Normal view
-
cs.AI, q-bio.NC updates on arXiv.org
-
MedScope: Incentivizing "Think with Videos" for Clinical Reasoning via Coarse-to-Fine Tool Calling
arXiv:2602.13332v1 Announce Type: cross Abstract: Long-form clinical videos are central to visual evidence-based decision-making, with growing importance for applications such as surgical robotics and related settings. However, current multimodal large language models typically process videos with passive sampling or weakly grounded inspection, which limits their ability to iteratively locate, verify, and justify predictions with temporally targeted evidence. To close this gap, we propose MedSc
-
Omics In Lung
-
Spatial and multi-omics transcriptomic dissects platinum resistance in lung adenocarcinoma: a five-gene predictive model with tumor microenvironment dynamics
Chem Biol Interact. 2026 Feb 7:111952. doi: 10.1016/j.cbi.2026.111952. Online ahead of print.ABSTRACTThe scarcity of reliable biomarkers and predictive models for platinum resistance in lung adenocarcinoma (LUAD) poses a significant clinical challenge. This study endeavors to identify molecular subtypes related to platinum resistance and construct a robust predictive model through multi-omics techniques. We performed integrative analysis of public datasets using advanced bioinformatics strategie
Spatial and multi-omics transcriptomic dissects platinum resistance in lung adenocarcinoma: a five-gene predictive model with tumor microenvironment dynamics
Chem Biol Interact. 2026 Feb 7:111952. doi: 10.1016/j.cbi.2026.111952. Online ahead of print.
ABSTRACT
The scarcity of reliable biomarkers and predictive models for platinum resistance in lung adenocarcinoma (LUAD) poses a significant clinical challenge. This study endeavors to identify molecular subtypes related to platinum resistance and construct a robust predictive model through multi-omics techniques. We performed integrative analysis of public datasets using advanced bioinformatics strategies, including spatial transcriptome deconvolution and consensus clustering. Bulk RNA deconvolution analysis was conducted to characterize tumor microenvironment heterogeneity. Feature selection was performed using the Supervised Principal Component (SuperPC) algorithm, followed by diagnostic model construction validated through receiver operating characteristic (ROC) analysis. Functional validation was performed through cytological experiments measuring cisplatin IC50 alterations following gene manipulation in LUAD cell lines. Consensus clustering revealed distinct LUAD subtypes, with Cluster1 demonstrating significant platinum resistance. We first subtyped the patients in the bulk transcriptome data based on consistency clustering, and then analyzed the differences between different platinum-resistant subtypes (Cluster 1 and Cluster 2), so as to screen 333 isotype-specific differentially expressed genes and 15 platinum resistance-related (PRR) genes were selected through machine learning. A refined 5-gene signature (ANKRD29/CACNA2D2/DSP/HSD17B6/SPP1) achieved exceptional predictive performance (AUC=0.9639). Spatial transcriptomics demonstrated compartmentalized expression patterns: SPP1/DSP localized to tumor niches, HSD17B6/CACNA2D2 to epithelial regions, and ANKRD29 depletion in stromal areas. Cellular colocalization analysis revealed malignant epithelial PH proximity to myeloid and mast cells. Functional validation confirmed that ANKRD29/CACNA2D2 overexpression sensitized A549/DDP cells to cisplatin, while DSP/SPP1/HSD17B6 overexpression induced resistance. Experiments in nude mice have shown that these genes are closely related to cisplatin resistance in LUAD. This study identifies the Cluster1 subtype and malignant epithelial PH as crucial determinants of platinum resistance in LUAD. Our innovative 5-gene predictive model exhibits clinical-grade diagnostic accuracy, and spatial transcriptomic characterization offers mechanistic insights into the dynamics of the tumor microenvironment.
