Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Beyond Prompts: Measuring and Optimizing LLM Tool-Agent Harnesses
arXiv:2609.05736v2 Announce Type: replace Abstract: LLM tool agents can be improved without retraining by modifying the runtime harness around a fixed model: prompts, tool interfaces, middleware, state handling, and recovery logic. We study this setting as resource-bounded harness selection for fixed-model multi-turn tool agents, with the search surface scoped to prompts and tool-boundary middleware: edits are guarded intercepts at the tool boundary, not arbitrary rewriting of agent execution l
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Omics In Lung
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Pan-cancer screening and integrative multi-omics and deep learning reveal the prognostic significance of an IBD-CRC shared host-microbe signature in bladder urothelial carcinoma
Transl Oncol. 2026 Sep 9;73:103020. doi: 10.1016/j.tranon.2026.103020. Online ahead of print.ABSTRACTBACKGROUND: The prognostic relevance of inflammatory bowel disease (IBD)-colorectal cancer (CRC) shared host-microbe signatures in non-intestinal epithelial malignancies remains unclear. This study aimed to evaluate the prognostic and biological significance of an IBD-CRC shared host-microbe interactome signature in bladder urothelial carcinoma (BLCA).METHODS: Gene set variation analysis (GSVA) w
Pan-cancer screening and integrative multi-omics and deep learning reveal the prognostic significance of an IBD-CRC shared host-microbe signature in bladder urothelial carcinoma
Transl Oncol. 2026 Sep 9;73:103020. doi: 10.1016/j.tranon.2026.103020. Online ahead of print.
ABSTRACT
BACKGROUND: The prognostic relevance of inflammatory bowel disease (IBD)-colorectal cancer (CRC) shared host-microbe signatures in non-intestinal epithelial malignancies remains unclear. This study aimed to evaluate the prognostic and biological significance of an IBD-CRC shared host-microbe interactome signature in bladder urothelial carcinoma (BLCA).
METHODS: Gene set variation analysis (GSVA) was used to assess the activity of the IBD-CRC shared signature across The Cancer Genome Atlas (TCGA) pan-cancer solid tumor cohorts, including lung, liver, colorectal, and urinary system tumors. In BLCA, weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO)-Cox regression were applied to construct a prognostic risk model, which was validated in independent transcriptomic cohorts. An attention-based multiple instance learning (MIL) model was developed to predict the LASSO-derived high- or low-risk group from H&E whole-slide images (WSIs), using TCGA cases for training and internal validation and an independent institutional cohort of 39 BLCA patients for external validation. Molecular subtype, immune infiltration, immunohistochemistry (IHC), machine learning, single nucleotide variation/copy number variation (SNV/CNV), single-cell/spatial transcriptomics, and WSI-based deep learning analyses were integrated to characterize the biological relevance of the signature.
RESULTS: High GSVA scores were significantly associated with poor prognosis in BLCA. The LASSO-derived high-risk group was enriched in basal/squamous molecular features and exhibited an immune-infiltrated but immunosuppressive tumor microenvironment, characterized by increased immunosuppressive cell infiltration and elevated immune checkpoint expression. Conventional IHC markers supported distinct subtype-related protein phenotypes between risk groups. Single-cell and spatial transcriptomic analyses revealed that malignant cells with high signature activity were enriched in Wnt, Hippo, and cell adhesion pathways. The WSI-based MIL model achieved an area under the curve (AUC) of 0.852 in the internal validation cohort. Machine learning and SNV/CNV analyses further characterized key molecular features associated with the LASSO risk score, including AKR1B1, LY6E, MEST, and others. Pan-cancer characterization of AKR1B1 across multiple malignancies, including lung adenocarcinoma (LUAD), liver hepatocellular carcinoma (LIHC), and kidney renal clear cell carcinoma (KIRC), revealed cancer-type-specific associations with immunosuppressive microenvironmental features and tumor stemness.
