Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Pretrain Value, Not Reward: Decoupled Value Policy Optimization
arXiv:2502.16944v2 Announce Type: replace-cross Abstract: In this paper, we explore how directly pretraining a value model simplifies and stabilizes reinforcement learning from human feedback (RLHF). In reinforcement learning, value estimation is the key to policy optimization, distinct from reward supervision. The value function predicts the \emph{return-to-go} of a partial answer, that is, how promising the partial answer is if it were continued to completion. In RLHF, however, the standard p
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Omics In Lung
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Recapitulating lung cancer metastasis in vitro: Advances in organoid models and challenges in clinical translation (Review)
Oncol Rep. 2026 Mar;55(3):49. doi: 10.3892/or.2026.9054. Epub 2026 Jan 23.ABSTRACTLung cancer remains a significant global health challenge, with metastatic progression being the leading driver of mortality. Organoid technology provides a tractable, physiologically relevant platform to model key aspects of lung cancer metastasis in vitro. The present review summarized methodologies for constructing and interrogating these models, covering tissue sources, culture modalities, gene editing and in v
Recapitulating lung cancer metastasis in vitro: Advances in organoid models and challenges in clinical translation (Review)
Oncol Rep. 2026 Mar;55(3):49. doi: 10.3892/or.2026.9054. Epub 2026 Jan 23.
ABSTRACT
Lung cancer remains a significant global health challenge, with metastatic progression being the leading driver of mortality. Organoid technology provides a tractable, physiologically relevant platform to model key aspects of lung cancer metastasis in vitro. The present review summarized methodologies for constructing and interrogating these models, covering tissue sources, culture modalities, gene editing and in vivo transplantation; applications in studying metastatic mechanisms, drug screening and capturing intra‑ and intertumoral heterogeneity are also highlighted. Persistent challenges include standardizing derivation and culture conditions, improving preservation of tumor‑microenvironmental interactions, expanding immune‑competent and vascularized models, and addressing scalability, cost, and regulatory and ethical considerations for clinical translation. Future directions include integrating multi‑omics approaches and spatial profiling, leveraging artificial intelligence for image and response analytics, advancing immune‑organoid models and establishing shared standards, reference materials and reporting guidelines to enhance reproducibility and clinical impact.
PMID:41574717 | DOI:10.3892/or.2026.9054
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cs.AI, q-bio.NC updates on arXiv.org
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PPGFlowECG: Latent Rectified Flow with Cross-Modal Encoding for PPG-Guided ECG Generation and Cardiovascular Disease Detection
arXiv:2509.19774v2 Announce Type: replace-cross Abstract: Electrocardiography (ECG) is the clinical gold standard for cardiovascular disease (CVD) assessment, yet continuous monitoring is constrained by the need for dedicated hardware and trained personnel. Photoplethysmography (PPG) is ubiquitous in wearable devices and readily scalable, but it lacks electrophysiological specificity, limiting diagnostic reliability. While generative methods aim to translate PPG into clinically useful ECG signa
PPGFlowECG: Latent Rectified Flow with Cross-Modal Encoding for PPG-Guided ECG Generation and Cardiovascular Disease Detection
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(Multiomics OR Omics) AND (Pancreatic)
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Research progress in diagnosis and treatment of pancreatic cancer with mismatch repair and microsatellite instability
Clin Transl Oncol. 2026 Jan 21. doi: 10.1007/s12094-025-04214-3. Online ahead of print.ABSTRACTPancreatic cancer (PC), predominantly pancreatic ductal adenocarcinoma, remains one of the most lethal malignancies, largely due to late diagnosis and intrinsic resistance to conventional therapies. In recent years, mismatch repair deficiency (dMMR) and microsatellite instability-high (MSI-H) have emerged as clinically actionable biomarkers in a small but distinct subset of PC, accounting for approxima
Research progress in diagnosis and treatment of pancreatic cancer with mismatch repair and microsatellite instability
Clin Transl Oncol. 2026 Jan 21. doi: 10.1007/s12094-025-04214-3. Online ahead of print.
