waypoint-bio
Supports work 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
- 1.3
- License
- MIT
- Compatibility
- Requires Python 3.10+ and waypoint-bio; the documented compatibility stack uses Transformers 4.57.6 and PEFT 0.18.1. Network access and approved Hugging Face access are needed for Hub downloads, but not for local conversion. Training benefits from a GPU.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/waypoint-bio/SKILL.md
- skills/waypoint-bio/SKILL_CN.md
- skills/waypoint-bio/references/cli-reference.md
- skills/waypoint-bio/references/compass-benchmark.md
- skills/waypoint-bio/references/data-preparation.md
- skills/waypoint-bio/references/python-api.md
- skills/waypoint-bio/references/upstream-review.md
- skills/waypoint-bio/scripts/profiler_to_waypoint.py
- skills/waypoint-bio/scripts/vocab_coverage.py
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