Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Geo-Expert: Towards Expert-Level Geological Reasoning via Parameter-Efficient Fine-Tuning
arXiv:2605.24844v1 Announce Type: new Abstract: While general-purpose Large Language Models (LLMs) applied to Geology often hallucinate when reasoning about subsurface structures and deep-time evolution, current AI in Earth sciences predominantly targets surface remote sensing and GIS. To bridge this gap, we introduce Geo-Expert, a family of parameter-efficient geological LLMs fine-tuned on a custom-curated, high-quality instruction dataset processed using our custom instruction synthesis pipel
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cs.AI, q-bio.NC updates on arXiv.org
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Distributionally Robust Transfer Learning with Structurally Missing Covariates, with Application to Cross-National Cardiac Arrest Prediction
arXiv:2605.24212v1 Announce Type: cross Abstract: Deploying clinical prediction models across healthcare systems often fails when key training covariates are unavailable at deployment and labeled outcomes are limited in the target domain. For example, high-performing models for out-of-hospital cardiac arrest (OHCA) rely on detailed prehospital measurements routinely collected in high-resource settings but unavailable in many international registries. Existing methods either discard missing cova
Distributionally Robust Transfer Learning with Structurally Missing Covariates, with Application to Cross-National Cardiac Arrest Prediction
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cs.AI, q-bio.NC updates on arXiv.org
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Cross-Domain Energy-Guided Diffusion Generation for Off-Dynamics Reinforcement Learning
arXiv:2605.24810v1 Announce Type: cross Abstract: Off-dynamics offline reinforcement learning seeks to learn a target-domain policy from a large source dataset and a limited target dataset under mismatched transition dynamics. Existing approaches such as reward augmentation and data filtering are constrained to the source dataset and cannot synthesize new target behavior to improve coverage beyond the collected source trajectories. While recent model-based methods attempt to address this by lea
Cross-Domain Energy-Guided Diffusion Generation for Off-Dynamics Reinforcement Learning
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cs.AI, q-bio.NC updates on arXiv.org
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DRScaffold: Boosting Dense-Scene Reasoning in Lightweight Vision Language Models
arXiv:2605.26038v1 Announce Type: cross Abstract: Lightweight vision-language models perform competitively on standard benchmarks yet fail systematically in dense-scene reasoning, where multiple objects, attributes, and relations must be jointly grounded and resolved through multi-step inference. Such capability is critical for real-world applications where models must reliably interpret cluttered environments. Yet existing training signals provide no explicit grounding between reasoning steps
DRScaffold: Boosting Dense-Scene Reasoning in Lightweight Vision Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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AutoResearchClaw: Self-Reinforcing Autonomous Research with Human-AI Collaboration
arXiv:2605.20025v2 Announce Type: replace Abstract: Automating scientific discovery requires more than generating papers from ideas. Real research is iterative: hypotheses are challenged from multiple perspectives, experiments fail and inform the next attempt, and lessons accumulate across cycles. Existing autonomous research systems often model this process as a linear pipeline: they rely on single-agent reasoning, stop when execution fails, and do not carry experience across runs. We present
AutoResearchClaw: Self-Reinforcing Autonomous Research with Human-AI Collaboration
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cs.AI, q-bio.NC updates on arXiv.org
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SoK: A Comprehensive Security Analysis of Jailbreak Resilience in GPT and DeepSeek Models
arXiv:2506.18543v2 Announce Type: replace-cross Abstract: The rapid proliferation of Large Language Models (LLMs) has heightened concerns regarding their exposure to jailbreak attacks, which craft adversarial inputs designed to elicit unsafe content. Although proprietary models such as GPT-4 have been extensively evaluated, the robustness of emerging open-source systems like DeepSeek remains insufficiently examined, despite their growing use in LLM applications. In this paper, we conduct the fi
SoK: A Comprehensive Security Analysis of Jailbreak Resilience in GPT and DeepSeek Models
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cs.AI, q-bio.NC updates on arXiv.org
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STAPO: Stabilizing Reinforcement Learning for LLMs by Silencing Rare Spurious Tokens
arXiv:2602.15620v5 Announce Type: replace-cross Abstract: Reinforcement Learning (RL) has significantly improved large language model reasoning, but existing RL fine-tuning methods rely heavily on heuristic techniques such as entropy regularization and reweighting to maintain stability. In practice, they often suffer from late-stage performance collapse, leading to degraded reasoning quality and unstable training. We identify a key factor behind this instability: a small fraction of tokens, ter
