AIMC Journal:
bioRxiv

Showing 31 to 40 of 4918 articles

Protein Language Model-Conditioned Graph Neural Networks for Multitask GPCR Ligand Activity Prediction

bioRxiv Oct 7, 2026
Predicting ligand activity across G protein-coupled receptors (GPCRs) requires models that capture both molecular structure and receptor-specific information while remaining robust to chemical and target-domain shift. We developed a multimodal graph ...
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ddkg.skill: A Compositional Agent Skill for Translating Biomedical and Bioinformatics Questions into Cypher for the Data Distillery Knowledge Graph

bioRxiv Oct 7, 2026
Biomedical knowledge graphs can connect information across genes, phenotypes, tissues, pathways, experiments, and clinical resources, but they are difficult to query correctly without detailed knowledge of the graph. Large language models can help wr...
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Genome-wide structural variants uncover strain-specific genes and evolutionary genomic determinants of a fungal maize pathogen

bioRxiv Oct 7, 2026
Genomic structural variants (SVs) are important sources of genetic diversity and contribute to the adaptation and evolution of plant-pathogenic fungi. Colletotrichum graminicola, the causal agent of maize (Zea mays L.) anthracnose, causes significant...
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Fully integrative species delimitation with machine learning and diverse data types in delimSOM 2.0

bioRxiv Oct 7, 2026
Species delimitation increasingly relies on multiple sources of evidence, but most frameworks are still limited to genetics and morphology or analyze data types separately and compare results qualitatively. We present delimSOM 2.0, an R package that ...
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A lightweight deep-learning detector for the real-time monitoring of the invasive frogs Rhinella marina and Polypedates leucomystax

bioRxiv Oct 7, 2026
Early detection of invasive species is critical to efficiently managing biological invasions. Passive acoustic monitoring combined with deep learning has become an effective tool for identifying invasive anurans from their species-specific mating cal...
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Machine Learning-Driven Phenotype Predictions based on Genome Annotations

bioRxiv Oct 7, 2026
The rapid expansion of isolate genome sequences and metagenome-assembled genomes has created a growing need for computational approaches that can infer microbial phenotypes directly from genome information. Here, we present a machine learning framewo...
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Limitations of Genomic Foundation Models for Decoding Regulatory Mechanisms in ALS

bioRxiv Oct 7, 2026
Genomic foundation models promise to infer regulatory consequences of genetic variants directly from DNA sequence, but how well these predictions translate to clinical utility remains unclear. To probe this question, we evaluate AlphaGenome (AG) for ...
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BettaAI: a machine-learning object detection model for the quantification of aggressive displays in the Siamese fighting fish Betta splendens

bioRxiv Oct 6, 2026
The Siamese fighting fish (Betta splendens) is well-known for its high levels of aggression and complex, stereotyped displays, making it an ideal model for testing deep learning-based tools for high-throughput, unbiased quantification of aggressive b...
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lisaR: An LLM-Inferred Semantic Annotation of biological categories for gene set enrichment analysis

bioRxiv Oct 6, 2026
Gene set enrichment analysis (GSEA) turns differential expression results into lists of enriched gene sets. These lists are often long and redundant and span several gene-set collections, which makes their biological interpretation difficult. We pres...
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Predicted structure of the complete CPLANE complex reveals novel interactors and mechanisms of Jbts17 during ciliogenesis

bioRxiv Oct 6, 2026
Cilia are highly conserved organelles that use hundreds of unique proteins to drive extracellular motility and serve as signaling hubs for eukaryotic cells. The Ciliogenesis and Planar Polarity Effector (CPLANE) protein complex controls basal body do...
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