Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Does Less Hallucination Mean Less Creativity? An Empirical Investigation in LLMs
arXiv:2512.11509v1 Announce Type: cross Abstract: Large Language Models (LLMs) exhibit remarkable capabilities in natural language understanding and reasoning, but suffer from hallucination: the generation of factually incorrect content. While numerous methods have been developed to reduce hallucinations, their impact on creative generations remains unexplored. This gap is particularly critical for AI-assisted scientific discovery, which requires both factual accuracy and creative hypothesis ge
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cs.AI, q-bio.NC updates on arXiv.org
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From Verification Burden to Trusted Collaboration: Design Goals for LLM-Assisted Literature Reviews
arXiv:2512.11661v1 Announce Type: cross Abstract: Large Language Models (LLMs) are increasingly embedded in academic writing practices. Although numerous studies have explored how researchers employ these tools for scientific writing, their concrete implementation, limitations, and design challenges within the literature review process remain underexplored. In this paper, we report a user study with researchers across multiple disciplines to characterize current practices, benefits, and \textit
From Verification Burden to Trusted Collaboration: Design Goals for LLM-Assisted Literature Reviews
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cs.AI, q-bio.NC updates on arXiv.org
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Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Quality
arXiv:2503.05860v3 Announce Type: replace-cross Abstract: Benchmarks are essential for unified evaluation and reproducibility. The rapid rise of Artificial Intelligence for Software Engineering (AI4SE) has produced numerous benchmarks for tasks such as code generation and bug repair. However, this proliferation has led to major challenges: (1) fragmented knowledge across tasks, (2) difficulty in selecting contextually relevant benchmarks, (3) lack of standardization in benchmark creation, and (
Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Quality
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cs.AI, q-bio.NC updates on arXiv.org
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Understanding Prompt Management in GitHub Repositories: A Call for Best Practices
arXiv:2509.12421v2 Announce Type: replace-cross Abstract: The rapid adoption of foundation models (e.g., large language models) has given rise to promptware, i.e., software built using natural language prompts. Effective management of prompts, such as organization and quality assurance, is essential yet challenging. In this study, we perform an empirical analysis of 24,800 open-source prompts from 92 GitHub repositories to investigate prompt management practices and quality attributes. Our find
Understanding Prompt Management in GitHub Repositories: A Call for Best Practices
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cs.AI, q-bio.NC updates on arXiv.org
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MetaVoxel: Joint Diffusion Modeling of Imaging and Clinical Metadata
arXiv:2512.10041v2 Announce Type: replace-cross Abstract: Modern deep learning methods have achieved impressive results across tasks from disease classification, estimating continuous biomarkers, to generating realistic medical images. Most of these approaches are trained to model conditional distributions defined by a specific predictive direction with a specific set of input variables. We introduce MetaVoxel, a generative joint diffusion modeling framework that models the joint distribution o
MetaVoxel: Joint Diffusion Modeling of Imaging and Clinical Metadata
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Omics In Lung
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High-Throughput Dissection of Inter-Organ Genetic Networks: A Multi-Omic Systems Biology Approach
SLAS Technol. 2025 Dec 11:100376. doi: 10.1016/j.slast.2025.100376. Online ahead of print.ABSTRACTThe existing multi-omic analyses are frequently confined to individual tissues, and the regulatory picture of the systemic regulator of complex physiology and disease is hidden. To fill this gap, we have created a unified systems biology model of the high-throughput dissection of inter-organ genetic networks. Our model incorporates transcriptomic, epigenomic and proteomic analysis of five major orga
High-Throughput Dissection of Inter-Organ Genetic Networks: A Multi-Omic Systems Biology Approach
SLAS Technol. 2025 Dec 11:100376. doi: 10.1016/j.slast.2025.100376. Online ahead of print.
