Upload README.md with huggingface_hub

README.md

@@ -0,0 +1,283 @@
+---
+license: cc-by-4.0
+language:
+  - en
+tags:
+  - biology
+  - proteins
+  - enzymes
+  - ec-number
+  - genomics
+  - protein-function-prediction
+pretty_name: GRIMM (EC) — Genomic Representation Inference for Microbial Metabolism
+task_categories:
+  - text-classification
+size_categories:
+  - 100K<n<1M
+configs:
+  - config_name: EC_v2_amino_acids
+    default: true
+    data_files:
+      - split: split1_train
+        path: EC_v2/amino_acids/split_1/train.csv
+      - split: split1_validation
+        path: EC_v2/amino_acids/split_1/validation.csv
+      - split: split1_test1
+        path: EC_v2/amino_acids/split_1/test1.csv
+      - split: split1_test2
+        path: EC_v2/amino_acids/split_1/test2.csv
+      - split: split2_train
+        path: EC_v2/amino_acids/split_2/train.csv
+      - split: split2_validation
+        path: EC_v2/amino_acids/split_2/validation.csv
+      - split: split2_test1
+        path: EC_v2/amino_acids/split_2/test1.csv
+      - split: split2_test2
+        path: EC_v2/amino_acids/split_2/test2.csv
+      - split: split3_train
+        path: EC_v2/amino_acids/split_3/train.csv
+      - split: split3_validation
+        path: EC_v2/amino_acids/split_3/validation.csv
+      - split: split3_test1
+        path: EC_v2/amino_acids/split_3/test1.csv
+      - split: split3_test2
+        path: EC_v2/amino_acids/split_3/test2.csv
+      - split: split4_train
+        path: EC_v2/amino_acids/split_4/train.csv
+      - split: split4_validation
+        path: EC_v2/amino_acids/split_4/validation.csv
+      - split: split4_test1
+        path: EC_v2/amino_acids/split_4/test1.csv
+      - split: split4_test2
+        path: EC_v2/amino_acids/split_4/test2.csv
+      - split: split5_train
+        path: EC_v2/amino_acids/split_5/train.csv
+      - split: split5_validation
+        path: EC_v2/amino_acids/split_5/validation.csv
+      - split: split5_test1
+        path: EC_v2/amino_acids/split_5/test1.csv
+      - split: split5_test2
+        path: EC_v2/amino_acids/split_5/test2.csv
+  - config_name: EC_v2_nucleotides
+    data_files:
+      - split: split1_train
+        path: EC_v2/nucleotides/split_1/train.csv
+      - split: split1_validation
+        path: EC_v2/nucleotides/split_1/validation.csv
+      - split: split1_test1
+        path: EC_v2/nucleotides/split_1/test1.csv
+      - split: split1_test2
+        path: EC_v2/nucleotides/split_1/test2.csv
+      - split: split2_train
+        path: EC_v2/nucleotides/split_2/train.csv
+      - split: split2_validation
+        path: EC_v2/nucleotides/split_2/validation.csv
+      - split: split2_test1
+        path: EC_v2/nucleotides/split_2/test1.csv
+      - split: split2_test2
+        path: EC_v2/nucleotides/split_2/test2.csv
+      - split: split3_train
+        path: EC_v2/nucleotides/split_3/train.csv
+      - split: split3_validation
+        path: EC_v2/nucleotides/split_3/validation.csv
+      - split: split3_test1
+        path: EC_v2/nucleotides/split_3/test1.csv
+      - split: split3_test2
+        path: EC_v2/nucleotides/split_3/test2.csv
+      - split: split4_train
+        path: EC_v2/nucleotides/split_4/train.csv
+      - split: split4_validation
+        path: EC_v2/nucleotides/split_4/validation.csv
+      - split: split4_test1
+        path: EC_v2/nucleotides/split_4/test1.csv
+      - split: split4_test2
+        path: EC_v2/nucleotides/split_4/test2.csv
+      - split: split5_train
+        path: EC_v2/nucleotides/split_5/train.csv
+      - split: split5_validation
+        path: EC_v2/nucleotides/split_5/validation.csv
+      - split: split5_test1
+        path: EC_v2/nucleotides/split_5/test1.csv
+      - split: split5_test2
+        path: EC_v2/nucleotides/split_5/test2.csv
+  - config_name: EC_v1_amino_acids
