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No-Human in the Loop: Agentic Evaluation at Scale for Recommendation
Explaining Decisions in ML Models: a Parameterized Complexity Analysis (Part I)
Digital Transformation Chatbot (DTchatbot): Integrating Large Language Model-based Chatbot in Acquiring Digital Transformation Needs
Mathematical exploration and discovery at scale
FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation
LGM: Enhancing Large Language Models with Conceptual Meta-Relations and Iterative Retrieval
Hybrid Fact-Checking that Integrates Knowledge Graphs, Large Language Models, and Search-Based Retrieval Agents Improves Interpretable Claim Verification
RAG-IT: Retrieval-Augmented Instruction Tuning for Automated Financial Analysis
REFA: Reference Free Alignment for multi-preference optimization
Evaluating Large Language Models for Detecting Antisemitism
Site-specific DNA insertion into the human genome with engineered recombinases
Nature Biotechnology, Published online: 06 November 2025; doi:10.1038/s41587-025-02895-3
Engineered DNA recombinases efficiently and specifically insert genetic cargos without the use of landing pads.Harnessing multi-omics approaches to decipher tumor evolution and improve diagnosis and therapy in lung cancer
Biomark Res. 2025 Nov 5;13(1):140. doi: 10.1186/s40364-025-00859-y.
ABSTRACT
With the advancement of novel technologies such as whole-genome sequencing, single-cell sequencing, and spatial transcriptomics, single-omics analyses have already promoted the research of tumorigenesis as well as development and have partly elucidated the evolutionary processes of lung cancer. However, it is still difficult to distinguish these confounding features via single dimensional approaches due to the complexity, heterogeneity and cell-cell interactions with the immune microenvironment in lung cancer. Multi-omics approaches provide a holistic framework for constructing detailed tumor ecosystem landscapes, thereby facilitating the development of a more robust classification system for precision diagnosis and treatment, and aiding in the discovery of novel cancer biomarkers. In this review, we summarize the potential and applications of multi-omics approaches in characterizing intratumor heterogeneity and the tumor microenvironment throughout the course of lung cancer development. By further discussing the discovery and application of diagnostic and therapeutic biomarkers across precancerous lesions, early-stage lung cancer, tumor progression, metastasis, and therapy resistance, we outline the current challenges and future prospects of using multi-omics to identify reliable biomarkers. Moreover, we emphasize that integrative multi-omics models hold great promise for elucidating the complex interactions within the lung cancer ecosystem, thereby contributing to improved diagnostic accuracy, optimized therapeutic strategies, and better patient outcomes.
PMID:41194170 | PMC:PMC12590604 | DOI:10.1186/s40364-025-00859-y
Improving dataset transparency in dermatologic Artificial Intelligence using a dataset nutrition label
npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02125-9
Biased and poorly documented dermatology datasets pose risks to the development of safe and generalizable artificial intelligence (AI) tools. We created a Dataset Nutrition Label (DNL) for multiple dermatology datasets to support transparent and responsible data use. The DNL offers a structured, digestible summary of key attributes, including metadata, limitations, and risks, enabling data users to better assess suitability and proactively address potential sources of bias in datasets.Evaluating clinical AI summaries with large language models as judges
npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02005-2
Evaluating clinical AI summaries with large language models as judgesLiquid biopsy in gastrointestinal oncology: clinical applications and translational integration of ctDNA, CTCs, and sEVs
Oncol Rev. 2025 Oct 20;19:1702932. doi: 10.3389/or.2025.1702932. eCollection 2025.
ABSTRACT
BACKGROUND AND AIMS: Liquid biopsy offers a minimally invasive tool to detect actionable mutations, monitor minimal residual disease (MRD), and guide therapy in gastrointestinal (GI) cancers. We critically review the clinical utility of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and small extracellular vesicles (sEVs) across GI malignancies and propose a framework for their integration into clinical practice.
METHODS: We synthesized evidence from over 200 studies, including prospective trials and translational research, to assess diagnostic accuracy, prognostic value, and clinical actionability of each biomarker type in esophageal, gastric, colorectal, pancreatic, hepatocellular, and biliary cancers.
RESULTS: ctDNA has shown strong potential for MRD detection and treatment monitoring, particularly in colorectal and pancreatic cancer. CTCs offer insights into metastatic risk and therapeutic resistance, while sEVs provide molecular cargo relevant to immunomodulation and disease progression. Emerging microfluidics and AI-driven multi-omics approaches may overcome current limitations.
CONCLUSION: The integration of liquid biopsy technologies into GI oncology holds promise for early detection and precision therapy. We propose a five-phase clinical roadmap and outine the key research gaps that need to be addressed before widespread implementation in routine care.
PMID:41190015 | PMC:PMC12580207 | DOI:10.3389/or.2025.1702932
Combining International Standards to Develop Clinical Decision Support for Parent Smoking Cessation in Pediatrics
Key Features of Digital Phenotyping for Monitoring Mental Disorders: Systematic Review
Curated and harmonised transcriptomics datasets of interstitial lung diseases
Data Brief. 2025 Oct 14;63:112139. doi: 10.1016/j.dib.2025.112139. eCollection 2025 Dec.
ABSTRACT
This study provides manually curated and homogenised transcriptomics data of interstitial lung disease (ILD) patients retrieved from the NCBI Gene Expression Omnibus and European Nucleotide Archive repositories. The compendium includes 30 transcriptomics datasets generated with DNA microarrays and RNA sequencing (RNA-seq) technologies for a total of 1371 samples. All the datasets underwent metadata curation and harmonisation, data quality check, and preprocessing with standardised procedures. Furthermore, a robust data model was developed to standardise phenotypic data, thereby enhancing comparability across heterogeneous datasets. Gene expression data and lists of differentially expressed genes computed between ILD and healthy samples are provided. Among the ILDs included in this study, idiopathic pulmonary fibrosis (IPF) is the most represented worldwide. Co-expression networks of IPF and healthy samples were inferred, which are also included in this study. This study enhances the Findability, Accessibility, Interoperability, and Reusability (FAIR) of publicly available transcriptomic datasets related to ILDs. The resulting resource provides a integrated platform for the implementation and validation of systems biology and pharmacology approaches, facilitating the development of novel diagnostic and therapeutic strategies for ILDs.
PMID:41189603 | PMC:PMC12581653 | DOI:10.1016/j.dib.2025.112139
A multimodal whole-slide foundation model for pathology
Nature Medicine, Published online: 05 November 2025; doi:10.1038/s41591-025-03982-3
Pretrained using 335,645 whole-slide images, a foundation model is developed to provide representations for slide- and patient-level tasks. It is capable of performing clinical tasks and generating reports even in data-scarce scenarios, such as rare cancer diagnosis and survival prediction, without requiring further fine-tuning.