Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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SelfAI: Building a Self-Training AI System with LLM Agents
arXiv:2512.00403v1 Announce Type: cross Abstract: Recent work on autonomous scientific discovery has leveraged LLM-based agents to integrate problem specification, experiment planning, and execution into end-to-end systems. However, these frameworks are often confined to narrow application domains, offer limited real-time interaction with researchers, and lack principled mechanisms for determining when to halt exploration, resulting in inefficiencies, reproducibility challenges, and under-utili
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cs.AI, q-bio.NC updates on arXiv.org
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Human Decision-making is Susceptible to AI-driven Manipulation
arXiv:2502.07663v3 Announce Type: replace Abstract: AI systems are increasingly intertwined with daily life, assisting users with various tasks and guiding decision-making. This integration introduces risks of AI-driven manipulation, where such systems may exploit users' cognitive biases and emotional vulnerabilities to steer them toward harmful outcomes. Through a randomized between-subjects experiment with 233 participants, we examined human susceptibility to such manipulation in financial (e
Human Decision-making is Susceptible to AI-driven Manipulation
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cs.AI, q-bio.NC updates on arXiv.org
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Uni-X: Mitigating Modality Conflict with a Two-End-Separated Architecture for Unified Multimodal Models
arXiv:2509.24365v2 Announce Type: replace-cross Abstract: Unified Multimodal Models (UMMs) built on shared autoregressive (AR) transformers are attractive for their architectural simplicity. However, we identify a critical limitation: when trained on multimodal inputs, modality-shared transformers suffer from severe gradient conflicts between vision and text, particularly in shallow and deep layers. We trace this issue to the fundamentally different low-level statistical properties of images an
Uni-X: Mitigating Modality Conflict with a Two-End-Separated Architecture for Unified Multimodal Models
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cs.AI, q-bio.NC updates on arXiv.org
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The AI Productivity Index (APEX)
arXiv:2509.25721v3 Announce Type: replace-cross Abstract: We present an extended version of the AI Productivity Index (APEX-v1-extended), a benchmark for assessing whether frontier models are capable of performing economically valuable tasks in four jobs: investment banking associate, management consultant, big law associate, and primary care physician (MD). This technical report details the extensions to APEX-v1, including an increase in the held-out evaluation set from n = 50 to n = 100 cases
The AI Productivity Index (APEX)
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(Multiomics OR Omics) AND (Pancreatic)
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Single-Cell Multi-Omics in Type 2 Diabetes Mellitus: Revealing Cellular Heterogeneity and Mechanistic Insights
Int J Mol Sci. 2025 Nov 13;26(22):11005. doi: 10.3390/ijms262211005.ABSTRACTType 2 diabetes mellitus (T2DM) is a prevalent and complex metabolic disorder characterized by insulin resistance, progressive β-cell dysfunction, and severe systemic complications. Advances in single-cell multi-omics-transcriptomics, chromatin accessibility profiling, and integrative analyses-have offered unprecedented insights into the cellular heterogeneity and regulatory networks of pancreatic islets. We highlight re
Single-Cell Multi-Omics in Type 2 Diabetes Mellitus: Revealing Cellular Heterogeneity and Mechanistic Insights
Int J Mol Sci. 2025 Nov 13;26(22):11005. doi: 10.3390/ijms262211005.
ABSTRACT
Type 2 diabetes mellitus (T2DM) is a prevalent and complex metabolic disorder characterized by insulin resistance, progressive β-cell dysfunction, and severe systemic complications. Advances in single-cell multi-omics-transcriptomics, chromatin accessibility profiling, and integrative analyses-have offered unprecedented insights into the cellular heterogeneity and regulatory networks of pancreatic islets. We highlight recent discoveries in islet cell heterogeneity and β-cell pathophysiology, with a particular focus on dysfunction and dedifferentiation. We further underscore the computational frameworks that enable these discoveries, spanning data preprocessing, multi-omics integration, and machine learning-driven analyses, which collectively enable the dissection of disease-relevant cell subpopulations and the reconstruction of developmental and regulatory trajectories. We also examine how impaired signaling within islets and chronic adipose inflammation contribute to T2DM pathogenesis. Finally, we discuss key challenges in clinical translation-including limited population diversity in single-cell atlases and the interpretability of computational models-and propose future directions toward precision diagnostics and therapeutic innovation in T2DM.