ABSTRACT
Pancreatic cancer (PC), predominantly pancreatic ductal adenocarcinoma, remains one of the most lethal malignancies, largely due to late diagnosis and intrinsic resistance to conventional therapies. In recent years, mismatch repair deficiency (dMMR) and microsatellite instability-high (MSI-H) have emerged as clinically actionable biomarkers in a small but distinct subset of PC, accounting for approximately 1-2% of cases. These tumors display unique molecular characteristics, including a high prevalence of wild-type KRAS and TP53, elevated tumor mutational burden, and recurrent kinase fusions, which together confer enhanced immunogenicity and increased sensitivity to immune checkpoint inhibitors (ICIs). In addition to their therapeutic relevance, dMMR/MSI-H status has important diagnostic implications for the identification of Lynch syndrome-associated pancreatic cancers, informing genetic counseling and familial risk assessment. This review summarizes current understanding of the molecular basis of mismatch repair deficiency and microsatellite instability in PC, evaluates available diagnostic approaches such as immunohistochemistry, polymerase chain reaction, and next-generation sequencing, and discusses the prognostic and predictive significance of dMMR/MSI-H status. Emerging clinical evidence supporting the use of ICIs in selected patients across neoadjuvant, adjuvant, and advanced disease settings is also reviewed, along with challenges related to assay discordance, tumor heterogeneity, and immunotherapy resistance. Finally, future directions are highlighted, emphasizing the need for standardized testing algorithms, integration of multi-omics and spatial profiling technologies, and prospective clinical studies to optimize precision treatment strategies for this rare but clinically meaningful subtype of pancreatic cancer.
PMID:41563663 | DOI:10.1007/s12094-025-04214-3
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cs.AI, q-bio.NC updates on arXiv.org
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SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understanding
arXiv:2601.12805v1 Announce Type: cross Abstract: Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, However, their ability to reliably reason from gene-level knowledge to functional understanding, a core requirement for knowledge-enhanced cell atlas interpretation, remains largely underexplored. To address this gap
SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understanding
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cs.AI, q-bio.NC updates on arXiv.org
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Zero-shot adaptable task planning for autonomous construction robots: a comparative study of lightweight single and multi-AI agent systems
arXiv:2601.14091v1 Announce Type: cross Abstract: Robots are expected to play a major role in the future construction industry but face challenges due to high costs and difficulty adapting to dynamic tasks. This study explores the potential of foundation models to enhance the adaptability and generalizability of task planning in construction robots. Four models are proposed and implemented using lightweight, open-source large language models (LLMs) and vision language models (VLMs). These model
Zero-shot adaptable task planning for autonomous construction robots: a comparative study of lightweight single and multi-AI agent systems
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cs.AI, q-bio.NC updates on arXiv.org
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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
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cs.AI, q-bio.NC updates on arXiv.org
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Mitigating Gender Bias via Fostering Exploratory Thinking in LLMs
arXiv:2505.17217v3 Announce Type: replace-cross Abstract: Large Language Models (LLMs) often exhibit gender bias, resulting in unequal treatment of male and female subjects across different contexts. To address this issue, we propose a novel data generation framework that fosters exploratory thinking in LLMs. Our approach prompts models to generate story pairs featuring male and female protagonists in structurally identical, morally ambiguous scenarios, then elicits and compares their moral jud
Mitigating Gender Bias via Fostering Exploratory Thinking in LLMs
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(Multiomics OR Omics) AND (Pancreatic)
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Complement-secreting CAFs are associated with better prognosis in pancreatic cancer: single-cell multiomics
Gut. 2026 Jan 13:gutjnl-2025-335683. doi: 10.1136/gutjnl-2025-335683. Online ahead of print.ABSTRACTBACKGROUND: Accumulating evidence has demonstrated that distinct tumour-promoting and tumour-restraining cancer-associated fibroblast (CAF) subtypes coexist in pancreatic ductal adenocarcinoma.OBJECTIVE: To develop targeted CAF therapeutic strategies by reprogramming tumour-promoting CAF subtypes.DESIGN: We leveraged multiomics technologies to systematically identify and characterise CAF subtypes
Complement-secreting CAFs are associated with better prognosis in pancreatic cancer: single-cell multiomics
Gut. 2026 Jan 13:gutjnl-2025-335683. doi: 10.1136/gutjnl-2025-335683. Online ahead of print.
ABSTRACT
BACKGROUND: Accumulating evidence has demonstrated that distinct tumour-promoting and tumour-restraining cancer-associated fibroblast (CAF) subtypes coexist in pancreatic ductal adenocarcinoma.
OBJECTIVE: To develop targeted CAF therapeutic strategies by reprogramming tumour-promoting CAF subtypes.
DESIGN: We leveraged multiomics technologies to systematically identify and characterise CAF subtypes transcriptionally, epigenetically and spatially and correlate them with clinicopathological features.
RESULTS: We found that complement-secreting CAFs (csCAFs), initially identified by our group and inflammatory CAFs (iCAFs) share significant overlap in their transcriptional profiles and chromatin accessibility. iCAFs specifically express transcription factors from the heme and oxidative homeostasis pathway and the activator protein 1 family, which are both involved in cellular response to oxidative stress. Notably, the composition of csCAFs among all CAFs declined during pancreatic carcinogenesis, while trajectory analysis showed that csCAFs could potentially differentiate into iCAFs. Spatially resolved analysis indicated that tumour regions with a higher csCAF composition were associated with lower levels of TGF-β ligands, fewer M2 tumour-associated macrophages and increased levels of lipid mediators. Additionally, we identified a spatially defined CXCL12-CXCR4 ligand-receptor interaction between csCAFs and T cells, but in distinct patterns between different metastatic organs. Patients with a higher composition of csCAFs have significantly longer overall survival and recurrence-free survival through multiplex immunohistochemistry and bulk RNA-seq deconvolution.