CONCLUSION: The IBD-CRC shared host-microbe signature has significant prognostic value in BLCA and is associated with basal/squamous differentiation, immunosuppressive microenvironmental features, genomic alteration patterns, and malignant cell functional heterogeneity. The integrated multi-omics framework and externally validated pathology AI model provide potential tools for BLCA risk stratification and biological interpretation.
PMID:42715652 | DOI:10.1016/j.tranon.2026.103020
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Pan-cancer screening and integrative multi-omics and deep learning reveal the prognostic significance of an IBD-CRC shared host-microbe signature in bladder urothelial carcinoma
Transl Oncol. 2026 Sep 9;73:103020. doi: 10.1016/j.tranon.2026.103020. Online ahead of print.ABSTRACTBACKGROUND: The prognostic relevance of inflammatory bowel disease (IBD)-colorectal cancer (CRC) shared host-microbe signatures in non-intestinal epithelial malignancies remains unclear. This study aimed to evaluate the prognostic and biological significance of an IBD-CRC shared host-microbe interactome signature in bladder urothelial carcinoma (BLCA).METHODS: Gene set variation analysis (GSVA) w
Pan-cancer screening and integrative multi-omics and deep learning reveal the prognostic significance of an IBD-CRC shared host-microbe signature in bladder urothelial carcinoma
Transl Oncol. 2026 Sep 9;73:103020. doi: 10.1016/j.tranon.2026.103020. Online ahead of print.
ABSTRACT
BACKGROUND: The prognostic relevance of inflammatory bowel disease (IBD)-colorectal cancer (CRC) shared host-microbe signatures in non-intestinal epithelial malignancies remains unclear. This study aimed to evaluate the prognostic and biological significance of an IBD-CRC shared host-microbe interactome signature in bladder urothelial carcinoma (BLCA).
METHODS: Gene set variation analysis (GSVA) was used to assess the activity of the IBD-CRC shared signature across The Cancer Genome Atlas (TCGA) pan-cancer solid tumor cohorts, including lung, liver, colorectal, and urinary system tumors. In BLCA, weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO)-Cox regression were applied to construct a prognostic risk model, which was validated in independent transcriptomic cohorts. An attention-based multiple instance learning (MIL) model was developed to predict the LASSO-derived high- or low-risk group from H&E whole-slide images (WSIs), using TCGA cases for training and internal validation and an independent institutional cohort of 39 BLCA patients for external validation. Molecular subtype, immune infiltration, immunohistochemistry (IHC), machine learning, single nucleotide variation/copy number variation (SNV/CNV), single-cell/spatial transcriptomics, and WSI-based deep learning analyses were integrated to characterize the biological relevance of the signature.
RESULTS: High GSVA scores were significantly associated with poor prognosis in BLCA. The LASSO-derived high-risk group was enriched in basal/squamous molecular features and exhibited an immune-infiltrated but immunosuppressive tumor microenvironment, characterized by increased immunosuppressive cell infiltration and elevated immune checkpoint expression. Conventional IHC markers supported distinct subtype-related protein phenotypes between risk groups. Single-cell and spatial transcriptomic analyses revealed that malignant cells with high signature activity were enriched in Wnt, Hippo, and cell adhesion pathways. The WSI-based MIL model achieved an area under the curve (AUC) of 0.852 in the internal validation cohort. Machine learning and SNV/CNV analyses further characterized key molecular features associated with the LASSO risk score, including AKR1B1, LY6E, MEST, and others. Pan-cancer characterization of AKR1B1 across multiple malignancies, including lung adenocarcinoma (LUAD), liver hepatocellular carcinoma (LIHC), and kidney renal clear cell carcinoma (KIRC), revealed cancer-type-specific associations with immunosuppressive microenvironmental features and tumor stemness.
CONCLUSION: The IBD-CRC shared host-microbe signature has significant prognostic value in BLCA and is associated with basal/squamous differentiation, immunosuppressive microenvironmental features, genomic alteration patterns, and malignant cell functional heterogeneity. The integrated multi-omics framework and externally validated pathology AI model provide potential tools for BLCA risk stratification and biological interpretation.
