Results for “implant-generation”

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Run KADATH (Kernel for Agentic Darwinian Adaptation, Tooling, and Heredity), a Docker-based evolutionary kernel that turns a goal into a locked, Architect-authored benchmark, then evolves a population of smolagents-based coding agents across epochs: each agent runs in an isolated container, gets graded against frozen evidence, and the population is culled, mutated, and reproduced generation over generation until it converges on the best-performing agent framework for that goal. Use when the user wants to propose/approve/run a KADATH evolutionary run, check a run's status or live dashboard, pause/resume/continue a run, export the winning agent population, or understand its Architect/Grader/Tweaker/Birther pipeline, evidence-freezing, or genome lineage/memory model. Triggers on: "kadath", "kadath.sh", "evolve an agent", "Darwinian agent evolution", "agent population fitness benchmark", "smolagents evolutionary run", "kadath dashboard", "genome lineage", "epoch champions".