STAPO: Stabilizing Reinforcement Learning for LLMs by Silencing Rare Spurious Tokens
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Pulmonary nodule
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Proteomic and lipidomic analyses reveal molecular subtypes and potential targets in early-stage lung adenocarcinoma among non-smokers
Cell Rep. 2026 May 26;45(5):117215. doi: 10.1016/j.celrep.2026.117215. Epub 2026 Apr 28.ABSTRACTEarly-stage lung adenocarcinoma (LUAD) in never smokers exhibits distinct biological features, yet the metabolic programs driving early invasion remain unclear. We integrate proteomic and lipidomic profiling of primary LUAD tumors from never smokers, matched normal adjacent tissues (NATs), and benign pulmonary nodules (BPNs). Integrated multi-omics analysis reveals coordinated dysregulation of lipid m
Proteomic and lipidomic analyses reveal molecular subtypes and potential targets in early-stage lung adenocarcinoma among non-smokers
Cell Rep. 2026 May 26;45(5):117215. doi: 10.1016/j.celrep.2026.117215. Epub 2026 Apr 28.
ABSTRACT
Early-stage lung adenocarcinoma (LUAD) in never smokers exhibits distinct biological features, yet the metabolic programs driving early invasion remain unclear. We integrate proteomic and lipidomic profiling of primary LUAD tumors from never smokers, matched normal adjacent tissues (NATs), and benign pulmonary nodules (BPNs). Integrated multi-omics analysis reveals coordinated dysregulation of lipid metabolism and immune signaling in early LUAD. Proteome-based network fusion stratifies invasive LUAD into immune-metabolic synergistic (IMS) and metabolic-stress-driven (MSD) subtypes. IMS tumors retain apolipoprotein-associated lipid modules and favorable immune features, whereas MSD tumors exhibit stress-response programs. Mechanistically, APOA1 and APOC1 emerge as key nodes linking lipid homeostasis to invasion, and their depletion promotes LUAD cell migration and invasion. We establish a two-protein, four-lipid diagnostic panel demonstrating robust performance across tissue and plasma cohorts. These findings provide a molecular basis for early detection and risk stratification in never smokers.
PMID:42054209 | DOI:10.1016/j.celrep.2026.117215
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Establishment and characterization of an immortalized porcine gastric epithelial cell line and identification of NPC1 as a key mediator of aflatoxin B1 toxicity
Gene. 2026 Apr 9:150160. doi: 10.1016/j.gene.2026.150160. Online ahead of print.ABSTRACTPorcine gastric epithelial cells (PGECs) serve as a valuable model for studying the molecular and pathogenic mechanisms of the stomach. However, PGECs face limitations such as isolation challenges, short lifespan, and restricted proliferation. To address this, we established an immortalized PGECs (i-PGECs) to enable in vitro investigation of pathogen infection mechanisms. Primary PGECs were isolated from the
Establishment and characterization of an immortalized porcine gastric epithelial cell line and identification of NPC1 as a key mediator of aflatoxin B1 toxicity
Gene. 2026 Apr 9:150160. doi: 10.1016/j.gene.2026.150160. Online ahead of print.
ABSTRACT
Porcine gastric epithelial cells (PGECs) serve as a valuable model for studying the molecular and pathogenic mechanisms of the stomach. However, PGECs face limitations such as isolation challenges, short lifespan, and restricted proliferation. To address this, we established an immortalized PGECs (i-PGECs) to enable in vitro investigation of pathogen infection mechanisms. Primary PGECs were isolated from the acid-secreting glands using stepwise digestion with multiple enzymes (dispase II/collagenase I/hyaluronidase). Immortalization was achieved via lentiviral vectors expressing simian virus 40 large T antigen (SV40T) and human telomerase reverse transcriptase (hTERT), with successful expression confirmed by qRT-PCR (P < 0.05). Epithelial identity of i-PGECs was confirmed by stable expression of CK18, EpCAM, and E-cadherin, as shown by qRT-PCR and immunofluorescence. i-PGECs retained the morphological and ultrastructural features of PGECs and exhibited enhanced proliferation, as demonstrated by WST-8 assays, apoptosis and cell cycle analysis, karyotyping, and transmission electron microscopy (TEM). Telomere length analysis and scratch wound assays demonstrated stable telomere maintenance and consistent migration capacity unaffected by passaging. RNA-sequencing and differential expressed genes (DEGs) analysis revealed significantly upregulating of genes involved in cell proliferation pathways (P < 0.01). Following aflatoxin B1 (AFB1) exposure, i-PGECs significantly upregulated immune-related factors, such as NPC1 and PLAUR (P < 0.01). CRISPR/Cas9-mediated knockout of NPC1 in i-PGECs conferred increased resistance to AFB1-induced cytotoxicity, as shown by WST-8 assay. The i-PGECs remained stable after more than 50 passages, supporting their use as a reliable for in vitro model investigating the mechanisms of toxicity infection in the porcine gastric epithelium.
