AIMC Journal:
bioRxiv

Showing 2021 to 2030 of 4956 articles

Fine-scale habitat partitioning of sympatric stingrays revealed by drone-based remote sensing and deep learning

bioRxiv Mar 17, 2026
Habitat partitioning supports the coexistence of sympatric species and shapes their ecological roles across coastal seascapes. Understanding how sympatric species move through and use coastal habitats therefore provides fundamental ecological insight...
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Learning Universal Representations of Intermolecular Interactions with ATOMICA

bioRxiv Mar 16, 2026
Molecular interactions underlie nearly all biological processes, but many representation learning models either focus on single entities or are trained for a narrow set of interaction settings. Here, we introduce ATOMICA, a geometric deep learning mo...
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An explainable boosting machine model for identifying artifacts caused by formalin-fixed paraffin embedding

bioRxiv Mar 16, 2026
Background: Formalin-fixed paraffin-embedding (FFPE) is a widely used, cost-effective method for long-term storage of clinical samples. However, fixation is known to introduce damage to nucleic acids that can present as artifactual bases in sequencin...
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Opening the Black Box of Neural Computation from Neural Recordings with Gain-Modulated Linear Dynamical System

bioRxiv Mar 16, 2026
Inferring computational mechanisms from neural recordings is a central goal in systems neuroscience. Recent developments have identified low-rank recurrent neural networks (RNNs) as an effective tool for fitting observed neural activity and extractin...
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An explanatory benchmark of spatial domain detection reveals key drivers of method performance

bioRxiv Mar 16, 2026
The spatial organization of cells within tissues is critical for understanding biological function and disease, and spatial transcriptomics enables genome-wide mapping of this organization. Numerous computational methods aim to identify spatial domai...
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Detecting Manuscripts Related to Computable Phenotypes Using a Transformer-based Language Model

bioRxiv Mar 16, 2026
Objective: The demand for a comprehensive phenomics library, which requires identifying computable phenotype definitions and associated metadata from an ever-expanding biomedical literature, presents a significant, labor-intensive, and unscalable cha...
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Chemically informed representations of amino acids enable learning beyond the canonical protein alphabet

bioRxiv Mar 16, 2026
Computational models of proteins typically represent sequences using a fixed twenty-letter alphabet describing canonical amino acids. Although this symbolic representation underlies most machine learning approaches to protein analysis, it abstracts a...
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HipSAFE: automating hip fracture detection on ultrasound imaging using deep learning

bioRxiv Mar 16, 2026
Falls among older adults can result in hip fractures that requires x-ray based assessment at emergency department (ED). Only 25.7% of patients presenting to EDs are diagnosed with a hip fracture, as such improved diagnosis prior to transportation to ...
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UniST: A Unified Computational Framework for 3D Spatial Transcriptomics Reconstruction

bioRxiv Mar 16, 2026
Spatial transcriptomics (ST) enables the measurement of gene expression in its native spatial context, yet most ST datasets are acquired as two-dimensional (2D) sections. Consequently, the underlying three-dimensional (3D) organization of tissues is ...
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pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction

bioRxiv Mar 16, 2026
Predicting genetic perturbation responses at a single-cell level is central to building models for cell state and disease. However, existing approaches are limited on predicting phenotypic outcomes beyond expression changes and generalizing predictio...
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