Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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OpenFinGym: A Verifiable Multi-Task Gym Environment for Evaluating Quant Agents
arXiv:2606.26350v2 Announce Type: replace Abstract: Although large language model agents are increasingly applied to quantitative-finance workflows, their evaluation remains fragmented across isolated tasks, while the financial relevance of benchmark tasks is often overlooked. Yet financial workflows are inherently multi-stage, spanning interdependent tasks such as forecasting, strategy construction, risk management, and trading. Existing platforms typically focus on a single task, and can ther
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cs.AI, q-bio.NC updates on arXiv.org
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AsyncFlow: An Asynchronous Streaming RL Framework for Efficient LLM Post-Training
arXiv:2507.01663v2 Announce Type: replace-cross Abstract: Reinforcement learning (RL) has become a pivotal technology in the post-training phase of large language models (LLMs). Traditional task-collocated RL frameworks suffer from significant scalability bottlenecks, while task-separated RL frameworks face challenges in managing complex dataflows and resolving resource idling. Furthermore, most existing frameworks are tightly coupled with LLM training or inference engines, making them difficul
AsyncFlow: An Asynchronous Streaming RL Framework for Efficient LLM Post-Training
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Pulmonary nodule
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Macrophage spatiotemporal plasticity in pulmonary diseases: decoding the niche at single-cell resolution
Front Immunol. 2026 Jun 18;17:1855906. doi: 10.3389/fimmu.2026.1855906. eCollection 2026.ABSTRACTPulmonary gas exchange and host defense depend on the dynamic coordination of resident and recruited macrophage populations. Historically, macrophage functions have often been interpreted through the classic M1/M2 dichotomy; however, this binary framework does not capture the heterogeneity and context-dependent plasticity of macrophage states within the lung microenvironment. Advances in single-cell
Macrophage spatiotemporal plasticity in pulmonary diseases: decoding the niche at single-cell resolution
Front Immunol. 2026 Jun 18;17:1855906. doi: 10.3389/fimmu.2026.1855906. eCollection 2026.
ABSTRACT
Pulmonary gas exchange and host defense depend on the dynamic coordination of resident and recruited macrophage populations. Historically, macrophage functions have often been interpreted through the classic M1/M2 dichotomy; however, this binary framework does not capture the heterogeneity and context-dependent plasticity of macrophage states within the lung microenvironment. Advances in single-cell RNA sequencing and spatial multi-omics have substantially refined our understanding of this complex macrophage network. Here, we synthesize evidence from human studies and experimental models to summarize macrophage functional states in homeostasis and across chronic obstructive pulmonary disease, asthma, idiopathic pulmonary fibrosis, pulmonary hypertension, acute lung injury/acute respiratory distress syndrome, and lung cancer. We highlight how macrophage transcriptional programs are shaped by ontogeny, tissue niche, and epigenetic-metabolic regulation, and how these programs are linked to disease-specific remodeling of the pulmonary microenvironment. Across diverse respiratory diseases, persistent tissue injury and microenvironmental stress remodel resident macrophage programs and are frequently accompanied by the expansion and context-dependent differentiation of recruited monocyte-derived macrophages. These macrophage states are associated with inflammatory amplification, epithelial and endothelial barrier dysfunction, extracellular matrix remodeling, and tumor immune evasion. Ligand-receptor and spatial analyses further identify candidate communication axes linking macrophages with stromal, epithelial, endothelial, and immune cells, some of which appear partially conserved across disease contexts. Emerging macrophage-targeted strategies are increasingly being explored beyond broad depletion, with growing interest in context-specific reprogramming and niche modulation, including antibody-based, nanocarrier-mediated, and engineered-cell approaches. Decoding the spatiotemporal trajectories and cell-cell communication networks of specific macrophage subsets, while considering tissue context, species differences, and levels of experimental support, may help clarify mechanisms of tissue remodeling, therapeutic resistance, and macrophage-targeted intervention in complex pulmonary diseases.
