| --- |
| 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.tsv |
| - split: split1_validation |
| path: EC_v2/amino_acids/split_1/validation.tsv |
| - split: split1_test1 |
| path: EC_v2/amino_acids/split_1/test1.tsv |
| - split: split1_test2 |
| path: EC_v2/amino_acids/split_1/test2.tsv |
| - split: split2_train |
| path: EC_v2/amino_acids/split_2/train.tsv |
| - split: split2_validation |
| path: EC_v2/amino_acids/split_2/validation.tsv |
| - split: split2_test1 |
| path: EC_v2/amino_acids/split_2/test1.tsv |
| - split: split2_test2 |
| path: EC_v2/amino_acids/split_2/test2.tsv |
| - split: split3_train |
| path: EC_v2/amino_acids/split_3/train.tsv |
| - split: split3_validation |
| path: EC_v2/amino_acids/split_3/validation.tsv |
| - split: split3_test1 |
| path: EC_v2/amino_acids/split_3/test1.tsv |
| - split: split3_test2 |
| path: EC_v2/amino_acids/split_3/test2.tsv |
| - split: split4_train |
| path: EC_v2/amino_acids/split_4/train.tsv |
| - split: split4_validation |
| path: EC_v2/amino_acids/split_4/validation.tsv |
| - split: split4_test1 |
| path: EC_v2/amino_acids/split_4/test1.tsv |
| - split: split4_test2 |
| path: EC_v2/amino_acids/split_4/test2.tsv |
| - split: split5_train |
| path: EC_v2/amino_acids/split_5/train.tsv |
| - split: split5_validation |
| path: EC_v2/amino_acids/split_5/validation.tsv |
| - split: split5_test1 |
| path: EC_v2/amino_acids/split_5/test1.tsv |
| - split: split5_test2 |
| path: EC_v2/amino_acids/split_5/test2.tsv |
| - config_name: EC_v2_nucleotides |
| data_files: |
| - split: split1_train |
| path: EC_v2/nucleotides/split_1/train.tsv |
| - split: split1_validation |
| path: EC_v2/nucleotides/split_1/validation.tsv |
| - split: split1_test1 |
| path: EC_v2/nucleotides/split_1/test1.tsv |
| - split: split1_test2 |
| path: EC_v2/nucleotides/split_1/test2.tsv |
| - split: split2_train |
| path: EC_v2/nucleotides/split_2/train.tsv |
| - split: split2_validation |
| path: EC_v2/nucleotides/split_2/validation.tsv |
| - split: split2_test1 |
| path: EC_v2/nucleotides/split_2/test1.tsv |
| - split: split2_test2 |
| path: EC_v2/nucleotides/split_2/test2.tsv |
| - split: split3_train |
| path: EC_v2/nucleotides/split_3/train.tsv |
| - split: split3_validation |
| path: EC_v2/nucleotides/split_3/validation.tsv |
| - split: split3_test1 |
| path: EC_v2/nucleotides/split_3/test1.tsv |
| - split: split3_test2 |
| path: EC_v2/nucleotides/split_3/test2.tsv |
| - split: split4_train |
| path: EC_v2/nucleotides/split_4/train.tsv |
| - split: split4_validation |
| path: EC_v2/nucleotides/split_4/validation.tsv |
| - split: split4_test1 |
| path: EC_v2/nucleotides/split_4/test1.tsv |
| - split: split4_test2 |
| path: EC_v2/nucleotides/split_4/test2.tsv |
| - split: split5_train |
| path: EC_v2/nucleotides/split_5/train.tsv |
| - split: split5_validation |
| path: EC_v2/nucleotides/split_5/validation.tsv |
| - split: split5_test1 |
| path: EC_v2/nucleotides/split_5/test1.tsv |
| - split: split5_test2 |
| path: EC_v2/nucleotides/split_5/test2.tsv |
| - 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 |
|
|
|
|
| **`EC_v2/`** should be used for all new work, as it corrects important bugs in v1 data generation pipeline. `EC_v1/` is maintained for reproducibility of existing citing work and should only be used to reproduce already-published v1 results |
| |
| ## Structure |
| |
| ``` |
| EC_v2/ amino_acids/ split_1 … split_5 / {train, validation, test1, test2}.tsv |
| nucleotides/ split_1 … split_5 / {train, validation, test1, test2}.tsv |
| EC_v1/ amino_acids/ split_1 … split_5 / {train, validation, test1, test2}.csv |
| nucleotides/ split_1 … split_5 / {train, validation, test1, test2}.csv |
| ``` |
| |
| All files are **tab-separated**. v2 uses the `.tsv` extension; v1 retains the original |
| `.csv` extension (tab-separated despite the name) for release stability — load v1 with |
| `pd.read_csv(path, sep="\t")`. |
| |
| Columns — amino acids: `Entry, EC number, EMBL, RefSeq, UniRef50, UniRef90, UniRef100, Sequence`; |
| nucleotides: `Entry` (EMBL CDS id), `EC number`, `Sequence`. |
| |
| 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**. |
|
|
| **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 GRIMM repo git history for full details. |
|
|
| ## Citation |
|
|
| Preprint: https://arxiv.org/abs/2602.16504 |
|
|
| Code: https://github.com/Hoarfrost-Lab/grimm |
|
|
