Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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EvoRS: On-Policy Self-Evolution of Reward Systems for Open-Ended Reinforcement Learning
arXiv:2609.12459v1 Announce Type: new Abstract: Open-ended reinforcement learning often relies on rubric-based rewards for tasks without directly verifiable answers. Yet the policy and reward system form a dynamic feedback loop: as the policy optimizes the current reward, an initially useful reward system may become unreliable due to reward hacking or reduced response discriminability. The reward system should therefore evolve rather than remain fixed during training. Existing dynamic-rubric me
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Omics In Lung
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From the invasive front to organotropic pre-metastatic niches: spatial immune regulatory networks governing cholangiocarcinoma dissemination and metastasis-intercepting immunotherapy
Front Immunol. 2026 Aug 20;17:1919864. doi: 10.3389/fimmu.2026.1919864. eCollection 2026.ABSTRACTCholangiocarcinoma is an aggressive biliary tract malignancy in which metastatic relapse and primary or acquired resistance to immunotherapy remain major causes of mortality. Although immune checkpoint inhibitors have improved first-line treatment for advanced biliary tract cancer, most patients do not achieve durable benefit, indicating that immune failure is not explained by a single checkpoint pat
From the invasive front to organotropic pre-metastatic niches: spatial immune regulatory networks governing cholangiocarcinoma dissemination and metastasis-intercepting immunotherapy
Front Immunol. 2026 Aug 20;17:1919864. doi: 10.3389/fimmu.2026.1919864. eCollection 2026.
ABSTRACT
Cholangiocarcinoma is an aggressive biliary tract malignancy in which metastatic relapse and primary or acquired resistance to immunotherapy remain major causes of mortality. Although immune checkpoint inhibitors have improved first-line treatment for advanced biliary tract cancer, most patients do not achieve durable benefit, indicating that immune failure is not explained by a single checkpoint pathway. In this Review, we propose a spatial immune-regulatory continuum for cholangiocarcinoma dissemination. Most direct single-cell and spatial evidence currently derives from intrahepatic cholangiocarcinoma, and its applicability to perihilar and distal disease remains to be established. This continuum begins in the tumor core and invasive front, where malignant cells, cancer-associated fibroblasts, tumor-associated macrophages, endothelial and lymphatic cells, regulatory T cells, immature neutrophils and excluded or dysfunctional cytotoxic T cells form a pro-invasive ecosystem. It then extends through extracellular vesicles, soluble mediators and lymphovascular routes that may educate organotropic pre-metastatic niches. Finally, lymph node, lung, liver, peritoneal and bone microenvironments provide organ-specific extracellular matrix, myeloid and stromal programs that enable immune evasion and metastatic colonization. By integrating clinical evidence, multi-omics studies, single-cell and spatial transcriptomics, extracellular vesicle biology, pre-metastatic niche concepts and emerging therapeutic strategies, we argue that cholangiocarcinoma metastasis should be targeted before overt dissemination whenever possible. In this Review, "metastasis-intercepting immunotherapy" is used as an author-defined conceptual framework for strategies intended to prevent or disrupt the immune-stromal conditions that enable dissemination and colonization, rather than merely shrink established metastatic lesions. Metastasis-intercepting immunotherapy will likely require rational combinations that reprogram the invasive front, restore dendritic-cell-mediated antigen presentation, block tumor-stroma-myeloid circuits, disrupt EV-mediated communication that may contribute to niche formation and select patients using spatial biomarkers rather than bulk immune markers alone.
PMID:42694469 | PMC:PMC13539491 | DOI:10.3389/fimmu.2026.1919864
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Omics in Gastric
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Gastrointestinal motility in microgravity: a critical review of multi-level mechanisms and model-dependent effects
Front Physiol. 2026 Aug 20;17:1930628. doi: 10.3389/fphys.2026.1930628. eCollection 2026.ABSTRACTBACKGROUND: Gastrointestinal motility disturbances rank among the most frequently reported medical complications of spaceflight. Astronauts experience delayed gastric emptying, erratic small intestinal transit and reduced colonic propulsion. The underlying mechanisms are multifactorial. Microgravity alters intra-abdominal physical mechanics, disrupts autonomic and enteric neural circuits, shifts gast
Gastrointestinal motility in microgravity: a critical review of multi-level mechanisms and model-dependent effects
Front Physiol. 2026 Aug 20;17:1930628. doi: 10.3389/fphys.2026.1930628. eCollection 2026.
