AIMC Journal:
bioRxiv

Showing 701 to 710 of 4938 articles

FloREN: Decoding Immune Regulatory Networks through Interpretable Graph Transformer Patient Representations.

bioRxiv Jul 20, 2026
Single-cell RNA sequencing (scRNA-seq) enables detailed characterization of cellular heterogeneity, yet understanding the full cellular and regulatory environment of complex tissues remains challenging. In the era of large single-cell atlases, this t...
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ProteinDock: A physics-informed layer to improve protein-protein docking reliability

bioRxiv Jul 20, 2026
Computational modeling provides geometric insight into protein-protein interactions without requiring the resources of experimentation. However, reliability can be hindered when modeling proteins with distinctive features, such as antibodies, that us...
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Deep learning representations of human Immune Health for precision immunology

bioRxiv Jul 20, 2026
The human immune system is composed of [~]30-50 distinct cell types, each of which can exist in different states of activation or differentiation. Indeed, the mammalian immune system has evolved to sense and respond to infections, cancers, injuries, ...
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From Hodgkin-Huxley to Pretrained Neural Inference AI

bioRxiv Jul 20, 2026
High-density probes record from thousands of neurons simultaneously, yet resolving single-neuron identity remains an ill-posed inverse problem. While detailed simulations precisely characterize the biophysical forward process, their utility for inter...
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Closed-loop control of in vitro neuronal activity using reinforcement learning after in silico pre-training

bioRxiv Jul 20, 2026
Controlling specific neuronal dynamics with electrical stimulation is critical for therapeutic neuromodulation, yet deriving optimal control policies remains challenging due to the complex and non-stationary nature of biological neuronal networks. Wh...
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GDTR: Layer-wise Settling Depth Reveals Biological Grammar in Genomic Foundation Models

bioRxiv Jul 20, 2026
Genomic foundation models capture sequence regularities, yet existing interpretability tools rarely ask where in the layer stack a biological grammar becomes stable. We introduce GDTR, the Genomic Deep-Thinking Ratio, a training-free residual-stream ...
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Neocortical astrocyte diversity stems from distinct developmental origins

bioRxiv Jul 20, 2026
Key regulators of neural network activity in multiple advanced cognitive processes and essential components of the blood-brain barrier, astrocytes constitute a highly heterogeneous population at the morphological, molecular, and functional levels. Ho...
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Diversity and evolution of the transcriptional regulatory networks of Pseudomonas strains revealed using machine learning

bioRxiv Jul 20, 2026
The genus Pseudomonas consists of diverse and ecologically significant species that form close associations with both plants and animals. This genus is widely studied due to the clinically relevant Pseudomonas aeruginosa, model plant pathogen Pseudom...
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Ensembles of in silico structures enable T cell peptide-MHC binding prediction

bioRxiv Jul 20, 2026
Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data remains a longstanding challenge in computational imm...
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Factorization and spatial encodings: a hypothesis about the foundations of the genomic code

bioRxiv Jul 20, 2026
The genomic mechanisms that efficiently encode the initial architecture and synaptic connectivity of neural circuits remain poorly understood. We hypothesise that two primary mechanisms -- spatial encoding and factorisation -- enable a limited genome...
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