Normal view
-
cs.AI, q-bio.NC updates on arXiv.org
-
TreeGaussian: Tree-Guided Cascaded Contrastive Learning for Hierarchical Consistent 3D Gaussian Scene Segmentation and Understanding
arXiv:2604.03309v1 Announce Type: cross Abstract: 3D Gaussian Splatting (3DGS) has emerged as a real-time, differentiable representation for neural scene understanding. However, existing 3DGS-based methods struggle to represent hierarchical 3D semantic structures and capture whole-part relationships in complex scenes. Moreover, dense pairwise comparisons and inconsistent hierarchical labels from 2D priors hinder feature learning, resulting in suboptimal segmentation. To address these limitation
-
cs.AI, q-bio.NC updates on arXiv.org
-
DIRECT: Video Mashup Creation via Hierarchical Multi-Agent Planning and Intent-Guided Editing
arXiv:2604.04875v1 Announce Type: cross Abstract: Video mashup creation represents a complex video editing paradigm that recomposes existing footage to craft engaging audio-visual experiences, demanding intricate orchestration across semantic, visual, and auditory dimensions and multiple levels. However, existing automated editing frameworks often overlook the cross-level multimodal orchestration to achieve professional-grade fluidity, resulting in disjointed sequences with abrupt visual transi
DIRECT: Video Mashup Creation via Hierarchical Multi-Agent Planning and Intent-Guided Editing
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
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
-
Omics In Lung
-
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
-
cs.AI, q-bio.NC updates on arXiv.org
-
SenseMath: Do LLMs Have Number Sense? Evaluating Shortcut Use, Judgment, and Generation
arXiv:2604.01988v1 Announce Type: new Abstract: Large language models often default to step-by-step computation even when efficient numerical shortcuts are available. This raises a basic question: do they exhibit number sense in a human-like behavioral sense, i.e., the ability to recognize numerical structure, apply shortcuts when appropriate, and avoid them when they are not? We introduce SenseMath, a controlled benchmark for evaluating structure-sensitive numerical reasoning in LLMs. SenseMat
SenseMath: Do LLMs Have Number Sense? Evaluating Shortcut Use, Judgment, and Generation
-
cs.AI, q-bio.NC updates on arXiv.org
-
Dual Optimal: Make Your LLM Peer-like with Dignity
arXiv:2604.00979v2 Announce Type: replace-cross Abstract: Current aligned language models exhibit a dual failure mode we term the Evasive Servant: they sycophantically validate flawed user beliefs while deflecting responsibility with boilerplate disclaimers. We propose the Dignified Peer framework, which counters servility with anti-sycophancy and trustworthiness, and mitigates evasiveness through empathy and creativity. Realizing this agent requires overcoming significant challenges in data su
Dual Optimal: Make Your LLM Peer-like with Dignity
-
cs.AI, q-bio.NC updates on arXiv.org
-
Almost Sure Convergence of Linear Temporal Difference Learning with Arbitrary Features
arXiv:2409.12135v3 Announce Type: replace-cross Abstract: Temporal difference (TD) learning with linear function approximation (linear TD) is a classic and powerful prediction algorithm in reinforcement learning. While it is well-understood that linear TD converges almost surely to a unique point, this convergence traditionally requires the assumption that the features used by the approximator are linearly independent. However, this linear independence assumption does not hold in many practical
Almost Sure Convergence of Linear Temporal Difference Learning with Arbitrary Features
-
cs.AI, q-bio.NC updates on arXiv.org
-
VLM-CAD: VLM-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing
arXiv:2601.07315v4 Announce Type: replace-cross Abstract: Vision Language Models (VLMs) have demonstrated remarkable potential in multimodal reasoning, yet they inherently suffer from spatial blindness and logical hallucinations when interpreting densely structured engineering content, such as analog circuit schematics. To address these challenges, we propose a Vision Language Model-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing (VLM-CAD) designed for robust, step-by-st
VLM-CAD: VLM-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing
-
cs.AI, q-bio.NC updates on arXiv.org
-
Visual-ERM: Reward Modeling for Visual Equivalence
arXiv:2603.13224v1 Announce Type: cross Abstract: Vision-to-code tasks require models to reconstruct structured visual inputs, such as charts, tables, and SVGs, into executable or structured representations with high visual fidelity. While recent Large Vision Language Models (LVLMs) achieve strong results via supervised fine-tuning, reinforcement learning remains challenging due to misaligned reward signals. Existing rewards either rely on textual rules or coarse visual embedding similarity, bo
Visual-ERM: Reward Modeling for Visual Equivalence
-
Nature Biotechnology - Issue - nature.com science feeds
-
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning
Nature Biotechnology, Published online: 11 March 2026; doi:10.1038/s41587-026-03059-7TnpB endonucleases are engineered for improved genome editing.