PMID:41662930 | DOI:10.1016/j.cbi.2026.111952
-
Journal of Medical Internet Research
-
Problems and Barriers Regarding the Admission, Financing, and Service Provision of Digital Health Apps: Qualitative Stakeholder Survey
Background: Since their introduction with the Digital Care Act in 2019, DiGA are a part of the German statutory healthcare system. In order to become a DiGA, mHealth apps have to complete a certification process covering both technical and evidence related aspects. After completion, DiGA are added to the DiGA-directory, containing a list of all reimbursable DiGA within German statutory health insurance (SHI). The first apps were added at the end of 2020 with the number steadily increasing. The n
Problems and Barriers Regarding the Admission, Financing, and Service Provision of Digital Health Apps: Qualitative Stakeholder Survey
-
cs.AI, q-bio.NC updates on arXiv.org
-
Yunjue Agent Tech Report: A Fully Reproducible, Zero-Start In-Situ Self-Evolving Agent System for Open-Ended Tasks
arXiv:2601.18226v2 Announce Type: replace Abstract: Conventional agent systems often struggle in open-ended environments where task distributions continuously drift and external supervision is scarce. Their reliance on static toolsets or offline training lags behind these dynamics, leaving the system's capability boundaries rigid and unknown. To address this, we propose the In-Situ Self-Evolving paradigm. This approach treats sequential task interactions as a continuous stream of experience, en
Yunjue Agent Tech Report: A Fully Reproducible, Zero-Start In-Situ Self-Evolving Agent System for Open-Ended Tasks
-
Nature Medicine
-
Reliability of LLMs as medical assistants for the general public: a randomized preregistered study
Nature Medicine, Published online: 09 February 2026; doi:10.1038/s41591-025-04074-yIn a randomized controlled study involving 1,298 participants from a general sample, performance of humans when assisted by a large language model (LLM) was sensibly inferior to that of the LLM alone when assessing ten medical scenarios leading to disease identification and recommendations for treatment.
Reliability of LLMs as medical assistants for the general public: a randomized preregistered study
Nature Medicine, Published online: 09 February 2026; doi:10.1038/s41591-025-04074-y
In a randomized controlled study involving 1,298 participants from a general sample, performance of humans when assisted by a large language model (LLM) was sensibly inferior to that of the LLM alone when assessing ten medical scenarios leading to disease identification and recommendations for treatment.-
Cell
-
EcDNA-borne structural variants drive oncogenic fusion transcript amplification
Extrachromosomal DNA (ecDNA) is a major source of oncogenic fusions across cancer types, generating tissue-specific fusion landscapes with diagnostic potential. EcDNA-borne PVT1 5′-end fusions stabilize partner RNAs and boost oncogene output.
EcDNA-borne structural variants drive oncogenic fusion transcript amplification
-
cs.AI, q-bio.NC updates on arXiv.org
-
From Data to Behavior: Predicting Unintended Model Behaviors Before Training
arXiv:2602.04735v1 Announce Type: cross Abstract: Large Language Models (LLMs) can acquire unintended biases from seemingly benign training data even without explicit cues or malicious content. Existing methods struggle to detect such risks before fine-tuning, making post hoc evaluation costly and inefficient. To address this challenge, we introduce Data2Behavior, a new task for predicting unintended model behaviors prior to training. We also propose Manipulating Data Features (MDF), a lightwei
From Data to Behavior: Predicting Unintended Model Behaviors Before Training
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
Extrachromosomal DNA drives molecular and clinical heterogeneity in hepatocellular carcinoma: a multi-omics analysis and prognostic model development
Hum Genomics. 2026 Feb 3. doi: 10.1186/s40246-026-00927-w. Online ahead of print.ABSTRACTBACKGROUND: Extrachromosomal DNA (ecDNA) is an emerging hallmark of cancer that promotes tumor evolution and heterogeneity. However, the molecular characteristics and clinical significance of ecDNA in hepatocellular carcinoma (HCC) remain incompletely understood.METHODS: The clinical outcomes, genomics, transcriptomics, proteomics, tumor microenvironment, and drug target landscapes of ecDNA-negative and ecDN
Extrachromosomal DNA drives molecular and clinical heterogeneity in hepatocellular carcinoma: a multi-omics analysis and prognostic model development
Hum Genomics. 2026 Feb 3. doi: 10.1186/s40246-026-00927-w. Online ahead of print.
