| # Data availability — ProtTale |
|
|
| Training data, dataset splits and the clusterings that define them. Together |
| with the code, these files reproduce ProtTale from scratch: Stage 1 alignment, |
| Stage 2 generation, the reliability head, and the held-out benchmark. |
|
|
| Figure and table source data are in the sibling `Supplementary_Data` folder. |
|
|
| ``` |
| Data_availability/ |
| stage1_pairs/ Stage 1, functionally similar protein pairs |
| stage2_swissprot/ Stage 2, proteins paired with curated function text |
| clustering/ the clustering that defines every split |
| ``` |
|
|
| All `.json` files are **JSON Lines**: one JSON record per line, not a single |
| JSON array. Read them line by line. |
|
|
| --- |
|
|
| ## stage1_pairs/ — pairwise functional alignment |
| |
| Protein pairs labelled by MIPS clustering, used to train the Q-Former and shift |
| the sequence pathway into the text-derived functional space. |
| |
| | File | Records | |
| |---|---| |
| | `train_set.json` | 119,546 | |
| | `valid_set.json` | 388 | |
| | `test_set.json` | 534 | |
|
|
| Each record is a 5-element list: |
|
|
| | Position | Content | |
| |---|---| |
| | 0 | Amino acid sequence of protein A | |
| | 1 | Amino acid sequence of protein B | |
| | 2 | Curated Swiss-Prot `FUNCTION` description of protein A | |
| | 3 | Curated Swiss-Prot `FUNCTION` description of protein B | |
| | 4 | MIPS label as a string, `"1"` if both proteins fall in the same MIPS cluster (functionally similar), `"0"` otherwise | |
|
|
| Positives and negatives are balanced by construction in every split: 267 / 267 |
| in the test set, 194 / 194 in the validation set, and equal counts in training. |
|
|
| Pairs were drawn independently within each split, so no pair crosses a split |
| boundary. The pairing is derived without curation; the two descriptions |
| attached to each pair are curated Swiss-Prot text. |
|
|
| The 534 test pairs are also the pairs used to validate the LLM-as-judge. That |
| analysis, with UniProt identifiers and judge labels attached, is |
| `Supplementary_Data_3_stage1_test_pairs.csv`. |
|
|
| --- |
|
|
| ## stage2_swissprot/ — sequence to function text |
| |
| Swiss-Prot proteins paired with their curated `FUNCTION` descriptions. The source |
| was the full Swiss-Prot database, 574,627 entries, of which 473,996 carry a |
| curated `FUNCTION` description. |
| |
| | File | Records | Role | |
| |---|---|---| |
| | `train_set.json` | 207,197 | Trains the generator | |
| | `valid_set.json` | 1,000 | Tunes the generator; its judge labels train the reliability head | |
| | `test_set.json` | 1,000 | Tunes the reliability head | |
| | `unseen_set.json` | 1,031 | Held-out benchmark, all final reporting | |
|
|
| Each record is a 6-element list: |
|
|
| | Position | Content | |
| |---|---| |
| | 0 | Amino acid sequence | |
| | 1 | Curated Swiss-Prot `FUNCTION` description, the generation target | |
| | 2 | LLM-as-judge label for ProtTale's own prediction, scored `1` = Yes, `0` = No, `0.5` = Maybe, `-1` = Vague. This is the reliability head's training target. Set to `-1` throughout `unseen_set.json`, where it is a placeholder rather than a label | |
| | 3 | Experimentally validated Molecular Function GO terms | |
| | 4 | Enzyme Commission numbers | |
| | 5 | Placeholder, not used | |
|
|
| In `valid_set.json` the judge labels split 328 Yes, 510 No, 90 Maybe and 72 |
| Vague, which is the class balance the reliability head is fitted against. |
|
|
| Validation and test proteins are the CD-HIT representatives of their 40% |
| identity clusters, one per cluster. |
|
|
| Every protein in `unseen_set.json` is a post-2022 Swiss-Prot deposition and |
| comes from a different 40% identity cluster, one protein per cluster, none of |
| whose members appears in training, validation or testing. Because the protein |
| was chosen by deposition date and annotation rather than by length, it is not |
| always the cluster's CD-HIT representative (683 of the 1,031 are). Each carries |
| at least one experimentally validated MF GO term and at least one EC number, and |
| does not appear in the released training data of any baseline method compared |
| in the paper. The EC requirement means the benchmark consists entirely of |
| enzymes. |
|
|
| --- |
|
|
| ## clustering/ — how the splits were defined |
|
|
| | File | Content | |
| |---|---| |
| | `swissprot_cdhit_40.clstr` | CD-HIT output at 40% sequence identity over Swiss-Prot, 93,610 clusters covering 573,398 sequences | |
|
|
| **CD-HIT clusters define the splits.** Train, validation, test and unseen are |
| partitioned at the level of these clusters, so no protein in one split shares a |
| 40% identity cluster with a protein in another, and each unseen protein comes |
| from a cluster none of whose members the model saw. |
| The split files themselves carry sequences rather than cluster assignments, so |
| this file is what makes that separation checkable: map the sequences of any two |
| splits back to their clusters and confirm the clusters do not intersect. |
|
|
| **MIPS clusters define the Stage 1 labels.** They were built by Louvain |
| community detection over a 5.5 billion edge similarity network spanning 5.2 |
| million UniRef90 representatives, yielding about 1.2 million communities. A |
| Swiss-Prot protein inherits the MIPS cluster of its UniRef90 representative; |
| proteins longer than 1,200 residues, and those whose UniRef90 cluster has fewer |
| than 10 members, have no MIPS cluster and contribute no Stage 1 pairs. The |
| resulting same-cluster / different-cluster label is recorded per pair in |
| `stage1_pairs/`, position 4 of each record. |
|
|
| --- |
|
|
| ## Reproducing the paper's counts |
|
|
| The record counts above are the dataset sizes reported in the main text: |
| 119,546 / 388 / 534 Stage 1 pairs and 207,197 / 1,000 / 1,000 / 1,031 Stage 2 |
| proteins. |
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|