ABSTRACT
The existing multi-omic analyses are frequently confined to individual tissues, and the regulatory picture of the systemic regulator of complex physiology and disease is hidden. To fill this gap, we have created a unified systems biology model of the high-throughput dissection of inter-organ genetic networks. Our model incorporates transcriptomic, epigenomic and proteomic analysis of five major organs (liver, kidney, heart, lung, brain) using the Multi-Omics Factor Analysis (MOFA+) tool, specifically, cross-tissue coordination. We characterized 27 evidence-heavy cross-tissue modules (FDR < 0.05) that are major hubs such as *HNF4Aenda NRF2cheng8loadmasterregulatingconstitutionembryonicstemcellularinfoncogenes recognize them. One notable observation was liver-kidney metabolic axis, significant cross-talks in hepatocyte organoids are confirmed with CRISPR knockdown, which suppresses the expression of transporters expressed by the kidney. Our work offers a scalable validated framework that goes beyond organ-centric perspectives, which can be used as a potent tool of systemic disease modelling and precision medicine.
PMID:41389879 | DOI:10.1016/j.slast.2025.100376
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Journal of Medical Internet Research
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Stakeholder Criteria for Trust in Artificial Intelligence–Based Computer Perception Tools in Health Care: Qualitative Interview Study
Background: Computer perception (CP) technologies hold significant promise for advancing precision mental health care systems, given their ability to leverage algorithmic analysis of continuous, passive sensing data from wearables and smartphones (eg, behavioral activity, geolocation, vocal features, and ambient environmental data) to infer clinically meaningful behavioral and physiological states. However, successful implementation critically depends on cultivating well-founded stakeholder trus
Stakeholder Criteria for Trust in Artificial Intelligence–Based Computer Perception Tools in Health Care: Qualitative Interview Study
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npj Digital Medicine
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Legal implications of AI standard of care integration on patients’ informed consent: lessons from surgery
npj Digital Medicine, Published online: 13 December 2025; doi:10.1038/s41746-025-02157-1Legal implications of AI standard of care integration on patients’ informed consent: lessons from surgery
Legal implications of AI standard of care integration on patients’ informed consent: lessons from surgery
npj Digital Medicine, Published online: 13 December 2025; doi:10.1038/s41746-025-02157-1
Legal implications of AI standard of care integration on patients’ informed consent: lessons from surgery-
TechCrunch
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Trump’s AI executive order promises ‘one rulebook’ — startups may get legal limbo instead
Trump signed an AI executive order targeting state laws and promising one national rulebook. Critics warn it could trigger court battles and prolong uncertainty for startups while Congress debates federal rules.
Trump’s AI executive order promises ‘one rulebook’ — startups may get legal limbo instead
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cs.AI, q-bio.NC updates on arXiv.org
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Exploring Health Misinformation Detection with Multi-Agent Debate
arXiv:2512.09935v1 Announce Type: new Abstract: Fact-checking health-related claims has become increasingly critical as misinformation proliferates online. Effective verification requires both the retrieval of high-quality evidence and rigorous reasoning processes. In this paper, we propose a two-stage framework for health misinformation detection: Agreement Score Prediction followed by Multi-Agent Debate. In the first stage, we employ large language models (LLMs) to independently evaluate retr
Exploring Health Misinformation Detection with Multi-Agent Debate
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cs.AI, q-bio.NC updates on arXiv.org
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Mind the Gap! Pathways Towards Unifying AI Safety and Ethics Research
arXiv:2512.10058v1 Announce Type: new Abstract: While much research in artificial intelligence (AI) has focused on scaling capabilities, the accelerating pace of development makes countervailing work on producing harmless, "aligned" systems increasingly urgent. Yet research on alignment has diverged along two largely parallel tracks: safety--centered on scaled intelligence, deceptive or scheming behaviors, and existential risk--and ethics--focused on present harms, the reproduction of social bi
Mind the Gap! Pathways Towards Unifying AI Safety and Ethics Research
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Cell
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Are ultrasensitive ctDNA assays ready for clinical use in early-stage NSCLC?
Disease recurrence in early-stage non-small cell lung cancer (NSCLC) remains a persistent clinical challenge, underscoring the need for better prognostic biomarkers. In this preview, we highlight the clinical implications of ultrasensitive ctDNA monitoring in lung cancer risk modeling reported by Black et al. in this issue of Cell.
Are ultrasensitive ctDNA assays ready for clinical use in early-stage NSCLC?
