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cs.AI, q-bio.NC updates on arXiv.org
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Distilling Game Code World Model Generation into Lightweight Large Language Models
arXiv:2605.24375v1 Announce Type: new Abstract: Large Language Models (LLMs) have shown great ability in generating executable code from natural language, opening the possibility of automatically constructing environments for AI agents. Recent work on Code World Models (CWMs) demonstrates that LLMs can translate game rules into Python implementations compatible with solvers like Monte Carlo Tree Search. We study this problem in game settings, where generated environments must implement rules, l
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Omics In Lung
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GPNMB Drives Brain Metastasis by Sculpting a Pathological Endothelial-Immune Interactome
Cancer Discov. 2026 Apr 15. doi: 10.1158/2159-8290.CD-25-1663. Online ahead of print.ABSTRACTBrain metastases (BM) remain a devastating disease with dismal prognosis. How circulating tumor cells (CTCs) penetrate the blood brain barrier (BBB) and reprogram the brain microenvironment remain unclear. Using spatially resolved multi-omic profiling of CTCs and brain metastases, integrated with experimental and clinical analyses, we identified Glycoprotein Non-Metastatic Melanoma Protein B (GPNMB) as a
GPNMB Drives Brain Metastasis by Sculpting a Pathological Endothelial-Immune Interactome
Cancer Discov. 2026 Apr 15. doi: 10.1158/2159-8290.CD-25-1663. Online ahead of print.
ABSTRACT
Brain metastases (BM) remain a devastating disease with dismal prognosis. How circulating tumor cells (CTCs) penetrate the blood brain barrier (BBB) and reprogram the brain microenvironment remain unclear. Using spatially resolved multi-omic profiling of CTCs and brain metastases, integrated with experimental and clinical analyses, we identified Glycoprotein Non-Metastatic Melanoma Protein B (GPNMB) as a CTC-secreted driver of vascular disruption and brain colonization. CBX3 upregulation induced GPNMB expression, which bound endothelial EGFR, triggering CBL-mediated ubiquitination and degradation. Attenuated EGFR signaling suppressed FTO and disrupted endothelial junctions via YTHDF2-dependent TJP1 m6A methylation. Remarkably, GPNMB-induced BBB remodeling promoted immune infiltration via CXCL12-CXCR4 axis, and induced time course-dependent T cell exhaustion within the brain microenvironment. Clinically, elevated CBX3⁺GPNMB⁺ CTCs and plasma CXCL12 were significantly associated with BM progression in lung cancer and melanoma. Therapeutically, dual blockade of GPNMB and PD1 enhanced anti-BM efficacy in mice, unveiling GPNMB as a promising target for precision immunotherapy.
PMID:41973996 | DOI:10.1158/2159-8290.CD-25-1663
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Nature - Issue - nature.com science feeds
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Engineered immunosuppressive dendritic cells protect against cardiac remodelling
Nature, Published online: 08 April 2026; doi:10.1038/s41586-026-10346-5Lesion-targeted immune modulation is a feasible strategy to control cardiac fibrosis, and engineered dendritic cells are a promising therapeutic platform for treating cardiac remodelling and heart failure.