PMID:41303487 | PMC:PMC12652634 | DOI:10.3390/ijms262211005
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cs.AI, q-bio.NC updates on arXiv.org
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Cognitive bias in LLM reasoning compromises interpretation of clinical oncology notes
arXiv:2511.20680v1 Announce Type: cross Abstract: Despite high performance on clinical benchmarks, large language models may reach correct conclusions through faulty reasoning, a failure mode with safety implications for oncology decision support that is not captured by accuracy-based evaluation. In this two-cohort retrospective study, we developed a hierarchical taxonomy of reasoning errors from GPT-4 chain-of-thought responses to real oncology notes and tested its clinical relevance. Using br
Cognitive bias in LLM reasoning compromises interpretation of clinical oncology notes
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cs.AI, q-bio.NC updates on arXiv.org
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How Do Companies Manage the Environmental Sustainability of AI? An Interview Study About Green AI Efforts and Regulations
arXiv:2505.07317v2 Announce Type: replace-cross Abstract: With the ever-growing adoption of artificial intelligence (AI), AI-based software and its negative impact on the environment are no longer negligible, and studying and mitigating this impact has become a critical area of research. However, it is currently unclear which role environmental sustainability plays during AI adoption in industry and how AI regulations influence Green AI practices and decision-making in industry. We therefore ai
How Do Companies Manage the Environmental Sustainability of AI? An Interview Study About Green AI Efforts and Regulations
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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scGALA advances graph link prediction-based cell alignment for comprehensive data integration and harmonization
Nat Commun. 2025 Nov 26. doi: 10.1038/s41467-025-66644-5. Online ahead of print.ABSTRACTSingle-cell technologies have transformed our understanding of cellular heterogeneity through multimodal data acquisition. However, robust cell alignment remains a major challenge for data integration and harmonization, including batch correction, label transfer, and multi-omics integration. Many existing methods constrain alignment based on rigid feature-wise distance metrics, limiting their ability to captu
scGALA advances graph link prediction-based cell alignment for comprehensive data integration and harmonization
Nat Commun. 2025 Nov 26. doi: 10.1038/s41467-025-66644-5. Online ahead of print.
ABSTRACT
Single-cell technologies have transformed our understanding of cellular heterogeneity through multimodal data acquisition. However, robust cell alignment remains a major challenge for data integration and harmonization, including batch correction, label transfer, and multi-omics integration. Many existing methods constrain alignment based on rigid feature-wise distance metrics, limiting their ability to capture accurate cell correspondence across diverse cell populations and conditions. We introduce scGALA, a graph-based learning framework that redefines cell alignment by combining graph attention networks with a score-driven, task-independent optimization strategy. scGALA constructs enriched graphs of cell-cell relationships by integrating gene expression profiles with auxiliary information, such as spatial coordinates, and iteratively refines alignment via self-supervised graph link prediction, where a deep neural network is trained to identify and reinforce high-confidence correspondences across datasets. In extensive benchmarks, scGALA identifies over 25 percent more high-confidence alignments without compromising accuracy. By improving the core step of cell alignment, scGALA serves as a versatile enhancer for a wide range of single-cell data integration tasks.
PMID:41298467 | DOI:10.1038/s41467-025-66644-5
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cs.AI, q-bio.NC updates on arXiv.org
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Clinician-Directed Large Language Model Software Generation for Therapeutic Interventions in Physical Rehabilitation
arXiv:2511.18274v1 Announce Type: cross Abstract: Digital health interventions are increasingly used in physical and occupational therapy to deliver home exercise programs via sensor equipped devices such as smartphones, enabling remote monitoring of adherence and performance. However, digital interventions are typically programmed as software before clinical encounters as libraries of parametrized exercise modules targeting broad patient populations. At the point of care, clinicians can only s
Clinician-Directed Large Language Model Software Generation for Therapeutic Interventions in Physical Rehabilitation
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Journal of Medical Internet Research
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AI-Assisted Cardiovascular Risk Assessment by General Practitioners in Resource-Constrained Indonesian Settings Using a Conceptual Prototype: Randomized Controlled Study
Background: Preventive strategies integrated with digital health and artificial intelligence (AI), have significant potential to mitigate the global burden of atherosclerotic cardiovascular disease (ASCVD). AI-enabled clinical decision support (CDS) systems increasingly provide patient-specific insights beyond traditional risk factors. Despite these advances, their capacity to enhance clinical decision-making in resource-constrained settings remains largely unexplored. Objective: We conducted a
AI-Assisted Cardiovascular Risk Assessment by General Practitioners in Resource-Constrained Indonesian Settings Using a Conceptual Prototype: Randomized Controlled Study
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Nature Medicine
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The missing value of medical artificial intelligence
Nature Medicine, Published online: 25 November 2025; doi:10.1038/s41591-025-04050-6The missing value of medical artificial intelligence
The missing value of medical artificial intelligence
Nature Medicine, Published online: 25 November 2025; doi:10.1038/s41591-025-04050-6
The missing value of medical artificial intelligence-
Omics in Hepatocellular
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Decoding the cholesterol-apoptosis axis in HCC: a machine learning-based multi-omics integration and single-cell transcriptomic analysis
Discov Oncol. 2025 Nov 25;16(1):2162. doi: 10.1007/s12672-025-04010-z.ABSTRACTLiver hepatocellular carcinoma (LIHC), a predominant form of primary hepatic malignancy, demonstrates a progressively escalating global incidence, imposing substantial health and economic burdens on patients and society. Early diagnosis remains challenging, often resulting in late-stage detection, which limits the efficacy of current therapeutic strategies. This study systematically examines the transcriptional signatu
Decoding the cholesterol-apoptosis axis in HCC: a machine learning-based multi-omics integration and single-cell transcriptomic analysis
Discov Oncol. 2025 Nov 25;16(1):2162. doi: 10.1007/s12672-025-04010-z.