PMID:42396453 | PMC:PMC13322945 | DOI:10.3389/fimmu.2026.1855906
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cs.AI, q-bio.NC updates on arXiv.org
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Test-Time Self-Adaptive Conditioning for Stable Audio-Driven Talking-Head Generation
arXiv:2605.25488v1 Announce Type: cross Abstract: Audio-driven talking-head generation has achieved remarkable progress with recent models such as AniTalker, FLOAT, and Sonic. Despite their success, most existing approaches rely on a single static reference image to condition the entire video generation process at inference stage. This static conditioning paradigm often creates a mismatch between fixed identity features and dynamically evolving facial motion, leading to identity drift, temporal
Test-Time Self-Adaptive Conditioning for Stable Audio-Driven Talking-Head Generation
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cs.AI, q-bio.NC updates on arXiv.org
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Dynamic Dual-Granularity Skill Bank for Agentic RL
arXiv:2603.28716v2 Announce Type: replace Abstract: Agentic RL can benefit substantially from reusable experience, yet existing skill-based methods mainly extract trajectory-level guidance and often lack principled mechanisms for maintaining an evolving skill memory. We propose D2Skill, a dynamic dual-granularity skill bank for agentic RL that organizes reusable experience into task skills for high-level guidance and step skills for fine-grained decision support and error correction. D2Skill jo
Dynamic Dual-Granularity Skill Bank for Agentic RL
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cs.AI, q-bio.NC updates on arXiv.org
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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
TreeGaussian: Tree-Guided Cascaded Contrastive Learning for Hierarchical Consistent 3D Gaussian Scene Segmentation and Understanding
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cs.AI, q-bio.NC updates on arXiv.org
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ToG-Bench: Task-Oriented Spatio-Temporal Grounding in Egocentric Videos
arXiv:2512.03666v2 Announce Type: replace-cross Abstract: A core capability towards general embodied intelligence lies in localizing task-relevant objects from an egocentric perspective, formulated as Spatio-Temporal Video Grounding (STVG). Despite recent progress, existing STVG studies remain largely confined to object-centric and descriptive instructions, neglecting the task-oriented reasoning that is crucial for embodied agents to accomplish goal-directed interactions. To bridge this gap, we
ToG-Bench: Task-Oriented Spatio-Temporal Grounding in Egocentric Videos
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cs.AI, q-bio.NC updates on arXiv.org
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Predicting Neuromodulation Outcome for Parkinson's Disease with Generative Virtual Brain Model
arXiv:2603.29176v1 Announce Type: new Abstract: Parkinson's disease (PD) affects over ten million people worldwide. Although temporal interference (TI) and deep brain stimulation (DBS) are promising therapies, inter-individual variability limits empirical treatment selection, increasing non-negligible surgical risk and cost. Previous explorations either resort to limited statistical biomarkers that are insufficient to characterize variability, or employ AI-driven methods which is prone to overf
Predicting Neuromodulation Outcome for Parkinson's Disease with Generative Virtual Brain Model
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(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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MRD
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Dynamic Targetable Extracellular Vesicle Surface Proteins Monitor Depth of Response to CAR T Therapy
Res Sq [Preprint]. 2026 Mar 18:rs.3.rs-8913641. doi: 10.21203/rs.3.rs-8913641/v1.ABSTRACTExtracellular vesicles (EVs) represent a promising liquid biopsy platform in multiple myeloma (MM). We developed an MM EV Surface Protein Assay to quantify and dynamically monitor four MM EV subpopulations defined by targetable MM surface proteins (BCMA, CD38, GPRC5D, and CD319) across 336 serial blood samples from 45 relapsed/refractory MM (RRMM) patients treated with anti-BCMA chimeric antigen receptor (CA
Dynamic Targetable Extracellular Vesicle Surface Proteins Monitor Depth of Response to CAR T Therapy
Res Sq [Preprint]. 2026 Mar 18:rs.3.rs-8913641. doi: 10.21203/rs.3.rs-8913641/v1.
