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cs.AI, q-bio.NC updates on arXiv.org
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Pelican-Sim 1.0: A General World Model Simulator for Embodied Intelligence
arXiv:2609.12036v1 Announce Type: cross Abstract: In this technical report, we propose Pelican-Sim 1.0, a general world model simulator for embodied intelligence that predicts future observations from visual context and robot actions to support downstream learning and decision making. The model incorporates four key design features: (1) Unified action representation: a 28-dimensional action value space covering most mainstream embodiments, keeping one model valid across heterogeneous devices. (
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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From Black Box to Biological Insight: AttentioFuse Unlocks Multi-Omics Dynamics in Lung Cancer
Cancers (Basel). 2026 Mar 9;18(5):878. doi: 10.3390/cancers18050878.ABSTRACTBACKGROUND: Lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), the major subtypes of non-small cell lung cancer (NSCLC), exhibit distinct molecular landscapes that demand precision in prognosis and therapy. While deep learning models can achieve high predictive accuracy, their black-box nature limits clinical translation.METHODS: We introduce AttentioFuse, an interpretable deep learning framework employing a
From Black Box to Biological Insight: AttentioFuse Unlocks Multi-Omics Dynamics in Lung Cancer
Cancers (Basel). 2026 Mar 9;18(5):878. doi: 10.3390/cancers18050878.
ABSTRACT
BACKGROUND: Lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), the major subtypes of non-small cell lung cancer (NSCLC), exhibit distinct molecular landscapes that demand precision in prognosis and therapy. While deep learning models can achieve high predictive accuracy, their black-box nature limits clinical translation.
METHODS: We introduce AttentioFuse, an interpretable deep learning framework employing a Reactome-guided mid-fusion strategy for multi-omics integration. AttentioFuse builds on three pillars: (i) dual-phase learning with omics-specific encoders to preserve modality-unique patterns, (ii) hierarchical attention mechanisms (cross-omics, feature-level, and fusion-layer) to quantify layer contributions dynamically, and (iii) integrated explainability combining DeepSHAP and global attention weights for gene-to-pathway interpretation. Two depth variants are instantiated under identical priors: a three-layer configuration (3F) for main discrimination and a five-layer configuration (AttentioFuse-5X) for deeper hierarchical interpretation; the 5X variant is trained end-to-end and yields comparable accuracy while enhancing pathway-level resolution.
RESULTS: Evaluated on The Cancer Genome Atlas (TCGA) LUAD/LUSC cohorts, AttentioFuse matches state-of-the-art performance in TNM staging while uncovering actionable biological insights, including pan-NSCLC AKT/mTOR metabolic control, histology-divergent Notch signaling roles, and additional pathways related to developmental reactivation, microbiota-associated metastasis, and extracellular matrix remodeling.
CONCLUSIONS: By design, AttentioFuse-5X bridges predictive performance with hierarchical, pathway-resolved explanations, advancing oncology by transforming black-box predictions into biologically grounded decision support.
PMID:41827812 | PMC:PMC12985206 | DOI:10.3390/cancers18050878
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Omics In Lung
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From Black Box to Biological Insight: AttentioFuse Unlocks Multi-Omics Dynamics in Lung Cancer
Cancers (Basel). 2026 Mar 9;18(5):878. doi: 10.3390/cancers18050878.ABSTRACTBACKGROUND: Lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), the major subtypes of non-small cell lung cancer (NSCLC), exhibit distinct molecular landscapes that demand precision in prognosis and therapy. While deep learning models can achieve high predictive accuracy, their black-box nature limits clinical translation.METHODS: We introduce AttentioFuse, an interpretable deep learning framework employing a
From Black Box to Biological Insight: AttentioFuse Unlocks Multi-Omics Dynamics in Lung Cancer
Cancers (Basel). 2026 Mar 9;18(5):878. doi: 10.3390/cancers18050878.
ABSTRACT
BACKGROUND: Lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), the major subtypes of non-small cell lung cancer (NSCLC), exhibit distinct molecular landscapes that demand precision in prognosis and therapy. While deep learning models can achieve high predictive accuracy, their black-box nature limits clinical translation.
METHODS: We introduce AttentioFuse, an interpretable deep learning framework employing a Reactome-guided mid-fusion strategy for multi-omics integration. AttentioFuse builds on three pillars: (i) dual-phase learning with omics-specific encoders to preserve modality-unique patterns, (ii) hierarchical attention mechanisms (cross-omics, feature-level, and fusion-layer) to quantify layer contributions dynamically, and (iii) integrated explainability combining DeepSHAP and global attention weights for gene-to-pathway interpretation. Two depth variants are instantiated under identical priors: a three-layer configuration (3F) for main discrimination and a five-layer configuration (AttentioFuse-5X) for deeper hierarchical interpretation; the 5X variant is trained end-to-end and yields comparable accuracy while enhancing pathway-level resolution.
RESULTS: Evaluated on The Cancer Genome Atlas (TCGA) LUAD/LUSC cohorts, AttentioFuse matches state-of-the-art performance in TNM staging while uncovering actionable biological insights, including pan-NSCLC AKT/mTOR metabolic control, histology-divergent Notch signaling roles, and additional pathways related to developmental reactivation, microbiota-associated metastasis, and extracellular matrix remodeling.
CONCLUSIONS: By design, AttentioFuse-5X bridges predictive performance with hierarchical, pathway-resolved explanations, advancing oncology by transforming black-box predictions into biologically grounded decision support.
PMID:41827812 | PMC:PMC12985206 | DOI:10.3390/cancers18050878
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cs.AI, q-bio.NC updates on arXiv.org
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Give Them an Inch and They Will Take a Mile:Understanding and Measuring Caller Identity Confusion in MCP-Based AI Systems
arXiv:2603.07473v1 Announce Type: cross Abstract: The Model Context Protocol (MCP) is an open and standardized interface that enables large language models (LLMs) to interact with external tools and services, and is increasingly adopted by AI agents. However, the security of MCP-based systems remains largely unexplored.In this work, we conduct a large-scale security analysis of MCP servers integrated within MCP clients. We show that treating MCP servers as trusted entities without authenticatin