Link the public Gaia benchmark notebooks

README.md

@@ -1,5 +1,66 @@
+---
+license: cc-by-nc-4.0
+tags:
+- oncology
+- spatial-biology
+- benchmarks
+---
+
 # Gaia
 
-Gaia is a world model for solid tumor oncology.
+Gaia is a world model for solid-tumor oncology.
+
+## Public benchmark notebooks
+
+The public benchmark release is separated by evaluation scale. Each notebook
+is fully executed, explains every reported score, and links its compact
+evaluation script and input tables.
+
+- **[Cohort-level benchmarks](https://github.com/alunalabs/gaia/blob/main/01_cohort_level_benchmarks.ipynb):** drug perturbation priors, the complete 44-row trial-ORR source ledger, direct predicted-versus-observed ORR comparisons, and controls.
+- **[Patient-level benchmarks](https://github.com/alunalabs/gaia/blob/main/02_patient_level_benchmarks.ipynb):** the current CRC and cSCC patient-response scores, ROC AUC evaluation, exact label controls, and CRC measured on-treatment biology.
+- **[Biology-level benchmarks](https://github.com/alunalabs/gaia/blob/main/03_biology_level_benchmarks.ipynb):** the 289-row BioBench protocol, exact KO/OE scoring rules, row-family inventory, and KO gene-direction audit.
+
+The complete benchmark package is in the
+**[public Gaia GitHub repository](https://github.com/alunalabs/gaia)**.
+
+## Released results
+
+| Evaluation | Result |
+| --- | --- |
+| Cohort ORR, 44 disease–drug rows | Pearson 0.650; Spearman 0.594; MAE 10.25 ORR percentage points |
+| CRC pretreatment response, 11 patients | ROC AUC 0.800 |
+| cSCC pretreatment response, 12 patients | ROC AUC 0.778 |
+| CRC measured on-treatment biology, 11 patients | Best descriptive mean cosine 0.304 at rollout step 4 |
+| BioBench sender knockout | 257/289 direction passes (88.9%) |
+| BioBench sender overexpression | 257/281 scoreable direction passes (91.5%); 8 rows not applicable |
+| BioBench KO gene-direction audit | 0/173 audited ligand rows had every observed pathway gene decrease; median fraction decreasing 61.9% |
+
+BioBench contains 183 ligand–receptor pathway rows and 106 regional
+tissue-program rows. The separate per-gene audit is available for 173 ligand
+rows. It rules out an all-pathway-genes-down explanation on those rows, not all
+possible global-shift confounding; 10 ligand rows and the 106 regional rows do
+not have the same archived gene-level audit.
+
+## Reproduction boundary
+
+The GitHub release reproduces metrics, controls, tables, and figures from
+compact exported benchmark data. A public model-adapter runner owns the cohort,
+patient, and BioBench orchestration and score construction; the actual model,
+weights, tissue loader, and encoder remain behind the adapter. The included
+released-table adapter is explicitly a deterministic smoke test, not fresh
+inference. The repository contains no training code.
+
+This Hugging Face repository currently contains the project card only; model
+weights are not currently published here.
+
+The released benchmarks are research evaluations, not prospective clinical
+validation or a clinical decision system.
+
+## License
+
+Repository-authored release material is available under
+[CC BY-NC 4.0](https://github.com/alunalabs/gaia/blob/main/LICENSE). Commercial
+use is not permitted under that license. Underlying publications, study
+records, databases, and source datasets retain their own terms.
 
 Project overview: https://blog.alunadata.com/