bioRxiv

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Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture

bioRxiv Jan 1, 2025
Understanding how genomic sequences shape three-dimensional (3D) genome architecture is funda-mental to interpreting diverse biological processes. Although previous studies have shown that sequence information can predict 3D genome architecture, they...
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Advancing Protein Ensemble Predictions Across the Order–Disorder Continuum

bioRxiv Jan 1, 2025
While deep learning has transformed structure prediction for ordered proteins, intrinsically disordered proteins remain poorly predicted due to systematic underrepresentation in training data, despite constituting approximately 30% of eukaryotic prot...
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iDeepLC: chemical structure information yields improved retention time prediction of peptides with unseen modifications

bioRxiv Jan 1, 2025
Deep learning has notably advanced the field of liquid chromatography–mass spectrometry-based proteomics. Accurate prediction of peptide retention times significantly enhances our ability to match LC-MS data with the correct peptides and proteins, es...
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Chemical Dice Integrator (CDI): A Scalable Framework for Multimodal Molecular Representation Learning

bioRxiv Jan 1, 2025
The machine learning landscape for molecular property prediction is fragmented, with numerous Featurizers each capturing a narrow, specialized view of chemical structure. This heterogeneity forces a suboptimal choice of representation a priori, limit...
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BioToken and BioFM – Biologically-Informed Tokenization Enables Accurate and Efficient Genomic Foundation Models

bioRxiv Jan 1, 2025
Genomic variation underlies human phenotypic diversity, disease susceptibility, and evolutionary adaptation. Although large-scale genomic sequencing has transformed our ability to map genetic variation, accurately modeling and interpreting this data ...
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Detection dog performance state estimation from pre-stimulus video and physiological signals using deep learning and Bayesian inference

bioRxiv Jan 1, 2025
Detection dogs play a critical role in operational settings ranging from explosives detection to medical diagnostics. Their unmatched olfactory capabilities allow them to locate trace-level targets that remain beyond the reach of current technology. ...
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From Tasks to Topology: Dorsal and Ventral Streams Emerge in Optimized Neural Networks

bioRxiv Jan 1, 2025
The primate visual system is organized into dorsal and ventral pathways, classically linked to visuomotor control and perception. A long-standing question is whether this division reflects intrinsic architectural priors or emerges from task demands. ...
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The blood proteome predicts the impact of circulating factors on age-related mitochondrial health

bioRxiv Jan 1, 2025
Circulating non-cellular factors, such as plasma proteins, contribute to various features of aging. To determine the impacts of endogenous circulating factors on human age-related bioenergetic decline, we treated primary human fibroblasts with serum ...
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Calibration-free single-frame super-resolution fluorescence microscopy

bioRxiv Jan 1, 2025
Molecular fluorescence microscopy is a leading approach to super-resolution and nanoscale imaging in life and material sciences. However, super-resolution fluorescence microscopy is often bottlenecked by system-specific calibrations and long acquisit...
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Harnessing Interpretable Deep Learning to Predict Meropenem Resistance in Klebsiella pneumoniae

bioRxiv Jan 1, 2025
Antimicrobial resistance represents an escalating global healthcare threat, complicating treatment and increasing both morbidity and mortality. Deep learning offers promising solutions, particularly for bacterial profiling using omics data. For insta...
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