+    data_files:
+      - split: split1_train
+        path: EC_v1/amino_acids/split_1/train.csv
+      - split: split1_validation
+        path: EC_v1/amino_acids/split_1/validation.csv
+      - split: split1_test1
+        path: EC_v1/amino_acids/split_1/test1.csv
+      - split: split1_test2
+        path: EC_v1/amino_acids/split_1/test2.csv
+      - split: split2_train
+        path: EC_v1/amino_acids/split_2/train.csv
+      - split: split2_validation
+        path: EC_v1/amino_acids/split_2/validation.csv
+      - split: split2_test1
+        path: EC_v1/amino_acids/split_2/test1.csv
+      - split: split2_test2
+        path: EC_v1/amino_acids/split_2/test2.csv
+      - split: split3_train
+        path: EC_v1/amino_acids/split_3/train.csv
+      - split: split3_validation
+        path: EC_v1/amino_acids/split_3/validation.csv
+      - split: split3_test1
+        path: EC_v1/amino_acids/split_3/test1.csv
+      - split: split3_test2
+        path: EC_v1/amino_acids/split_3/test2.csv
+      - split: split4_train
+        path: EC_v1/amino_acids/split_4/train.csv
+      - split: split4_validation
+        path: EC_v1/amino_acids/split_4/validation.csv
+      - split: split4_test1
+        path: EC_v1/amino_acids/split_4/test1.csv
+      - split: split4_test2
+        path: EC_v1/amino_acids/split_4/test2.csv
+      - split: split5_train
+        path: EC_v1/amino_acids/split_5/train.csv
+      - split: split5_validation
+        path: EC_v1/amino_acids/split_5/validation.csv
+      - split: split5_test1
+        path: EC_v1/amino_acids/split_5/test1.csv
+      - split: split5_test2
+        path: EC_v1/amino_acids/split_5/test2.csv
+  - config_name: EC_v1_nucleotides
+    data_files:
+      - split: split1_train
+        path: EC_v1/nucleotides/split_1/train.csv
+      - split: split1_validation
+        path: EC_v1/nucleotides/split_1/validation.csv
+      - split: split1_test1
+        path: EC_v1/nucleotides/split_1/test1.csv
+      - split: split1_test2
+        path: EC_v1/nucleotides/split_1/test2.csv
+      - split: split2_train
+        path: EC_v1/nucleotides/split_2/train.csv
+      - split: split2_validation
+        path: EC_v1/nucleotides/split_2/validation.csv
+      - split: split2_test1
+        path: EC_v1/nucleotides/split_2/test1.csv
+      - split: split2_test2
+        path: EC_v1/nucleotides/split_2/test2.csv
+      - split: split3_train
+        path: EC_v1/nucleotides/split_3/train.csv
+      - split: split3_validation
+        path: EC_v1/nucleotides/split_3/validation.csv
+      - split: split3_test1
+        path: EC_v1/nucleotides/split_3/test1.csv
+      - split: split3_test2
+        path: EC_v1/nucleotides/split_3/test2.csv
+      - split: split4_train
+        path: EC_v1/nucleotides/split_4/train.csv
+      - split: split4_validation
+        path: EC_v1/nucleotides/split_4/validation.csv
+      - split: split4_test1
+        path: EC_v1/nucleotides/split_4/test1.csv
+      - split: split4_test2
+        path: EC_v1/nucleotides/split_4/test2.csv
+      - split: split5_train
+        path: EC_v1/nucleotides/split_5/train.csv
+      - split: split5_validation
+        path: EC_v1/nucleotides/split_5/validation.csv
+      - split: split5_test1
+        path: EC_v1/nucleotides/split_5/test1.csv
+      - split: split5_test2
+        path: EC_v1/nucleotides/split_5/test2.csv
+---
+
+# GRIMM-EC
+
+GRIMM is a benchmark for predicting enzyme function (EC number) from biological
+sequence. Sequences are reviewed (SwissProt) prokaryotic proteins with EC
+annotations; partitions are stratified per label by UniRef50 cluster so that
+homologous sequences do not leak between train and evaluation splits.
+
+Two modalities are provided: **amino acids** (per-protein SwissProt sequences) and
+**nucleotides** (per-CDS sequences from ENA).