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning
Nature Biotechnology, Published online: 11 March 2026; doi:10.1038/s41587-026-03059-7
TnpB endonucleases are engineered for improved genome editing.-
cs.AI, q-bio.NC updates on arXiv.org
-
Discriminative Perception via Anchored Description for Reasoning Segmentation
arXiv:2603.04002v1 Announce Type: cross Abstract: Reasoning segmentation increasingly employs reinforcement learning to generate explanatory reasoning chains that guide Multimodal Large Language Models. While these geometric rewards are primarily confined to guiding the final localization, they are incapable of discriminating whether the reasoning process remains anchored on the referred region or strays into irrelevant context. Lacking this discriminative guidance, the model's reasoning often
Discriminative Perception via Anchored Description for Reasoning Segmentation
-
cs.AI, q-bio.NC updates on arXiv.org
-
Beyond Prompt Degradation: Prototype-guided Dual-pool Prompting for Incremental Object Detection
arXiv:2603.02286v1 Announce Type: cross Abstract: Incremental Object Detection (IOD) aims to continuously learn new object categories without forgetting previously learned ones. Recently, prompt-based methods have gained popularity for their replay-free design and parameter efficiency. However, due to prompt coupling and prompt drift, these methods often suffer from prompt degradation during continual adaptation. To address these issues, we propose a novel prompt-decoupled framework called PDP.
Beyond Prompt Degradation: Prototype-guided Dual-pool Prompting for Incremental Object Detection
-
cs.AI, q-bio.NC updates on arXiv.org
-
Learning Memory-Enhanced Improvement Heuristics for Flexible Job Shop Scheduling
arXiv:2603.02846v1 Announce Type: cross Abstract: The rise of smart manufacturing under Industry 4.0 introduces mass customization and dynamic production, demanding more advanced and flexible scheduling techniques. The flexible job-shop scheduling problem (FJSP) has attracted significant attention due to its complex constraints and strong alignment with real-world production scenarios. Current deep reinforcement learning (DRL)-based approaches to FJSP predominantly employ constructive methods.
Learning Memory-Enhanced Improvement Heuristics for Flexible Job Shop Scheduling
-
cs.AI, q-bio.NC updates on arXiv.org
-
Enhancing Generative Auto-bidding with Offline Reward Evaluation and Policy Search
arXiv:2509.15927v4 Announce Type: replace-cross Abstract: Auto-bidding is a critical tool for advertisers to improve advertising performance. Recent progress has demonstrated that AI-Generated Bidding (AIGB), which learns a conditional generative planner from offline data, achieves superior performance compared to typical offline reinforcement learning (RL)-based auto-bidding methods. However, existing AIGB methods still face a performance bottleneck due to their inherent inability to explore b
Enhancing Generative Auto-bidding with Offline Reward Evaluation and Policy Search
-
cs.AI, q-bio.NC updates on arXiv.org
-
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
-
cs.AI, q-bio.NC updates on arXiv.org
-
VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention
arXiv:2602.19622v1 Announce Type: cross Abstract: Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational complexity, making it difficult to scale to large graphs; (2) attention mechanisms based on node-level operations limit the flexibility of the model and result in poor generalization performance in out-of-distribution
VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention
-
cs.AI, q-bio.NC updates on arXiv.org
-
MAS-FIRE: Fault Injection and Reliability Evaluation for LLM-Based Multi-Agent Systems
arXiv:2602.19843v1 Announce Type: cross Abstract: As LLM-based Multi-Agent Systems (MAS) are increasingly deployed for complex tasks, ensuring their reliability has become a pressing challenge. Since MAS coordinate through unstructured natural language rather than rigid protocols, they are prone to semantic failures (e.g., hallucinations, misinterpreted instructions, and reasoning drift) that propagate silently without raising runtime exceptions. Prevailing evaluation approaches, which measure
MAS-FIRE: Fault Injection and Reliability Evaluation for LLM-Based Multi-Agent Systems
-
cs.AI, q-bio.NC updates on arXiv.org
-
Rethinking the Design of Reinforcement Learning-Based Deep Research Agents
arXiv:2510.15862v4 Announce Type: replace Abstract: Large language models (LLMs) augmented with external tools are increasingly deployed as deep research agents that gather, reason over, and synthesize web information to answer complex queries. Although recent open-source systems achieve strong empirical performance via reinforcement learning from web interactions, the impact of key design choices remains under-explored. We formalize deep research as reinforcement learning in an episodic finite