ABSTRACT
BACKGROUND: Gastrointestinal motility disturbances rank among the most frequently reported medical complications of spaceflight. Astronauts experience delayed gastric emptying, erratic small intestinal transit and reduced colonic propulsion. The underlying mechanisms are multifactorial. Microgravity alters intra-abdominal physical mechanics, disrupts autonomic and enteric neural circuits, shifts gastrointestinal hormone secretion profiles, inflicts oxidative stress upon effector cells, and perturbs gut microbial communities. Cross-model comparisons reveal substantial disagreement, suggesting that no single ground-based analog fully captures the pathophysiology of orbital flight.
AIM: To critically review how weightlessness affects gastric emptying, small intestinal transit and colonic motility; to critically evaluate contradictory findings across simulation platforms; and to delineate the neural, humoral, cellular and microbiological mechanisms involved.
METHODS: We searched PubMed, Web of Science and the NASA Technical Reports Server for articles published between January 1990 and June 2026 (last search 30 June 2026). Search terms included: "microgravity", "weightlessness", "spaceflight", "gastrointestinal motility", "gastric emptying", "intestinal transit", "gut microbiome", "interstitial cells of Cajal" and "oxidative stress". Studies using head-down bed rest, hindlimb unloading, clinorotation, parabolic flight and actual spaceflight were included. The review follows a critical narrative design; the full search strategy and the framework used to appraise the evidence are described in Section 1.1.
RESULTS: Altered-gravity studies suggest that gastrointestinal dysmotility may involve neurohumoral dysregulation, oxidative injury to interstitial cells of Cajal and smooth muscle, barrier dysfunction and altered enteric signaling; however, most mechanistic evidence derives from simulated models and has not been directly validated during human spaceflight. Direct human motility measurements remain sparse, and the evidence comprises a mixture of direct observations, model-dependent inferences and testable hypotheses. Cross-study agreement is poor: some head-down bed rest trials report accelerated small-bowel transit, whereas tail-suspension models and limited flight observations suggest motor suppression. These divergences may reflect model-specific confounding rather than a uniform effect of microgravity.
CONCLUSION: Current ground-based models each capture only partial aspects of orbital GI pathophysiology. Future work should combine multi-omics profiling with next-generation simulation platforms to develop evidence-based countermeasures for long-duration missions.
PMID:42694486 | PMC:PMC13539599 | DOI:10.3389/fphys.2026.1930628
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cs.AI, q-bio.NC updates on arXiv.org
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FrontierOR: Benchmarking LLMs' Capacity for Efficient Algorithm Design in Large-Scale Optimization
arXiv:2605.25246v2 Announce Type: new Abstract: Large language models (LLMs) are increasingly used for optimization modeling and solver-code generation, yet practical operations research and optimization problems often require a harder capability: designing scalable algorithms that exploit problem structure and outperform direct formulation-and-solve baselines. Existing benchmarks are limited to small or simplified examples far below real-world scale and complexity. We introduce FrontierOR, amo
FrontierOR: Benchmarking LLMs' Capacity for Efficient Algorithm Design in Large-Scale Optimization
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cs.AI, q-bio.NC updates on arXiv.org
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IVR-R1: Refining Trajectories through Iterative Visual-Grounded Reasoning in Reinforcement Learning
arXiv:2605.23997v1 Announce Type: cross Abstract: Multimodal large language models via reinforcement learning (RL) have demonstrated remarkable capabilities in complex visual reasoning tasks, yet they remain limited in long-horizon multimodal scenarios, often suffering from visual hallucination and logical error. Current methods typically pre-encode high-dimensional visual scenes into discrete textual proxies to facilitate downstream reasoning. As the reasoning chain unfolds, however, the inher
IVR-R1: Refining Trajectories through Iterative Visual-Grounded Reasoning in Reinforcement Learning
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cs.AI, q-bio.NC updates on arXiv.org
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Agent Learning via Early Experience
arXiv:2510.08558v3 Announce Type: replace Abstract: A long-term goal of language agents is to learn and improve through their own experience, ultimately outperforming humans in complex, real-world tasks. However, training agents from experience data with reinforcement learning remains difficult in many environments, which either lack verifiable rewards (e.g., websites) or require inefficient long-horizon rollouts (e.g., multi-turn tool use). As a result, most current agents rely on supervised f
Agent Learning via Early Experience
