| --- |
| pretty_name: SwissTest |
| license: mit |
| language: |
| - en |
| task_categories: |
| - text-generation |
| tags: |
| - biology |
| - protein-design |
| - protein-sequence |
| - interpro |
| - gene-ontology |
| - benchmark |
| size_categories: |
| - 1K<n<10K |
| configs: |
| - config_name: go |
| data_files: |
| - split: test |
| path: data/go/test-00000-of-00001.parquet |
| - config_name: ipr |
| data_files: |
| - split: test |
| path: data/ipr/test-00000-of-00001.parquet |
| - config_name: ipr_go |
| default: true |
| data_files: |
| - split: test |
| path: data/ipr_go/test-00000-of-00001.parquet |
| --- |
| |
| # SwissTest |
|
|
| SwissTest contains English instructions for function-guided protein sequence design, |
| reference protein sequences, and GO molecular function or InterPro annotations. |
| It is a test dataset used in PDFBench. The three subsets (Hugging Face configurations) represent different |
| conditioning information for overlapping sets of reference sequences. |
|
|
| The dataset is packaged as one repository, `Knlife/SwissTest`, with three selectable |
| subsets: `go`, `ipr`, and `ipr_go`. The default subset is `ipr_go`. |
|
|
| ## Subsets and splits |
|
|
| | Subset (configuration) | Split | Task records | Unique reference sequences | Excess exact duplicate records | |
| | --- | --- | ---: | ---: | ---: | |
| | `go` | test | 693 | 689 | 3 | |
| | `ipr` | test | 870 | 865 | 5 | |
| | `ipr_go` | test | 674 | 670 | 3 | |
|
|
| `go` provides GO molecular function annotations, `ipr` provides InterPro annotations, |
| and `ipr_go` provides both. Only `test` is supplied; no training or validation split |
| has been created. The default configuration is `ipr_go`. |
|
|
| The 2,237 task records contain 884 distinct reference sequences across all configurations. |
| The sets for `go` and `ipr` share 670 distinct sequences. All 670 distinct sequences |
| in `ipr_go` also occur in both other configurations. Configurations must not be treated |
| as disjoint train/test partitions. Annotations present in multiple configurations agree |
| for their shared reference sequences. |
|
|
| ## Loading |
|
|
| Select a subset by passing its name as the second argument: |
|
|
| ```python |
| from datasets import load_dataset |
| |
| test = load_dataset("Knlife/SwissTest", "ipr_go", split="test") |
| go_test = load_dataset("Knlife/SwissTest", "go", split="test") |
| ipr_test = load_dataset("Knlife/SwissTest", "ipr", split="test") |
| ``` |
|
|
| For a local copy, pass its directory instead of the repository ID. The README declares |
| the data files for each configuration, so the original JSON archives and audit metadata |
| are excluded from loading. |
|
|
| ## Record schema |
|
|
| All configurations use the same schema. Unavailable annotation types are empty lists; |
| annotations are never copied from another configuration to fill those lists. |
|
|
| | Field | Type | Meaning | |
| | --- | --- | --- | |
| | `id` | string | Configuration and zero-based source row, such as `go-000000`. Unique per task record in this snapshot. | |
| | `source_index` | int64 | Zero-based row index in the corresponding original JSON array. | |
| | `protein_id` | string | `sha256:` followed by the SHA-256 digest of the exact reference sequence. Shared by identical sequences; not a UniProt accession. | |
| | `instruction` | string | Original design instruction, including whitespace and punctuation. | |
| | `reference` | string | Original reference protein sequence. | |
| | `sequence_length` | int64 | Number of characters in `reference`. | |
| | `go_molecular_function` | list of structs | GO annotations with string fields `id` and `name`. | |
| | `interpro` | list of structs | InterPro annotations with string fields `id`, `name`, `type` and int64 fields `begin`, `end`. | |
|
|
| GO fields are renamed from `GO-ID` and `GO-Name`. InterPro fields are renamed from |
| `InterPro-ID`, `InterPro-Name`, `InterPro-Type`, `Beg`, and `End`. Their values and list |
