| --- |
| dataset_info: |
| features: |
| - name: A |
| dtype: string |
| - name: B |
| dtype: string |
| - name: SeqA |
| dtype: string |
| - name: SeqB |
| dtype: string |
| - name: OrgA |
| dtype: string |
| - name: OrgB |
| dtype: string |
| - name: NameA |
| dtype: string |
| - name: NameB |
| dtype: string |
| - name: GeneA |
| dtype: string |
| - name: GeneB |
| dtype: string |
| - name: labels |
| dtype: int8 |
| - name: source_dataset |
| dtype: string |
| - name: evidence |
| dtype: string |
| - name: y2h_v1_result |
| dtype: string |
| - name: y2h_v4_result |
| dtype: string |
| - name: mappit_result |
| dtype: string |
| - name: gpca_result |
| dtype: string |
| - name: score |
| dtype: float32 |
| - name: contact_probability |
| dtype: float32 |
| - name: model_confidence |
| dtype: float32 |
| - name: pDockQ |
| dtype: float32 |
| - name: iPAE |
| dtype: float32 |
| - name: CCC |
| dtype: float32 |
| - name: novel |
| dtype: int8 |
| splits: |
| - name: afrf_y2h_yeast |
| num_bytes: 542861 |
| num_examples: 597 |
| - name: afrf_y2h_human |
| num_bytes: 3953209 |
| num_examples: 4046 |
| - name: yeri |
| num_bytes: 1810228 |
| num_examples: 1970 |
| - name: y2h_union_25 |
| num_bytes: 4625430 |
| num_examples: 4556 |
| - name: valbin_25 |
| num_bytes: 15517114 |
| num_examples: 12706 |
| - name: prs_rrs_yeast |
| num_bytes: 335754 |
| num_examples: 306 |
| - name: prs_rrs_human |
| num_bytes: 787687 |
| num_examples: 729 |
| - name: orthogonal_assays |
| num_bytes: 9027406 |
| num_examples: 8846 |
| download_size: 15030614 |
| dataset_size: 36599689 |
| configs: |
| - config_name: default |
| data_files: |
| - split: afrf_y2h_yeast |
| path: data/afrf_y2h_yeast-* |
| - split: afrf_y2h_human |
| path: data/afrf_y2h_human-* |
| - split: yeri |
| path: data/yeri-* |
| - split: y2h_union_25 |
| path: data/y2h_union_25-* |
| - split: valbin_25 |
| path: data/valbin_25-* |
| - split: prs_rrs_yeast |
| path: data/prs_rrs_yeast-* |
| - split: prs_rrs_human |
| path: data/prs_rrs_human-* |
| - split: orthogonal_assays |
| path: data/orthogonal_assays-* |
| license: cc-by-4.0 |
| language: |
| - en |
| tags: |
| - protein |
| - protein-protein-interaction |
| - interactome |
| - biology |
| - alphafold |
| pretty_name: CCSB AI Interactome Benchmark |
| --- |
| |
| # CCSB-AI-Interactome |
|
|
| Harmonized protein-protein interaction benchmark built from the Supplementary Data of: |
|
|
| > Lambourne, L., Yadav, A., Wang, Y. et al. **Experimental assessment of AI-based interactome mapping.** *Nature Communications* **17**, 4894 (2026). https://doi.org/10.1038/s41467-026-70942-x |
|
|
| The study screened a near-complete *S. cerevisiae* ORFeome (5,854 sequence-validated ORFs, 99.5% coverage) with an improved yeast two-hybrid assay to produce YeRI, then put proteome-scale AlphaFold/RoseTTAFold predictions through the same wet-lab pipeline. Its headline finding is that high-confidence AI predictions match experimental data in quality but recover far fewer strictly novel interactions in proteome-wide screening. |
|
|
| Every table has been resolved to amino acid sequences and coerced to a single schema, so all splits share identical columns and can be iterated without special-casing. |
|
|
| ## Splits |
|
|
| | Split | Rows | Positive | Negative | Unscorable | Organism | What it is | |
| |---|---|---|---|---|---|---| |
| | `afrf_y2h_yeast` | 597 | 17 | 559 | 21 | yeast | AlphaFold/RoseTTAFold-predicted pairs, each given a wet-lab Y2H verdict (Supp. Data 19) | |
| | `afrf_y2h_human` | 4,046 | 402 | 2,916 | 728 | human | Zhang et al. AF/RF human predictions, each given a Y2H verdict (Supp. Data 22) | |
| | `yeri` | 1,970 | 1,970 | 0 | 0 | yeast | The yeast reference interactome, with AlphaFold metrics and orthogonal assays joined (Supp. Data 16 + 24) | |
| | `y2h_union_25` | 4,556 | 4,556 | 0 | 0 | yeast | Union of four systematic yeast Y2H maps (Supp. Data 17) | |
| | `valbin_25` | 12,706 | 12,706 | 0 | 0 | yeast | Validated binary yeast PPIs across structural, literature, and Y2H evidence (Supp. Data 21) | |
| | `prs_rrs_yeast` | 306 | 108 | 198 | 0 | yeast | scPRS-v2 positive and scRRS-v2 random reference sets, with every assay readout attached (Supp. Data 2, 3, 4, 23) | |
| | `prs_rrs_human` | 729 | 342 | 387 | 0 | human | hsPRS-v2 / hsRRS-v2 plus the literature and random comparators tested alongside (Supp. Data 22) | |
| | `orthogonal_assays` | 8,846 | 858 | 6,484 | 1,504 | yeast | Raw MAPPIT and GPCA assay-level results, one row per assayed configuration (Supp. Data 11) | |
|
|
| ## The interesting one |
|
|
| `afrf_y2h_yeast` and `afrf_y2h_human` are pairs that a structure-based AI method called an interaction, each carrying an experimental verdict. Every negative is a structural near-miss rather than a random pair, which makes them a far harder discrimination target than the usual random-negative benchmarks, and a direct test of whether a sequence-only model recovers signal that structure-based virtual screening got wrong. |