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Nature Biotechnology - Issue - nature.com science feeds
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A framework for building a synthetic cell from the SynCell Asia Initiative
Nature Biotechnology, Published online: 26 May 2026; doi:10.1038/s41587-026-03153-wBuilding a living cell from scratch requires overcoming a bottleneck that has remained unresolved despite decades of progress: orchestrating the spatiotemporal integration of core functional modules. To tackle this barrier, the SynCell Asia Initiative outlines a strategy for developing core functional modules followed by their systems-level integration through the establishment of a centralized, artificial intelli
A framework for building a synthetic cell from the SynCell Asia Initiative
Nature Biotechnology, Published online: 26 May 2026; doi:10.1038/s41587-026-03153-w
Building a living cell from scratch requires overcoming a bottleneck that has remained unresolved despite decades of progress: orchestrating the spatiotemporal integration of core functional modules. To tackle this barrier, the SynCell Asia Initiative outlines a strategy for developing core functional modules followed by their systems-level integration through the establishment of a centralized, artificial intelligence (AI)-driven biofoundry.-
cs.AI, q-bio.NC updates on arXiv.org
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Beyond Retrieval: Modeling Confidence Decay and Deterministic Agentic Platforms in Generative Engine Optimization
arXiv:2604.03656v1 Announce Type: new Abstract: Generative Engine Optimization (GEO) is rapidly reshaping digital marketing paradigms in the era of Large Language Models (LLMs). However, current GEO strategies predominantly rely on Retrieval-Augmented Generation (RAG), which inherently suffers from probabilistic hallucinations and the "zero-click" paradox, failing to establish sustainable commercial trust. In this paper, we systematically deconstruct the probabilistic flaws of existing RAG-base
Beyond Retrieval: Modeling Confidence Decay and Deterministic Agentic Platforms in Generative Engine Optimization
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cs.AI, q-bio.NC updates on arXiv.org
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BAAI Cardiac Agent: An intelligent multimodal agent for automated reasoning and diagnosis of cardiovascular diseases from cardiac magnetic resonance imaging
arXiv:2604.04078v1 Announce Type: cross Abstract: Cardiac magnetic resonance (CMR) is a cornerstone for diagnosing cardiovascular disease. However, it remains underutilized due to complex, time-consuming interpretation across multi-sequences, phases, quantitative measures that heavily reliant on specialized expertise. Here, we present BAAI Cardiac Agent, a multimodal intelligent system designed for end-to-end CMR interpretation. The agent integrates specialized cardiac expert models to perform
BAAI Cardiac Agent: An intelligent multimodal agent for automated reasoning and diagnosis of cardiovascular diseases from cardiac magnetic resonance imaging
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cs.AI, q-bio.NC updates on arXiv.org
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Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics
arXiv:2510.09901v2 Announce Type: replace Abstract: Computing has long served as a cornerstone of scientific discovery. Recently, a paradigm shift has emerged with the rise of large language models (LLMs), introducing autonomous systems, referred to as agents, that accelerate discovery across varying levels of autonomy. These language agents provide a flexible and versatile framework that orchestrates interactions with human scientists, natural language, computer language and code, and physics.
Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics
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cs.AI, q-bio.NC updates on arXiv.org
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SelfGrader: Stable Jailbreak Detection for Large Language Models using Token-Level Logits
arXiv:2604.01473v1 Announce Type: cross Abstract: Large Language Models (LLMs) are powerful tools for answering user queries, yet they remain highly vulnerable to jailbreak attacks. Existing guardrail methods typically rely on internal features or textual responses to detect malicious queries, which either introduce substantial latency or suffer from the randomness in text generation. To overcome these limitations, we propose SelfGrader, a lightweight guardrail method that formulates jailbreak
SelfGrader: Stable Jailbreak Detection for Large Language Models using Token-Level Logits
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Cell
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Editing strigolactone hormone receptor for robust antiviral silencing in rice
Precise genome editing of the rice strigolactone receptor DWARF14 confers robust, transgene-free antiviral resistance by blocking viral suppression of endogenous RNA silencing, offering a promising strategy for durable disease protection without a yield penalty.