| order are preserved. Coordinate values are retained exactly as supplied; no offset |
| conversion is applied. They satisfy `1 <= begin <= end <= sequence_length` in these files. |
| These locations describe annotations on the reference sequence. |
|
|
| The original `response#1` field equals `reference` in every one of the 2,237 records. |
| It is omitted from the normalized table. It must not be interpreted as a model-generated |
| prediction in these source files. The complete original records remain available in |
| `original/`. |
|
|
| ## Preservation and validation |
|
|
| The conversion preserves every task record, its source order, the exact reference |
| sequence and instruction, and all annotation values and ordering. Exact duplicate |
| records are retained to preserve the original benchmark size and weighting. |
| Distinct reference proteins can share the same instruction. |
|
|
| All 2,930 GO annotation names contain leading or trailing whitespace. This whitespace |
| is preserved, together with the original punctuation and repeated terms in instructions. |
| Reference sequences range from 10 to 7,785 characters. The `ipr` configuration includes |
| the unknown residue symbol `X`; sequences are not truncated, filtered, or rewritten. |
| Several InterPro hits can refer to the same entry at different locations; these are retained. |
|
|
| Each Parquet file was reloaded with `datasets.load_dataset`, and every field was checked |
| against the normalized records. Reversing the field renaming and restoring `response#1` |
| reconstructed all original records. Archived JSON files match their source SHA-256 hashes. |
| Counts, duplicate row indices, sequence overlaps, checksums, and validation results are |
| recorded in [metadata/audit.json](metadata/audit.json). |
|
|
| ## Repository files |
|
|
| ```text |
| README.md |
| data/ |
| go/test-00000-of-00001.parquet |
| ipr/test-00000-of-00001.parquet |
| ipr_go/test-00000-of-00001.parquet |
| original/ |
| go.json |
| ipr.json |
| ipr_go.json |
| metadata/ |
| audit.json |
| upstream_comparison.json |
| ``` |
|
|
| ## Source and construction |
|
|
| These records match the test files in |
| [Knlife/SwiwwProtIPG](https://huggingface.co/datasets/Knlife/SwiwwProtIPG/tree/888930029b5c9ea0a0801f3d86732173c987056c), |
| at revision `888930029b5c9ea0a0801f3d86732173c987056c`: |
| `go_test.json`, `ipr_test.json`, and `ipr_go_test.json`. |
| The local source files replace the upstream `sequence` field with identical |
| `reference` and `response#1` fields. All other fields and the record order match. |
| The comparison and file hashes are recorded in |
| [metadata/upstream_comparison.json](metadata/upstream_comparison.json). |
|
|
| The [upstream card](https://huggingface.co/datasets/Knlife/SwiwwProtIPG/blob/888930029b5c9ea0a0801f3d86732173c987056c/README.md) |
| reports selection from UniProt/SwissProt between 2025-01-01 and 2025-08-25, with |
| InterPro and GO molecular function annotations. It describes constructing instructions |
| from annotation descriptions following Mol-Instructions. This construction history |
| is reported by the upstream publisher; it has not been independently reproduced here. |
| The task files contain no UniProt accessions or exact database release identifiers. |
|
|
| ## License |
|
|
| This dataset is released under the MIT license, following the upstream dataset card. |
|
|
| ## Citation |
|
|
| The upstream card provides the following PDFBench citation: |
|
|
| ```bibtex |
| @misc{kuang2025pdfbenchbenchmarknovoprotein, |
| title={PDFBench: A Benchmark for De novo Protein Design from Function}, |
| author={Jiahao Kuang and Nuowei Liu and Changzhi Sun and Tao Ji and Yuanbin Wu}, |
| year={2025}, |
| eprint={2505.20346}, |
| archivePrefix={arXiv}, |
| primaryClass={cs.LG}, |
| url={https://arxiv.org/abs/2505.20346} |
| } |
| ``` |
|
|
| See the [PDFBench project](https://pdfbench.github.io/) for project context. |
|
|
