AIMC Journal:
bioRxiv

Showing 1061 to 1070 of 4938 articles

Super Learner Ensemble Modeling of CPTAC Proteomic Data for Survival Prediction in Head and Neck Squamous Cell Carcinoma

bioRxiv Jun 16, 2026
Survival analysis in head and neck squamous cell carcinoma (HNSCC) is traditionally performed using Cox proportional hazards models, alongside some exploration into black-box machine learning methods. The Super Learner (SL) algorithm addresses this m...
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PhenoBIC: operator-free single-cell spatial phenotyping in multiplex imaging data using deep learning of cell staining patterns

bioRxiv Jun 16, 2026
Multiplex imaging is a valuable tool for spatially examining tissue microenvironments at the single-cell level to uncover biological and clinical insights. However, most multiplex image analysis workflows currently require manual intervention for cel...
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A Transformer-derived transcriptomic score associates with ex-vivo drug response in AML

bioRxiv Jun 16, 2026
Background Drug-tolerant persister (DTP) cell states have been implicated in relapse across multiple cancers, including acute myeloid leukaemia (AML) [1,2]. Methods that score such states from transcriptomic data, generalise to held-out samples, expo...
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scIsoAgent enables autonomous isoform-resolved characterization and sequence-informed interpretation of long-read single-cell transcriptomes

bioRxiv Jun 16, 2026
Alternative isoform usage can alter gene function independently of total gene expression, creating a need to resolve transcript isoforms at single-cell resolution. Long-read single-cell RNA sequencing meets this need by linking cellular identity to t...
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Machine learning surrogate forward models for biomechanical laryngeal control

bioRxiv Jun 16, 2026
Accurate modeling of laryngeal motor control is key to understanding typical and disordered voice production. However, traditional biomechanical plant models based on ordinary differential equations (ODEs) often involve high computational costs and n...
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OmicOS: A Comprehensive Omics Ecosystem Infrastructure and Agent System for the AI Era

bioRxiv Jun 16, 2026
Biology has accumulated a vast ecosystem of omics methods, but much of this ecosystem remains built for expert humans rather than scientific agents. Methods are scattered across Python packages, R/Bioconductor and CRAN workflows, command-line tools, ...
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Dissecting and directing pathology foundation models

bioRxiv Jun 16, 2026
Foundation models (FMs) are central to digital pathology, encoding histology images into dense embeddings for facilitating diagnostic classification, molecular alteration prediction, and clinical outcome modeling. However, the opacity of these embedd...
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DeltaQ: Value-Guided Hebbian Learning in Spiking Neuronal Networks for Multi-Goal Navigation

bioRxiv Jun 16, 2026
Animals must often navigate environments where feedback about progress toward a goal is sparse or delayed, requiring internal representations of space and memory of prior experience. The hippocampal-entorhinal system is believed to support this capab...
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Linking automated image analysis to ecological inference: high-throughput monitoring of soil fauna

bioRxiv Jun 16, 2026
1 - Automated in situ sensors - e.g., buried scanners - are transforming biodiversity monitoring by generating data at spatio-temporal resolutions unattainable through traditional sampling, including in cryptic environments such as soil that have rem...
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PolyFold: Evaluation of Open-Use Molecular Structure Prediction Algorithms to Inform Their Utility in Diverse Biological Applications

bioRxiv Jun 16, 2026
With the growing use of machine-learning-assisted pipelines for designing, characterizing, and optimizing biomolecules, the reliability of structure prediction models is increasingly important. PolyFold is a benchmarking framework developed to evalua...
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