Publish AlphaEnzyme input data and checksums

.gitattributes

@@ -58,3 +58,9 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+inputs/kinetics/train.csv filter=lfs diff=lfs merge=lfs -text
+inputs/mutation/component_inputs_unlabelled.csv filter=lfs diff=lfs merge=lfs -text
+inputs/mutation/proteingym_rows.csv filter=lfs diff=lfs merge=lfs -text
+inputs/specificity/eval/eval.csv filter=lfs diff=lfs merge=lfs -text
+inputs/specificity/tables/train.csv filter=lfs diff=lfs merge=lfs -text
+inputs/specificity/tables/valid.csv filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,29 @@
+---
+pretty_name: AlphaEnzyme data
+tags:
+- enzyme
+- protein
+- biology
+---
+
+# AlphaEnzyme data
+
+Released input tables and supporting assets for the AlphaEnzyme specificity, kinetics, and mutation tasks. The corresponding code is available in the [`liuyong` branch of the AlphaEnzyme repository](https://github.com/yliust/AlphaEnzyme/tree/liuyong). Model checkpoints are published separately at [GENTEL-Lab/AlphaEnzyme](https://huggingface.co/GENTEL-Lab/AlphaEnzyme).
+
+## Contents
+
+- `inputs/specificity/`: training, validation, and evaluation tables; reference banks and reaction fingerprints.
+- `inputs/kinetics/`: training, validation, and test tables; row-level auxiliary data, normalization statistics, and descriptor banks.
+- `inputs/mutation/`: variant tables, fold definitions, fold row/index files, normalization files, and component inputs.
+- `inputs/CONTRACT.json`: machine-readable file layout.
+- `inputs/README.md`: detailed directory instructions.
+
+Download into the AlphaEnzyme project root:
+
+```bash
+hf download GENTEL-Lab/AlphaEnzyme-data --type dataset --local-dir data
+```
+
+This recreates `data/inputs/`. Large per-pair Pairformer/ESMC feature caches are not included; see `docs/NEW_DATA.md` in the code repository for feature-generation commands. The repository contains task input files, not a single table directly loadable by the Hugging Face `datasets` library.
+
+`SHA256SUMS` records the SHA-256 digest of each released file.

SHA256SUMS

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inputs/CONTRACT.json

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+{
+  "release": "AlphaEnzyme",
+  "tasks": {
+    "specificity": {
+      "tables": [
+        "inputs/specificity/tables/train.csv",
+        "inputs/specificity/tables/valid.csv",
+        "inputs/specificity/eval/eval.csv"
+      ],
+      "reference_banks": [
+        "inputs/specificity/features/reference/positive_context.npz",
+        "inputs/specificity/features/reference/positive_protein_pocket.npz"
+      ],
+      "reaction_fingerprints": "inputs/specificity/features/drfp/reaction_fingerprints.pkl"
+    },
+    "kinetics": {
+      "tables": [
+        "inputs/kinetics/train.csv",
+        "inputs/kinetics/valid.csv",
+        "inputs/kinetics/test.csv"
+      ],
+      "sources": "inputs/kinetics/alpha_sources.json",
+      "row_extra": [
+        "inputs/kinetics/alpha_train_row_extra.npz",
+        "inputs/kinetics/alpha_valid_row_extra.npz",
+        "inputs/kinetics/alpha_test_row_extra.npz"
+      ],
+      "training_stats": "inputs/kinetics/alpha_training_zscore_stats.npz",
+      "substrate_fingerprints": "inputs/kinetics/features/substrate/substrate_fp_ecfp4_2048.pkl",
+      "reaction_fingerprints": "inputs/kinetics/features/drfp/rxn2fp_public_kinetics.pkl",
+      "protein_pocket_bank": "inputs/kinetics/features/protein_pocket/all_protein_pocket.npz"
+    },
+    "mutation": {
+      "labels": "inputs/mutation/inputs/rows.csv",
+      "variants": "inputs/mutation/variants.csv",
+      "references": "inputs/mutation/references.csv",
+      "full_raw_table": "inputs/mutation/proteingym_rows.csv",
+      "folds": "inputs/mutation/folds.json",
+      "protocol": "inputs/mutation/protocol.json",
+      "component_scores": "inputs/mutation/component_inputs_unlabelled.csv",
+      "fold_normalization": "inputs/mutation/features/fold_*_normalization.npz"
+    }
+  },
+  "precomputed_features": "Not included. Generate Pairformer/ESMC features from the raw tables with code/scripts/data_preprocessing/prepare_pairs.py; see docs/NEW_DATA.md.",
+  "checkpoints": "Distributed separately in AlphaEnzyme_checkpoints.zip.",
+  "path_base": "Repository root after unzipping the data archive into data/"
+}

inputs/README.md

@@ -0,0 +1,28 @@
+# AlphaEnzyme raw data
+
+This archive contains the raw tables and the small released input assets used
+by the three tasks: specificity reference banks, reaction fingerprints,
+kinetics descriptor banks and the eight mutation fold-normalization files.
+
+Unpack into `data/` so that the paths are:
+
+```text
+data/inputs/specificity/tables/{train,valid}.csv
+data/inputs/specificity/eval/eval.csv
+data/inputs/specificity/features/reference/positive_context.npz
+data/inputs/specificity/features/reference/positive_protein_pocket.npz
+data/inputs/specificity/features/drfp/reaction_fingerprints.pkl
+data/inputs/kinetics/{train,valid,test}.csv
+data/inputs/mutation/{variants,references,proteingym_rows}.csv
+data/inputs/mutation/{folds,protocol}.json
+data/inputs/mutation/component_inputs_unlabelled.csv
+data/inputs/mutation/inputs/rows.csv
+data/inputs/mutation/inputs/fold_*_{train,valid,test}_{rows,indices}.*
+data/inputs/mutation/features/fold_*_normalization.npz
+```
+
+The large per-pair Pairformer/ESMC feature caches are not included. The mutation
+`inputs/` directory contains the released fold row tables and index arrays. See
+`docs/NEW_DATA.md` for the feature-generation commands.
+
+`CONTRACT.json` lists the machine-readable layout.

inputs/kinetics/alpha_sources.json

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+{
+  "public_strict_iteration1_fulltrue_msa": {
+    "embedding_dir": "features/pairformer/all",
+    "drfp_path": "features/drfp/rxn2fp_public_kinetics.pkl",
+    "bank_path": "features/protein_pocket/all_protein_pocket.npz"
+  }
+}
+

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