AIMC Journal:
bioRxiv

Showing 1931 to 1940 of 4956 articles

Predicting Unseen Gene Perturbation Response Using Graph Neural Networks with Biological Priors

bioRxiv Mar 26, 2026
Predicting transcriptional responses to genetic perturbations is a central challenge in functional genomics. CRISPR Perturb-seq experiments measure gene expression changes induced by targeted perturbations, yet experimentally testing all possible per...
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Age-related cerebellar genetic, neuronal and functional impairments are reversed by specific magnetic stimulation protocols

bioRxiv Mar 26, 2026
Age-related cognitive decline reflects progressive atrophic changes that advance through broad neural networks. There is no effective treatment. However, brain ageing is not homogenous, so treating the earliest-affected circuits may be successful in ...
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OPTIMIS: Optimizing Personalized Therapies through Integrated Multiscale Intelligent Simulation

bioRxiv Mar 26, 2026
Controlling complex biological systems across multiple scales remains a major challenge in computational medicine, because whole-body disease behavior is closely shaped by noisy cellular events at much smaller scales. Standard deterministic models of...
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Self-supervised learning for a gene program-centric view of cell states

bioRxiv Mar 26, 2026
Single-cell omics has extended the biological interrogation of cell state from examining the expression of individual genes to unbiased profiling of tens of thousands of genes at once. However, extracting biological insights from such high-dimensiona...
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Evaluating Evo 2 for plant variant effect prediction

bioRxiv Mar 26, 2026
The genomic foundation model Evo 2 enables zero-shot variant effect prediction. Here, we evaluate its performance using Arabidopsis thaliana reproductive barrier genes with experimentally confirmed gain- and loss-of-function variants, and show that E...
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LAMBDA: A Prophage Detection Benchmark for Genomic Language Models

bioRxiv Mar 26, 2026
Transformer-based genomic sequence models represent an emerging frontier in computational biology. Yet, their embeddings have not yet shown the same level of predictive power as natural and protein language models, indicating a gap between current im...
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Identification of letters distorted by physiologically-inspired spatial scrambling

bioRxiv Mar 25, 2026
In the geniculostriate pathway of the human visual system, neuronal projections carry signals from a particular retinal locus in parallel from one anatomical area to the next. Imprecision in the fidelity of these projections would place constraints o...
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VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs

bioRxiv Mar 25, 2026
Automated extraction of molecular interactions from scientific literature has outpaced the development of systematic methods for integrating this information with curated models and knowledge graphs. Here we present VIOLIN (Versatile Interaction Orga...
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Mosaic integration of spatial multi-omics with SpaMosaic

bioRxiv Mar 25, 2026
With the advent of spatial multi-omics, mosaic integration of diverse datasets with partially overlapping modalities enables construction of comprehensive multi-modal spatial atlases from heterogeneous sources. Here, we present SpaMosaic, a tool that...
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Tokenization to Transfer: Do Genomic Foundation Models Learn Good Representations?

bioRxiv Mar 25, 2026
The success of Large Language Models has inspired the development of Genomic Foundation Models (GFMs) through similar pretraining techniques. However, the relationship between pretraining performance and effectiveness in downstream genomic tasks rema...
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