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Cell
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Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy
MiTEs are myeloid-targeted immunocytokine prodrugs that block TREM2+ tumor-associated macrophages while activating cytotoxic lymphocytes via TME-specific IL-2 activity, eliciting strong anti-tumor efficacy in preclinical models with minimal systemic toxicity.
Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy
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(Multiomics OR Omics) AND (Pancreatic)
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Pancreatic Cancer Organoids: Modeling Disease and Guiding Therapy
Cancers (Basel). 2025 Nov 30;17(23):3850. doi: 10.3390/cancers17233850.ABSTRACTPancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies. An unmet need exists for reliable biomarkers and in vitro models capable of predicting patient drug response to advance personalized medicine. Traditional models fail to represent the tumor's complexity and the role of the stromal environment in chemoresistance. Patient-derived organoids (PDOs) overcome these limitations, enabling multi-om
Pancreatic Cancer Organoids: Modeling Disease and Guiding Therapy
Cancers (Basel). 2025 Nov 30;17(23):3850. doi: 10.3390/cancers17233850.
ABSTRACT
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies. An unmet need exists for reliable biomarkers and in vitro models capable of predicting patient drug response to advance personalized medicine. Traditional models fail to represent the tumor's complexity and the role of the stromal environment in chemoresistance. Patient-derived organoids (PDOs) overcome these limitations, enabling multi-omics profiling and reliable drug testing for functional precision medicine. This review provides a comprehensive overview of PDAC PDO research, emphasizing the following major areas: (i) the genetic and phenotypic fidelity of PDOs, (ii) their predictive value for drug response and chemoresistance, (iii) the integration of the extracellular matrix and tumor microenvironment (TME) components, and (iv) emerging technologies. Studies confirm that PDOs faithfully represent the primary tumor's specific genetic features and retain intratumoral heterogeneity. PDO-based platforms have demonstrated a strong correlation between in vitro drug sensitivity and in vivo efficacy in xenograft models, validating their utility for identifying drug candidates, repurposing existing drugs, and determining effective combinations. Efforts are ongoing to integrate crucial TME components, like cancer-associated fibroblasts, using innovative co-culture platforms such as fused PDOs and InterOMaX, to better model desmoplasia and chemoresistance mechanisms. Furthermore, PDO technology is converging with microphysiological systems and artificial intelligence tools to facilitate high-throughput drug screening and dynamic, real-time monitoring of therapeutic effects. The integration of PDOs into biobanks and advanced screening platforms holds the potential to accelerate drug discovery and improve therapeutic outcomes for PDAC patients, if challenges related to protocol standardization and regulatory acceptance are addressed.
PMID:41375051 | PMC:PMC12690986 | DOI:10.3390/cancers17233850
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Omics In Lung
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Integrative network pharmacology, transcriptomics, and microbiomics elucidate the therapeutic mechanism of <em>Polygala tenuifolia</em> Willd water extract in chronic obstructive pulmonary disease
Front Microbiol. 2025 Nov 25;16:1703853. doi: 10.3389/fmicb.2025.1703853. eCollection 2025.ABSTRACTBACKGROUND: Polygala tenuifolia Willd (PT) is a plant with both medicinal and edible values. Traditionally, it has been used for sedation, enhancing cognition, resolving phlegm, and relieving cough. However, its protective effects and mechanisms against chronic obstructive pulmonary disease (COPD) remain unclear.AIM OF THE STUDY: This study aims to observe the protective effects of the water extrac
Integrative network pharmacology, transcriptomics, and microbiomics elucidate the therapeutic mechanism of <em>Polygala tenuifolia</em> Willd water extract in chronic obstructive pulmonary disease
Front Microbiol. 2025 Nov 25;16:1703853. doi: 10.3389/fmicb.2025.1703853. eCollection 2025.
ABSTRACT
BACKGROUND: Polygala tenuifolia Willd (PT) is a plant with both medicinal and edible values. Traditionally, it has been used for sedation, enhancing cognition, resolving phlegm, and relieving cough. However, its protective effects and mechanisms against chronic obstructive pulmonary disease (COPD) remain unclear.
AIM OF THE STUDY: This study aims to observe the protective effects of the water extract of Polygala tenuifolia Willd (WEPT) on COPD, and to preliminarily elucidate its potential therapeutic mechanisms by integrating network pharmacology, molecular docking, multi-omics analysis, and molecular experiments.
