AIMC Journal:
bioRxiv

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CellAwareGNN: Single-Cell Enhanced Knowledge Graph Foundation Model for Drug Indication Prediction

bioRxiv Feb 23, 2026
Graph foundation models have emerged as powerful tools for drug repurposing by enabling the prediction of novel drug-disease indications from large biomedical knowledge graphs. A representative example is TxGNN, which was previously developed and tra...
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A Comprehensive Atlas and Machine-Learning Framework for Predicting IDR-Protein Binding Affinity

bioRxiv Feb 23, 2026
Intrinsically disordered regions (IDRs) enable pervasive, regulatable protein interactions, yet predicting their binding affinities remains challenging because disorder permits heterogeneous interfaces and context-dependent recognition. Here we intro...
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Pixel2Gene enables histology-guided reconstruction and prediction of spatial gene expression

bioRxiv Feb 23, 2026
Advances in spatial transcriptomics (ST) have fundamentally transformed our understanding of tissue biology by enabling gene expression profiling within intact spatial contexts and uncovering tissue organization and microenvironmental interactions. H...
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Hierarchical Multi-Omics Trajectory Prediction forFecal Microbiota Transplantation: A Novel MachineLearning Framework for Small-Sample LongitudinalMulti-Omics Integration

bioRxiv Feb 23, 2026
Fecal microbiota transplantation (FMT) has emerged as a highly effective treatment for recurrent Clostridioides difficile infection and is being actively investigated for numerous other conditions. While multi-omics studies have revealed dynamic chan...
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Structure-Based TCR-pMHC Binding Prediction and Generalization to Unseen Peptides

bioRxiv Feb 23, 2026
The interaction between T-cell receptors (TCRs) with the peptide-bound major histocompatibility complex (MHC) intricately impacts the functional specificity of T-cell-mediated adaptive immune response. Consequently, implication in immunotherapy has c...
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Geometric-Evolutionary Deep Learning Decodes the Human GPCR-Metabolome Interactome and Enables Systematic De-Orphanization

bioRxiv Feb 23, 2026
G protein-coupled receptors (GPCRs) are the largest class of drug targets, yet hundreds of orphan GPCRs lack known endogenous ligands, limiting our understanding of human physiology and therapeutic development. Existing computational approaches often...
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Reservoir Computing with Ultra-Sparse Rings

bioRxiv Feb 23, 2026
Many existing models of computation in recurrent neural networks assume dense, unconstrained initial connectivity, where any pair of neurons may be coupled to generate the rich dynamics needed for learning complex temporal patterns. Inspired by inver...
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Deep learning extracts MoA-specific signatures from high-throughput images of chemically and genetically perturbed Corynebacteria

bioRxiv Feb 23, 2026
Tuberculosis (TB) is the worldwide leading infectious killer due to a single pathogen and increasing antimicrobial resistance (AMR) makes it imperative to discover and develop new drugs with novel modes of action (MoAs) to treat TB infections. Phenot...
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Genomic Evolution of SARS-CoV-2 Delta Variants Pre- and Post-Omicron Emergence using Alignment-free Machine Learning models

bioRxiv Feb 23, 2026
The SARS-CoV-2 Delta variant (B.1.617.2), initially classified as a variant of concern due to its enhanced transmissibility and vaccine-escape mutations, underwent further genomic changes following the emergence of the Omicron variant (B.1.1.529). Th...
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Dynamic, single-cell monitoring of CAR T cell identity and activation with Raman spectroscopy

bioRxiv Feb 23, 2026
Chimeric antigen receptor (CAR) T cell therapies have reshaped treatment for cancers and immune-mediated diseases, yet their safety and efficacy depend on both the proliferation of engineered cells and their dynamic functional state - features that r...
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