name: "linnaeus" description: "Public linnaeus repo knowledge for model architecture, training/inference entry points, and profiling workflows. Inject before editing polli-labs/linnaeus or integrating with typus taxonomy surfaces."
linnaeus
Public Linnaeus repository knowledge for taxonomy-aware biodiversity modeling.
Quick facts
- Repo:
polli-labs/linnaeus(public) - Core model families:
mFormerV0,mFormerV1,DINOv3MultiHead - Config system: YACS defaults in
linnaeus/config.py+ YAML experiment configs - Package manager:
uv(prefer overpip)
Core entry points
linnaeus/main.py- training entry pointlinnaeus/config.py- default config schema and hierarchylinnaeus/models/- model implementations and blockslinnaeus/h5data/- dataset + dataloader stacklinnaeus/profiling/cli.py- profiling analysis CLIlinnaeus/tools/profiling/run_profiling_trials.py- profiling runner CLI
Fast workflow
cd ~/repo/linnaeus
uv sync --extra dev --extra profiling --extra cpu
# Inspect CLI surfaces
linnaeus-prof --help
linnaeus-prof-run --help
# Local smoke train
python -m linnaeus.main \
--cfg configs/experiments/examples/aves_smoke.yaml \
--opts TRAIN.EPOCHS 1 DEBUG.PROFILER.ENABLED False
Guardrails
- Keep public repo configs free of secrets/private infra details.
- Place internal experiment/runtime configs in private repo surfaces, not under public
configs/. - Prefer reproducible trial definitions with explicit branch + commit pinning.
References
docs/profiling/README.mddocs/profiling/prof-cli.mddocs/profiling/prof-run.mddocs/dev/