Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Schema-Aware Planning and Hybrid Knowledge Toolset for Reliable Knowledge Graph Triple Verification
arXiv:2604.04190v1 Announce Type: new Abstract: Knowledge Graphs (KGs) serve as a critical foundation for AI systems, yet their automated construction inevitably introduces noise, compromising data trustworthiness. Existing triple verification methods, based on graph embeddings or language models, often suffer from single-source bias by relying on either internal structural constraints or external semantic evidence, and usually follow a static inference paradigm. As a result, they struggle with
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation
Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.ABSTRACTBACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-
Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation
Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.
ABSTRACT
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.
METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-cell and spatial transcriptomics, as well as peripheral blood multi-omics data to uncover key molecular signatures in IPF. Furthermore, machine learning techniques were utilized to identify core genes, whereas functional analyses and Mendelian randomization were conducted to evaluate the causal relationships among gut microbiota, immune cells, and IPF. Additionally, experimental validation using qPCR and ELISA assays was conducted in vitro, in vivo, and in patient plasma to confirm the expression patterns of key genes.
RESULTS: Across integrated public bulk, single-cell, spatial, and blood multi-omics, CXCL13, IL33, TLR4, and IGF1 were identified as core IPF genes consistently linked to immune infiltration and fibrotic remodeling. Deconvolution, scRNA-seq, and spatial mapping localized their dysregulation to fibroblasts and immune compartments (notably B-cell, macrophage, and mast-cell axes), highlighting fibroblast-immune crosstalk in fibrotic foci. A four-gene model robustly distinguished IPF from controls across cohorts. Mendelian randomization supported a gut-immune-lung axis, indicating causal effects of specific gut taxa on IPF risk via immune phenotypes. qPCR/ELISA in TGF-β1-stimulated fibroblasts, bleomycin mouse lungs, and patient plasma corroborated upregulation of IL33, CXCL13, IGF1 and downregulation of TLR4. Drug-signature reversal nominated cucurbitacin I and temsirolimus; molecular docking was performed as a preliminary in silico, computer-simulation-based assessment of potential ligand-protein interactions between these compounds and the four core targets.
CONCLUSION: This study provides new insights into the importance of gut-immune-lung axis in IPF and identifies CXCL13, IL33, TLR4, and IGF1 as diagnostic signatures and therapeutic targets. By integrating public multi-omics resources with experimental validation, our findings offer a foundation for future diagnostic and treatment strategies aimed at modulating the gut microbiota and immune system in IPF.
PMID:41939867 | PMC:PMC13043422 | DOI:10.3389/fimmu.2026.1730289
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Omics In Lung
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Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation
Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.ABSTRACTBACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-
Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation
Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.
ABSTRACT
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.
METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-cell and spatial transcriptomics, as well as peripheral blood multi-omics data to uncover key molecular signatures in IPF. Furthermore, machine learning techniques were utilized to identify core genes, whereas functional analyses and Mendelian randomization were conducted to evaluate the causal relationships among gut microbiota, immune cells, and IPF. Additionally, experimental validation using qPCR and ELISA assays was conducted in vitro, in vivo, and in patient plasma to confirm the expression patterns of key genes.
RESULTS: Across integrated public bulk, single-cell, spatial, and blood multi-omics, CXCL13, IL33, TLR4, and IGF1 were identified as core IPF genes consistently linked to immune infiltration and fibrotic remodeling. Deconvolution, scRNA-seq, and spatial mapping localized their dysregulation to fibroblasts and immune compartments (notably B-cell, macrophage, and mast-cell axes), highlighting fibroblast-immune crosstalk in fibrotic foci. A four-gene model robustly distinguished IPF from controls across cohorts. Mendelian randomization supported a gut-immune-lung axis, indicating causal effects of specific gut taxa on IPF risk via immune phenotypes. qPCR/ELISA in TGF-β1-stimulated fibroblasts, bleomycin mouse lungs, and patient plasma corroborated upregulation of IL33, CXCL13, IGF1 and downregulation of TLR4. Drug-signature reversal nominated cucurbitacin I and temsirolimus; molecular docking was performed as a preliminary in silico, computer-simulation-based assessment of potential ligand-protein interactions between these compounds and the four core targets.