ABSTRACT
Extracellular vesicles (EVs) represent a promising liquid biopsy platform in multiple myeloma (MM). We developed an MM EV Surface Protein Assay to quantify and dynamically monitor four MM EV subpopulations defined by targetable MM surface proteins (BCMA, CD38, GPRC5D, and CD319) across 336 serial blood samples from 45 relapsed/refractory MM (RRMM) patients treated with anti-BCMA chimeric antigen receptor (CAR) T-cell therapy. All four MM EV subpopulations significantly decreased in 43 patients with initial response, while BCMA+, GPRC5D+, and CD319+ MM EVs increased in 19 patients with progression, and antigen escape was detected by BCMA+ MM EVs. MM EV subpopulations differentiated minimal residual disease (MRD) status and complemented MRD for detecting early relapse before clinical progression. Notably, CD319+ MM EVs were early predictors of progression-free and overall survival in MRD-negative patients. This assay enables noninvasive monitoring of deep response, progression, and antigen escape, and stratifies survival in MRD-negative patients with RRMM.
PMID:41890853 | PMC:PMC13015583 | DOI:10.21203/rs.3.rs-8913641/v1
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Unraveling the Link Between Azathioprine and Acute Pancreatitis: Integrating Network Toxicology, Machine Learning, and Mendelian Randomization
CPT Pharmacometrics Syst Pharmacol. 2026 Mar;15(3):e70178. doi: 10.1002/psp4.70178.ABSTRACTAzathioprine (AZA), a widely used immunosuppressant, can induce acute pancreatitis (AP), yet the underlying molecular mechanisms remain unclear. This study employed an integrative multiomics strategy-combining network toxicology, machine learning, Mendelian randomization (MR), and molecular docking-to elucidate the biological basis of AZA-induced AP. AZA-associated genes were first identified through bioin
Unraveling the Link Between Azathioprine and Acute Pancreatitis: Integrating Network Toxicology, Machine Learning, and Mendelian Randomization
CPT Pharmacometrics Syst Pharmacol. 2026 Mar;15(3):e70178. doi: 10.1002/psp4.70178.
ABSTRACT
Azathioprine (AZA), a widely used immunosuppressant, can induce acute pancreatitis (AP), yet the underlying molecular mechanisms remain unclear. This study employed an integrative multiomics strategy-combining network toxicology, machine learning, Mendelian randomization (MR), and molecular docking-to elucidate the biological basis of AZA-induced AP. AZA-associated genes were first identified through bioinformatics databases and analyzed using protein-protein interaction networks and GO/KEGG functional enrichment. Least absolute shrinkage and selection operator (LASSO) regression and support vector machine recursive feature elimination (SVM-RFE) were applied to prioritize key differentially expressed genes for diagnostic modeling. MR was then used to examine potential causal links between gene expression and AP risk, followed by molecular docking to assess AZA-protein interactions. Sixty-eight candidate genes related to AZA-induced AP were identified. Enrichment analyses indicated involvement in lipid metabolic regulation, inflammatory pathways, and energy homeostasis. Machine learning highlighted seven key genes-CES1, CTSK, JAK1, NR3C2, PLIN5, WEE1, and RORA-as central to AP development. MR analysis further demonstrated that decreased expression of CES1 and CTSK may mediate AZA-related AP susceptibility. Docking simulations revealed strong, specific binding between AZA and both CES1 and CTSK. Overall, this study identifies CES1 and CTSK as genetically protective factors and mechanistic mediators in AZA-triggered AP. These findings offer new molecular insights into the genomic and biochemical pathways underlying this adverse drug reaction.