Engineered immunosuppressive dendritic cells protect against cardiac remodelling
Nature, Published online: 08 April 2026; doi:10.1038/s41586-026-10346-5
Lesion-targeted immune modulation is a feasible strategy to control cardiac fibrosis, and engineered dendritic cells are a promising therapeutic platform for treating cardiac remodelling and heart failure.-
cs.AI, q-bio.NC updates on arXiv.org
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MoltNet: Understanding Social Behavior of AI Agents in the Agent-Native MoltBook
arXiv:2602.13458v2 Announce Type: replace-cross Abstract: Large-scale communities of AI agents are becoming increasingly prevalent, creating new environments for agent-agent social interaction. Prior work has examined multi-agent behavior primarily in controlled or small-scale settings, limiting our understanding of emergent social dynamics at scale. The recent emergence of MoltBook, a social networking platform designed explicitly for AI agents, presents a unique opportunity to study whether a
MoltNet: Understanding Social Behavior of AI Agents in the Agent-Native MoltBook
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cs.AI, q-bio.NC updates on arXiv.org
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Think, Act, Build: An Agentic Framework with Vision Language Models for Zero-Shot 3D Visual Grounding
arXiv:2604.00528v2 Announce Type: replace-cross Abstract: 3D Visual Grounding (3D-VG) aims to localize objects in 3D scenes via natural language descriptions. While recent advancements leveraging Vision-Language Models (VLMs) have explored zero-shot possibilities, they typically suffer from a static workflow relying on preprocessed 3D point clouds, essentially degrading grounding into proposal matching. To bypass this reliance, our core motivation is to decouple the task: leveraging 2D VLMs to
Think, Act, Build: An Agentic Framework with Vision Language Models for Zero-Shot 3D Visual Grounding
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cs.AI, q-bio.NC updates on arXiv.org
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RAAP: Retrieval-Augmented Affordance Prediction with Cross-Image Action Alignment
arXiv:2603.29419v1 Announce Type: cross Abstract: Understanding object affordances is essential for enabling robots to perform purposeful and fine-grained interactions in diverse and unstructured environments. However, existing approaches either rely on retrieval, which is fragile due to sparsity and coverage gaps, or on large-scale models, which frequently mislocalize contact points and mispredict post-contact actions when applied to unseen categories, thereby hindering robust generalization.
RAAP: Retrieval-Augmented Affordance Prediction with Cross-Image Action Alignment
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Nature - Issue - nature.com science feeds
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DNA damage burden causes selective CUX2 neuron loss in neuroinflammation
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10310-3DNA damage burden and inadequate repair in CUX2+ cortical layer 2/3 excitatory neurons contributes to selective vulnerability in neuroinflammatory injury.
DNA damage burden causes selective CUX2 neuron loss in neuroinflammation
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10310-3
DNA damage burden and inadequate repair in CUX2+ cortical layer 2/3 excitatory neurons contributes to selective vulnerability in neuroinflammatory injury.-
Nature - Issue - nature.com science feeds
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Expansion of outer cortical CUX2 neurons requires adaptations for DNA repair
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10290-4The transcription factor ATF4 is shown to regulate double-stranded DNA repair within vulnerable CUX2+ upper-layer 2/3 cortical neurons, enabling their survival during development.
Expansion of outer cortical CUX2 neurons requires adaptations for DNA repair
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10290-4
The transcription factor ATF4 is shown to regulate double-stranded DNA repair within vulnerable CUX2+ upper-layer 2/3 cortical neurons, enabling their survival during development.-
(Multiomics OR Omics) AND (Pancreatic)
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Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma
Cell Rep Med. 2026 Mar 30:102708. doi: 10.1016/j.xcrm.2026.102708. Online ahead of print.ABSTRACTIntratumor heterogeneity (ITH) undermines transcriptome-based stratification in intrahepatic cholangiocarcinoma (iCCA). Here, we integrate multi-omics data from multi-region, single-region, and single-cell RNA sequencing cohorts to systematically characterize gene expression ITH. We uncover that immune and stromal heterogeneity are primary drivers of ITH, leading to misclassification of a median 27.8
Robust transcriptomic hallmarks targeting intratumor heterogeneity in intrahepatic cholangiocarcinoma
Cell Rep Med. 2026 Mar 30:102708. doi: 10.1016/j.xcrm.2026.102708. Online ahead of print.