PMID:42715652 | DOI:10.1016/j.tranon.2026.103020
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Omics in Hepatocellular
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Pan-cancer screening and integrative multi-omics and deep learning reveal the prognostic significance of an IBD-CRC shared host-microbe signature in bladder urothelial carcinoma
Transl Oncol. 2026 Sep 9;73:103020. doi: 10.1016/j.tranon.2026.103020. Online ahead of print.ABSTRACTBACKGROUND: The prognostic relevance of inflammatory bowel disease (IBD)-colorectal cancer (CRC) shared host-microbe signatures in non-intestinal epithelial malignancies remains unclear. This study aimed to evaluate the prognostic and biological significance of an IBD-CRC shared host-microbe interactome signature in bladder urothelial carcinoma (BLCA).METHODS: Gene set variation analysis (GSVA) w
Pan-cancer screening and integrative multi-omics and deep learning reveal the prognostic significance of an IBD-CRC shared host-microbe signature in bladder urothelial carcinoma
Transl Oncol. 2026 Sep 9;73:103020. doi: 10.1016/j.tranon.2026.103020. Online ahead of print.
ABSTRACT
BACKGROUND: The prognostic relevance of inflammatory bowel disease (IBD)-colorectal cancer (CRC) shared host-microbe signatures in non-intestinal epithelial malignancies remains unclear. This study aimed to evaluate the prognostic and biological significance of an IBD-CRC shared host-microbe interactome signature in bladder urothelial carcinoma (BLCA).
METHODS: Gene set variation analysis (GSVA) was used to assess the activity of the IBD-CRC shared signature across The Cancer Genome Atlas (TCGA) pan-cancer solid tumor cohorts, including lung, liver, colorectal, and urinary system tumors. In BLCA, weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO)-Cox regression were applied to construct a prognostic risk model, which was validated in independent transcriptomic cohorts. An attention-based multiple instance learning (MIL) model was developed to predict the LASSO-derived high- or low-risk group from H&E whole-slide images (WSIs), using TCGA cases for training and internal validation and an independent institutional cohort of 39 BLCA patients for external validation. Molecular subtype, immune infiltration, immunohistochemistry (IHC), machine learning, single nucleotide variation/copy number variation (SNV/CNV), single-cell/spatial transcriptomics, and WSI-based deep learning analyses were integrated to characterize the biological relevance of the signature.
RESULTS: High GSVA scores were significantly associated with poor prognosis in BLCA. The LASSO-derived high-risk group was enriched in basal/squamous molecular features and exhibited an immune-infiltrated but immunosuppressive tumor microenvironment, characterized by increased immunosuppressive cell infiltration and elevated immune checkpoint expression. Conventional IHC markers supported distinct subtype-related protein phenotypes between risk groups. Single-cell and spatial transcriptomic analyses revealed that malignant cells with high signature activity were enriched in Wnt, Hippo, and cell adhesion pathways. The WSI-based MIL model achieved an area under the curve (AUC) of 0.852 in the internal validation cohort. Machine learning and SNV/CNV analyses further characterized key molecular features associated with the LASSO risk score, including AKR1B1, LY6E, MEST, and others. Pan-cancer characterization of AKR1B1 across multiple malignancies, including lung adenocarcinoma (LUAD), liver hepatocellular carcinoma (LIHC), and kidney renal clear cell carcinoma (KIRC), revealed cancer-type-specific associations with immunosuppressive microenvironmental features and tumor stemness.
CONCLUSION: The IBD-CRC shared host-microbe signature has significant prognostic value in BLCA and is associated with basal/squamous differentiation, immunosuppressive microenvironmental features, genomic alteration patterns, and malignant cell functional heterogeneity. The integrated multi-omics framework and externally validated pathology AI model provide potential tools for BLCA risk stratification and biological interpretation.
