waypoint-bio
Category: life-sciences · License: MIT · Version: 1.1 · Includes scripts
Tags: microbiome, foundation models, metagenomics, benchmarks
When to use it
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 thewaypoint 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.
Example requests
Ask your agent in plain language, for example:- “How do I get embeddings for my gut 16S samples from the 45M Waypoint model?”
- “I have a MetaPhlAn merged table, merged_abundance_table.txt, from 240 shotgun stool samples (IBD vs healthy, several timepoints per patient). I want to fine-tune Waypoint-6m to classify IBD.
waypoint prepare-datasetchoked on the pipe-separated clade names. How do I convert it and set this up properly?” - “I’ve got about 60k public gut metagenome profiles from MGnify and want to train my own transformer that treats each sample like a sentence of taxa ordered by abundance, then see how it compares with the published numbers on the standard eight-task set. Where do I start?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.