bioRxiv

Showing 4711 to 4720 of 5021 articles

On the use of generative models for evolutionary inference of malaria vectors from genomic data

bioRxiv Jan 1, 2025
Malaria in sub-Saharan Africa is transmitted by mosquitoes, in particular the Anopheles gambiae complex. Efforts to control the spread of malaria have often focused on these vectors, but less is known about the demographic history of populations and ...
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Interpretable Thermodynamic Score-based Classification of Relaxation Excursions

bioRxiv Jan 1, 2025
Classification and regression are cornerstones of computational biology and science at large, from identifying cell types to stratifying patients by disease state. Current deep learning classifiers provide accurate predictions but offer neither uncer...
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Integrative Genomic and Functional Analyses Reveal NINL as a Modulator of Tau Aggregation

bioRxiv Jan 1, 2025
Proteostasis dysfunction is a hallmark of frontotemporal dementia (FTD) and Alzheimer’s disease (AD), yet the genetic and molecular pathways that disrupt protein homeostasis remain poorly understood. We integrated human genetics, transcriptomics, and...
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A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction

bioRxiv Jan 1, 2025
Genomic prediction and design require models that integrate local sequence features with long-range regulatory dependencies spanning hundreds of kilobases to megabases. Existing approaches have made substantial progress along complementary axes: supe...
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SpineDL: a Deep Learning-based approach for neuron and anatomical structure segmentation in immunofluorescence images of damaged spinal cords

bioRxiv Jan 1, 2025
In this study, we present SpineDL, an open-source deep learning (DL) approach for neurons and anatomical structure segmentation of the spinal cord in fluorescence images immunostained with NeuN and DAPI, within the context of murine models of spinal ...
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Parallel hierarchical encoding of linguistic representations in the human auditory cortex and recurrent automatic speech recognition systems

bioRxiv Jan 1, 2025
Transforming continuous acoustic speech signals into discrete linguistic meaning is a remarkable computational feat accomplished by both the human brain and modern artificial intelligence. A key scientific question is whether these biological and art...
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Ultra-fast and highly sensitive protein structure alignment with segment-level representations and block-sparse optimization

bioRxiv Jan 1, 2025
Deep learning models for protein structure prediction have given rise to extreme growth in 3D structure data. As a result, traditional methods for geometric structure alignment are too slow to effectively search modern structure libraries. In this st...
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Molecular Biointerface Characterisation for an Implanted Medical Device Using Cryogenic Orbitrap Secondary Ion Mass Spectrometry (Cryo-OrbiSIMS)

bioRxiv Jan 1, 2025
Implanted medical devices often fail due to foreign body reaction (FBR), a process still not fully understood. This work presents a new depth profiling approach to provide insight into the spatial metabolomics of the biointerface of implants, reveali...
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A Biologically Grounded Structural Causal Model Enables cfRNA Specific In-Context Learning

bioRxiv Jan 1, 2025
Cell-free RNA (cfRNA) in human plasma provides a minimally invasive readout of tissue physiology, yet its extreme sparsity, heavy-tailed abundance distributions, and weak but structured correlation patterns create major challenges for machine learnin...
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Benchmarking datasets for machine learning in protein function prediction

bioRxiv Jan 1, 2025
Remarkable progress has been achieved by machine learning, particularly in accurate prediction of protein tertiary structures. Despite these advances, accurately annotating protein functions through machine learning approaches remains challenging, pr...
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