bioRxiv

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Earth-Observation and Environmental Vision Transformers Reveal Genome–Environment Associations in Macroalgae

bioRxiv Jan 1, 2025
Macroalgae thrive in extreme environments, yet the genomic basis of their tolerance remains poorly resolved. We describe nine Arabian Gulf macroalgae and integrate them with 117 published genomes (126 total; 70 Rhodophyta, 43 Ochrophyta, 13 Chlorophy...
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Classpose: foundation model-driven whole slide image-scale cell phenotyping in H&E

bioRxiv Jan 1, 2025
Cell segmentation and phenotyping in histopathology samples are essential techniques applied across diagnostic and research workflows. However, annotation by human experts requires significant time and domain expertise and is affected by inter-observ...
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Mechanism-Aware Inductive Bias Enhances Generalization in Protein-Protein Interaction Prediction

bioRxiv Jan 1, 2025
Robust prediction of protein–protein interactions (PPIs) requires models that generalize beyond the training distribution. Here, we present PLMDA-PPI, a mechanism-aware framework that incorporates biophysical inductive biases into a dual-attention ar...
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Deep Mediation Analysis for Multimodal Genotype-Imaging Associations with Disease Phenotypes

bioRxiv Jan 1, 2025
Both genotype and imaging data carry entangled information about the phenotypes. Associations between genotypes and phenotypes can be manifested or absent on biomedical images. While there are abundant multimodal association studies integrating genot...
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Multi-model reinforcement learning with online retrospective change point detection

bioRxiv Jan 1, 2025
Humans continuously adapt to uncertain and changing situations. However, most reinforcement learning models of human behavior struggle to explain this capability. We propose a novel reinforcement learning agent for uncertain and volatile Markov decis...
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Sampling Function-Related Metastable States of Proteins With DASH

bioRxiv Jan 1, 2025
Rational discovery of function-specific protein modulators as well as activity-enhanced engineering proteins underscore the need to identify function-related metastable states (FMSs) of proteins. However, current experimental and computational method...
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Connectome of a human foveal retina

bioRxiv Jan 1, 2025
The foveal retina is a primate specialization which presents a feasible site for obtaining a complete connectome of a human CNS structure. In the fovea, cells and circuits are miniaturized and compressed to densely sample the visual image at high res...
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Orthographic training finetunes a neuronal letter position code in primate visual cortex

bioRxiv Jan 1, 2025
Reading is an acquired skill that enhances brain activity in human visual cortex and is thought to repurpose preexisting ventral visual circuitry for the fast parallel processing of letter strings. However, the neuronal code underlying position-invar...
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DeepAden: An explainable machine learning method for predicting the substrate specificity of nonribosomal peptide synthetases

bioRxiv Jan 1, 2025
Microbial non-ribosomal peptides (NRPs) exhibit remarkable structural diversity and serve as valuable sources of lead compounds for clinical drug development. The biosynthesis of NRPs relies on non-ribosomal peptide synthetases (NRPSs), in which aden...
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DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning

bioRxiv Jan 1, 2025
Gaining structural insights into the interactions between antibodies and their corresponding antigens is essential for understanding immune recognition and for guiding therapeutic antibody design. However, accurately modelling these complexes remains...
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