ABSTRACT
Intratumor heterogeneity (ITH) undermines transcriptome-based stratification in intrahepatic cholangiocarcinoma (iCCA). Here, we integrate multi-omics data from multi-region, single-region, and single-cell RNA sequencing cohorts to systematically characterize gene expression ITH. We uncover that immune and stromal heterogeneity are primary drivers of ITH, leading to misclassification of a median 27.8% of tumors by existing subtyping systems. To overcome this, we identify a low-intratumor-heterogeneity/high-intertumor-variability (LIHV) gene set and develop an ITH-insensitive classification system defining five subgroups: inflammatory (SI), metabolic (SII), atypical (SIII-1), immune-silent (SIII-2), and neurodegenerative (SIII-3). These subgroups exhibit distinct clinical outcomes, molecular features, immune landscapes, and therapeutic vulnerabilities. GPRC5A and VTCN1 serve as robust immunohistochemical biomarkers for SI and SIII tumors, while serum CEA and CA19-9 identify inflammatory iCCA. Therapeutically, HSP90 inhibition synergizes with anti-PD1 in inflammatory iCCA, whereas combined anti-PD1 and anti-TIM3 suppresses neurodegenerative iCCA. Collectively, our study provides a robust molecular framework and actionable therapeutic strategies for iCCA.
PMID:41916296 | DOI:10.1016/j.xcrm.2026.102708
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Omics In Lung
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Trem1 regulates neutrophil metabolism and recruitment in lung ischemia-reperfusion injury
Redox Biol. 2026 Jan 14;92:104026. doi: 10.1016/j.redox.2026.104026. Online ahead of print.ABSTRACTPrimary graft dysfunction (PGD) caused by ischemia-reperfusion injury (IRI) is a major complication after lung transplantation, yet its underlying mechanisms remain unclear. Triggering receptor expressed on myeloid cells 1 (Trem1) is an important mediator of inflammation, but its role in neutrophil function and metabolic reprogramming during lung IRI is not well understood. In this study, we used a
Trem1 regulates neutrophil metabolism and recruitment in lung ischemia-reperfusion injury
Redox Biol. 2026 Jan 14;92:104026. doi: 10.1016/j.redox.2026.104026. Online ahead of print.
ABSTRACT
Primary graft dysfunction (PGD) caused by ischemia-reperfusion injury (IRI) is a major complication after lung transplantation, yet its underlying mechanisms remain unclear. Triggering receptor expressed on myeloid cells 1 (Trem1) is an important mediator of inflammation, but its role in neutrophil function and metabolic reprogramming during lung IRI is not well understood. In this study, we used a murine orthotopic lung transplantation model with cold ischemia and reperfusion, and Trem1 knockout (Trem1-/-) and myeloid-specific Trem1 conditional knockout mice (LysmCreTrem1fl) to explore the role of Trem1 in neutrophil recruitment, neutrophil extracellular trap (NET) formation, and metabolism. Our results show that Trem1 expression increases in both mouse and human lungs after reperfusion and correlates with neutrophil infiltration and lung injury. Trem1 deficiency significantly reduced neutrophil and macrophage recruitment, NET formation, and tissue damage. Multi-omics analysis revealed that Trem1 deletion suppressed oxidative phosphorylation (OXPHOS) and induced a metabolic shift in neutrophils toward glycolysis. In clinical samples, the abundance of TREM1+ neutrophils was correlated with PGD severity and OXPHOS activity. These findings identify Trem1 as a key regulator of neutrophil metabolism and recruitment in lung IRI, and suggest that targeting Trem1 may provide a novel therapeutic strategy to mitigate PGD and improve lung transplant outcomes.