ABSTRACT
Liver hepatocellular carcinoma (LIHC), a predominant form of primary hepatic malignancy, demonstrates a progressively escalating global incidence, imposing substantial health and economic burdens on patients and society. Early diagnosis remains challenging, often resulting in late-stage detection, which limits the efficacy of current therapeutic strategies. This study systematically examines the transcriptional signatures of apoptosis-associated and cholesterol metabolic pathways in LIHC, providing insights into its underlying mechanisms and identifying potential prognostic markers. We employed multi-omics and machine learning to evaluate gene expression variations and construct a prognostic risk scoring model. This study identified apoptosis- and cholesterol metabolism-related differentially expressed genes (ACMRDEGs). Importantly, LASSO regression analysis identified six hub genes (EPHX2, FABP5, SQLE, ADH4, HMGCS2, and CYP7A1) as critical prognostic biomarkers, demonstrating significant correlation with overall survival (OS). Furthermore, immune cell infiltration analysis indicated significant differences in 12 immune cell types within LIHC microenvironment, underscoring the immune system's involvement in disease progression. cholesterol and alcohol metabolism pathways were significantly enriched among hub gene modules, as quantified by multiple gene enrichment analyses. Single-cell analysis identified six major cell types, providing a deeper understanding of the cellular heterogeneity within LIHC. In summarize, this study presents the first integrated apoptosis-cholesterol metabolic pathway-based six-gene prognostic model for LIHC, validated for robustness across multiple cohorts, which may facilitate personalized therapeutic strategies and refined risk assessment in clinical practice.
PMID:41288805 | PMC:PMC12647489 | DOI:10.1007/s12672-025-04010-z
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Decoding the cholesterol-apoptosis axis in HCC: a machine learning-based multi-omics integration and single-cell transcriptomic analysis
Discov Oncol. 2025 Nov 25;16(1):2162. doi: 10.1007/s12672-025-04010-z.ABSTRACTLiver hepatocellular carcinoma (LIHC), a predominant form of primary hepatic malignancy, demonstrates a progressively escalating global incidence, imposing substantial health and economic burdens on patients and society. Early diagnosis remains challenging, often resulting in late-stage detection, which limits the efficacy of current therapeutic strategies. This study systematically examines the transcriptional signatu
Decoding the cholesterol-apoptosis axis in HCC: a machine learning-based multi-omics integration and single-cell transcriptomic analysis
Discov Oncol. 2025 Nov 25;16(1):2162. doi: 10.1007/s12672-025-04010-z.
ABSTRACT
Liver hepatocellular carcinoma (LIHC), a predominant form of primary hepatic malignancy, demonstrates a progressively escalating global incidence, imposing substantial health and economic burdens on patients and society. Early diagnosis remains challenging, often resulting in late-stage detection, which limits the efficacy of current therapeutic strategies. This study systematically examines the transcriptional signatures of apoptosis-associated and cholesterol metabolic pathways in LIHC, providing insights into its underlying mechanisms and identifying potential prognostic markers. We employed multi-omics and machine learning to evaluate gene expression variations and construct a prognostic risk scoring model. This study identified apoptosis- and cholesterol metabolism-related differentially expressed genes (ACMRDEGs). Importantly, LASSO regression analysis identified six hub genes (EPHX2, FABP5, SQLE, ADH4, HMGCS2, and CYP7A1) as critical prognostic biomarkers, demonstrating significant correlation with overall survival (OS). Furthermore, immune cell infiltration analysis indicated significant differences in 12 immune cell types within LIHC microenvironment, underscoring the immune system's involvement in disease progression. cholesterol and alcohol metabolism pathways were significantly enriched among hub gene modules, as quantified by multiple gene enrichment analyses. Single-cell analysis identified six major cell types, providing a deeper understanding of the cellular heterogeneity within LIHC. In summarize, this study presents the first integrated apoptosis-cholesterol metabolic pathway-based six-gene prognostic model for LIHC, validated for robustness across multiple cohorts, which may facilitate personalized therapeutic strategies and refined risk assessment in clinical practice.
