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Human Decision-making is Susceptible to AI-driven Manipulation
Uni-X: Mitigating Modality Conflict with a Two-End-Separated Architecture for Unified Multimodal Models
The AI Productivity Index (APEX)
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
Cognitive bias in LLM reasoning compromises interpretation of clinical oncology notes
How Do Companies Manage the Environmental Sustainability of AI? An Interview Study About Green AI Efforts and Regulations
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
Clinician-Directed Large Language Model Software Generation for Therapeutic Interventions in Physical Rehabilitation
AI-Assisted Cardiovascular Risk Assessment by General Practitioners in Resource-Constrained Indonesian Settings Using a Conceptual Prototype: Randomized Controlled Study
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 intelligenceDecoding 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
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
When Alignment Fails: Multimodal Adversarial Attacks on Vision-Language-Action Models
ConCISE: A Reference-Free Conciseness Evaluation Metric for LLM-Generated Answers
SMILE: A Composite Lexical-Semantic Metric for Question-Answering Evaluation
Artificial Intelligence Index Report 2025
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 cancerTen 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