PMID:41861599 | DOI:10.1016/j.redox.2026.104026
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cs.AI, q-bio.NC updates on arXiv.org
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Delta1 with LLM: symbolic and neural integration for credible and explainable reasoning
arXiv:2603.12953v1 Announce Type: cross Abstract: Neuro-symbolic reasoning increasingly demands frameworks that unite the formal rigor of logic with the interpretability of large language models (LLMs). We introduce an end to end explainability by construction pipeline integrating the Automated Theorem Generator Delta1 based on the full triangular standard contradiction (FTSC) with LLMs. Delta1 deterministically constructs minimal unsatisfiable clause sets and complete theorems in polynomial ti
Delta1 with LLM: symbolic and neural integration for credible and explainable reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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Don't Freeze, Don't Crash: Extending the Safe Operating Range of Neural Navigation in Dense Crowds
arXiv:2603.06729v1 Announce Type: cross Abstract: Navigating safely through dense crowds requires collision avoidance that generalizes beyond the densities seen during training. Learning-based crowd navigation can break under out-of-distribution crowd sizes due to density-sensitive observation normalization and social-cost scaling, while analytical solvers often remain safe but freeze in tight interactions. We propose a reinforcement learning approach for dense, variable-density navigation that
Don't Freeze, Don't Crash: Extending the Safe Operating Range of Neural Navigation in Dense Crowds
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cs.AI, q-bio.NC updates on arXiv.org
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Cross-Modal Taxonomic Generalization in (Vision-) Language Models
arXiv:2603.07474v1 Announce Type: cross Abstract: What is the interplay between semantic representations learned by language models (LM) from surface form alone to those learned from more grounded evidence? We study this question for a scenario where part of the input comes from a different modality -- in our case, in a vision-language model (VLM), where a pretrained LM is aligned with a pretrained image encoder. As a case study, we focus on the task of predicting hypernyms of objects represent
Cross-Modal Taxonomic Generalization in (Vision-) Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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LifeBench: A Benchmark for Long-Horizon Multi-Source Memory
arXiv:2603.03781v1 Announce Type: new Abstract: Long-term memory is fundamental for personalized agents capable of accumulating knowledge, reasoning over user experiences, and adapting across time. However, existing memory benchmarks primarily target declarative memory, specifically semantic and episodic types, where all information is explicitly presented in dialogues. In contrast, real-world actions are also governed by non-declarative memory, including habitual and procedural types, and need
LifeBench: A Benchmark for Long-Horizon Multi-Source Memory
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cs.AI, q-bio.NC updates on arXiv.org
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Dynamic Manifold Hopfield Networks for Context-Dependent Associative Memory
arXiv:2506.01303v3 Announce Type: replace-cross Abstract: Neural population activity in cortical and hippocampal circuits can be flexibly reorganized by context, suggesting that cognition relies on dynamic manifolds rather than static representations. However, how such dynamic organization can be realized mechanistically within a unified dynamical system remains unclear. Continuous Hopfield networks provide a classical attractor framework in which neural dynamics follow gradient descent on a fi
Dynamic Manifold Hopfield Networks for Context-Dependent Associative Memory
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cs.AI, q-bio.NC updates on arXiv.org
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MoltNet: Understanding Social Behavior of AI Agents in the Agent-Native MoltBook
arXiv:2602.13458v1 Announce Type: cross Abstract: Large-scale communities of AI agents are becoming increasingly prevalent, creating new environments for agent-agent social interaction. Prior work has examined multi-agent behavior primarily in controlled or small-scale settings, limiting our understanding of emergent social dynamics at scale. The recent emergence of MoltBook, a social networking platform designed explicitly for AI agents, presents a unique opportunity to study whether and how t
MoltNet: Understanding Social Behavior of AI Agents in the Agent-Native MoltBook
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cs.AI, q-bio.NC updates on arXiv.org
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InnoEval: On Research Idea Evaluation as a Knowledge-Grounded, Multi-Perspective Reasoning Problem
arXiv:2602.14367v1 Announce Type: cross Abstract: The rapid evolution of Large Language Models has catalyzed a surge in scientific idea production, yet this leap has not been accompanied by a matching advance in idea evaluation. The fundamental nature of scientific evaluation needs knowledgeable grounding, collective deliberation, and multi-criteria decision-making. However, existing idea evaluation methods often suffer from narrow knowledge horizons, flattened evaluation dimensions, and the in