|
|
| ## Schema |
|
|
| All splits share these columns. |
|
|
| | Column | Type | Meaning | |
| |---|---|---| |
| | `A`, `B` | string | UniProt accession | |
| | `SeqA`, `SeqB` | string | Amino acid sequence | |
| | `OrgA`, `OrgB` | string | Organism binomial | |
| | `NameA`, `NameB` | string | Systematic ORF name (yeast) or source accession (human) | |
| | `GeneA`, `GeneB` | string | Common gene name | |
| | `labels` | int8 | `1` interacting, `0` non-interacting, `-1` not scorable | |
| | `source_dataset` | string | Provenance set within the paper | |
| | `evidence` | string | `;`-joined evidence flags, for example `I3D-exp-24;Lit-BM-24` | |
| | `y2h_v1_result`, `y2h_v4_result` | string | Raw Y2H verdict, empty when not tested | |
| | `mappit_result`, `gpca_result` | string | Orthogonal assay verdict, empty when not tested | |
| | `score` | float32 | Assay score, or YeRI manual growth score | |
| | `contact_probability`, `model_confidence`, `pDockQ`, `iPAE`, `CCC` | float32 | AlphaFold confidence metrics, `NaN` when unavailable | |
| | `novel` | int8 | `1` if strictly novel at publication, `0` if not, `-1` unknown | |
|
|
| ### Label semantics differ by split |
|
|
| This is the one thing to read before using `labels`. |
|
|
| - `afrf_y2h_yeast`, `afrf_y2h_human`, `orthogonal_assays`: the label is the **assay outcome**. This is the adjudication being benchmarked. |
| - `prs_rrs_yeast`, `prs_rrs_human`: the label is **reference-set membership** (PRS positive, RRS random). The assay outcome is in the result columns instead, since reference-set membership is the ground truth and the assay is what is being calibrated. |
| - `yeri`, `y2h_union_25`, `valbin_25`: positive-only interaction lists, so every label is `1`. Supply your own negatives. |
|
|
| `labels = -1` marks rows that cannot be scored: autoactivators, failed tests, and clones that failed sequence confirmation. They are retained rather than dropped so nothing is silently lost. Filter with `ds.filter(lambda x: x["labels"] >= 0)`. |
|
|
| ## Usage |
|
|
| ```python |
| from datasets import load_dataset |
| |
| # The AI-adjudicated benchmark |
| ds = load_dataset("GleghornLab/CCSB-AI-Interactome", split="afrf_y2h_human") |
| ds = ds.filter(lambda x: x["labels"] >= 0) # 3,318 scorable pairs |
| |
| # The yeast reference interactome |
| yeri = load_dataset("GleghornLab/CCSB-AI-Interactome", split="yeri") |
| ``` |
|
|
| ## Caveats |
|
|
| - **Y2H negatives are not verified non-interactions.** The assay recovers roughly 20 to 30% of scPRS-v2 positives, so a `Negative` means "not detected in this assay" and not "these proteins do not interact." Treat `afrf_y2h_*` as a Y2H-verifiability benchmark, not a ground-truth interaction benchmark. |
| - **Yeast is well represented in common PPI training corpora** (STRING, BioGRID). Any evaluation on the yeast splits needs a homology or cluster-level leakage control against the model's training set. The `novel` column on `yeri` marks the 1,446 rows that were strictly novel at publication and are the least likely to be memorized. |
| - **`yeri` and `prs_rrs_human` contain both-orientation rows.** `yeri` has 1,970 rows over 1,910 unique unordered pairs, matching the paper's reported 1,910 PPIs; `prs_rrs_human` has 729 rows over 590 unique pairs. Deduplicate on a sorted `(NameA, NameB)` key if you need one row per pair. |
| - **`mappit_result` and `gpca_result` are a pair-level collapse** of the assay-level table, scoring a pair positive if any tested configuration was positive. This does not exactly reproduce the per-assay counts in the paper's Figure 2a, which applies additional quality control that is not recoverable from the released tables. Use the `orthogonal_assays` split to recompute under a different rule. |
| - **10 rows lack sequences.** Four human accessions referenced by the source tables are now inactive in UniProt (`A0A0C4DGZ8`, `O43930` and `Q8WV35` deleted, `P01562` demerged). Their rows are retained with empty `SeqA` / `SeqB`. |
|
|
| ## Provenance |
|
|
| Sequences were resolved from UniProt reference proteomes `UP000002311` (*S. cerevisiae* S288C) and `UP000005640` (*H. sapiens*), with per-identifier lookups for entries outside those proteomes. Yeast ORF names were matched on the UniProt ordered locus name field. |
|
|
| ## License and citation |
|
|
| Source Supplementary Data are distributed under CC BY 4.0 as part of the open access article, and this derived dataset carries the same license. Cite the original paper: |
|
|
| ```bibtex |
| @article{lambourne2026interactome, |
| title = {Experimental assessment of AI-based interactome mapping}, |
| author = {Lambourne, Luke and Yadav, Anupama and Wang, Yang and others}, |
| journal = {Nature Communications}, |
| volume = {17}, |
| number = {1}, |
| pages = {4894}, |
| year = {2026}, |
| doi = {10.1038/s41467-026-70942-x} |
| } |
| ``` |
|
|
| The yeast interaction maps are also browsable at the [Yeast Interactome Portal](https://yeast.interactome-atlas.org/). |
|
|