Editing strigolactone hormone receptor for robust antiviral silencing in rice
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cs.AI, q-bio.NC updates on arXiv.org
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Learning to Generate Formally Verifiable Step-by-Step Logic Reasoning via Structured Formal Intermediaries
arXiv:2603.29500v1 Announce Type: new Abstract: Large language models (LLMs) have recently demonstrated impressive performance on complex, multi-step reasoning tasks, especially when post-trained with outcome-rewarded reinforcement learning Guo et al. 2025. However, it has been observed that outcome rewards often overlook flawed intermediate steps, leading to unreliable reasoning steps even when final answers are correct. To address this unreliable reasoning, we propose PRoSFI (Process Reward o
Learning to Generate Formally Verifiable Step-by-Step Logic Reasoning via Structured Formal Intermediaries
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cs.AI, q-bio.NC updates on arXiv.org
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$V_0$: A Generalist Value Model for Any Policy at State Zero
arXiv:2602.03584v2 Announce Type: replace-cross Abstract: Policy gradient methods rely on a baseline to measure the relative advantage of an action, ensuring the model reinforces behaviors that outperform its current average capability. In the training of Large Language Models (LLMs) using Actor-Critic methods (e.g., PPO), this baseline is typically estimated by a Value Model (Critic) often as large as the policy model itself. However, as the policy continuously evolves, the value model require
$V_0$: A Generalist Value Model for Any Policy at State Zero
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Nature Medicine
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In vivo generation of anti-BCMA CAR-T cells in relapsed or refractory multiple myeloma: a phase 1 study
Nature Medicine, Published online: 25 March 2026; doi:10.1038/s41591-026-04244-6In a phase 1 trial, the in vivo generation of anti-BCMA CAR-T cells by lentiviral delivery was feasible and did not lead to dose-limiting toxicities in five patients with relapsed or refractory multiple myeloma.
In vivo generation of anti-BCMA CAR-T cells in relapsed or refractory multiple myeloma: a phase 1 study
Nature Medicine, Published online: 25 March 2026; doi:10.1038/s41591-026-04244-6
In a phase 1 trial, the in vivo generation of anti-BCMA CAR-T cells by lentiviral delivery was feasible and did not lead to dose-limiting toxicities in five patients with relapsed or refractory multiple myeloma.-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Research on the compatibility mechanism of the Tingli Dazao Xiefei Decoction by multi-organ metabolomics strategy
J Ethnopharmacol. 2026 Mar 21:121548. doi: 10.1016/j.jep.2026.121548. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: The Tingli Dazao Xiefei Decoction (TD) is a traditional phlegm-eliminating prescription composed of Descurainia sophia (L.) Webb. ex Prantl (TLZ) and Ziziphus jujuba Mill. (DZ), which can relieve lung, heart and kidney injury in asthma. TLZ acts as the monarch drug in the TD. Based on the research mode of "material basis of traditional Chinese medicinal properties c
Research on the compatibility mechanism of the Tingli Dazao Xiefei Decoction by multi-organ metabolomics strategy
J Ethnopharmacol. 2026 Mar 21:121548. doi: 10.1016/j.jep.2026.121548. Online ahead of print.
ABSTRACT
ETHNOPHARMACOLOGICAL RELEVANCE: The Tingli Dazao Xiefei Decoction (TD) is a traditional phlegm-eliminating prescription composed of Descurainia sophia (L.) Webb. ex Prantl (TLZ) and Ziziphus jujuba Mill. (DZ), which can relieve lung, heart and kidney injury in asthma. TLZ acts as the monarch drug in the TD. Based on the research mode of "material basis of traditional Chinese medicinal properties can be divided and combined", we have confirmed that the flavonoid glycosides components /the oligosaccharide components/the fatty oil component (FG/Oli/FO) are effective components of TLZ. However, the compatibility mechanism of the TD, and the contribution of the effective components of TLZ to the efficacy were still unclear.