ABSTRACT
BACKGROUND: Extrachromosomal DNA (ecDNA) is an emerging hallmark of cancer that promotes tumor evolution and heterogeneity. However, the molecular characteristics and clinical significance of ecDNA in hepatocellular carcinoma (HCC) remain incompletely understood.
METHODS: The clinical outcomes, genomics, transcriptomics, proteomics, tumor microenvironment, and drug target landscapes of ecDNA-negative and ecDNA-positive HCC in the Cancer Genome Atlas (TCGA) were compared. Next, the least absolute shrinkage and selection operator (LASSO) and random survival forest (RSF) algorithms were used to screen the ecDNA gene signature. A nomogram was constructed and evaluated based on the risk score and clinicopathological features. Finally, the role of DNASE1L3 was validated through in vitro experiments.
RESULTS: EcDNA-positive tumors showed increased vascular invasion, higher AFP levels, and more TP53 mutations. These tumors displayed unique activation of proliferation pathways, decreased stromal infiltration, and heightened immune activation. Our validated six-gene signature (RNF186, BMP6, AOC1, FBLL1, MYBL2, and DNASE1L3) demonstrated strong prognostic value when combined with tumor stage in the nomogram. Notably, DNASE1L3 was downregulated in HCC, showed endothelial cell-specific expression, and suppressed the proliferation and migration of Hep3B2.1-7 cells.
CONCLUSION: Our study characterizes the molecular and clinical distinctions between ecDNA-negative and ecDNA-positive HCC and establishes a clinically applicable gene signature for patient prognosis. These findings advance our understanding of ecDNA-driven tumor heterogeneity and provide potential strategies for personalized HCC management.
PMID:41634868 | DOI:10.1186/s40246-026-00927-w
-
Omics in Gastric
-
Integrative proteogenomics maps multifactorial aetiology, progression and therapeutic vulnerabilities in gastric cancer
Gut. 2026 Jan 30:gutjnl-2025-337247. doi: 10.1136/gutjnl-2025-337247. Online ahead of print.ABSTRACTBACKGROUND: Gastric cancer, with disproportionately higher incidence in East Asia, arises from complex host-microbiome-environment interactions beyond Helicobacter pylori (HP) infection. However, the molecular architecture linking environmental carcinogens, microbial succession and host response remains unclear.OBJECTIVE: To delineate multifactorial aetiologies and clinically actionable subtypes/b
Integrative proteogenomics maps multifactorial aetiology, progression and therapeutic vulnerabilities in gastric cancer
Gut. 2026 Jan 30:gutjnl-2025-337247. doi: 10.1136/gutjnl-2025-337247. Online ahead of print.
ABSTRACT
BACKGROUND: Gastric cancer, with disproportionately higher incidence in East Asia, arises from complex host-microbiome-environment interactions beyond Helicobacter pylori (HP) infection. However, the molecular architecture linking environmental carcinogens, microbial succession and host response remains unclear.
OBJECTIVE: To delineate multifactorial aetiologies and clinically actionable subtypes/biomarkers of gastric cancer through integrative proteogenomic, microbial and environmental exposure profiling.
DESIGN: We established a multiomics atlas of paired tumour, adjacent mucosa tissues and blood from 154 treatment-naïve Taiwanese patients, integrating whole-exome sequencing, RNA-seq, proteome and phosphoproteome profiling with carcinogen signatures, HP status, microbiome composition and refined anatomical mapping. Cell-based functional assays tested carcinogen effects. Microbial subtype was assessed in an independent cohort.