PMID:42715652 | DOI:10.1016/j.tranon.2026.103020
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cs.AI, q-bio.NC updates on arXiv.org
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From Prompt Optimization to Multi-Dimensional Credibility Evaluation: Enhancing Trustworthiness of Chinese LLM-Generated Liver MRI Reports -- with Preliminary Extension to Lung Cancer
arXiv:2510.23008v3 Announce Type: replace Abstract: Large language models (LLMs) have demonstrated promising performance in generating diagnostic conclusions from imaging findings, thereby supporting radiology reporting, trainee education, and quality control. However, systematic guidance on how to optimize prompt design across different clinical contexts remains underexplored. Moreover, a comprehensive and standardized framework for assessing the trustworthiness of LLM-generated radiology repo
From Prompt Optimization to Multi-Dimensional Credibility Evaluation: Enhancing Trustworthiness of Chinese LLM-Generated Liver MRI Reports -- with Preliminary Extension to Lung Cancer
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cs.AI, q-bio.NC updates on arXiv.org
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Unifying Speech Editing Detection and Content Localization via Prior-Enhanced Audio LLMs
arXiv:2601.21463v3 Announce Type: replace-cross Abstract: Existing speech editing detection (SED) datasets are predominantly constructed using manual splicing or limited editing operations, resulting in restricted diversity and poor coverage of realistic editing scenarios. Meanwhile, current SED methods rely heavily on frame-level supervision to detect observable acoustic anomalies, which fundamentally limits their ability to handle deletion-type edits, where the manipulated content is entirely
Unifying Speech Editing Detection and Content Localization via Prior-Enhanced Audio LLMs
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npj Digital Medicine
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The landscape of virtual simulation in undergraduate dental education with implications for artificial intelligence incorporation
npj Digital Medicine, Published online: 26 May 2026; doi:10.1038/s41746-026-02806-zThe landscape of virtual simulation in undergraduate dental education with implications for artificial intelligence incorporation
The landscape of virtual simulation in undergraduate dental education with implications for artificial intelligence incorporation
npj Digital Medicine, Published online: 26 May 2026; doi:10.1038/s41746-026-02806-z
The landscape of virtual simulation in undergraduate dental education with implications for artificial intelligence incorporation-
cs.AI, q-bio.NC updates on arXiv.org
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Beyond Static Vision: Scene Dynamic Field Unlocks Intuitive Physics Understanding in Multi-modal Large Language Models
arXiv:2604.03302v1 Announce Type: cross Abstract: While Multimodal Large Language Models (MLLMs) have demonstrated impressive capabilities in image and video understanding, their ability to comprehend the physical world has become an increasingly important research focus. Despite their improvements, current MLLMs struggle significantly with high-level physics reasoning. In this work, we investigate the first step of physical reasoning, i.e., intuitive physics understanding, revealing substantia
Beyond Static Vision: Scene Dynamic Field Unlocks Intuitive Physics Understanding in Multi-modal Large Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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ROSClaw: A Hierarchical Semantic-Physical Framework for Heterogeneous Multi-Agent Collaboration
arXiv:2604.04664v1 Announce Type: cross Abstract: The integration of large language models (LLMs) with embodied agents has improved high-level reasoning capabilities; however, a critical gap remains between semantic understanding and physical execution. While vision-language-action (VLA) and vision-language-navigation (VLN) systems enable robots to perform manipulation and navigation tasks from natural language instructions, they still struggle with long-horizon sequential and temporally struct
ROSClaw: A Hierarchical Semantic-Physical Framework for Heterogeneous Multi-Agent Collaboration
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Journal of Medical Internet Research
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Predictive Value of Machine Learning for Poststroke Mortality Risk: Systematic Review and Meta-Analysis
Background: People with stroke face a high mortality risk, and an accurate prediction model is essential to the guidance of clinical decision-making in this population. Recently, with growing attention paid to machine learning (ML) in stroke care, some researchers have investigated the effectiveness of ML in predicting the mortality risk in stroke. However, systematic evidence is still lacking for its effectiveness. Objective: This systematic review aims to evaluate the value of ML in predicting
Predictive Value of Machine Learning for Poststroke Mortality Risk: Systematic Review and Meta-Analysis
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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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Nature - Issue - nature.com science feeds
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Gene regulatory landscape dissected by single-cell four-omics sequencing
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10322-zCombining single-cell parallel profiling of genome conformation, histone modifications, chromatin accessibility and gene expression reveals dynamics and intranuclear spatial clustering of epigenome profiles, enabling sophisticated analysis of the regulatory landscape across cell types and tissues.