CONCLUSION: This study provides new insights into the importance of gut-immune-lung axis in IPF and identifies CXCL13, IL33, TLR4, and IGF1 as diagnostic signatures and therapeutic targets. By integrating public multi-omics resources with experimental validation, our findings offer a foundation for future diagnostic and treatment strategies aimed at modulating the gut microbiota and immune system in IPF.
PMID:41939867 | PMC:PMC13043422 | DOI:10.3389/fimmu.2026.1730289
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Oncogene - Issue - nature.com science feeds
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SRSF10 promotes cisplatin resistance in bladder cancer via BIN1 Exon 12 retention and ANXA1 activation
Oncogene, Published online: 06 April 2026; doi:10.1038/s41388-026-03735-7SRSF10 promotes cisplatin resistance in bladder cancer via BIN1 Exon 12 retention and ANXA1 activation
SRSF10 promotes cisplatin resistance in bladder cancer via BIN1 Exon 12 retention and ANXA1 activation
Oncogene, Published online: 06 April 2026; doi:10.1038/s41388-026-03735-7
SRSF10 promotes cisplatin resistance in bladder cancer via BIN1 Exon 12 retention and ANXA1 activation-
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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Scaling Whole-Body Human Musculoskeletal Behavior Emulation for Specificity and Diversity
arXiv:2603.29332v1 Announce Type: cross Abstract: The embodied learning of human motor control requires whole-body neuro-actuated musculoskeletal dynamics, while the internal muscle-driven processes underlying movement remain inaccessible to direct measurement. Computational modeling offers an alternative, but inverse dynamics methods struggled to resolve redundant control from observed kinematics in the high-dimensional, over-actuated system. Forward imitation approaches based on deep reinforc
Scaling Whole-Body Human Musculoskeletal Behavior Emulation for Specificity and Diversity
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cs.AI, q-bio.NC updates on arXiv.org
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X-World: Controllable Ego-Centric Multi-Camera World Models for Scalable End-to-End Driving
arXiv:2603.19979v2 Announce Type: replace-cross Abstract: Scalable and reliable evaluation is increasingly critical in the end-to-end era of autonomous driving, where vision--language--action (VLA) policies directly map raw sensor streams to driving actions. Yet, current evaluation pipelines still rely heavily on real-world road testing, which is costly, biased toward limited scenario coverage, and difficult to reproduce. These challenges motivate a real-world simulator that can generate realis
X-World: Controllable Ego-Centric Multi-Camera World Models for Scalable End-to-End Driving
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cs.AI, q-bio.NC updates on arXiv.org
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EVA: Aligning Video World Models with Executable Robot Actions via Inverse Dynamics Rewards
arXiv:2603.17808v2 Announce Type: replace-cross Abstract: Video generative models are increasingly used as world models for robotics, where a model generates a future visual rollout conditioned on the current observation and task instruction, and an inverse dynamics model (IDM) converts the generated frames into executable robot actions. However, current video world models lack explicit executability constraints. As a result, visually coherent rollouts may still violate rigid-body and kinematic
EVA: Aligning Video World Models with Executable Robot Actions via Inverse Dynamics Rewards
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npj Digital Medicine
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Boosting foundation models for rare eye disease diagnosis via a multimodal text-to-image generative framework
npj Digital Medicine, Published online: 24 March 2026; doi:10.1038/s41746-026-02560-2Boosting foundation models for rare eye disease diagnosis via a multimodal text-to-image generative framework
Boosting foundation models for rare eye disease diagnosis via a multimodal text-to-image generative framework
npj Digital Medicine, Published online: 24 March 2026; doi:10.1038/s41746-026-02560-2
Boosting foundation models for rare eye disease diagnosis via a multimodal text-to-image generative framework-
cs.AI, q-bio.NC updates on arXiv.org
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daVinci-Env: Open SWE Environment Synthesis at Scale
arXiv:2603.13023v1 Announce Type: cross Abstract: Training capable software engineering (SWE) agents demands large-scale, executable, and verifiable environments that provide dynamic feedback loops for iterative code editing, test execution, and solution refinement. However, existing open-source datasets remain limited in scale and repository diversity, while industrial solutions are opaque with unreleased infrastructure, creating a prohibitive barrier for most academic research groups. We pres
