bioRxiv

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Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods

bioRxiv Jan 1, 2025
The diverse regulatory functions, protein production capacity, and stability of natural and synthetic RNAs are closely tied to their ability to fold into intricate structures. Determining RNA structure is thus fundamental to RNA biology and bioengine...
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The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

bioRxiv Jan 1, 2025
Saccharomycotina yeasts are a highly diverse and widely distributed subphylum of ascomycete fungi that exhibit diversity in their asexual growth morphologies; the human commensal yeast Candida albicans exhibits both unicellular and filamentous growth...
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Shared neural geometries for bilingual semantic representations

bioRxiv Jan 1, 2025
The human brain has the remarkable ability to understand and express similar concepts in multiple languages. To understand how it does so, we examined responses of hippocampal neurons during passive listening, directed speaking, and spontaneous conve...
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Machine Learning Identifies Common Risk Variants and Implicates Abnormal Vision Physiology in ASD

bioRxiv Jan 1, 2025
Genomic technology advancements have facilitated associations between genetic variants and disease risk. Rare deleterious variants can independently induce disease, while common variants collectively enhance susceptibility with minimal individual eff...
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Locally balanced inhibition allows for robust learning of input-output associations in feedforward networks with Hebbian plasticity

bioRxiv Jan 1, 2025
In neural networks within the brain, the activity of a post-synaptic neuron is determined by the combined influence of many pre-synaptic neurons. This distributed processing enables mechanisms like Hebbian plasticity to associate sensory inputs with ...
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Using Large Language Models to Assemble, Audit, and Prioritize the Therapeutic Landscape

bioRxiv Jan 1, 2025
We present an AI-assisted pipeline for disease-specific drug landscape analysis. Given a disease name, the system assembles a comprehensive, evidence-based view of therapeutic assets by integrating structured sources (such as ClinicalTrials.gov and C...
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SKiM-GPT: Combining Biomedical Literature-Based Discovery with Large Language Model Hypothesis Evaluation

bioRxiv Jan 1, 2025
Generating and testing hypotheses is a critical aspect of biomedical science. Typically, researchers generate hypotheses by carefully analyzing available information and making logical connections, which are then tested. The accelerating growth of bi...
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A Lightweight Deep Learning Architecture for Potato Leaf Disease Detection: A Comprehensive Survey

bioRxiv Jan 1, 2025
Potato leaf diseases pose a serious challenge to global food security, often leading to considerable yield losses if not detected promptly. The growing maturity of deep learning has enabled automated, high-precision plant disease recognition, even on...
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Automated spermatogenic staging in PAS-stained testes of Sprague-Dawley rats using a deep learning model for normal and atrophied tissues

bioRxiv Jan 1, 2025
The spermatogenic stage serves as a vital criterion for assessing normal spermatogenesis and is central to evaluating reproductive toxicity. Current manual methods for spermatogenic stage evaluation are time-intensive, require expert knowledge, and a...
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De novo design of light-regulated dynamic proteins using deep learning

bioRxiv Jan 1, 2025
Recent advances in deep learning have enabled accurate design of static protein structures, but the de novo design of protein functions controlled by programmable, intramolecular conformational changes remains an unsolved challenge. Here, we present ...
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