AIMC Journal:
bioRxiv

Showing 2191 to 2200 of 4956 articles

VascFlexMap: Microvascular Ultrasound Imaging at Low Frame Rates Using Sparse Data and a Transformer-Decoder Network

bioRxiv Mar 2, 2026
Objective: Superresolution ultrasound (SR US) reveals microvascular structures with exquisite resolution, but clinical translation remains limited by the need for ultrafast frame rates, massive data volumes, and long reconstruction times. This work p...
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Detecting Extrachromosomal DNA from Routine Histopathology

bioRxiv Mar 2, 2026
Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, tumour heterogeneity and poor clinical outcomes [1-3], yet its detection relies on specialised genomic assays that are not integrated into routine diagnostics. Here, we show th...
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Genomic language models improve cross-species gene expression prediction and accurately capture regulatory variant effects in Brachypodium mutant lines

bioRxiv Mar 2, 2026
Predicting gene expression from cis-regulatory DNA sequences at the promoter and terminator regions is a central challenge in plant genomics. This capability is also a prerequisite for assessing the effects of regulatory mutations on gene expression....
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DNA fragment length analysis using machine learning assisted vibrational spectroscopy

bioRxiv Mar 2, 2026
DNA length analysis is essential for genomic workflows including next-generation sequencing and fragmentomics based diagnostics. Conventional approaches typically require large, expensive instrumentation and sample-destructive protocols with long pro...
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Evaluation of deep learning tools for chromatin contact prediction

bioRxiv Mar 2, 2026
Three-dimensional chromatin organization is essential for gene regulation and is commonly measured using Hi-C contact maps. Recent deep learning models have been developed to predict Hi-C maps from genomic and epigenomic features. However, their rela...
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t2pmhc: A Structure-Informed Graph Neural Network to predict TCR-pMHC Binding

bioRxiv Mar 2, 2026
Mapping of T cell receptors (TCRs) to their cognate MHC-presented peptides (pMHC) is central for the development of precision immunotherapies and vaccine design. However, accurate prediction of TCR affinity to peptide antigens remains an open challen...
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Explainable AI for end-to-end pathogen target discovery and molecular design

bioRxiv Mar 2, 2026
Drug discovery is often constrained by target identification, a bottleneck especially acute in antimicrobial development and the fight against emerging fungicide resistance. We present APEX (Attention-based Protein EXplainer), an explainable AI frame...
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MONICA: A Web Application for Automated Whole Optic Nerve Contour Extraction and Morphometric Analysis Validated Across Taxonomic Orders and Image Quality Levels

bioRxiv Mar 2, 2026
Quantitative assessment of optic nerve health requires metrics beyond axon counts alone. Axon density and glial coverage fraction correlate with clinical measures of visual function, yet no existing automated tool extracts optic nerve cross-sectional...
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GTA-5: A Unified Graph Transformer Framework for Ligands and Protein Binding Sites - Part I: Constructing the PDB Pocket and Ligand Space

bioRxiv Mar 2, 2026
Structural recognition between a protein target and a ligand underpins therapeutic innovation, yet computational representations of protein binding sites and small molecules remain largely disjoint. Here we introduce GTA-5, a unified graph transforme...
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EnzySeek: Efficient Exploration of Enzyme Reaction Pathways Using AI Agents

bioRxiv Mar 2, 2026
With the rapid development of Large Language Models (LLMs) and Agent technologies, AI can assist in solving a variety of real-world problems across multiple domains, such as autonomous driving, drug discovery, and materials design. In this work, we p...
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