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cs.AI, q-bio.NC updates on arXiv.org
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Hybrid Fact-Checking that Integrates Knowledge Graphs, Large Language Models, and Search-Based Retrieval Agents Improves Interpretable Claim Verification
arXiv:2511.03217v1 Announce Type: cross Abstract: Large language models (LLMs) excel in generating fluent utterances but can lack reliable grounding in verified information. At the same time, knowledge-graph-based fact-checkers deliver precise and interpretable evidence, yet suffer from limited coverage or latency. By integrating LLMs with knowledge graphs and real-time search agents, we introduce a hybrid fact-checking approach that leverages the individual strengths of each component. Our sys
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Nature Biotechnology - Issue - nature.com science feeds
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Site-specific DNA insertion into the human genome with engineered recombinases
Nature Biotechnology, Published online: 06 November 2025; doi:10.1038/s41587-025-02895-3Engineered DNA recombinases efficiently and specifically insert genetic cargos without the use of landing pads.
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.-
npj Digital Medicine
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Improving dataset transparency in dermatologic Artificial Intelligence using a dataset nutrition label
npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02125-9Biased 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 ass
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.-
npj Digital Medicine
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Evaluating clinical AI summaries with large language models as judges
npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02005-2Evaluating clinical AI summaries with large language models as judges
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 judges-
MRD
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Liquid 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.ABSTRACTBACKGROUND 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 i
Liquid 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
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Journal of Medical Internet Research
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Combining International Standards to Develop Clinical Decision Support for Parent Smoking Cessation in Pediatrics
Smoking has severe health consequences, and secondhand smoke (SHS) exposure among children increases the risk of sudden infant death syndrome, chronic respiratory diseases, such as asthma, and lung cancer in adulthood. For many parents, pediatricians are the primary source of interaction with the healthcare system. Nevertheless, in pediatric settings, appropriate tobacco treatments are rarely, if ever, provided to parents who smoke. To best address tobacco use among parents, it is ideal to devel
Combining International Standards to Develop Clinical Decision Support for Parent Smoking Cessation in Pediatrics
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Nature Medicine
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A multimodal whole-slide foundation model for pathology
Nature Medicine, Published online: 05 November 2025; doi:10.1038/s41591-025-03982-3Pretrained 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.
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.-
Nature - Issue - nature.com science feeds
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Fair human-centric image dataset for ethical AI benchmarking
Nature, Published online: 05 November 2025; doi:10.1038/s41586-025-09716-2The Fair Human-Centric Image Benchmark (FHIBE, pronounced ‘Feebee’)—an image dataset that implements best practices for consent, privacy, compensation, safety, diversity and utility—can be used responsibly as a fairness evaluation dataset for many human-centric computer vision applications.
Fair human-centric image dataset for ethical AI benchmarking
Nature, Published online: 05 November 2025; doi:10.1038/s41586-025-09716-2
The Fair Human-Centric Image Benchmark (FHIBE, pronounced ‘Feebee’)—an image dataset that implements best practices for consent, privacy, compensation, safety, diversity and utility—can be used responsibly as a fairness evaluation dataset for many human-centric computer vision applications.-
cs.AI, q-bio.NC updates on arXiv.org
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How can we assess human-agent interactions? Case studies in software agent design
arXiv:2510.09801v2 Announce Type: replace Abstract: LLM-powered agents are both a promising new technology and a source of complexity, where choices about models, tools, and prompting can affect their usefulness. While numerous benchmarks measure agent accuracy across domains, they mostly assume full automation, failing to represent the collaborative nature of real-world use cases. In this paper, we make two major steps towards the rigorous assessment of human-agent interactions. First, we prop
How can we assess human-agent interactions? Case studies in software agent design
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cs.AI, q-bio.NC updates on arXiv.org
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Digital Twin based Automatic Reconfiguration of Robotic Systems in Smart Environments
arXiv:2511.00094v1 Announce Type: 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 operation
Digital Twin based Automatic Reconfiguration of Robotic Systems in Smart Environments
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cs.AI, q-bio.NC updates on arXiv.org
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Will Humanity Be Rendered Obsolete by AI?
arXiv:2510.22814v2 Announce Type: replace Abstract: This article analyzes the existential risks artificial intelligence (AI) poses to humanity, tracing the trajectory from current AI to ultraintelligence. Drawing on Irving J. Good and Nick Bostrom's theoretical work, plus recent publications (AI 2027; If Anyone Builds It, Everyone Dies), it explores AGI and superintelligence. Considering machines' exponentially growing cognitive power and hypothetical IQs, it addresses the ethical and existenti
Will Humanity Be Rendered Obsolete by AI?