AIM OF THE STUDY: To clarify the compatibility mechanism of TD, and the contribution of the effective components of TLZ to the efficacy from a comprehensive perspective of lung, heart, and kidney.
METHODS: First, we chose the asthma model corresponding to the efficacy of TD in purging the lungs and relieving asthma, and the rats were divided into the normal (NC) group, model (M) group, dexamethasone (DEX) group, and treatment groups of TD/TLZ/DZ/FO+DZ/Oli+DZ/FG+DZ. Second, metabolomics and network pharmacology were applied to elucidate the comprehensive protective effect of TD/FG+DZ/Oli+DZ/FO+DZ. Third, the multi-omics results were validated using Western blotting, RT-qPCR, flow cytometry, and immunofluorescence.
RESULTS: FO+DZ/Oli+DZ/FG+DZ had different degrees of protective effects against lung/heart/kidney injury in asthma. In metabolomics research, the principal component analysis (PCA) and cluster analysis results showed that the TLZ group was closer to TD group than DZ group, the FO+DZ and Oli+DZ group clustered with TD/NC groups in the lung and kidney, and the FO+DZ and FG+DZ group clustered with TD/NC groups in the heart. Pathway enrichment analysis suggested that the comprehensive protective effect of TLZ and its effective components combined with DZ on lung/heart/kidney may be achieved by regulating the arginine and proline metabolism, alanine, aspartate and glutamate metabolism, and unsaturated fatty acid biosynthesis. Multi-organ metabolomics and network pharmacology revealed consistent biological functions in KEGG pathways. Validation experiment showed that TLZ and its effective components combined with DZ could reverse the abnormal expression of proteins and RNA related to inflammation, airway remodeling, excitotoxicity, and energy-supply, apoptosis at different levels. Furthermore, FO+DZ may reduce asthma damage by inhibiting the FABP4/PPAR-γ/NF-κB signaling pathway.
CONCLUSION: TLZ played the key role in TD, and FO had the best therapeutic effect on each organ; the efficacy of Oli was mainly reflected in reducing lung and kidney damage, and FG was mainly involved in enhancing energy metabolism in the heart. These findings proved that traditional Chinese medicine could exert comprehensive efficacy in a 'multi-components trigger multi-channel' way.
PMID:41871629 | DOI:10.1016/j.jep.2026.121548
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Omics In Lung
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Research on the compatibility mechanism of the Tingli Dazao Xiefei Decoction by multi-organ metabolomics strategy
J Ethnopharmacol. 2026 Mar 21:121548. doi: 10.1016/j.jep.2026.121548. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: The Tingli Dazao Xiefei Decoction (TD) is a traditional phlegm-eliminating prescription composed of Descurainia sophia (L.) Webb. ex Prantl (TLZ) and Ziziphus jujuba Mill. (DZ), which can relieve lung, heart and kidney injury in asthma. TLZ acts as the monarch drug in the TD. Based on the research mode of "material basis of traditional Chinese medicinal properties c
Research on the compatibility mechanism of the Tingli Dazao Xiefei Decoction by multi-organ metabolomics strategy
J Ethnopharmacol. 2026 Mar 21:121548. doi: 10.1016/j.jep.2026.121548. Online ahead of print.
ABSTRACT
ETHNOPHARMACOLOGICAL RELEVANCE: The Tingli Dazao Xiefei Decoction (TD) is a traditional phlegm-eliminating prescription composed of Descurainia sophia (L.) Webb. ex Prantl (TLZ) and Ziziphus jujuba Mill. (DZ), which can relieve lung, heart and kidney injury in asthma. TLZ acts as the monarch drug in the TD. Based on the research mode of "material basis of traditional Chinese medicinal properties can be divided and combined", we have confirmed that the flavonoid glycosides components /the oligosaccharide components/the fatty oil component (FG/Oli/FO) are effective components of TLZ. However, the compatibility mechanism of the TD, and the contribution of the effective components of TLZ to the efficacy were still unclear.
AIM OF THE STUDY: To clarify the compatibility mechanism of TD, and the contribution of the effective components of TLZ to the efficacy from a comprehensive perspective of lung, heart, and kidney.