PMID:41966285 | DOI:10.1016/j.gene.2026.150160
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Omics In Lung
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Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.ABSTRACTIdiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide associatio
Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.
ABSTRACT
Idiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide association study for IPF to elucidate the causal effects of the CpG sites on IPF. Totally, 452 CpG sites has shown putative causal effects on IPF risk after Bonferroni correction. Among them, 13 CpG sites have shown strong colocalization evidence with genetic factors associated with IPF. Specifically, DNA methylation at CpG sites within MAN2A2 and TRIM27 shows significant differences between IPF lungs and controls, correlating with altered mRNA expressions of these genes in lung tissues. The CpG site in MAN2A2 is a binding site of ZNF384 according to transcription factor databases. RNA sequencing in the TGFβ1-induced alveolar epithelia confirms significantly reduced expression of MAN2A2 and ZNF384 comparing to the controls. Collectively, our study suggests a putative causal link between DNA methylation within MAN2A2 and IPF risk, wherein lung-specific DNA methylation in MAN2A2 may perturb the interaction between ZNF384 and MAN2A2, revealing novel roles for these genes in IPF pathogenesis.
PMID:41965819 | DOI:10.1038/s42003-026-10033-1
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.ABSTRACTIdiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide associatio
Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.
ABSTRACT
Idiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide association study for IPF to elucidate the causal effects of the CpG sites on IPF. Totally, 452 CpG sites has shown putative causal effects on IPF risk after Bonferroni correction. Among them, 13 CpG sites have shown strong colocalization evidence with genetic factors associated with IPF. Specifically, DNA methylation at CpG sites within MAN2A2 and TRIM27 shows significant differences between IPF lungs and controls, correlating with altered mRNA expressions of these genes in lung tissues. The CpG site in MAN2A2 is a binding site of ZNF384 according to transcription factor databases. RNA sequencing in the TGFβ1-induced alveolar epithelia confirms significantly reduced expression of MAN2A2 and ZNF384 comparing to the controls. Collectively, our study suggests a putative causal link between DNA methylation within MAN2A2 and IPF risk, wherein lung-specific DNA methylation in MAN2A2 may perturb the interaction between ZNF384 and MAN2A2, revealing novel roles for these genes in IPF pathogenesis.