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cs.AI, q-bio.NC updates on arXiv.org
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The Denario project: Deep knowledge AI agents for scientific discovery
arXiv:2510.26887v1 Announce Type: new Abstract: We present Denario, an AI multi-agent system designed to serve as a scientific research assistant. Denario can perform many different tasks, such as generating ideas, checking the literature, developing research plans, writing and executing code, making plots, and drafting and reviewing a scientific paper. The system has a modular architecture, allowing it to handle specific tasks, such as generating an idea, or carrying out end-to-end scientific
The Denario project: Deep knowledge AI agents for scientific discovery
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cs.AI, q-bio.NC updates on arXiv.org
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Frame Semantic Patterns for Identifying Underreporting of Notifiable Events in Healthcare: The Case of Gender-Based Violence
arXiv:2510.26969v1 Announce Type: cross Abstract: We introduce a methodology for the identification of notifiable events in the domain of healthcare. The methodology harnesses semantic frames to define fine-grained patterns and search them in unstructured data, namely, open-text fields in e-medical records. We apply the methodology to the problem of underreporting of gender-based violence (GBV) in e-medical records produced during patients' visits to primary care units. A total of eight pattern
Frame Semantic Patterns for Identifying Underreporting of Notifiable Events in Healthcare: The Case of Gender-Based Violence
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cs.AI, q-bio.NC updates on arXiv.org
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A Systematic Literature Review of Spatio-Temporal Graph Neural Network Models for Time Series Forecasting and Classification
arXiv:2410.22377v3 Announce Type: replace-cross Abstract: In recent years, spatio-temporal graph neural networks (GNNs) have attracted considerable interest in the field of time series analysis, due to their ability to capture, at once, dependencies among variables and across time points. The objective of this systematic literature review is hence to provide a comprehensive overview of the various modeling approaches and application domains of GNNs for time series classification and forecasting
A Systematic Literature Review of Spatio-Temporal Graph Neural Network Models for Time Series Forecasting and Classification
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cs.AI, q-bio.NC updates on arXiv.org
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Deep Learning-based Prediction of Clinical Trial Enrollment with Uncertainty Estimates
arXiv:2507.23607v2 Announce Type: replace-cross Abstract: Clinical trials are a systematic endeavor to assess the safety and efficacy of new drugs or treatments. Conducting such trials typically demands significant financial investment and meticulous planning, highlighting the need for accurate predictions of trial outcomes. Accurately predicting patient enrollment, a key factor in trial success, is one of the primary challenges during the planning phase. In this work, we propose a novel deep l
Deep Learning-based Prediction of Clinical Trial Enrollment with Uncertainty Estimates
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cs.AI, q-bio.NC updates on arXiv.org
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A Process Mining-Based System For The Analysis and Prediction of Software Development Workflows
arXiv:2510.25935v2 Announce Type: replace-cross Abstract: CodeSight is an end-to-end system designed to anticipate deadline compliance in software development workflows. It captures development and deployment data directly from GitHub, transforming it into process mining logs for detailed analysis. From these logs, the system generates metrics and dashboards that provide actionable insights into PR activity patterns and workflow efficiency. Building on this structured representation, CodeSight
A Process Mining-Based System For The Analysis and Prediction of Software Development Workflows
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cs.AI, q-bio.NC updates on arXiv.org
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On the limitation of evaluating machine unlearning using only a single training seed
arXiv:2510.26714v2 Announce Type: replace-cross Abstract: Machine unlearning (MU) aims to remove the influence of certain data points from a trained model without costly retraining. Most practical MU algorithms are only approximate and their performance can only be assessed empirically. Care must therefore be taken to make empirical comparisons as representative as possible. A common practice is to run the MU algorithm multiple times independently starting from the same trained model. In this w
On the limitation of evaluating machine unlearning using only a single training seed
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MRD
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International expert consensus on the clinical integration of circulating tumor cells in solid tumors
Eur J Cancer. 2025 Dec 9;231:116050. doi: 10.1016/j.ejca.2025.116050. Epub 2025 Oct 20.ABSTRACTBACKGROUND: Circulating tumor cells (CTCs) are a versatile biomarker in solid tumors. Extensive research supports their clinical relevance and led to regulatory approval in breast, prostate, and colorectal cancers. However, clinical adoption remains limited mainly due to the lack of consensus and standardized technologies. Additionally, CTC research lacks unified direction. To address these gaps, an in
International expert consensus on the clinical integration of circulating tumor cells in solid tumors
Eur J Cancer. 2025 Dec 9;231:116050. doi: 10.1016/j.ejca.2025.116050. Epub 2025 Oct 20.
