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cs.AI, q-bio.NC updates on arXiv.org
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Thought Communication in Multiagent Collaboration
arXiv:2510.20733v1 Announce Type: cross Abstract: Natural language has long enabled human cooperation, but its lossy, ambiguous, and indirect nature limits the potential of collective intelligence. While machines are not subject to these constraints, most LLM-based multi-agent systems still rely solely on natural language, exchanging tokens or their embeddings. To go beyond language, we introduce a new paradigm, thought communication, which enables agents to interact directly mind-to-mind, akin
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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HALO: hierarchical causal modeling for single cell multi-omics data
Nat Commun. 2025 Oct 7;16(1):8892. doi: 10.1038/s41467-025-63921-1.ABSTRACTThough open chromatin may promote active transcription, gene expression responses may not be directly coordinated with changes in chromatin accessibility. Most existing methods for single-cell multi-omics data focus only on learning stationary, shared information among these modalities, overlooking modality-specific information delineating cellular states and dynamics resulting from causal relations among modalities. To a
HALO: hierarchical causal modeling for single cell multi-omics data
Nat Commun. 2025 Oct 7;16(1):8892. doi: 10.1038/s41467-025-63921-1.
ABSTRACT
Though open chromatin may promote active transcription, gene expression responses may not be directly coordinated with changes in chromatin accessibility. Most existing methods for single-cell multi-omics data focus only on learning stationary, shared information among these modalities, overlooking modality-specific information delineating cellular states and dynamics resulting from causal relations among modalities. To address this, the epigenome-transcriptome relationship can be characterized in relation to time as coupled (changing dependently) or decoupled (changing independently). We propose the framework HALO, adopting a causal approach to model these temporal causal relations on two levels. On the representation level, HALO factorizes these two modalities into both coupled and decoupled latent representations, revealing their dynamic interplay. On the individual gene level, HALO matches gene-peak pairs and characterizes their changes over time. HALO discovers analogous biological functions between modalities, distinguishes epigenetic factors for lineage specification, and identifies temporal cis-regulation interactions relevant to cellular differentiation and human diseases.
PMID:41057364 | PMC:PMC12504611 | DOI:10.1038/s41467-025-63921-1
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Cell
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How to build the virtual cell with artificial intelligence: Priorities and opportunities
Advances in AI and omics enable the creation of AI virtual cells (AIVCs)—multi-scale, multimodal neural network models that simulate molecules, cells, and tissues across diverse states. This vision outlines their design and collaborative development, promising to transform biological research through high-fidelity simulations, accelerating discoveries, and fostering interdisciplinary open science collaborations.