bioRxiv

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Structure-based Predictions of Conformational B Cell Epitopes by Protein Language Model and Deep Learning

bioRxiv Jan 1, 2025
Mapping conformational B-cell epitopes remains a central challenge for antibody discovery: experiments are costly and most computational tools trained on generic protein–protein interfaces transfer poorly to antibody–antigen recognition. We introduce...
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An anatomical substrate of credit assignment in reinforcement learning

bioRxiv Jan 1, 2025
A key problem in learning is credit assignment. Biological systems lack a plausible mechanism to implement the backpropagation approach, a method that underlies much of the dramatic progress in artificial intelligence. Here, we use automated connecto...
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An Interpretable Deep Learning Framework for Biomarker Discovery in Complex Disease Survival Outcomes

bioRxiv Jan 1, 2025
Identification of important biomarkers associated with complex disease survival outcomes is fundamental for gaining an in-depth understanding of disease mechanisms and advancing precision medicine in conditions such as cancer and cardiovascular disor...
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Feature-Mask-Based Strategies for Subtype-Specific Freezing of Gait Detection using CNNs

bioRxiv Jan 1, 2025
Freezing of gait (FOG), a disabling symptom of Parkinson’s disease, varies in manifestations and motion contexts. Its heterogeneity motivates subtype categorization such as manifestation-specific subtypes (akinesia, trembling or shuffling) or motion-...
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Tahoe-x1: Scaling Perturbation-Trained Single-Cell Foundation Models to 3 Billion Parameters

bioRxiv Jan 1, 2025
Foundation models have transformed natural language processing and computer vision, yet their potential in single-cell biology—particularly for complex diseases such as cancer— remains underexplored. We present Tahoe-x1 (Tx1), a family of perturbatio...
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Integrating Multi-Structure Covalent Docking with Machine Learning Consensus Scoring Enhances Virtual Screening of Human Acetylcholinesterase Inhibitors

bioRxiv Jan 1, 2025
Acetylcholinesterase (AChE) inhibition is a key mechanism in the treatment of neurodegenerative diseases and in counteracting toxic exposures to pesticides and nerve agents. However, virtual screening of AChE remains challenging due to the enzyme’s s...
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The Impact of Acute High-Intensity Activity on Perceptual Decision-Making Dynamics

bioRxiv Jan 1, 2025
This study investigates the acute impact of high-intensity activity on perceptual decision-making, using computational modeling to assess changes during and after physical activity. Participants performed a two-alternative forced choice perceptual de...
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ppLM-CO:Pre-trained Protein Language Model for Codon Optimization

bioRxiv Jan 1, 2025
Messenger ribonucleic acid (mRNA) vaccines represent a major advancement in synthetic biology, yet their efficacy remains limited by how efficiently the encoded protein is translated within the host. Since multiple codons can code for the same amino ...
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PlasmoFP: leveraging deep learning to predict protein function of uncharacterized proteins across the malaria parasite genus

bioRxiv Jan 1, 2025
The first malaria parasite Plasmodium falciparum genome published in 2002 jump-started functional studies, but a large fraction of all predicted proteins remains partially annotated and of ‘unknown function’. Here, we introduce Plasmodium Function Pr...
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Protein Dimension DB: A Unified Protein Repository for Representation Learning and Functional Analysis

bioRxiv Jan 1, 2025
Inspired by the success of large language models in areas like natural language processing, researchers have applied similar architectures, notably the Transformer, to protein sequences. Thanks to these developments, Protein Language Models (PLMs) ha...
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