AIMC Journal:
bioRxiv

Showing 691 to 700 of 4938 articles

Deep learning design and in vivo validation of Mùˆller glia-specific cis-regulatory elements

bioRxiv Jul 21, 2026
Effective recombinant adeno-associated virus gene therapies require promoters that are compact and cell-type-specific. Ideally, promoters should also exhibit functional conservation when tested in model organisms to ensure that preclinical findings t...
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Multicenter self-supervised computational pathology identifies prognostic histomorphological phenotypes in colorectal cancer

bioRxiv Jul 21, 2026
H&E whole-slide images capture prognostic information encoded in tumor morphology and the surrounding microenvironment, but these signals remain difficult to extract and interpret at scale. Here, we developed a self-supervised computational pathology...
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Extracellular Matrix Proteomic Signatures Associate with Disease-Free Survival in Later Events of Ductal Carcinoma In Situ or Invasive Breast Cancer

bioRxiv Jul 21, 2026
Background: Ductal carcinoma in situ (DCIS) is a noninvasive breast lesion with variable risk of progression to invasive breast cancer (IBC). Current transcription and cell marker investigations suggest ECM decreases in later events but are limited i...
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A metric for comparing complex systems by their dynamics

bioRxiv Jul 21, 2026
Comparisons are fundamental to science: experiment against model, one organism against another, a system against itself across time. Because many systems, from brains to climate, are characterized by how they evolve in time, it is a natural goal to c...
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Organism-scale annotation with Pan-human Azimuth

bioRxiv Jul 21, 2026
Single-cell atlases now span many human tissues, but inconsistent annotations across studies limit their utility as a unified reference. We introduce Pan-human Azimuth, a supervised neural network that maps human cells from diverse tissues and datase...
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Binary node clustering via contrastive learning for haplotype phasing in de novo genome assembly

bioRxiv Jul 21, 2026
Accurate haplotype phasing is essential for high-quality genome assembly, yet de novo phasing of complex genomes without parental data remains challenging. We formulate haplotype phasing as a node clustering problem with overlapping clusters on augme...
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SPgen: Proteome-wide Spatial Proteomics generation using multi-modality foundation models

bioRxiv Jul 21, 2026
Spatial proteomics (SP) measures the spatial distribution of proteins within tissues, providing important insights into tissue function, disease, and therapeutic response. However, current SP technologies profile only a small fraction of the proteome...
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Representative vs. Load-bearing Layers: A Dissociation in Genomic Foundation Models

bioRxiv Jul 21, 2026
Downstream use of genomic foundation models follows one of three conventions: aggregating representations across all layers (Pearce et al., 2026), defaulting to the last hidden state as a fixed feature extractor (Dalla-Torre et al., 2024), or picking...
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Multi-model Segmentation and Morphometric Quantification of Cerebral Amyloid Angiopathy in Alzheimer's Disease Whole Slide Histopathology Images

bioRxiv Jul 21, 2026
Introduction: Cerebral amyloid angiopathy (CAA) is characterized by amyloid-beta deposition in cortical and leptomeningeal vessels and associated with cognitive impairment and hemorrhage. Current neuropathological assessments rely on semiquantitative...
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Leveraging multiplicity in biologically informed neural networks to uncover disease heterogeneity

bioRxiv Jul 20, 2026
Biologically inspired neural networks (BINNs) embed pathway, ontology, or protein-interaction structure directly into neural networks, promising interpretable disease prediction where hidden nodes map to named biological entities. Yet BINNs have been...
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