PMID:41832938 | DOI:10.1002/psp4.70178
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Oncogene - Issue - nature.com science feeds
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LINC-AC092535.5 regulates MICAL2 mRNA level to inhibit p53-mediated ferroptosis in nasopharyngeal carcinoma
Oncogene, Published online: 14 March 2026; doi:10.1038/s41388-026-03714-yLINC-AC092535.5 regulates MICAL2 mRNA level to inhibit p53-mediated ferroptosis in nasopharyngeal carcinoma
LINC-AC092535.5 regulates MICAL2 mRNA level to inhibit p53-mediated ferroptosis in nasopharyngeal carcinoma
Oncogene, Published online: 14 March 2026; doi:10.1038/s41388-026-03714-y
LINC-AC092535.5 regulates MICAL2 mRNA level to inhibit p53-mediated ferroptosis in nasopharyngeal carcinoma-
cs.AI, q-bio.NC updates on arXiv.org
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CaMeLs Can Use Computers Too: System-level Security for Computer Use Agents
arXiv:2601.09923v2 Announce Type: replace Abstract: AI agents are vulnerable to prompt injection attacks, where malicious content hijacks agent behavior to steal credentials or cause financial loss. The only known robust defense is architectural isolation that strictly separates trusted task planning from untrusted environment observations. However, applying this design to Computer Use Agents (CUAs) -- systems that automate tasks by viewing screens and executing actions -- presents a fundamenta
CaMeLs Can Use Computers Too: System-level Security for Computer Use Agents
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cs.AI, q-bio.NC updates on arXiv.org
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Unified Medical Image Segmentation with State Space Modeling Snake
arXiv:2507.12760v2 Announce Type: replace-cross Abstract: Unified Medical Image Segmentation (UMIS) is critical for comprehensive anatomical assessment but faces challenges due to multi-scale structural heterogeneity. Conventional pixel-based approaches, lacking object-level anatomical insight and inter-organ relational modeling, struggle with morphological complexity and feature conflicts, limiting their efficacy in UMIS. We propose Mamba Snake, a novel deep snake framework enhanced by state s
Unified Medical Image Segmentation with State Space Modeling Snake
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cs.AI, q-bio.NC updates on arXiv.org
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MemSifter: Offloading LLM Memory Retrieval via Outcome-Driven Proxy Reasoning
arXiv:2603.03379v1 Announce Type: cross Abstract: As Large Language Models (LLMs) are increasingly used for long-duration tasks, maintaining effective long-term memory has become a critical challenge. Current methods often face a trade-off between cost and accuracy. Simple storage methods often fail to retrieve relevant information, while complex indexing methods (such as memory graphs) require heavy computation and can cause information loss. Furthermore, relying on the working LLM to process
MemSifter: Offloading LLM Memory Retrieval via Outcome-Driven Proxy Reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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Chain of World: World Model Thinking in Latent Motion
arXiv:2603.03195v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models are a promising path toward embodied intelligence, yet they often overlook the predictive and temporal-causal structure underlying visual dynamics. World-model VLAs address this by predicting future frames, but waste capacity reconstructing redundant backgrounds. Latent-action VLAs encode frame-to-frame transitions compactly, but lack temporally continuous dynamic modeling and world knowledge. To overcome thes
Chain of World: World Model Thinking in Latent Motion
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cs.AI, q-bio.NC updates on arXiv.org
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FineRef: Fine-Grained Error Reflection and Correction for Long-Form Generation with Citations
arXiv:2602.18437v1 Announce Type: cross Abstract: Generating with citations is crucial for trustworthy Large Language Models (LLMs), yet even advanced LLMs often produce mismatched or irrelevant citations. Existing methods over-optimize citation fidelity while overlooking relevance to the user query, which degrades answer quality and robustness in real-world settings with noisy or irrelevant retrieved content. Moreover, the prevailing single-pass paradigm struggles to deliver optimal answers in
FineRef: Fine-Grained Error Reflection and Correction for Long-Form Generation with Citations
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cs.AI, q-bio.NC updates on arXiv.org
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Are We Measuring Oversmoothing in Graph Neural Networks Correctly?
arXiv:2502.04591v4 Announce Type: replace-cross Abstract: Oversmoothing is a fundamental challenge in graph neural networks (GNNs): as the number of layers increases, node embeddings become increasingly similar, and model performance drops sharply. Traditionally, oversmoothing has been quantified using metrics that measure the similarity of neighbouring node features, such as the Dirichlet energy. We argue that these metrics have critical limitations and fail to reliably capture oversmoothing i