bioRxiv

Showing 3131 to 3140 of 4993 articles

An Artificial Intelligence Model for Translating Natural Language into Functional de Novo Proteins

bioRxiv Jan 1, 2025
Traditional protein design is fundamentally constrained by known sequences and folds. To break free from these limitations, we introduce a new alternative: designing proteins directly from plain-language specifications. To achieve this, we trained MP...
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Organelle bridges and nanodomain partitioning govern targeting of membrane-embedded proteins to lipid droplets

bioRxiv Jan 1, 2025
Numerous metabolic enzymes translocate from the ER membrane bilayer to the lipid droplet (LD) monolayer, where they perform essential functions. Mislocalization of certain LD-targeted membrane proteins, including HSD17B13 and PNPLA3, is implicated in...
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MicrobioRel: A Set of Datasets for Microbiome Relation Extraction

bioRxiv Jan 1, 2025
Biomedical knowledge curation relies on a variety of Natural Language Processing tasks, including biomedical entity recognition and document-level relation extraction. With the growing size and capabilities of Language Models, effectively deploying t...
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FORCE trained spiking networks do not benefit from faster learning while parameter matched rate networks do

bioRxiv Jan 1, 2025
Training spiking recurrent neural networks (SRNNs) presents significant challenges compared to standard recurrent neural networks (RNNs) that model neural firing rates more directly. Here, we investigate the origins of these difficulties by training ...
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Facial expression discrimination emerges from neural subspaces shared with detection and identity

bioRxiv Jan 1, 2025
Understanding how the human brain decodes facial expressions remains a fundamental challenge, requiring computational models that tightly connect neural responses to behavior. Here, we demonstrate that rhesus macaques provide a unique and powerful an...
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Benchmarking antigen-aware inverse folding methods for antibody design

bioRxiv Jan 1, 2025
Computational antibody design has seen many recent advances pioneered via the use of language models and advanced structure prediction tools. Developing a de novo antibody against a specific antigen requires structural awareness that most language mo...
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Learning from B Cell Evolution: Adaptive Multi-Expert Diffusion for Antibody Design via Online Optimization

bioRxiv Jan 1, 2025
Recent advances in diffusion models have shown remarkable potential for antibody design, yet existing approaches apply uniform generation strategies that cannot adapt to each antigen’s unique requirements. Inspired by B cell affinity maturation—where...
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DNA Sequence Trace Reconstruction Using Deep Learning

bioRxiv Jan 1, 2025
Deciphering DNA sequences is fundamental to unlocking the mysteries of life, but the high dimensionality and complexity of biological sequence data significantly hinder knowledge discovery. In particular, the challenges of sequence length, repetitive...
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Deep Learning for Predicting Stem Cell Efficiency for use in Beta Cell Differentiation

bioRxiv Jan 1, 2025
Recent clinical trial data have shown that cell therapy holds curative potential for type-1 diabetes, however the large amounts of lab-grown cells required is a substantial bottleneck. The necessary cell differentiation process exhibits substantial v...
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Conceptualization and Feasibility Testing of a Vibro-Acoustic Solution for Tumor Detection

bioRxiv Jan 1, 2025
Accurate detection of tumors is critical for the success of oncologic surgical intervention. Along with any modality for the localization of tumors, surgeons achieve important information with direct palpation as long as direct touch of the tumor is ...
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