AIMC Journal:
bioRxiv

Showing 1261 to 1270 of 4956 articles

ORIGAMI: Orientation-Aware Graph Neural Network for Assessing Multimeric Interfaces of Protein Complex Structures

bioRxiv Jun 3, 2026
Deep learning-based protein structure prediction methods have led to a paradigm-shift in computational structural biology, yet reliably assessing the quality of computationally predicted multimeric structures remains challenging. Recent methods have ...
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sstar2: A Python Package for S*-based Archaic Introgression Detection with Machine Learning

bioRxiv Jun 3, 2026
Detecting introgressed genomic fragments from unsampled or extinct source populations remains challenging. The S* statistic is widely used for this purpose, but the original sstar implementation relies on generalized additive models to smooth quantil...
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ViTAMIn-O: Democratizing computer vision-based machine learning for stem cell research

bioRxiv Jun 3, 2026
Deep Learning (DL) holds exciting potential in automating the prediction of organoid differentiation results. Nevertheless, current models lack adaptability, openness, and robustness in performance. Additionally, broad employments of predictive model...
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Integrating Histology with Spatial Molecular Programs Using a Multimodal Foundation Model

bioRxiv Jun 3, 2026
Histopathological assessment remains central to cancer diagnosis and stratification, yet its mechanistic interpretation remains limited without molecular context. To address this, we developed SQUALL, a multimodal foundation model integrating histolo...
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Data-Efficient Exploration of Enzyme Function Using Family-Specific Machine Learning

bioRxiv Jun 3, 2026
Enzymes are essential biocatalysts across diverse industries, driving demand for high-performing variants. Foundation models are attractive for guiding enzyme discovery, but often lack the resolution to model subtle variations driving function within...
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Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses

bioRxiv Jun 3, 2026
Grasses (Poaceae) dominate terrestrial ecosystems and sustain global food security, yet the genomic principles enabling their repeated adaptation to extreme environments remain unresolved. Combining dense phylogenomic sampling, global environmental d...
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Multiplex Proteomics of Lewy Body Dementia Reveals Cerebrospinal Fluid Biomarkers of Clinical and Neuropathological Heterogeneity

bioRxiv Jun 2, 2026
Lewy body dementia (LBD), which encompasses Parkinson's disease dementia (PDD) and Dementia with Lewy bodies (DLB), lacks established biofluid markers of its complex clinical and neuropathological heterogeneity. Multiplex proteomic tools, such as the...
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Vermeer: Autoregressive generative modeling of microscopy predicts protein localization

bioRxiv Jun 2, 2026
Fluorescent microscopy provides a rich view into how proteins localize within cells, but it remains experimentally infeasible to image human proteins across all of the different factors that can impact localization. We introduce Vermeer, a channel-ad...
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Physics-guided design of intrinsically disordered proteins

bioRxiv Jun 2, 2026
Intrinsically disordered protein regions (IDPs) are found across the tree of life and characterized by the lack of a stable 3D fold, encoding function through a vast ensemble of conformations. This plasticity makes rational design of IDPs challenging...
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Quantifying and Predicting the Difficulty of Multiple Sequence Alignment with AlDiScore

bioRxiv Jun 2, 2026
Multiple Sequence Alignment (MSA) constitutes an important and frequent operation in molecular sequence data analysis. There exist numerous tools, algorithms, and criteria to infer an MSA. This plethora of available approaches to MSA may induced an e...
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