+
+## ⭐ Which version to use
+
+| Path | Status | Use it? |
+|------|--------|---------|
+| **`EC_v2/`** | corrected, leakage-free, matches the current preprint | ✅ **Yes — all new work** |
+| `EC_v1/`     | original release (v1 preprint + parallel works); legacy | only to reproduce already-published v1 results |
+
+## Structure
+
+```
+EC_v2/  (and EC_v1/)
+  amino_acids/   split_1 … split_5 / {train, validation, test1, test2}.csv
+  nucleotides/   split_1 … split_5 / {train, validation, test1, test2}.csv
+```
+
+Columns — amino acids: `Entry, EC number, EMBL, RefSeq, UniRef50, UniRef90, UniRef100, Sequence`;
+nucleotides: `Entry` (EMBL CDS id), `EC number`, `Sequence`. Files are tab-separated.
+
+The 5 folds are **not** a standard k-fold: each is an independent train/valid/test
+partition that preserves UniRef50 clusters. Train and evaluate the 5 folds as
+independent models (individually or as an ensemble), not as rotating CV folds.
+
+### Splits
+
+- **train / validation / test1** — closed-set: evaluation sequences whose labels also
+  appear in training, but held out by UniRef50 cluster.
+- **test2** — open-set: sequences from labels **absent from training** (out-of-distribution).
+
+### Labels
+
+EC numbers (4th level). Proteins with multiple EC annotations are kept as a single
+**compound label string** (e.g. `1.1.99.1;1.2.1.8`), distinct from its component
+labels — they are **not** expanded into separate rows.
+
+### Sizes (GRIMM-EC v2, average per fold)
+
+| Modality | train | validation | test1 | test2 |
+|----------|------:|-----------:|------:|------:|
+| amino acids | ~178,053 | ~28,719 | ~29,689 | ~959 |
+| nucleotides | ~251,745 | ~42,557 | ~45,185 | ~1,755 |
+
+237,421 proteins · 6,393 EC labels (1,321 compound) · 65,996 UniRef50 clusters.
+Sequences from UniProt release **2025_02**.
+
+## How GRIMM-EC v2 is built (and how it differs from v1)
+
+v2 reuses v1's UniRef50 cluster assignments but regenerates the splits to match the
+documented method:
+
+- **Per-protein SwissProt sequences** (release 2025_02) — v1's AA data instead held
+  the UniRef50 *representative* sequence.
+- **Low-support labels split by UniRef50 cluster** — labels with 1–2 clusters are
+  partitioned by whole cluster (2 clusters → 1 train / 1 test1; 1 cluster → orphan,
+  ~80% train / ~20% test2 across folds), not by individual sequence as in v1.
+- **Independent, shuffled folds**; **seeded** for reproducibility.
+- **`test2` is held-out only** (true open-set) — v1 inadvertently also wrote the
+  held-out orphans into train.
+- EC labels normalized (stray whitespace stripped).
+
+**Verified for v2 (all 5 folds, both modalities):** 0 `(sequence, EC)` overlap between
+`train` and any evaluation split; 0 accession overlap between splits; `test2` labels
+absent from train. Identical sequences carrying *different* EC labels may appear in
+different splits — this is intended cross-label difficulty under per-label
+stratification, not leakage.
+
+## Known limitations of GRIMM-EC v1 (fixed in v2)
+
+`EC_v1/` is retained for reproducibility of already-published results. Its `test2`
+has been **corrected** to be fully disjoint from `train`/`validation`/`test1`;
+`train`/`validation`/`test1` are **unchanged** from the original release. Remaining
+v1 limitations (all fixed in v2):
+
+1. AA sequences are UniRef50 **representatives**, not per-protein SwissProt sequences
+   (the nucleotide modality used real per-CDS sequences and is unaffected).
+2. ~5.8% of AA `test1` rows (and ~4.1% of `validation`) share an exact sequence with
+   `train`, because 1–2 cluster labels were split by sequence rather than by cluster
+   (nucleotides: ~0.4%).
+
+See the repository / preprint for full details.
+
+## Citation
+
+> Hoarfrost et al. GRIMM: Genomic Representation Inference for Microbial Metabolism. (preprint)
+
+Code: https://github.com/Hoarfrost-Lab/grimm