bioRxiv

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Accurate and efficient phylogenetic inference through end-to-end deep learning

bioRxiv Jan 1, 2025
Accurate phylogenetic inference is crucial for understanding evolutionary relationships among species. Deep learning technique has been introduced for phylogenetic inference; however, the existing deep learning-based approaches either suffer from lim...
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System-level health profiling from blood DNA methylation with explainable deep learning

bioRxiv Jan 1, 2025
Genome-scale DNA methylation (DNAm) profiles capture organismal physiology, but most predictive models lack transparency and multi-level applicability. Here we develop an explainable framework that quantifies respiratory, cardiovascular, and metaboli...
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Belief updating in uncertain environments are differentially sensitive to reward and punishment learning: Evidence from ERP

bioRxiv Jan 1, 2025
Learning from rewards and punishments is crucial for adaptive decision-making, but it is still unclear how individuals integrate prediction errors to update beliefs in uncertain environments, particularly the distinctions between reward and punishmen...
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Integrative machine learning predicts activating kinase mutations for precision oncology

bioRxiv Jan 1, 2025
Kinases are enzymes that catalyze phosphorylation and play crucial roles in a myriad of cellular regulatory processes and hemostasis. Patient-specific genetic mutations that aberrantly activate kinases can profoundly influence cancer progression and ...
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Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells

bioRxiv Jan 1, 2025
Multicellular self-organization relies on complex interactions across multiple length scales, shaping the transcriptional activity and molecular phenotype of individual cells. Despite advances in spatial omics technologies, mapping protein state comp...
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High-throughput multi-camera array microscope platform for automated 3D behavioral analysis of swimming zebrafish larvae

bioRxiv Jan 1, 2025
Understanding the behavioral and morphological dynamics of moving model organisms like the zebrafish larvae requires accurate, high-throughput 3D analysis. However, traditional single-view 2D video tracking fails to capture the full scope of natural ...
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Uncertainty-Aware Tau Detection in Progressive Supranuclear Palsy Using Object Detection Models

bioRxiv Jan 1, 2025
Abnormal tau accumulation is a hallmark of neurodegenerative tauopathies such as Progressive Supranuclear Palsy (PSP). Traditional post-mortem assessments rely on manual lesion annotation, which is time-consuming and subjective. Existing machine lear...
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Functional MRI signals as fast as 1Hz are coupled to brain states and predict spontaneous neural activity

bioRxiv Jan 1, 2025
fMRI signals were traditionally seen as slow and sampled in the order of seconds, but recent technological advances have enabled much faster sampling rates. We hypothesized that high-frequency fMRI signals can capture spontaneous neural activity that...
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A deep learning framework for understanding cochlear implants

bioRxiv Jan 1, 2025
Sensory prostheses replace dysfunctional sensory organs with electrical stimulation but currently fail to restore normal perception. Outcomes may be limited by stimulation strategies, neural degeneration, or suboptimal decoding by the brain. We propo...
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Adolescent alcohol consumption alters sex-specific behaviors associated with prefrontal functional connectivity in mice

bioRxiv Jan 1, 2025
The prefrontal cortex (PFC) is one of the last brain regions to fully mature, making it particularly sensitive to drug use early in life. Both human and rodent studies find long-lasting behavioral changes after adolescent alcohol exposure that implic...
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