bioRxiv

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OMNI: Optimized Multi-view Network Integration with Heterogeneous Graph Attention for Biomedical Interaction Prediction

bioRxiv Jan 1, 2025
Accurate prediction of biomedical relationships, such as chemical–gene interactions, is fundamental to understanding disease mechanisms and advancing drug discovery. With the rapid growth of heterogeneous biological data, modeling large-scale, multi-...
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Dopamine and serotonin transients predict depressive symptom relief following deep brain stimulation of human subcallosal cingulate cortex

bioRxiv Jan 1, 2025
Recent advances in deep brain stimulation (DBS) of the subcallosal cingulate (SCC) show promise in mitigating the symptoms of treatment-resistant depression (TRD) in humans1–3. Monoamines, such as dopamine and serotonin, mediate the effects of pharma...
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An EMG Foundation Model for Neural Decoding

bioRxiv Jan 1, 2025
Decoding algorithms can be used to predict motor behaviour from patterns of neural activity. However, most studies rely on subject-optimized models, limiting generalization and scalability to novel subjects and tasks. Building on recent advances in d...
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Paying Attention to Other Animal Detections Improves Camera Trap Classification Models

bioRxiv Jan 1, 2025
In ecological studies, automated species classification models are increasingly used to process large volumes of camera trap images. Most current classification models rely on a two-step pipeline: a detector first locates and crops animals, followed ...
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Airborne Nanoplastics Perturb Mitochondrial Complex I via the ND6 Axis: Polymer-Specific Mitoepigenetic Remodeling Integrating Experimental, In Silico, and Machine Learning Analyses

bioRxiv Jan 1, 2025
Airborne nanoplastics constitute an emerging class of environmental contaminants, but their mitoepigenetic effects on human immune cells have not been systematically investigated. Ex vivo human lymphocytes were used to investigate integrated mitochon...
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DeepGEOSearch: LLM-Powered Schemaless Retrieval for Biomedical Data Discovery

bioRxiv Jan 1, 2025
Public biomedical repositories contain extensive, valuable datasets, yet identifying datasets that precisely match specific study requirements remains inefficient. Conventional keyword- and schema-based systems frequently fall short when queries enco...
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Interpreting Convolutional Neural Networks in Population Genetics

bioRxiv Jan 1, 2025
Machine learning approaches have become a powerful alternative to traditional methods in population genetics. Convolutional neural networks (CNNs) in particular have been successful in inferring natural selection, recombination rate estimation, intro...
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Tryptophan Chemistry Driven by a Widespread Cytochrome P422 Enzyme Family

bioRxiv Jan 1, 2025
Tryptophan serves as a versatile biosynthetic precursor across living organisms. While heme-binding proteins (HBPs) mediate key reactions in tryptophan transformation, the full diversity of HBPs remains largely unexplored. Here, we developed the nove...
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Query-driven generative AI synthesizes multi-modal spatial omics from histology

bioRxiv Jan 1, 2025
Spatial omics technologies offer unprecedented insights into the cellular organization of tissues; however, they are not yet scalable for routine clinical use. In contrast, images of histological staining remain the foundation of pathological diagnos...
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PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery

bioRxiv Jan 1, 2025
As biology becomes increasingly data-driven, so too does the field of phage lysins, enzymes that degrade bacterial cell walls and hold promise as alternatives to traditional antibiotics. Five years ago, we introduced PhaLP, a centralized resource for...
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