METHODS AND MATERIALS: HPLC quantified WEPT constituents. COPD mice models established via chronic smoke exposure underwent WEPT treatment, and the therapeutic effect was evaluated by lung function test, histopathology and cytokine profiling. Integrated multi-omics analyses (network pharmacology, transcriptomics, microbiomics) identified bioactive compounds, therapeutic targets, pathway regulations, and microbiota dynamics. Molecular docking validated compound-target interactions, while immunohistochemical/fluorescence assays confirmed key protein expression in lung tissues.
RESULTS: WEPT administration effectively reduced inflammatory cytokine levels in COPD mice, improved lung function, and alleviated histopathological damage like alveolar structural injury and airway inflammation. Network pharmacology and transcriptomic analyses identified Norhyoscyamine and Onjixanthone I as key active components, targeting PIK3CA and AKT1 via PI3K-AKT pathway regulation. Microbiome analysis showed WEPT restored gut microbiota balance. Molecular docking confirmed strong binding of bioactive compounds to core targets, while immunostaining assays demonstrated WEPT suppressed p-PI3K and p-AKT protein expression.
CONCLUSION: WEPT may exert its intervention effects on COPD through a multi-target and multi-level comprehensive regulatory mechanism.
PMID:41377050 | PMC:PMC12685879 | DOI:10.3389/fmicb.2025.1703853
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npj Digital Medicine
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AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential
npj Digital Medicine, Published online: 11 December 2025; doi:10.1038/s41746-025-02198-6AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential
npj Digital Medicine, Published online: 11 December 2025; doi:10.1038/s41746-025-02198-6
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential-
npj Digital Medicine
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Potential for Algorithmic Bias in Clinical Decision Instrument Development
npj Digital Medicine, Published online: 10 December 2025; doi:10.1038/s41746-025-02119-7Potential for Algorithmic Bias in Clinical Decision Instrument Development
Potential for Algorithmic Bias in Clinical Decision Instrument Development
npj Digital Medicine, Published online: 10 December 2025; doi:10.1038/s41746-025-02119-7
Potential for Algorithmic Bias in Clinical Decision Instrument Development-
cs.AI, q-bio.NC updates on arXiv.org
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Toward an AI Reasoning-Enabled System for Patient-Clinical Trial Matching
arXiv:2512.08026v1 Announce Type: new Abstract: Screening patients for clinical trial eligibility remains a manual, time-consuming, and resource-intensive process. We present a secure, scalable proof-of-concept system for Artificial Intelligence (AI)-augmented patient-trial matching that addresses key implementation challenges: integrating heterogeneous electronic health record (EHR) data, facilitating expert review, and maintaining rigorous security standards. Leveraging open-source, reasoning
Toward an AI Reasoning-Enabled System for Patient-Clinical Trial Matching
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cs.AI, q-bio.NC updates on arXiv.org
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Beyond Traditional Diagnostics: Transforming Patient-Side Information into Predictive Insights with Knowledge Graphs and Prototypes
arXiv:2512.08261v1 Announce Type: new Abstract: Predicting diseases solely from patient-side information, such as demographics and self-reported symptoms, has attracted significant research attention due to its potential to enhance patient awareness, facilitate early healthcare engagement, and improve healthcare system efficiency. However, existing approaches encounter critical challenges, including imbalanced disease distributions and a lack of interpretability, resulting in biased or unreliab
Beyond Traditional Diagnostics: Transforming Patient-Side Information into Predictive Insights with Knowledge Graphs and Prototypes
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cs.AI, q-bio.NC updates on arXiv.org
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Principles2Plan: LLM-Guided System for Operationalising Ethical Principles into Plans
arXiv:2512.08536v1 Announce Type: new Abstract: Ethical awareness is critical for robots operating in human environments, yet existing automated planning tools provide little support. Manually specifying ethical rules is labour-intensive and highly context-specific. We present Principles2Plan, an interactive research prototype demonstrating how a human and a Large Language Model (LLM) can collaborate to produce context-sensitive ethical rules and guide automated planning. A domain expert provid