AIMC Journal:
bioRxiv

Showing 71 to 80 of 4935 articles

The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics

bioRxiv Oct 6, 2026
The ModelSEED Biochemistry Database (https://modelseed.org/biochem) supplies foundational mass- and charge-balanced reaction networks for metabolic reconstructions. Here we present an update on the biochemistry where the database has been expanded to...
View on bioRxiv DOI

Tractable and Thermodynamically Consistent pKa Prediction via First-Dissociation Aggregation

bioRxiv Oct 6, 2026
Ionization governs molecular behavior, yet predicting aqueous pKa accurately and tractably remains a fundamental challenge. Rigorous ensemble methods require enumerating a protonation-state space that grows exponentially with the number of ionizable ...
View on bioRxiv DOI

pre-miRBench: a multispecies benchmark and reference model for animal precursor microRNA prediction

bioRxiv Oct 6, 2026
Motivation: Precursor microRNA (pre-miRNA) prediction is used to prioritize genomic hairpins for miRNA annotation. Published predictors are trained and evaluated on different species collections, negative sets and data partitions, making reported gai...
View on bioRxiv DOI

Flock: A Negative-Enriched Protein-Protein Interaction Dataset

bioRxiv Oct 6, 2026
Protein-protein interactions (PPIs) govern fundamental biological processes and are central to therapeutic discovery, yet computational prediction methods remain severely limited by a lack of high-quality negative data (non-interacting PPIs). Existin...
View on bioRxiv DOI

Slide-level batch structure limits histology-guided supervision of transcriptomic foundation models

bioRxiv Oct 5, 2026
Spatial transcriptomics pairs spatially resolved gene expression with tissue morphology in the same tissue section. Transcriptomic foundation models encode such expression profiles into general-purpose representations, but these representations can r...
View on bioRxiv DOI

Iterative computational bioprospecting of hydroxymethylfurfural oxidases combining molecular simulation and machine learning

bioRxiv Oct 5, 2026
The enzymatic oxidation of 5-hydroxymethylfurfural (HMF) to 2,5-furandicarboxylic acid (FDCA) is a key step in the sustainable production of polyethylene furanoate (PEF), yet the final oxidation of 5-formyl-2-furancarboxylic acid (FFCA) to FDCA remai...
View on bioRxiv DOI

Evaluating in-context learning with prompting regimes for transformer-based synthetic health tabular data generation

bioRxiv Oct 5, 2026
Tabular synthetic data generation (SDG) can facilitate research and development in the health domain, as access to health data is restricted. To accommodate for its structural complexity, such as multimodal distributions and fragmentation, transforme...
View on bioRxiv DOI

Diffusion MRI of cortical organoids reveals protocol-associated spatial reproducibility and increasing diffusivity with diffusion time

bioRxiv Oct 5, 2026
Early human cortical development involves rapid changes in cytoarchitecture that remain difficult to interrogate non-invasively. Biophysical diffusion MRI models provide a potential window onto this microstructure, including water exchange across cel...
View on bioRxiv DOI

AI-assisted quantification of the clonogenic assay

bioRxiv Oct 5, 2026
The clonogenic assay is the foundational standard for evaluating cellular radiosensitivity, yet its manual quantification is limited by labor-intensive processing, high inter-observer variability, and a reductive binary scoring system. Here, we prese...
View on bioRxiv DOI

Predicting the long-term impact of AI assistants on collective intelligence

bioRxiv Oct 5, 2026
Artificial intelligence (AI) assistants can improve individual performance but may weaken unaided performance and limit interest diversity, raising questions about their long-term effects on collective intelligence (CI). Here, we consider an evolutio...
View on bioRxiv DOI
Popular Topics
Popular Journals