RESULTS: A polycyclic-aromatic-hydrocarbon signature, dibenz[a,h]acridine, emerged as a high-risk exposure promoting invasion, immune suppression and poor survival, significantly exceeding nitrosamine-linked risk in this cohort. Multilayer integration defined three initiation ecologies: HP-driven inflammatory, non-HP microbiome-enriched immune-silent and HP-free microbially depleted states. Among HP-negative tumours, a Streptococcus-enriched subtype associated with tight-junction (CLDN18.2/ZO-1/OCLN) disruption and epithelial-mesenchymal transition, whereas a subset of clinically aggressive cases retained CLDN18.2-high epithelial-stable subtype for therapeutic accessibility. An independent cohort revealed gastric juice-derived Streptococcus anginosus abundance inversely correlated with tight-junction proteins. Anatomical mapping reveals location-specific, sex-specific, subtype-specific oncogenic networks and kinase activity, including CDK4 activation in clinical biomarker-negative tumours. Decision-tree models combining exposure and proteome-immune states refined recurrence and survival prediction beyond stage.
CONCLUSION: This proteogenomic framework defines exposure-informed and microbiome-informed gastric cancer subtypes, providing a molecular schema for patient stratification, prevention and actionable therapeutic vulnerabilities.
PMID:41617485 | DOI:10.1136/gutjnl-2025-337247
-
npj Digital Medicine
-
Publisher Correction: Best practice recommendations and considerations for designing and electronically implementing event-driven diaries in clinical trials
npj Digital Medicine, Published online: 27 January 2026; doi:10.1038/s41746-026-02396-wPublisher Correction: Best practice recommendations and considerations for designing and electronically implementing event-driven diaries in clinical trials
Publisher Correction: Best practice recommendations and considerations for designing and electronically implementing event-driven diaries in clinical trials
npj Digital Medicine, Published online: 27 January 2026; doi:10.1038/s41746-026-02396-w
Publisher Correction: Best practice recommendations and considerations for designing and electronically implementing event-driven diaries in clinical trials-
cs.AI, q-bio.NC updates on arXiv.org
-
Federated Proximal Optimization for Privacy-Preserving Heart Disease Prediction: A Controlled Simulation Study on Non-IID Clinical Data
arXiv:2601.17183v1 Announce Type: cross Abstract: Healthcare institutions have access to valuable patient data that could be of great help in the development of improved diagnostic models, but privacy regulations like HIPAA and GDPR prevent hospitals from directly sharing data with one another. Federated Learning offers a way out to this problem by facilitating collaborative model training without having the raw patient data centralized. However, clinical datasets intrinsically have non-IID (no
Federated Proximal Optimization for Privacy-Preserving Heart Disease Prediction: A Controlled Simulation Study on Non-IID Clinical Data
-
cs.AI, q-bio.NC updates on arXiv.org
-
The Limits of AI Data Transparency Policy: Three Disclosure Fallacies
arXiv:2601.18127v1 Announce Type: cross Abstract: Data transparency has emerged as a rallying cry for addressing concerns about AI: data quality, privacy, and copyright chief among them. Yet while these calls are crucial for accountability, current transparency policies often fall short of their intended aims. Similar to nutrition facts for food, policies aimed at nutrition facts for AI currently suffer from a limited consideration of research on effective disclosures. We offer an institutional
The Limits of AI Data Transparency Policy: Three Disclosure Fallacies
-
npj Digital Medicine
-
Multimodal digital biopsy for preoperative prediction of occult peritoneal metastasis in gastric cancer
npj Digital Medicine, Published online: 26 January 2026; doi:10.1038/s41746-025-02268-9Multimodal digital biopsy for preoperative prediction of occult peritoneal metastasis in gastric cancer
Multimodal digital biopsy for preoperative prediction of occult peritoneal metastasis in gastric cancer
npj Digital Medicine, Published online: 26 January 2026; doi:10.1038/s41746-025-02268-9
Multimodal digital biopsy for preoperative prediction of occult peritoneal metastasis in gastric cancer-
cs.AI, q-bio.NC updates on arXiv.org
-