ABSTRACT
BACKGROUND: Circulating tumor cells (CTCs) are a versatile biomarker in solid tumors. Extensive research supports their clinical relevance and led to regulatory approval in breast, prostate, and colorectal cancers. However, clinical adoption remains limited mainly due to the lack of consensus and standardized technologies. Additionally, CTC research lacks unified direction. To address these gaps, an international expert panel was established to assess the current and future clinical utility of CTCs.
METHODS: A panel of 11 CTC experts identified key areas of controversy, informing a structured survey distributed to 55 international multidisciplinary experts. Consensus was predefined as ≥ 70 % agreement. Areas without consensus were discussed in a virtual meeting, leading to final statements on the clinical integration of CTCs.
RESULTS: Thirty-seven experts completed the survey. Consensus was reached on the clinical utility of CTCs for prognosis and treatment monitoring in metastatic breast (BC) and prostate (PC) cancers, including AR-V7 testing in metastatic castration-resistant PC for therapy selection. In other tumors, CTCs remain investigational. Experts agreed that while clinical utility is not yet established in early-stage disease, CTCs show promise in early BC, especially combined with cell-free DNA (cfDNA) for minimal residual disease detection. CellSearch® is currently the only platform with high-level evidence for clinical use, though emerging technologies are promising. Key challenges include improving detection sensitivity/specificity, standardizing workflows, generating robust data, and clinician education. Experts emphasized shifting from enumeration to phenotypic and molecular characterization, particularly for treatment guidance, and highlighted the complementary role of CTCs and cfDNA, advocating for integrated liquid biopsy approaches.
CONCLUSIONS: This consensus offers practical guidance for clinical integration of CTCs and outlines strategic research priorities to unlock their full potential in precision oncology.
PMID:41172567 | DOI:10.1016/j.ejca.2025.116050
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Animal models in tuberculosis metabolomics: a systematic review of current evidence and the road to translational relevance
Front Mol Biosci. 2025 Oct 15;12:1688882. doi: 10.3389/fmolb.2025.1688882. eCollection 2025.ABSTRACTBACKGROUND: Animal models are important for tuberculosis (TB) research, offering controlled settings to study disease mechanisms. However, their ability to replicate TB-induced metabolic responses in humans is uncertain. This systematic review evaluated the current use of animal models in metabolomics studies aimed at characterising active pulmonary TB.METHODS: PubMed, Scopus, and Web of Science w
Animal models in tuberculosis metabolomics: a systematic review of current evidence and the road to translational relevance
Front Mol Biosci. 2025 Oct 15;12:1688882. doi: 10.3389/fmolb.2025.1688882. eCollection 2025.
ABSTRACT
BACKGROUND: Animal models are important for tuberculosis (TB) research, offering controlled settings to study disease mechanisms. However, their ability to replicate TB-induced metabolic responses in humans is uncertain. This systematic review evaluated the current use of animal models in metabolomics studies aimed at characterising active pulmonary TB.
METHODS: PubMed, Scopus, and Web of Science were systematically searched for metabolomics studies of pulmonary TB in humans and animal models, following PRISMA guidelines. Eligible studies were screened, and quality was assessed using QUDOMICS and STAIR tools. Data were synthesised by species, sample matrix, experimental design, and reported differential metabolites. Differential metabolite names were compared between species and subjected to pathway analysis in MetaboAnalyst 6.0.
RESULTS: Of the 80 eligible studies, nine involved animal models, predominantly mice. These models captured only 4.7% of human TB-associated differential metabolites, with the highest overlap (3.8%) in mouse lung tissue. Despite low concordance at metabolite level, conserved disruptions were observed in amino acid, glutathione, and one-carbon metabolism pathways. Interspecies variation was evident, influenced by host species, sample matrix, infection protocol, and analytical method.
CONCLUSION: Animal models partially replicated key metabolic features of human TB, particularly at the pathway level. However, variability across studies hampers current translational interpretation. Broader model use, standardised protocols, and integrated multi-platform omics approaches are needed to improve the relevance and comparability of animal models in TB metabolomics research.
PMID:41169614 | PMC:PMC12568366 | DOI:10.3389/fmolb.2025.1688882
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Journal of Medical Internet Research
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Digital Health Technology Compliance With Clinical Safety Standards In the National Health Service in England: National Cross-Sectional Study
Background: To be authorized for use in the National Health Service (NHS) in England, digital health technologies (DHTs) must meet 2 mandatory clinical risk management standards, Data Coordination Board (DCB) 0129 and 0160, demonstrating that risks from design and use have been assessed and mitigated. NHS organizations must not procure a DHT without DCB0129 assurance and must not deploy one without DCB0160 assurance. Despite legal requirement, no public data exist on how many DHTs are in use in