METHODS: First, we chose the asthma model corresponding to the efficacy of TD in purging the lungs and relieving asthma, and the rats were divided into the normal (NC) group, model (M) group, dexamethasone (DEX) group, and treatment groups of TD/TLZ/DZ/FO+DZ/Oli+DZ/FG+DZ. Second, metabolomics and network pharmacology were applied to elucidate the comprehensive protective effect of TD/FG+DZ/Oli+DZ/FO+DZ. Third, the multi-omics results were validated using Western blotting, RT-qPCR, flow cytometry, and immunofluorescence.
RESULTS: FO+DZ/Oli+DZ/FG+DZ had different degrees of protective effects against lung/heart/kidney injury in asthma. In metabolomics research, the principal component analysis (PCA) and cluster analysis results showed that the TLZ group was closer to TD group than DZ group, the FO+DZ and Oli+DZ group clustered with TD/NC groups in the lung and kidney, and the FO+DZ and FG+DZ group clustered with TD/NC groups in the heart. Pathway enrichment analysis suggested that the comprehensive protective effect of TLZ and its effective components combined with DZ on lung/heart/kidney may be achieved by regulating the arginine and proline metabolism, alanine, aspartate and glutamate metabolism, and unsaturated fatty acid biosynthesis. Multi-organ metabolomics and network pharmacology revealed consistent biological functions in KEGG pathways. Validation experiment showed that TLZ and its effective components combined with DZ could reverse the abnormal expression of proteins and RNA related to inflammation, airway remodeling, excitotoxicity, and energy-supply, apoptosis at different levels. Furthermore, FO+DZ may reduce asthma damage by inhibiting the FABP4/PPAR-γ/NF-κB signaling pathway.
CONCLUSION: TLZ played the key role in TD, and FO had the best therapeutic effect on each organ; the efficacy of Oli was mainly reflected in reducing lung and kidney damage, and FG was mainly involved in enhancing energy metabolism in the heart. These findings proved that traditional Chinese medicine could exert comprehensive efficacy in a 'multi-components trigger multi-channel' way.
PMID:41871629 | DOI:10.1016/j.jep.2026.121548
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cs.AI, q-bio.NC updates on arXiv.org
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Tiny but Mighty: A Software-Hardware Co-Design Approach for Efficient Multimodal Inference on Battery-Powered Small Devices
arXiv:2510.05109v5 Announce Type: replace-cross Abstract: Large Multimodal Models (LMMs) are inherently modular, consisting of vision and audio encoders, projectors, and large language models. Yet, they are almost always executed monolithically, which underutilizes the heterogeneous accelerators (NPUs, GPUs, DSPs) in modern SoCs and leads to high end-to-end latency. In this paper, we present NANOMIND, a hardware--software co-design inference framework for Large Multimodal Models (LMMs) that bre
Tiny but Mighty: A Software-Hardware Co-Design Approach for Efficient Multimodal Inference on Battery-Powered Small Devices
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cs.AI, q-bio.NC updates on arXiv.org
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Towards Efficient Federated Learning of Networked Mixture-of-Experts for Mobile Edge Computing
arXiv:2511.01743v2 Announce Type: replace-cross Abstract: Recent advancements in large artificial intelligence models (LAMs) are driving significant innovations in mobile edge computing within next-generation wireless networks. However, the substantial demands for computational resources and larges-cale training data required to train LAMs conflict with the limited storage and computational capacity of edge devices, posing significant challenges to training and deploying LAMs at the edge. In th
Towards Efficient Federated Learning of Networked Mixture-of-Experts for Mobile Edge Computing
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cs.AI, q-bio.NC updates on arXiv.org
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Zero-Permission Manipulation: Can We Trust Large Multimodal Model Powered GUI Agents?
arXiv:2601.12349v2 Announce Type: replace-cross Abstract: Large multimodal model powered GUI agents are emerging as high-privilege operators on mobile platforms, entrusted with perceiving screen content and injecting inputs. However, their design operates under the implicit assumption of Visual Atomicity: that the UI state remains invariant between observation and action. We demonstrate that this assumption is fundamentally invalid in Android, creating a critical attack surface. We present Ac