AIMC Journal:
bioRxiv

Showing 541 to 550 of 4935 articles

ProtFinder: An efficient machine learning framework for protein model selection on real data

bioRxiv Aug 7, 2026
Model selection is a fundamental step in phylogenetic analysis that determines the best-fit model of sequence evolution for a given multiple sequence alignment. Popular model selection methods, such as ModelFinder, rely on statistical information cri...
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De novo transformer modeling improves recovery of genetic cell types from sparse single-cell RNA sequencing

bioRxiv Aug 7, 2026
Single-cell RNA sequencing (scRNA-seq) simultaneously provides gene-expression profiles and genetic variants from individual cells, creating an opportunity to relate cellular phenotypes to their somatic evolutionary histories. However, delineation of...
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Schema-Grounded Multitask Instruction Fine-tuning for Joint Biomedical Named Entity Recognition and Relation Extraction in Pharmacovigilance

bioRxiv Aug 6, 2026
Motivation: Pharmacovigilance relies on accurate extraction of structured biomedical entities and their semantic relationships from scientific literature. However, most biomedical information extraction systems address named entity recognition (NER) ...
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Structural basis for alternative 3' splice site selection in the human spliceosome active center

bioRxiv Aug 6, 2026
Accurate alternative splicing requires discrimination between adjacent 3' splice sites (3'-ss) during catalysis and is disrupted by pathogenic AG-gain mutations that create competing 3'-ss. Here, we present cryo-EM structures of human spliceosomes as...
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Invasion status stratifies the composition of the human pancreatic cancer perineural niche

bioRxiv Aug 6, 2026
The peripheral nervous system innervates the pancreatic ductal adenocarcinoma (PDAC) microenvironment, and perineural invasion (PNI), the invasion of cancer cells in and around nerves, correlates with metastatic burden and poor outcomes. Though PDAC ...
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BRIDGE: A Computational Workflow from Single Neurons to Network of Mean-Field Models

bioRxiv Aug 6, 2026
Mean-field models are extensively used in large-scale brain simulations because they provide a wieldy description of population dynamics while preserving key features of neural activity. Despite their widespread adoption, no common and reproducible m...
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HDOCK-Multimer: integrating docking and combinatorial assembly for structure prediction of large protein complexes

bioRxiv Aug 6, 2026
Deep learning methods, such as AlphaFold and RosettaFold, achieve high accuracy in protein structure prediction. However, predicting the structure of large protein complexes remains challenging due to their large size and intricate multi-chain intera...
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LabGrymace: Automated Analysis of Mouse Grimace for Quantitative Assessment of Pain Dynamics

bioRxiv Aug 6, 2026
Accurate assessment of pain in animal models is essential for understanding pain mechanisms, developing analgesics, and ensuring animal welfare. The Mouse Grimace Scale (MGS) provides a sensitive, non-invasive measure of spontaneous pain by quantifyi...
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Multi-modal foundation model with whole-slide attention enables transferrable digital pathology at single-cell resolution

bioRxiv Aug 6, 2026
Paired histopathology and spatial transcriptomics data are advancing our understanding of tissue biology and disease, but modeling both modalities at single-cell resolution while mapping local and distal cell-cell interdependencies remains computatio...
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A Unified Deep Learning-Based Framework for Reference-Based and Reference-Free Local Ancestry Inference

bioRxiv Aug 6, 2026
Local ancestry inference (LAI) identifies the ancestral origin of genomic segments within admixed individuals and is an important tool for population genetics and disease association studies. Existing LAI methods generally rely on reference panels co...
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