bioRxiv

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TissueFormer: a neural network for labeling tissue from grouped single-cell RNA profiles

bioRxiv Jan 1, 2025
Single-cell RNA sequencing technologies have enabled unprecedented insights into gene expression and are poised to transform clinical diagnostics. At present, most computational approaches for interpreting single-cell data operate at the level of ind...
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Semi-Automated Seal Detection on the Western Antarctic Peninsula: An Unsupervised Machine Learning Approach for Detecting Ice Seals in Aerial Survey Data

bioRxiv Jan 1, 2025
Over the past 25 years, the Western Antarctic Peninsula (WAP) has experienced dramatic shifts in sea ice extent. This change has coincided with rapid alterations in ice-dependent ecosystems, including those supporting crabeater seals - the most abund...
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Machine Learning Reveals Intrinsic Determinants of siRNA Efficacy

bioRxiv Jan 1, 2025
Small interfering RNAs (siRNAs) are widely used in therapeutics and agriculture for sequence-specific gene silencing. However, siRNA efficacy remains difficult to predict due to complex dependencies on sequence, structure, and thermodynamic propertie...
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Deep Learning Improves Parameter Estimation in Reinforcement Learning Models

bioRxiv Jan 1, 2025
Cognitive models are widely used in psychology and neuroscience to formulate and test hypotheses about cognitive processes. These processes are characterized by model parameters, which are then used for scientific inference. The reliability of scient...
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Superior batch alignment and hyper-dimensional cytometry representations allow ultra-sensitive classification of disease phenotypes

bioRxiv Jan 1, 2025
Analysis of cytometry data predominantly relies on clustering and dimensionality reduction approaches for computational tractability. This is particularly relevant for modern spectral flow cytometers, which can simultaneously measure an increasingly ...
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Integrating Artificial Intelligence-Driven Digital Pathology and Genomics to Establish Patient-Derived Organoids as a Novel Alternative Model for Drug Response in Head and Neck Cancer

bioRxiv Jan 1, 2025
Patient-derived organoids (PDOs) are emerging as advanced 3D ex vivo novel alternative method (NAM) preclinical models, offering significant advantages over traditional cell lines and monolayer cultures for therapeutic development. In this study, we ...
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De novo single-cell biological analysis of drug resistance in human melanoma through a novel deep learning-powered approach

bioRxiv Jan 1, 2025
Elucidating drug response mechanisms in human melanoma is crucial for improving treatment outcomes. Although scRNA-seq captures gene expression at the individual cell level, existing tools to gain deeper insights into a studied population pertaining ...
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Semi-supervised detection of natural selection with positive-unlabeled learning

bioRxiv Jan 1, 2025
Identifying genomic regions shaped by natural selection is a central goal in evolutionary ge-nomics. Existing machine learning methods for this task are typically trained using simulated genomic data labeled according to specific evolutionary scenari...
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Variant effect prediction with reliability estimation across priority viruses

bioRxiv Jan 1, 2025
Viruses pose a significant threat to global health due to their rapid evolution, adaptability, and increasing potential for cross-species transmission. While advances in machine learning and the growing availability of sequence and structure data off...
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Hi-Cformer enables multi-scale chromatin contact map modeling for single-cell Hi-C data analysis

bioRxiv Jan 1, 2025
Single-cell Hi-C captures the three-dimensional organization of chromatin in individual cells and provides insights into fundamental genomic processes such as gene regulation and transcription. While analyses of bulk Hi-C data have revealed multi-sca...
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