PMID:41288805 | DOI:10.1007/s12672-025-04010-z
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cs.AI, q-bio.NC updates on arXiv.org
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When Alignment Fails: Multimodal Adversarial Attacks on Vision-Language-Action Models
arXiv:2511.16203v2 Announce Type: replace-cross Abstract: Vision-Language-Action models (VLAs) have recently demonstrated remarkable progress in embodied environments, enabling robots to perceive, reason, and act through unified multimodal understanding. Despite their impressive capabilities, the adversarial robustness of these systems remains largely unexplored, especially under realistic multimodal and black-box conditions. Existing studies mainly focus on single-modality perturbations and ov
When Alignment Fails: Multimodal Adversarial Attacks on Vision-Language-Action Models
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cs.AI, q-bio.NC updates on arXiv.org
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ConCISE: A Reference-Free Conciseness Evaluation Metric for LLM-Generated Answers
arXiv:2511.16846v1 Announce Type: cross Abstract: Large language models (LLMs) frequently generate responses that are lengthy and verbose, filled with redundant or unnecessary details. This diminishes clarity and user satisfaction, and it increases costs for model developers, especially with well-known proprietary models that charge based on the number of output tokens. In this paper, we introduce a novel reference-free metric for evaluating the conciseness of responses generated by LLMs. Our m
ConCISE: A Reference-Free Conciseness Evaluation Metric for LLM-Generated Answers
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cs.AI, q-bio.NC updates on arXiv.org
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SMILE: A Composite Lexical-Semantic Metric for Question-Answering Evaluation
arXiv:2511.17432v1 Announce Type: cross Abstract: Traditional evaluation metrics for textual and visual question answering, like ROUGE, METEOR, and Exact Match (EM), focus heavily on n-gram based lexical similarity, often missing the deeper semantic understanding needed for accurate assessment. While measures like BERTScore and MoverScore leverage contextual embeddings to address this limitation, they lack flexibility in balancing sentence-level and keyword-level semantics and ignore lexical si
SMILE: A Composite Lexical-Semantic Metric for Question-Answering Evaluation
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cs.AI, q-bio.NC updates on arXiv.org
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Artificial Intelligence Index Report 2025
arXiv:2504.07139v3 Announce Type: replace Abstract: Welcome to the eighth edition of the AI Index report. The 2025 Index is our most comprehensive to date and arrives at an important moment, as AI's influence across society, the economy, and global governance continues to intensify. New in this year's report are in-depth analyses of the evolving landscape of AI hardware, novel estimates of inference costs, and new analyses of AI publication and patenting trends. We also introduce fresh data on
Artificial Intelligence Index Report 2025
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npj Digital Medicine
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Multimodal analysis of whole slide images in colorectal cancer
npj Digital Medicine, Published online: 24 November 2025; doi:10.1038/s41746-025-02095-yMultimodal analysis of whole slide images in colorectal cancer
Multimodal analysis of whole slide images in colorectal cancer
npj Digital Medicine, Published online: 24 November 2025; doi:10.1038/s41746-025-02095-y
Multimodal analysis of whole slide images in colorectal cancer-
Oncogene - Issue - nature.com science feeds
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Ten years of oncogene editorship: a decade of transformation
Oncogene, Published online: 24 November 2025; doi:10.1038/s41388-025-03648-xTen years of oncogene editorship: a decade of transformation
Ten years of oncogene editorship: a decade of transformation
Oncogene, Published online: 24 November 2025; doi:10.1038/s41388-025-03648-x
Ten years of oncogene editorship: a decade of transformation-
Journal of Medical Internet Research
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Health care Experiences of Educated Young Adults With Blindness in the Digital Age: Qualitative Study
Background: The rapid advancement of digital health technologies (DHTs) offers substantial potential for improving healthcare access, yet it simultaneously risks exacerbating existing inequities for marginalized populations. Previous research on the digital divide has often treated individuals with blindness as a homogenous group, primarily focusing on barriers related to digital access and skills. However, less is known about the nuanced experiences of specific subgroups, such as educated and d