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.

arXiv:2512.23508v1 Announce Type: new Abstract: How can we ensure that AI systems are aligned with human values and remain safe? We can study this problem through the frameworks of the AI assistance and the AI shutdown games. The AI assistance problem concerns designing an AI agent that helps a human to maximise their utility function(s). However, only the human knows these function(s); the AI assistant must learn them. The shutdown problem instead concerns designing AI agents that: shut down when a shutdown button is pressed; neither try to prevent nor cause the pressing of the shutdown button; and otherwise accomplish their task competently. In this paper, we show that addressing these challenges requires AI agents that can reason under uncertainty and handle both incomplete and non-Archimedean preferences.

arXiv:2512.22181v1 Announce Type: cross Abstract: Artificial intelligence (AI) is transforming cancer diagnosis and treatment. The intricate nature of this disease necessitates the collaboration of diverse stakeholders with varied expertise to ensure the effectiveness of cancer research. Despite its importance, forming effective interdisciplinary research teams remains challenging. Understanding and predicting collaboration patterns can help researchers, organizations, and policymakers optimize resources and foster impactful research. We examined co-authorship networks as a proxy for collaboration within AI-driven cancer research. Using 7,738 publications (2000-2017) from Scopus, we constructed 36 overlapping co-authorship networks representing new, persistent, and discontinued collaborations. We engineered both attribute-based and structure-based features and built four machine learning classifiers. Model interpretability was performed using Shapley Additive Explanations (SHAP). Random forest achieved the highest recall for all three types of examined collaborations. The discipline similarity score emerged as a crucial factor, positively affecting new and persistent patterns while negatively impacting discontinued collaborations. Additionally, high productivity and seniority were positively associated with discontinued links. Our findings can guide the formation of effective research teams, enhance interdisciplinary cooperation, and inform strategic policy decisions.

arXiv:2512.22385v1 Announce Type: cross Abstract: In this paper, we propose an LLM-Guided Exemplar Selection framework to address a key limitation in state-of-the-art Human Activity Recognition (HAR) methods: their reliance on large labeled datasets and purely geometric exemplar selection, which often fail to distinguish similar weara-ble sensor activities such as walking, walking upstairs, and walking downstairs. Our method incorporates semantic reasoning via an LLM-generated knowledge prior that captures feature importance, inter-class confusability, and exemplar budget multipliers, and uses it to guide exemplar scoring and selection. These priors are combined with margin-based validation cues, PageRank centrality, hubness penalization, and facility-location optimization to obtain a compact and informative set of exemplars. Evaluated on the UCI-HAR dataset under strict few-shot conditions, the framework achieves a macro F1-score of 88.78%, outperforming classical approaches such as random sampling, herding, and $k$-center. The results show that LLM-derived semantic priors, when integrated with structural and geometric cues, provide a stronger foundation for selecting representative sensor exemplars in few-shot wearable-sensor HAR.

arXiv:2512.23304v1 Announce Type: cross Abstract: Multimodal Large Language Models (LLMs) introduce an emerging paradigm for medical imaging by interpreting scans through the lens of extensive clinical knowledge, offering a transformative approach to disease classification. This study presents a critical comparison between two fundamentally different AI architectures: the specialized open-source agent MedGemma and the proprietary large multimodal model GPT-4 for diagnosing six different diseases. The MedGemma-4b-it model, fine-tuned using Low-Rank Adaptation (LoRA), demonstrated superior diagnostic capability by achieving a mean test accuracy of 80.37% compared to 69.58% for the untuned GPT-4. Furthermore, MedGemma exhibited notably higher sensitivity in high-stakes clinical tasks, such as cancer and pneumonia detection. Quantitative analysis via confusion matrices and classification reports provides comprehensive insights into model performance across all categories. These results emphasize that domain-specific fine-tuning is essential for minimizing hallucinations in clinical implementation, positioning MedGemma as a sophisticated tool for complex, evidence-based medical reasoning.

arXiv:2512.00127v2 Announce Type: replace-cross Abstract: Teaching language models to reason about code execution remains a fundamental challenge. While Chain-of-Thought (CoT) prompting has shown promise, current synthetic training data suffers from a critical weakness: the reasoning steps are often plausible-sounding explanations generated by teacher models, not verifiable accounts of what the code actually does. This creates a troubling failure mode where models learn to mimic superficially convincing but logically flawed reasoning patterns. We address this by grounding CoT generation directly in program execution traces. Our pipeline instruments code to capture its dynamic behavior, then narrates these execution traces into natural language and factually-grounded rationales that are verifiable by design. This execution-grounded approach ensures every reasoning step reflects what the program computes, eliminating logical hallucinations at the source. We evaluate our method on code reasoning tasks, code generation and explanation tasks from HumanEval. Models trained on our bi-directional trace-grounded data achieve substantial improvements on reasoning tasks, with gains of up to 30 points on output prediction and 28 points on input prediction over base models, alongside competitive explanation and code generation performance. https://github.ibm.com/IBM-Research-AI/Verified-Code-CoT

Cell Death Discovery, Published online: 29 December 2025; doi:10.1038/s41420-025-02917-8

Modeling hepatocellular carcinoma and its microenvironment on a chip

Many people use peer online forums to seek support for health-related problems. More research is needed to understand the impacts of forum use, and how these are generated. However, there are significant ethical and practical challenges with the methods available to do the required research. We examine the key challenges associated with conducting each of the most commonly used online data collection methods: surveys, interviews, forum post analysis; and triangulation of these methods. Based on our learning from the Improving Peer Online Forums (iPOF) study, an inter-disciplinary realist informed mixed methods evaluation of peer online forums, we outline strategies that can be used to address key issues pertaining to assessing important outcomes, facilitating participation, validating participants (users who consent to take part in one or more parts of the study), protecting anonymity, gaining consent, managing risk, multi-stakeholder engagement, and triangulation. We share this learning to support researchers, reviewers, and ethics committees faced with deciding how best to address these challenges. We highlight the need for ongoing open, transparent discussion to ensure the research field keeps pace with evolving technology design and societal attitudes to online data use.