waypoint-bio

Use when working with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pretraining corpus, the Compass eight-task benchmark, or the waypoint CLI from the waypoint-bio package. Covers embedding microbiome samples, fine-tuning on taxonomic abundance data, benchmarking a checkpoint on Compass, pretraining a GPT-2 model on taxonomic abundance profiles, and converting MetaPhlAn, Kraken2, QIIME 2, or MGnify abundance tables into waypoint format.

Version

1.0

License

MIT

Compatibility

Requires Python 3.10+ with `waypoint-bio` (pulls torch, transformers, datasets, peft, scikit-learn). Needs network access and a Hugging Face token with access granted to the gated outpost-bio repos. A GPU is strongly recommended for pretraining and benchmarking.