abstract: The proliferation of Large Language Models (LLMs) has intensified concerns about manipulative or deceptive behaviors that can undermine user autonomy, trust, and well-being. Existing safety benchmarks predominantly rely on coarse binary labels and fail to capture the nuanced psychological and social mechanisms constituting manipulation. We introduce \textbf{DarkPatterns-LLM}, a comprehensive benchmark dataset and diagnostic framework for fine-grained assessment of manipulative content in LLM outputs across seven harm categories: Legal/Power, Psychological, Emotional, Physical, Autonomy, Economic, and Societal Harm. Our framework implements a four-layer analytical pipeline comprising Multi-Granular Detection (MGD), Multi-Scale Intent Analysis (MSIAN), Threat Harmonization Protocol (THP), and Deep Contextual Risk Alignment (DCRA). The dataset contains 401 meticulously curated examples with instruction-response pairs and expert annotations. Through evaluation of state-of-the-art models including GPT-4, Claude 3.5, and LLaMA-3-70B, we observe significant performance disparities (65.2\%--89.7\%) and consistent weaknesses in detecting autonomy-undermining patterns. DarkPatterns-LLM establishes the first standardized, multi-dimensional benchmark for manipulation detection in LLMs, offering actionable diagnostics toward more trustworthy AI systems.