Gene regulatory landscape dissected by single-cell four-omics sequencing
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10322-z
Combining single-cell parallel profiling of genome conformation, histone modifications, chromatin accessibility and gene expression reveals dynamics and intranuclear spatial clustering of epigenome profiles, enabling sophisticated analysis of the regulatory landscape across cell types and tissues.-
npj Digital Medicine
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WiseMind: a knowledge-guided multi-agent framework for accurate and empathetic psychiatric diagnosis
npj Digital Medicine, Published online: 25 March 2026; doi:10.1038/s41746-026-02559-9WiseMind: a knowledge-guided multi-agent framework for accurate and empathetic psychiatric diagnosis
WiseMind: a knowledge-guided multi-agent framework for accurate and empathetic psychiatric diagnosis
npj Digital Medicine, Published online: 25 March 2026; doi:10.1038/s41746-026-02559-9
WiseMind: a knowledge-guided multi-agent framework for accurate and empathetic psychiatric diagnosis-
cs.AI, q-bio.NC updates on arXiv.org
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A Robust Incomplete Multimodal Low-Rank Adaptation Approach for Emotion Recognition
arXiv:2507.11202v1 Announce Type: cross Abstract: Multimodal Emotion Recognition (MER) often encounters incomplete multimodality in practical applications due to sensor failures or privacy protection requirements. While existing methods attempt to address various incomplete multimodal scenarios by balancing the training of each modality combination through additional gradients, these approaches face a critical limitation: training gradients from different modality combinations conflict with eac
A Robust Incomplete Multimodal Low-Rank Adaptation Approach for Emotion Recognition
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cs.AI, q-bio.NC updates on arXiv.org
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More Bang for the Buck: Process Reward Modeling with Entropy-Driven Uncertainty
arXiv:2503.22233v4 Announce Type: replace-cross Abstract: We introduce the Entropy-Driven Uncertainty Process Reward Model (EDU-PRM), a novel entropy-driven training framework for process reward modeling that enables dynamic, uncertainty-aligned segmentation of complex reasoning steps, eliminating the need for costly manual step annotations. Unlike previous Process Reward Models (PRMs) that rely on static partitioning and human labeling, EDU-PRM automatically anchors step boundaries at tokens w
More Bang for the Buck: Process Reward Modeling with Entropy-Driven Uncertainty
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cs.AI, q-bio.NC updates on arXiv.org
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Step 3.5 Flash: Open Frontier-Level Intelligence with 11B Active Parameters
arXiv:2602.10604v2 Announce Type: replace-cross Abstract: We introduce Step 3.5 Flash, a sparse Mixture-of-Experts (MoE) model that bridges frontier-level agentic intelligence and computational efficiency. We focus on what matters most when building agents: sharp reasoning and fast, reliable execution. Step 3.5 Flash pairs a 196B-parameter foundation with 11B active parameters for efficient inference. It is optimized with interleaved 3:1 sliding-window/full attention and Multi-Token Prediction
Step 3.5 Flash: Open Frontier-Level Intelligence with 11B Active Parameters
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cs.AI, q-bio.NC updates on arXiv.org
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Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation
arXiv:2602.15022v1 Announce Type: cross Abstract: Many generative tasks in chemistry and science involve distributions invariant to group symmetries (e.g., permutation and rotation). A common strategy enforces invariance and equivariance through architectural constraints such as equivariant denoisers and invariant priors. In this paper, we challenge this tradition through the alternative canonicalization perspective: first map each sample to an orbit representative with a canonical pose or orde