| --- |
| license: other |
| license_name: cc-by-4.0-and-apache-2.0 |
| license_link: LICENSE |
| pretty_name: Protein concept probing |
| task_categories: |
| - text-classification |
| - token-classification |
| tags: |
| - biology |
| - protein |
| - probing |
| - interpretability |
| configs: |
| - config_name: functional_sites |
| data_files: |
| - split: train |
| path: functional_sites/train.parquet |
| - split: validation |
| path: functional_sites/validation.parquet |
| - split: test |
| path: functional_sites/test.parquet |
| - config_name: go_bp |
| data_files: |
| - split: train |
| path: go_bp/train.parquet |
| - split: validation |
| path: go_bp/validation.parquet |
| - split: test |
| path: go_bp/test.parquet |
| - config_name: go_cc |
| data_files: |
| - split: train |
| path: go_cc/train.parquet |
| - split: validation |
| path: go_cc/validation.parquet |
| - split: test |
| path: go_cc/test.parquet |
| - config_name: go_mf |
| data_files: |
| - split: train |
| path: go_mf/train.parquet |
| - split: validation |
| path: go_mf/validation.parquet |
| - split: test |
| path: go_mf/test.parquet |
| - config_name: interpro_active_site |
| data_files: |
| - split: train |
| path: interpro_active_site/train.parquet |
| - split: validation |
| path: interpro_active_site/validation.parquet |
| - split: test |
| path: interpro_active_site/test.parquet |
| - config_name: interpro_binding_site |
| data_files: |
| - split: train |
| path: interpro_binding_site/train.parquet |
| - split: validation |
| path: interpro_binding_site/validation.parquet |
| - split: test |
| path: interpro_binding_site/test.parquet |
| - config_name: interpro_conserved_site |
| data_files: |
| - split: train |
| path: interpro_conserved_site/train.parquet |
| - split: validation |
| path: interpro_conserved_site/validation.parquet |
| - split: test |
| path: interpro_conserved_site/test.parquet |
| - config_name: interpro_domain |
| data_files: |
| - split: train |
| path: interpro_domain/train.parquet |
| - split: validation |
| path: interpro_domain/validation.parquet |
| - split: test |
| path: interpro_domain/test.parquet |
| - config_name: interpro_family |
| data_files: |
| - split: train |
| path: interpro_family/train.parquet |
| - split: validation |
| path: interpro_family/validation.parquet |
| - split: test |
| path: interpro_family/test.parquet |
| - config_name: interpro_homologous_superfamily |
| data_files: |
| - split: train |
| path: interpro_homologous_superfamily/train.parquet |
| - split: validation |
| path: interpro_homologous_superfamily/validation.parquet |
| - split: test |
| path: interpro_homologous_superfamily/test.parquet |
| - config_name: interpro_repeat |
| data_files: |
| - split: train |
| path: interpro_repeat/train.parquet |
| - split: validation |
| path: interpro_repeat/validation.parquet |
| - split: test |
| path: interpro_repeat/test.parquet |
| - config_name: lipidation |
| data_files: |
| - split: train |
| path: lipidation/train.parquet |
| - split: validation |
| path: lipidation/validation.parquet |
| - split: test |
| path: lipidation/test.parquet |
| - config_name: localization |
| data_files: |
| - split: train |
| path: localization/train.parquet |
| - split: validation |
| path: localization/validation.parquet |
| - split: test |
| path: localization/test.parquet |
| - config_name: metal_ion_binding |
| data_files: |
| - split: train |
| path: metal_ion_binding/train.parquet |
| - split: validation |
| path: metal_ion_binding/validation.parquet |
| - split: test |
| path: metal_ion_binding/test.parquet |
| - config_name: peptide |
| data_files: |
| - split: train |
| path: peptide/train.parquet |
| - split: validation |
| path: peptide/validation.parquet |
| - split: test |
| path: peptide/test.parquet |
| - config_name: phosphorylation |
| data_files: |
| - split: train |
| path: phosphorylation/train.parquet |
| - split: validation |
| path: phosphorylation/validation.parquet |
| - split: test |
| path: phosphorylation/test.parquet |
| - config_name: post_translational_modification |
| data_files: |
| - split: train |
| path: post_translational_modification/train.parquet |
| - split: validation |
| path: post_translational_modification/validation.parquet |
| - split: test |
| path: post_translational_modification/test.parquet |
| - config_name: prot_param |
| data_files: |
| - split: train |
| path: prot_param/train.parquet |
| - split: validation |
| path: prot_param/validation.parquet |
| - split: test |
| path: prot_param/test.parquet |
| - config_name: secondary_structure |
| data_files: |
| - split: train |
| path: secondary_structure/train.parquet |
| - split: validation |
| path: secondary_structure/validation.parquet |
| - split: test |
| path: secondary_structure/test.parquet |
| - config_name: ssp_q3 |
| data_files: |
| - split: train |
| path: ssp_q3/train.parquet |
| - split: validation |
| path: ssp_q3/validation.parquet |
| - split: test |
| path: ssp_q3/test.parquet |
| - config_name: ssp_q8 |
| data_files: |
| - split: train |
| path: ssp_q8/train.parquet |
| - split: validation |
| path: ssp_q8/validation.parquet |
| - split: test |
| path: ssp_q8/test.parquet |
| - config_name: topology |
