evo2-genome-modeling

name	evo2-genome-modeling
description	Run pinned Evo 2 DNA sequence scoring, embeddings, variant scoring, or controlled generation. Use for long-context genomic foundation-model analyses when compatible local GPU hardware and explicit genome/strand provenance are available.
license	MIT

Evo 2 Genome Modeling

Gate

Ask once before installing pinned Evo 2/Vortex dependencies, downloading large checkpoints, using GPU/remote compute, or sending sequence to a hosted API. State hardware compatibility and estimated memory/time. Follow $cx-compute-environment.

Workflow

1. Record assembly, chromosome/contig, coordinates, strand, reference allele, sequence window, organism, and intended task. Validate reference alleles and keep reverse complements/overlapping loci together in evaluation splits.
2. Pin Evo 2 version/commit, checkpoint and checksum, tokenizer, context length, embedding layer or scoring rule, precision, hardware, seeds, and generation parameters/budget.
3. Run the official installation smoke test, then execute into artifacts/<run-id>/evo2/; retain exact sequences, coordinate maps, logits or embeddings, generations, configs, environment, logs, and failures.
4. For variants, compare matched reference/alternate windows and both strand conventions when appropriate. For generation, report memorization, novelty, composition, constraints, filter failures, and nearest database neighbors.
5. Record with $science-provenance; review with $science-review.

Boundaries

• Likelihood is not pathogenicity, fitness, expression, or clinical evidence.
• Generated DNA is a computational hypothesis; do not automatically synthesize, deploy, or optimize for harmful biological function.