Dev/v1.5 MassSpecGym#68
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harrylaucngd wants to merge 41 commits into
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Merge the MIST-CF branch history while keeping the v1.5 closure tree focused on the corrected oracle implementation. Co-authored-by: Cursor <cursoragent@cursor.com>
v1.5 model zoo implementation.
…o feat/llm-skills
feat: level 1 model card impl
* tmp feat: test out with diffms (v0 model card) * chore: update model card * fix: suibmission dir * cho9re: remove pubication field * chore: remove superfluous comments * chore: add .claude to gitignore * chore: update scripts in llm skills * feat: diffms implementation * feat: add mist molforge submission * tmp fix: remove model card for llm skills
…SpecGym into feat/llm-skills
This reverts commit dae836a.
Revert "Feat/llm skills lv2"
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This PR merges
dev/v1.5intopluskal-lab/MassSpecGym. On top of upstreammain, it adds the v1.5 benchmark / model zoo, data and download paths, implementations for encoders, retrieval, de novo, simulation, and oracles, plus scripts, dependencies, and tests.What changed (by area)
Data & Hub
massspecgym/data/:download,fp2mol_dataset, MIST-related modules,subformulae,transforms,sanity_check, etc., for v1.5-style loading and inferred-formula workflows.data/exclude_inchikeys.csv.scripts/download_data.py,scripts/convert_to_parquet.py.Model zoo / v1.5
diffms,frigid,molforge, sharedfp2molbase.generative_retrieval,iceberg_retrieval,mist_retrieval, updates toretrieval/baseand related code.predict,fast_filter,sirius, etc.).Scripts
scripts/run.py,run_simulation.py, etc., for v1.5 runs.Packaging & docs
setup.py(e.g. pyarrow and related deps).README.md,checkpoints/README.md.