gkrieg13/mimyr

Local-first, conversational AI research partner for multi-omics analysis with CLI, desktop app, and 95+ reproducible skills; keeps raw data local while routing natural-language requests to Python/R/CLI tools with persistent memory, autonomous analysis paths, and multi-method consensus workflows (TianGzlab, 155+ stars, Apache 2.0, 2026)

A diffusion language model for genome-scale perturbation prediction across diverse cellular contexts.

An Ontix autoencoder with an explainable, 16-dimensional latent space, trained on single-cell RNA-seq data. Each latent dimension is constrained by a gene ontology term generated with Claude Opus 5, making the embedding directly interpretable in terms of biological processes.

ScVI is a variational inference model for single-cell RNA-seq data that can learn an underlying latent space, integrate technical batches and impute dropouts. The learned low-dimensional latent representation of the data can be used for visualization and clustering.

CondSCVI is a variational inference model for single-cell RNA-seq data that can learn an underlying latent space. The predictions of the model are meant to be afterward used for deconvolution of a second spatial transcriptomics dataset in DestVI.

Stack is a large-scale encoder-decoder foundation model for single-cell biology. It introduces a novel tabular attention architecture that enables both intra- and inter-cellular information flow, setting cell-by-gene matrix chunks as the basic input data unit.