AIMC Journal:
bioRxiv

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Machine Learning Resolves Functional Phenotypes and Therapeutic Responses in KCNQ2 Developmental Epileptic Encephalopathy iPSC Models

bioRxiv Jan 1, 2025
Pathogenic KCNQ2 variants are associated with developmental and epileptic encephalopathy (KCNQ2-DEE), a devastating disorder characterized by neonatal-onset seizures and impaired neurodevelopment with no effective treatments. KCNQ2 encodes the voltag...
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scYeast: a Biological-knowledge-guided Foundation Model on Yeast Single-Cell Transcriptomics

bioRxiv Jan 1, 2025
Pre-trained large models have emerged as a pivotal technological approach for foundational cell modeling. However, existing deep learning-based foundational models for cells have predominantly focused on human or murine systems, with a relative scarc...
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Systematic feature and architecture evaluation reveals tokenized learned embeddings enhance siRNA efficacy prediction

bioRxiv Jan 1, 2025
Recent advances in machine learning have improved the prediction of siRNA efficacy, with graph neural networks and transformer-based encodings leading the way. However, existing models still face challenges, including potential inaccuracies in thermo...
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PolyRNN: A time-resolved model of polyphonic musical expectations aligned with human brain responses

bioRxiv Jan 1, 2025
Musical expectations shape how we perceive and process music, yet current computational models are limited to monophonic or simplified stimuli. The study of the neural processes underlying musical expectations in real-world music therefore requires s...
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Predicting molecular recognition features in protein sequences with MoRFchibi 2.0

bioRxiv Jan 1, 2025
Molecular Recognition Features (MoRFs) are segments within disordered protein regions (IDRs) that undergo a disorder-to-order transition upon binding to their partners. Identifying MoRFs remains a significant challenge. This paper introduces MoRFchib...
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Deep-learning triage of 3D pathology datasets for comprehensive and efficient pathologist assessments

bioRxiv Jan 1, 2025
Standard-of-care slide-based 2D histopathology severely undersamples spatially heterogeneous tissue specimens, with each thin 2D section representing <1% of the entire tissue volume (in the case of a biopsy). Recent advances in non-destructive 3D pat...
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Inferring the landscapes of mutation and recombination in the common marmoset (Callithrix jacchus) in the presence of twinning and hematopoietic chimerism

bioRxiv Jan 1, 2025
The common marmoset is an important model in biomedical and clinical research, particularly for the study of age-related, neurodegenerative, and neurodevelopmental disorders (due to their biological similarities with humans), infectious disease (due ...
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Computational Tracking of Cell Origins Using CellSexID from Single-Cell Transcriptomes

bioRxiv Jan 1, 2025
Cell tracking in chimeric models is essential yet challenging, particularly in developmental biology, regenerative medicine, and transplantation research. Existing methods such as fluorescent labeling and genetic barcoding are technically demanding, ...
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Quantum Cognition Machine Learning for Forecasting Chromosomal Instability

bioRxiv Jan 1, 2025
The accurate prediction of chromosomal instability from the morphology of circulating tumor cells (CTCs) enables real-time detection of CTCs with high metastatic potential in the context of liquid biopsy diagnostics. However, it presents a significan...
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Rapid and Reproducible Multimodal Biological Foundation Model Development with AIDO.ModelGenerator

bioRxiv Jan 1, 2025
Foundation models (FMs) for DNA, RNA, proteins, cells, and tissues have begun to close long-standing performance gaps in biological prediction tasks, yet each modality is usually studied in isolation. Bridging them requires software that can ingest h...
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