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docs: clarify TargetID data inputs #15

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15 changes: 15 additions & 0 deletions README.md
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Expand Up @@ -348,6 +348,21 @@ python main.py --task targetID --scfm TranscriptFormer --disease ss
python main.py --task targetID --disease blastoma --scfm PINNACLE --sample-seed 44
```

TargetID evaluation files are loaded from:

```text
evaluation/
targetID/
source/targetid-<disease>-<seed>.csv
evaluation_samples/targetid-<disease>-query-<seed>.csv
```

The source CSVs include `disease`, `celltype`, `candidate_genes`, and `y`.
The query CSVs add `user_question` and `full_query` prompts generated from
those inputs. Disease-specific embeddings and processed single-cell resources
are expected to come from MedeaDB and the selected single-cell foundation model
configuration, such as `PINNACLE` or `TranscriptFormer`.

##### Synthetic Lethality Task

```bash
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