AIMC Journal:
bioRxiv

Showing 1031 to 1040 of 4938 articles

Nonlinear influence of reward volatility on arbitration between multiple learning strategies reflects cost-benefit optimization

bioRxiv Jun 19, 2026
Action selection involves two systems: a model-free reinforcement learning strategy, which relies on experience with action-outcome pairs, and a model-based reinforcement learning strategy, which enables more flexible behavior via inference using a m...
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FeatureMSEA: Metabolic Feature-based Metabolite Set Enrichment Analysis

bioRxiv Jun 19, 2026
Liquid chromatography-mass spectrometry (LC-MS) untargeted metabolomics detects thousands of metabolic features, but converting these chemical signals into metabolite set-level biological knowledge remains challenging. This is because most features l...
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Sequence-to-function modeling uncovers the context-specific grammar of Drosophila chromatin insulation

bioRxiv Jun 19, 2026
Chromatin is organized into self-interacting topologically associating domains partitioned by boundary elements that insulate adjacent domains and restrict regulatory interactions. Yet, how sequence context and combinations of factors dictate boundar...
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Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket)

bioRxiv Jun 19, 2026
RNAs are important therapeutic targets, however identifying ligandable small-molecule binding pockets remains a major barrier to RNA-targeted drug discovery. Here, SMARTPocket, an atomic-level geometric deep learning framework for predicting RNA-smal...
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Tox21mer, A transformer foundation model for Tox21 high-throughput concentration-response curves data

bioRxiv Jun 19, 2026
The U.S. Tox21 collaboration has generated a large reference library of high-throughput concentration-response assays. Here we present Tox21mer, a 43.5-million-parameter transformer that encodes each Tox21 concentration-response curve together with a...
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High-Frequency Spatial Feature Fusion with 3D CNN for Early Stage Schizophrenia Classification

bioRxiv Jun 19, 2026
Early detection of schizophrenia (SZ) remains challenging due to the subtlety of early-stage brain alterations and reliance on subjective clinical assessment. We propose a frequency-aware 3D convolutional neural network (CNN) pipeline that integrates...
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Host-derived bile acids drive dysbiosis by selecting bile-resistant epimerizing bacteria in inflammatory bowel disease

bioRxiv Jun 19, 2026
Microbial dysbiosis is a hallmark of inflammatory bowel diseases (IBD); however, its drivers and impact on disease pathophysiology are poorly understood. Applying neural network-based feature attribution to metabolomics and metagenomics datasets from...
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Muscle Loss as a Foundational Step in the Development and Evolution of the Turtle Shell

bioRxiv Jun 18, 2026
Modern biodiversity is built on a series of disparate body plans whose origins are obscured by deep time. Our most direct source of clarifying data is the fossilized skeleton, where morphology reflects an evolving functionality realized through the d...
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Benchmarking gene expression reconstruction from single-cell latent representations

bioRxiv Jun 18, 2026
Single-cell transcriptomics is typically modeled in low-dimensional latent representations that improve the signal-to-noise ratio of the data. Such representations underpin data integration, cell state discovery, and perturbation prediction, with app...
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Benchmarking attention-based methods for vision transformers' interpretability in retinal fundus imaging

bioRxiv Jun 18, 2026
Deep learning models based on Vision Transformers (ViTs) have shown strong performance in retinal fundus imaging, but their interpretability remains poorly understood. In particular, attention-based attribution methods are widely used to explain ViT ...
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