bioRxiv

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Understanding Language Model Scaling on Protein Fitness Prediction

bioRxiv Jan 1, 2025
Protein language models, and models that incorporate structure or homologous sequences, estimate sequence likelihoods p(sequence) that reflect the protein fitness landscape and are commonly used in mutation effect prediction and protein design. It is...
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Limitations of de novo sequencing in resolving sequence ambiguity

bioRxiv Jan 1, 2025
De novo peptide sequencing enables peptide identification from fragmentation spectra without relying on sequence databases. However, incomplete spectra create ambiguity, making unambiguous identification challenging. Recent deep learning advances hav...
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Concept2Brain: An AI model for predicting subject-level neurophysiological responses to text and pictures

bioRxiv Jan 1, 2025
The current growth of artificial intelligence (AI) tools provides an unprecedented opportunity to extract deeper insights from neurophysiological data while also enabling the reproduction and prediction of brain responses to a wide range of events an...
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AVATAR: AI Vision Analysis for Three-dimensional Action in Real-time

bioRxiv Jan 1, 2025
Artificial intelligence (AI) is an emerging tool for high-resolution behavioural analysis and conduction of human-free behavioural experiments. Here, we applied an AI-based system, AVATAR, which automatically virtualises 3D motions from the detection...
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Identifying pyrogenic contaminants using transcriptomic profiling of monocyte activation test with machine learning

bioRxiv Jan 1, 2025
The monocyte activation test is an in vitro pyrogenicity assessment method that can utilise human peripheral blood mononuclear cells to detect pyrogens in injectable drugs, providing a binary outcome that indicates the presence or absence of a pyroge...
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Generating Bounded Linear Temporal Logic in Systems Biology with Large Language Models

bioRxiv Jan 1, 2025
In computational modeling, Bounded Linear Temporal Logic (BLTL) is a valuable formalism for describing and verifying the temporal behavior of biological systems. However, translating natural language (NL) descriptions of system behaviors into accurat...
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DynaRepo: The repository of macromolecular conformational dynamics

bioRxiv Jan 1, 2025
Proteins, RNA, and DNA are central to virtually all cellular processes, often assembling into macro-molecular complexes to perform their functions. While these molecules are inherently dynamic, most methods for studying their mechanisms focus on stat...
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Interpretable Machine Learning Uncovers Structural Determinants of Wnt-Wls Binding Specificity from Extended Atomistic Simulations

bioRxiv Jan 1, 2025
The Wnt protein family plays a critical role in cell development, with each Wnt protein interacting differently with the Wls membrane protein through distinct binding residues. A direct comparison and elucidation of the molecular mechanisms underlyin...
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Rapid CE–MS with Real-Time Eco–AI Resolves Proteomic Heterogeneity Among Single Human Neutrophils

bioRxiv Jan 1, 2025
Single-cell proteomics by mass spectrometry is advancing rapidly, yet throughput and sensitivity remain limiting—particularly for small, protein-poor cell types such as neutrophils. As the most abundant circulating leukocytes in humans, neutrophils a...
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Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins

bioRxiv Jan 1, 2025
Intrinsically disordered proteins (IDPs) exhibit highly dynamic and heterogeneous conformational ensembles that are strongly influenced by sequence features. While global properties such as chain compaction and scaling behavior have been widely studi...
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