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... read more
Cancer driver mutations shape the tumor microenvironment (TME), yet whether TME composition alone can predict genotype has not been systematically evaluated across cancers with external validation. We trained machine learning models to predict driver... read more
Abstract Epigenetic biomarkers offer critical insight into biological aging and disease risk, yet most deep learning models lack interpretability and generalization across tissues. We present a reproducible pipeline for interpretable age classificati... read more
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... read more
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... read more
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... read more
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... read more
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... read more
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... read more
Protein-protein binding affinity is important for understanding protein interactions within a protein complex and for identifying strong drug-peptide binders to a target protein. Many structure-based models were built previously with reasonable perfo... read more
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