daVinci-Env: Open SWE Environment Synthesis at Scale
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cs.AI, q-bio.NC updates on arXiv.org
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Thinking with Gaze: Sequential Eye-Tracking as Visual Reasoning Supervision for Medical VLMs
arXiv:2603.06697v1 Announce Type: cross Abstract: Vision--language models (VLMs) process images as visual tokens, yet their intermediate reasoning is often carried out in text, which can be suboptimal for visually grounded radiology tasks. Radiologists instead diagnose via sequential visual search; eye-tracking captures this process as time-ordered gaze trajectories that reveal how evidence is acquired over time. We use eye-gaze as supervision to guide VLM reasoning by introducing a small set o
Thinking with Gaze: Sequential Eye-Tracking as Visual Reasoning Supervision for Medical VLMs
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cs.AI, q-bio.NC updates on arXiv.org
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Hit-RAG: Learning to Reason with Long Contexts via Preference Alignment
arXiv:2603.07023v1 Announce Type: cross Abstract: Despite the promise of Retrieval-Augmented Generation in grounding Multimodal Large Language Models with external knowledge, the transition to extensive contexts often leads to significant attention dilution and reasoning hallucinations. The surge in information density causes critical evidence to be submerged by voluminous noise, which complicates the discernment of relevant fragments within a dense input. In this paper, we propose \textbf{Hit-
Hit-RAG: Learning to Reason with Long Contexts via Preference Alignment
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cs.AI, q-bio.NC updates on arXiv.org
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IntPro: A Proxy Agent for Context-Aware Intent Understanding via Retrieval-conditioned Inference
arXiv:2603.03325v1 Announce Type: cross Abstract: Large language models (LLMs) have become integral to modern Human-AI collaboration workflows, where accurately understanding user intent serves as a crucial step for generating satisfactory responses. Context-aware intent understanding, which involves inferring user intentions from situational environments, is inherently challenging because it requires reasoning over both the immediate context and the user's underlying motivations that drive the
IntPro: A Proxy Agent for Context-Aware Intent Understanding via Retrieval-conditioned Inference
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cs.AI, q-bio.NC updates on arXiv.org
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Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset
arXiv:2406.06512v2 Announce Type: replace-cross Abstract: The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings
Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset
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cs.AI, q-bio.NC updates on arXiv.org
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xLLM Technical Report
arXiv:2510.14686v2 Announce Type: replace-cross Abstract: We introduce xLLM, an intelligent and efficient Large Language Model (LLM) inference framework designed for high-performance, large-scale enterprise-grade serving, with deep optimizations for diverse AI accelerators. To address these challenges, xLLM builds a novel decoupled service-engine architecture. At the service layer, xLLM-Service features an intelligent scheduling module that efficiently processes multimodal requests and co-locat
xLLM Technical Report
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cs.AI, q-bio.NC updates on arXiv.org
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A Very Big Video Reasoning Suite
arXiv:2602.20159v1 Announce Type: cross Abstract: Rapid progress in video models has largely focused on visual quality, leaving their reasoning capabilities underexplored. Video reasoning grounds intelligence in spatiotemporally consistent visual environments that go beyond what text can naturally capture, enabling intuitive reasoning over spatiotemporal structure such as continuity, interaction, and causality. However, systematically studying video reasoning and its scaling behavior is hindere
A Very Big Video Reasoning Suite
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cs.AI, q-bio.NC updates on arXiv.org
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ALOE: Action-Level Off-Policy Evaluation for Vision-Language-Action Model Post-Training
arXiv:2602.12691v2 Announce Type: replace-cross Abstract: We study how to improve large foundation vision-language-action (VLA) systems through online reinforcement learning (RL) in real-world settings. Central to this process is the value function, which provides learning signals to guide VLA learning from experience. In practice, the value function is estimated from trajectory fragments collected from different data sources, including historical policies and intermittent human interventions.