PMID:41965819 | DOI:10.1038/s42003-026-10033-1
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cs.AI, q-bio.NC updates on arXiv.org
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ClawArena: Benchmarking AI Agents in Evolving Information Environments
arXiv:2604.04202v1 Announce Type: cross Abstract: AI agents deployed as persistent assistants must maintain correct beliefs as their information environment evolves. In practice, evidence is scattered across heterogeneous sources that often contradict one another, new information can invalidate earlier conclusions, and user preferences surface through corrections rather than explicit instructions. Existing benchmarks largely assume static, single-authority settings and do not evaluate whether a
ClawArena: Benchmarking AI Agents in Evolving Information Environments
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cs.AI, q-bio.NC updates on arXiv.org
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Representation learning to advance multi-institutional studies with electronic health record data from US and France
arXiv:2502.08547v2 Announce Type: replace Abstract: The widespread adoption of electronic health records has created new opportunities for translational clinical research, yet this promise remains constrained by fragmented data across privacy-siloed institutions and substantial heterogeneity in local coding practices. While privacy-preserving collaborative learning allows institutions to work together without sharing patient-level data, it does not address inconsistencies in how clinical concep
Representation learning to advance multi-institutional studies with electronic health record data from US and France
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cs.AI, q-bio.NC updates on arXiv.org
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A Model Can Help Itself: Reward-Free Self-Training for LLM Reasoning
arXiv:2510.18814v2 Announce Type: replace-cross Abstract: Can language models improve their reasoning performance without external rewards, using only their own sampled responses for training? We show that they can. We propose Self-evolving Post-Training (SePT), a simple post-training method that alternates between self-generation and training on self-generated responses. It repeatedly samples questions, uses the model itself to generate low-temperature responses, and then finetunes the model o
A Model Can Help Itself: Reward-Free Self-Training for LLM Reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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Hierarchical Memory Orchestration for Personalized Persistent Agents
arXiv:2604.01670v1 Announce Type: new Abstract: While long-term memory is essential for intelligent agents to maintain consistent historical awareness, the accumulation of extensive interaction data often leads to performance bottlenecks. Naive storage expansion increases retrieval noise and computational latency, overwhelming the reasoning capacity of models deployed on constrained personal devices. To address this, we propose Hierarchical Memory Orchestration (HMO), a framework that organizes
Hierarchical Memory Orchestration for Personalized Persistent Agents
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cs.AI, q-bio.NC updates on arXiv.org
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DarwinNet: An Evolutionary Network Architecture for Agent-Driven Protocol Synthesis
arXiv:2604.01236v1 Announce Type: cross Abstract: Traditional network architectures suffer from severe protocol ossification and structural fragility due to their reliance on static, human-defined rules that fail to adapt to the emergent edge cases and probabilistic reasoning of modern autonomous agents. To address these limitations, this paper proposes DarwinNet, a bio-inspired, self-evolving network architecture that transitions communication protocols from a \textit{design-time} static parad
DarwinNet: An Evolutionary Network Architecture for Agent-Driven Protocol Synthesis
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cs.AI, q-bio.NC updates on arXiv.org
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Omni-SimpleMem: Autoresearch-Guided Discovery of Lifelong Multimodal Agent Memory
arXiv:2604.01007v2 Announce Type: replace Abstract: AI agents increasingly operate over extended time horizons, yet their ability to retain, organize, and recall multimodal experiences remains a critical bottleneck. Building effective lifelong memory requires navigating a vast design space spanning architecture, retrieval strategies, prompt engineering, and data pipelines; this space is too large and interconnected for manual exploration or traditional AutoML to explore effectively. We deploy a
Omni-SimpleMem: Autoresearch-Guided Discovery of Lifelong Multimodal Agent Memory
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Journal of Medical Internet Research
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Well-Being and Cognitive Factors Influencing Health Care Workers’ Adherence to Internet-Based Stress Management: Mixed Methods Analysis of a Nonrandomized Controlled Study
Background: High stress levels are common among health care workers (HCWs), threatening their health and workforce stability. Internet-based mobile stress management (MSM) is a promising intervention for reducing work-related stress; however, poor adherence limits effectiveness. Exploring factors influencing HCWs’ adherence may thus aid in developing optimal interventions. Objective: The research aimed to investigate (1) how HCWs’ well-being and cognitive factors influenced MSM treatment adheren
Well-Being and Cognitive Factors Influencing Health Care Workers’ Adherence to Internet-Based Stress Management: Mixed Methods Analysis of a Nonrandomized Controlled Study
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Cell
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Efficient amyloid-β degradation in Alzheimer’s disease using SPYTACs
SPYTAC is a synthetic peptide-programmed targeted protein degradation platform harnessing LRP1 to drive lysosomal degradation of extracellular amyloid-β in the brain and periphery. In 5×FAD mice, SPYTAC treatment efficiently degrades amyloid-β, preserves neurons, and improves cognition with reduced neuroinflammation and microhemorrhage when compared with antibody therapy.
Efficient amyloid-β degradation in Alzheimer’s disease using SPYTACs
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Cell
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Restoring circadian rhythms in the hypothalamic paraventricular nucleus reverses aging biomarkers and extends lifespan in male mice
Enhancing circadian amplitude in mouse hypothalamic paraventricular nucleus neurons by 3′-deoxyadenosine treatment alleviates age-related pathologies and extends lifespan.