PyHealth 2.0: A Comprehensive Open-Source Toolkit for Accessible and Reproducible Clinical Deep Learning
arXiv:2601.16414v1 Announce Type: cross Abstract: Difficulty replicating baselines, high computational costs, and required domain expertise create persistent barriers to clinical AI research. To address these challenges, we introduce PyHealth 2.0, an enhanced clinical deep learning toolkit that enables predictive modeling in as few as 7 lines of code. PyHealth 2.0 offers three key contributions: (1) a comprehensive toolkit addressing reproducibility and compatibility challenges by unifying 15+
PyHealth 2.0: A Comprehensive Open-Source Toolkit for Accessible and Reproducible Clinical Deep Learning
-
cs.AI, q-bio.NC updates on arXiv.org
-
DeepEra: A Deep Evidence Reranking Agent for Scientific Retrieval-Augmented Generated Question Answering
arXiv:2601.16478v1 Announce Type: cross Abstract: With the rapid growth of scientific literature, scientific question answering (SciQA) has become increasingly critical for exploring and utilizing scientific knowledge. Retrieval-Augmented Generation (RAG) enhances LLMs by incorporating knowledge from external sources, thereby providing credible evidence for scientific question answering. But existing retrieval and reranking methods remain vulnerable to passages that are semantically similar but
DeepEra: A Deep Evidence Reranking Agent for Scientific Retrieval-Augmented Generated Question Answering
-
cs.AI, q-bio.NC updates on arXiv.org
-
An Optimized Decision Tree-Based Framework for Explainable IoT Anomaly Detection
arXiv:2601.14305v1 Announce Type: cross Abstract: The increase in the number of Internet of Things (IoT) devices has tremendously increased the attack surface of cyber threats thus making a strong intrusion detection system (IDS) with a clear explanation of the process essential towards resource-constrained environments. Nevertheless, current IoT IDS systems are usually traded off with detection quality, model elucidability, and computational effectiveness, thus the deployment on IoT devices. T
An Optimized Decision Tree-Based Framework for Explainable IoT Anomaly Detection
-
TechCrunch
-
OpenEvidence hits $12B valuation, with new round led by Thrive, DST
The medical info database has doubled in valuation since last raise in October, despite encroachment from model makers.
OpenEvidence hits $12B valuation, with new round led by Thrive, DST
-
cs.AI, q-bio.NC updates on arXiv.org
-
OpenNovelty: An LLM-powered Agentic System for Verifiable Scholarly Novelty Assessment
arXiv:2601.01576v2 Announce Type: replace-cross Abstract: Evaluating novelty is critical yet challenging in peer review, as reviewers must assess submissions against a vast, rapidly evolving literature. This report presents OpenNovelty, an LLM-powered agentic system for transparent, evidence-based novelty analysis. The system operates through four phases: (1) extracting the core task and contribution claims to generate retrieval queries; (2) retrieving relevant prior work based on extracted que
OpenNovelty: An LLM-powered Agentic System for Verifiable Scholarly Novelty Assessment
-
npj Digital Medicine
-
An artificial intelligence-powered learning health system to improve sepsis detection and quality of care: a before-and-after study
npj Digital Medicine, Published online: 20 January 2026; doi:10.1038/s41746-025-02180-2An artificial intelligence-powered learning health system to improve sepsis detection and quality of care: a before-and-after study
An artificial intelligence-powered learning health system to improve sepsis detection and quality of care: a before-and-after study
npj Digital Medicine, Published online: 20 January 2026; doi:10.1038/s41746-025-02180-2
An artificial intelligence-powered learning health system to improve sepsis detection and quality of care: a before-and-after study-
npj Digital Medicine
-
LLM-driven collaborative framework for knowledge-enhanced cancer pain assessment and management
npj Digital Medicine, Published online: 19 January 2026; doi:10.1038/s41746-026-02362-6LLM-driven collaborative framework for knowledge-enhanced cancer pain assessment and management
LLM-driven collaborative framework for knowledge-enhanced cancer pain assessment and management
npj Digital Medicine, Published online: 19 January 2026; doi:10.1038/s41746-026-02362-6
LLM-driven collaborative framework for knowledge-enhanced cancer pain assessment and management