CONCLUSION: Our study demonstrates that csCAFs may represent an early-stage iCAF subtype and suggests a promising strategy for reprogramming iCAFs into csCAFs.
PMID:41534892 | DOI:10.1136/gutjnl-2025-335683
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npj Digital Medicine
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Geometric multi-instance learning for weakly supervised gastric cancer segmentation
npj Digital Medicine, Published online: 13 January 2026; doi:10.1038/s41746-025-02287-6Geometric multi-instance learning for weakly supervised gastric cancer segmentation
Geometric multi-instance learning for weakly supervised gastric cancer segmentation
npj Digital Medicine, Published online: 13 January 2026; doi:10.1038/s41746-025-02287-6
Geometric multi-instance learning for weakly supervised gastric cancer segmentation-
cs.AI, q-bio.NC updates on arXiv.org
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Interoperability in AI Safety Governance: Ethics, Regulations, and Standards
arXiv:2601.06153v1 Announce Type: cross Abstract: This policy report draws on country studies from China, South Korea, Singapore, and the United Kingdom to identify effective tools and key barriers to interoperability in AI safety governance. It offers practical recommendations to support a globally informed yet locally grounded governance ecosystem. Interoperability is a central goal of AI governance, vital for reducing risks, fostering innovation, enhancing competitiveness, promoting standard
Interoperability in AI Safety Governance: Ethics, Regulations, and Standards
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cs.AI, q-bio.NC updates on arXiv.org
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FairMedQA: Benchmarking Bias in Large Language Models for Medical Question Answering
arXiv:2505.19562v2 Announce Type: replace Abstract: Large language models (LLMs) are approaching expert-level performance in medical question answering (QA), demonstrating strong potential to improve public healthcare. However, underlying biases related to sensitive attributes such as sex and race pose life-critical risks. The extent to which such sensitive attributes affect diagnosis remains an open question and requires comprehensive empirical investigation. Additionally, even the latest Coun
FairMedQA: Benchmarking Bias in Large Language Models for Medical Question Answering
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cs.AI, q-bio.NC updates on arXiv.org
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Streamlining evidence based clinical recommendations with large language models
arXiv:2505.10282v2 Announce Type: replace-cross Abstract: Clinical evidence underpins informed healthcare decisions, yet integrating it into real-time practice remains challenging due to intensive workloads, complex procedures, and time constraints. This study presents Quicker, an LLM-powered system that automates evidence synthesis and generates clinical recommendations following standard guideline development workflows. Quicker delivers an end-to-end pipeline from clinical questions to recomm
Streamlining evidence based clinical recommendations with large language models
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Omics In Lung
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The role of PCMT1 in prognosis tumor immune microenvironment and therapeutic responses across cancers
Discov Oncol. 2026 Jan 5. doi: 10.1007/s12672-025-04366-2. Online ahead of print.ABSTRACTBACKGROUND: Emerging evidence highlights the overexpression of Protein-L-isoaspartate (D-aspartate) O-methyltransferase (PCMT1) in multiple malignancies. However, its pan-cancer prognostic significance, tumor immune microenvironment (TIME) interactions, and therapeutic implications remain underexplored.METHODS: Multi-omics data were integrated from UCSC Xena, GTEx, UALCAN, and published cohorts. PCMT1 expres
The role of PCMT1 in prognosis tumor immune microenvironment and therapeutic responses across cancers
Discov Oncol. 2026 Jan 5. doi: 10.1007/s12672-025-04366-2. Online ahead of print.
ABSTRACT
BACKGROUND: Emerging evidence highlights the overexpression of Protein-L-isoaspartate (D-aspartate) O-methyltransferase (PCMT1) in multiple malignancies. However, its pan-cancer prognostic significance, tumor immune microenvironment (TIME) interactions, and therapeutic implications remain underexplored.
METHODS: Multi-omics data were integrated from UCSC Xena, GTEx, UALCAN, and published cohorts. PCMT1 expression patterns were systematically analyzed across 33 cancer types. Associations between PCMT1 and clinical outcomes, immune infiltration, immune checkpoint genes (ICGs), tumor mutation burden (TMB), microsatellite instability (MSI), and drug sensitivity were evaluated using bioinformatics pipelines.