| data_files: |
| - split: train |
| path: topology/train.parquet |
| - split: validation |
| path: topology/validation.parquet |
| - split: test |
| path: topology/test.parquet |
| --- |
| |
| # Protein concept probing |
|
|
| Twenty-two protein annotation tasks for probing what a protein language model's internal states encode, from |
| amino-acid composition to Gene Ontology terms. Thirteen tasks label a whole protein and nine label each residue. The |
| human tasks are reviewed *Homo sapiens* UniProtKB entries shorter than 1,024 residues; four further tasks are |
| xTrimoPGLM benchmark tables. |
|
|
| | Config | Level | Task | Proteins | Labels | Train / validation / test | |
| |---|---|---|---|---|---| |
| | `functional_sites` | residue | multiclass | 6,893 | 6 | 4,778 / 1,106 / 1,009 | |
| | `go_bp` | protein | multilabel | 12,255 | 304 | 8,591 / 1,888 / 1,776 | |
| | `go_cc` | protein | multilabel | 16,443 | 164 | 11,409 / 2,457 / 2,577 | |
| | `go_mf` | protein | multilabel | 11,504 | 123 | 8,010 / 1,786 / 1,708 | |
| | `interpro_active_site` | protein | multilabel | 718 | 58 | 482 / 116 / 120 | |
| | `interpro_binding_site` | protein | multilabel | 640 | 39 | 446 / 87 / 107 | |
| | `interpro_conserved_site` | protein | multilabel | 2,948 | 334 | 2,062 / 450 / 436 | |
| | `interpro_domain` | protein | multilabel | 8,003 | 364 | 5,307 / 1,371 / 1,325 | |
| | `interpro_family` | protein | multilabel | 3,601 | 239 | 2,097 / 678 / 826 | |
| | `interpro_homologous_superfamily` | protein | multilabel | 8,198 | 100 | 5,499 / 1,368 / 1,331 | |
| | `interpro_repeat` | protein | multilabel | 1,189 | 65 | 819 / 189 / 181 | |
| | `lipidation` | residue | multiclass | 978 | 25 | 654 / 129 / 195 | |
| | `localization` | protein | multiclass | 7,530 | 10 | 5,321 / 590 / 1,619 | |
| | `metal_ion_binding` | protein | binary | 7,242 | 1 | 5,346 / 599 / 1,297 | |
| | `peptide` | residue | multiclass | 4,977 | 4 | 3,485 / 700 / 792 | |
| | `phosphorylation` | residue | multiclass | 8,648 | 6 | 6,057 / 1,304 / 1,287 | |
| | `post_translational_modification` | residue | multiclass | 15,349 | 12 | 10,722 / 2,400 / 2,227 | |
| | `prot_param` | protein | regression | 18,126 | 31 | 12,747 / 2,777 / 2,602 | |
| | `secondary_structure` | residue | multiclass | 8,986 | 4 | 6,310 / 1,351 / 1,325 | |
| | `ssp_q3` | residue | multiclass | 11,479 | 3 | 9,731 / 1,083 / 665 | |
| | `ssp_q8` | residue | multiclass | 11,479 | 8 | 9,731 / 1,083 / 665 | |
| | `topology` | residue | multiclass | 4,777 | 17 | 3,378 / 754 / 645 | |
|
|
| ## Homology leakage |
|
|
| The human tasks keep their published cluster splits: MMseqs2 clusters at 20% identity (30% for InterPro active |
| site, binding site, conserved site and repeat) are assigned whole to train plus validation or to test, and |
| validation clusters are drawn at 50% identity from the rest, with 80% coverage of the target sequence. The four |
| benchmark tasks keep their published test split, and validation is a random 10% of their train split, so they hold |
| no homology guarantee between train and validation. |
|
|
| ## How it was built |
|
|
| 1. Read each curated human table and its recorded train, validation and test assignment. |
| 2. Turn its targets into one `label` column: a multi-hot vector over the InterPro entries or Gene Ontology terms, |
| 31 ProtParam values, or one class index per residue in the contiguous order of the classes the table holds. |
| 3. For Gene Ontology, keep the terms with more than six positive proteins in both validation and test. |
| 4. For the four benchmark tables, split 10% of train off as validation with seed 184502, then drop sequences of |
| 1,024 residues or more. |
|
|
| ## Columns |
|
|
| | Column | Meaning | |
| |---|---| |
| | `id` | UniProt accession for the human tasks; a stable sequence-derived id for the benchmark tasks | |
| | `sequence` | amino-acid sequence | |
| | `label` | multi-hot list (multilabel), list of 31 floats (regression), integer (binary or multiclass), or one integer per residue (residue tasks) | |
|
|
| Each config folder also holds `metadata.json` with the task level, task type and label names. The benchmark tables |
| publish their classes but not the order of their integers, so their label names are `class_<n>`. |
|
|
| ## What a model trained on it may say |
|
|
| These are probing benchmarks. InterPro entries and many UniProt features are curated with computational evidence, |
| so a probe here measures agreement with the annotations, not experimentally measured function. Residue tasks count |
| unannotated residues as their own class (`-`), which dominates most of them. |
|
|
| ## Sources and licence |
|
|
| The human tasks are the curated tables of Figshare record 10.6084/m9.figshare.31169506, released under CC BY 4.0, |
| built from UniProtKB (accessed 2025-09-09) and the InterPro entry list (accessed 2025-09-16). The four benchmark |
| tasks (`metal_ion_binding`, `localization`, `ssp_q3`, `ssp_q8`) are from `biomap-research` on Hugging Face under |
| Apache 2.0. |
|
|
| ## Files |
|
|
| `<config>/train.parquet`, `<config>/validation.parquet`, `<config>/test.parquet` and `<config>/metadata.json` for each |
| of the 22 configs. |
|
|
