Artificial Intelligence Medical Compendium

Single-cell foundation models perform well on cell-type classification, but their value for disease-state prediction and their advantage over classical representations remains unclear. We benchmarked cell-representations from four foundation models u... read more 

Background and aims. Inflammatory Bowel Disease (IBD) is a complex immune-mediated condition with a strong genetic contribution. The genetics of IBD are highly complex, with inflammation, autoimmunity, and mucosal immunity pathways involved in its pa... read more 

Electrical stimulation of brain activity has emerged as a key therapeutic intervention for neurological diseases. The success of these approaches relies on precisely tuned stimulation parameters. A major challenge is that these parameters should idea... read more 

Single-cell foundation models (scFMs) are commonly benchmarked using final-layer embeddings, although useful depth may depend on the task. We evaluate Geneformer, scBERT, scGPT, and scFoundation as frozen feature extractors for cell-type and perturba... read more 

When nanoparticles enter biological environments, their surfaces are rapidly coated by proteins, forming a protein corona that governs their biological identity and downstream responses. Existing computational methods treat each protein as an indepen... read more 

Understanding tissue organization requires accurate molecular quantification and faithful spatial localization. Spatial omics, particularly spatial transcriptomics (ST), face measurement trade-offs that limit simultaneous achievement of molecular and... read more 

RNA therapeutics are increasingly moving from empirical screening towards rational, computation-guided design. Recent advances in RNA language models, generative models and structure-aware learning have improved sequence representation, candidate gen... read more 

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Periodontal nerves, comprising sensory, sympathetic, and parasympathetic fibers, are essential components of the periodontium. Beyond their classic sensory and proprioceptive functions, these neural networks actively modulate periodontal immune respo... read more 

MOTIVATION: Gene function prediction is pivotal in genomic and metagenomic data analysis. Current annotation tools typically rely on the most similar sequence from the query database and struggle to robustly set meaningful hit thresholds, causing a m... read more