RESULTS: Our pan-cancer analysis revealed differential expression patterns of PCMT1 across various malignancies, with significant upregulation in 20 cancer types and downregulation in 3 cancer types. Notably, PCMT1 overexpression was predominantly observed in epithelial-origin tumors, such as ACC (adrenocortical carcinoma), BRCA (breast invasive carcinoma), COAD (colon adenocarcinoma), and LUAD (lung adenocarcinoma). Survival analysis demonstrated that elevated PCMT1 expression was significantly correlated with unfavorable prognosis in multiple epithelial tumors, particularly in BRCA, esophageal carcinoma (ESCA), head and neck squamous cell carcinoma (HNSC), liver hepatocellular carcinoma (LIHC), and mesothelioma (MESO). Furthermore, comprehensive analysis identified significant associations between PCMT1 expression and various tumor microenvironment features, including immune scores, six distinct immune cell types, four immunosuppressive cell populations, cancer-associated fibroblasts (CAFs)-related markers, and immunosuppressive factors. PCMT1 expression also showed significant correlations with tumor mutation burden (TMB), microsatellite instability (MSI), DNA stemness score (DNAss), and RNA stemness score (RNAss). Particularly noteworthy was the strong positive correlation between PCMT1 expression and CAFs infiltration, along with their associated factors. These findings were further validated in independent immunotherapy cohorts, where PCMT1 consistently demonstrated immunosuppressive characteristics.
CONCLUSION: Multi-omics analysis suggests that PCMT1 may serve as a potential prognostic biomarker and a novel immunotherapy target for pan-cancer.
PMID:41491065 | DOI:10.1007/s12672-025-04366-2
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cs.AI, q-bio.NC updates on arXiv.org
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Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models
arXiv:2601.01321v1 Announce Type: new Abstract: Digital twins, as precise digital representations of physical systems, have evolved from passive simulation tools into intelligent and autonomous entities through the integration of artificial intelligence technologies. This paper presents a unified four-stage framework that systematically characterizes AI integration across the digital twin lifecycle, spanning modeling, mirroring, intervention, and autonomous management. By synthesizing existing
Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models
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cs.AI, q-bio.NC updates on arXiv.org
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OpenNovelty: An LLM-powered Agentic System for Verifiable Scholarly Novelty Assessment
arXiv:2601.01576v1 Announce Type: 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 queries via
OpenNovelty: An LLM-powered Agentic System for Verifiable Scholarly Novelty Assessment
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cs.AI, q-bio.NC updates on arXiv.org
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PathFound: An Agentic Multimodal Model Activating Evidence-seeking Pathological Diagnosis
arXiv:2512.23545v1 Announce Type: cross Abstract: Recent pathological foundation models have substantially advanced visual representation learning and multimodal interaction. However, most models still rely on a static inference paradigm in which whole-slide images are processed once to produce predictions, without reassessment or targeted evidence acquisition under ambiguous diagnoses. This contrasts with clinical diagnostic workflows that refine hypotheses through repeated slide observations
PathFound: An Agentic Multimodal Model Activating Evidence-seeking Pathological Diagnosis
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npj Digital Medicine
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Context matching is not reasoning when performing generalized clinical evaluation of generative language models
npj Digital Medicine, Published online: 27 December 2025; doi:10.1038/s41746-025-02253-2Context matching is not reasoning when performing generalized clinical evaluation of generative language models
Context matching is not reasoning when performing generalized clinical evaluation of generative language models
npj Digital Medicine, Published online: 27 December 2025; doi:10.1038/s41746-025-02253-2
Context matching is not reasoning when performing generalized clinical evaluation of generative language models-
npj Digital Medicine
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A novel evaluation benchmark for medical LLMs illuminating safety and effectiveness in clinical domains
npj Digital Medicine, Published online: 26 December 2025; doi:10.1038/s41746-025-02277-8A novel evaluation benchmark for medical LLMs illuminating safety and effectiveness in clinical domains
A novel evaluation benchmark for medical LLMs illuminating safety and effectiveness in clinical domains
npj Digital Medicine, Published online: 26 December 2025; doi:10.1038/s41746-025-02277-8
A novel evaluation benchmark for medical LLMs illuminating safety and effectiveness in clinical domains-
cs.AI, q-bio.NC updates on arXiv.org
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aiXiv: A Next-Generation Open Access Ecosystem for Scientific Discovery Generated by AI Scientists
arXiv:2508.15126v2 Announce Type: replace Abstract: Recent advances in large language models (LLMs) have enabled AI agents to autonomously generate scientific proposals, conduct experiments, author papers, and perform peer reviews. Yet this flood of AI-generated research content collides with a fragmented and largely closed publication ecosystem. Traditional journals and conferences rely on human peer review, making them difficult to scale and often reluctant to accept AI-generated research con