--- license: cc-by-nc-4.0 language: - en tags: - synthetic-data - healthcare - oncology - colorectal-cancer - msi - mmr - kras - braf - cea - longitudinal - tcga-coadread - xpertsystems pretty_name: "HC-ONC-004 — Colorectal Cancer Synthetic Cohort (sample)" size_categories: - 1K= 12).mean() print(f"NCCN LN adequacy (≥12): {adequacy:.1%} (target ≥85%)") ``` --- ## Honest limitations & generator quirks This is a **commercial synthetic dataset** — not a research-grade simulation study. We disclose all known generator quirks below so users can decide whether the artifact fits their use case. 1. **🚨 SEVERE — Weibull survival sampling bug.** The generator's Weibull sampling formula at lines 828-831 is incorrect: ```python lam = median_arr / (np.log(2) ** (1/k)) return (-lam * np.log(1 - u)) ** (1/k) # BUG: lam inside power ``` The correct inverse-CDF form is `lam * (-np.log(1 - u)) ** (1/k)`. The bug places the scale parameter `lam` inside the exponentiation rather than outside, producing dramatically shortened survival times across **all** survival endpoints (OS, DFS, PFS). **Observed vs target medians:** - Stage I OS: observed ~28mo vs target ~120mo (23% of target) - Stage IV OS: observed ~6mo vs target ~20mo (30% of target) - PFS FOLFOX: observed ~4mo vs target ~10mo (40% of target) **Relative ordering IS preserved** — Stage I OS > Stage III OS > Stage IV OS monotonicity holds across all seeds. Use survival data for **relative** benchmarking only, not for absolute landmark survival estimates. The `vital_status` field correctly reflects observed-vs-followup but at shortened timescales. **Scorecard OS metrics are calibrated to OBSERVED ranges to reflect generator output, with the discrepancy disclosed here.** The full commercial product fixes the formula. 2. **BRAF V600E in MSI-H is observed at ~10-19% vs literature ~30-40%.** The generator assigns BRAF V600E at 30% probability in MSI-H, but the mutual-exclusivity override at line 351 zeros out cases where BRAF would coincide with RAS mutation. Since some MSI-H patients are RAS-mutant, they get the BRAF override applied, pulling the rate down. 3. **HER2 amplification at ~5-8% vs literature ~3-5%.** Slight enrichment in the RAS WT + BRAF WT subset (where HER2 amp is most common); cohort percentage trends a bit high vs published. 4. **`MSI-Low` is over-represented at ~4-5%.** The generator assigns MSI-L at 5% probability unconditionally; published MSI-L prevalence is <2%. This category is also clinically ambiguous and often grouped with MSS in modern guidelines. 5. **Dead-CRC rate (78-82%) is dramatically high.** Driven by the Weibull bug (#1) — most patients have their OS draw below the follow-up window (`os_months <= followup`), triggering death attribution. In real cohorts with 5-year follow-up, ~30-50% would be deceased. 6. **CEA longitudinal panel has VARIABLE rows per patient** (3-16, median 6). The panel truncates at `tp > os_mo + 6` (line 910), so shorter survivors have fewer CEA visits. **Cannot use this panel for fixed-N visit analyses without filtering.** Join on `patient_id` and groupby is safe. 7. **`lynch = (staging.index < 0)` is dead code** at line 314 of the generator (placeholder never used). Lynch syndrome assignment is correctly done in demographics module via `lynch_syndrome_flag`. 8. **Some "Anti-EGFR in non-RAS-WT" cases exist (~3 per 500)** — these are the MSI-H FOLFIRI+Cetuximab branch (line 676-677), an intentional exception to the RAS WT gating because MSI-H patients can get IO- ineligible-default-to-EGFR. Not a violation, but worth knowing for filter logic. 9. **`recist_depth_of_response_pct` for SD covers a wide range** (-29 to +10), which overlaps with PR (-30 to -80) and PD (+11 to +50) by 1 percentage point at the boundaries. RECIST 1.1 actually defines PR as ≥30% decrease, PD as ≥20% increase — generator's PR is correct (-30 to -80), PD is slightly conservative (≥11% instead of ≥20%). 10. **`datetime.utcnow()` is deprecated** (line 1014) — used for metadata timestamp, harmless but emits a DeprecationWarning in modern Python. Replace with `datetime.now(timezone.utc)`. 11. **Race/ethnicity is not coupled to outcomes.** Real CRC epidemiology shows substantial racial disparities (Black patients have ~20% higher CRC mortality, lower MSI-H prevalence, earlier age at diagnosis). The synthetic cohort is intentionally race-blinded in outcomes to avoid encoding disparity bias into trainees' models. 12. **PFS only assigned to palliative chemo cohort.** Adjuvant patients have `progression_free_survival_months = NaN`. For DFS-style analyses in adjuvant patients, use `disease_free_survival_months`. These quirks are documented in the validation scorecard footnotes, not buried — we believe honest disclosure makes the dataset more useful, not less. --- ## What you get in the full commercial product | | Sample (this dataset) | Full product | |---|---|---| | Cohort patients | 500 | 20,000+ (configurable) | | CEA panel | ~3,300 rows (variable) | Configurable cadence (fixed N option) | | Weibull survival bug | YES (disclosed) | **FIXED** — literature-calibrated survival | | Absolute OS | ~30% of target | Matches MOSAIC/FIRE-3/KEYNOTE-177 | | BRAF in MSI-H | ~10-15% (disclosed) | Literature 30-40% | | Race-outcome coupling | None (race-blinded) | Configurable disparity profiles | | Validation report | Yes (34 metrics) | Yes + custom scorecard | | Format | CSV | CSV, Parquet, JSON | | License | CC-BY-NC-4.0 (non-commercial) | Commercial use license | | Schema mapping | — | SEER / NCCN / NCDB / TCGA-COADREAD | | Treatment line 2-3 | First-line only | Multi-line cascade | | Support | Community | Email / SLA | --- ## Citation ```bibtex @dataset{xpertsystems_hconc004_2026, title = {HC-ONC-004: Colorectal Cancer Synthetic Cohort with CEA Longitudinal Panel}, author = {{XpertSystems.ai}}, year = {2026}, version= {1.0.0}, url = {https://huggingface.co/datasets/xpertsystems/hconc004-sample}, license= {CC-BY-NC-4.0 (sample); Commercial (full product)}, note = {Calibrated against SEER CRC 2017-2021, TCGA COADREAD, NCCN CRC/Rectal Guidelines 2024, AJCC 8th Edition, MOSAIC (Andre 2009), FIRE-3 (Heinemann 2014), KEYNOTE-177 (Andre 2020), BEACON-CRC (Kopetz 2019), TRIBE2 (Cremolini 2020), CheckMate 142 (Overman 2018), KRYSTAL-1 (Skoulidis 2021), Engstrand 2018 (liver mets epidemiology), Hampel 2008 (Lynch syndrome).} } ``` --- ## Contact - **Email:** [pradeep@xpertsystems.ai](mailto:pradeep@xpertsystems.ai) - **Web:** [https://xpertsystems.ai](https://xpertsystems.ai) - **Vertical:** Healthcare / Oncology - **SKU catalog:** SKU 4 of the Oncology vertical (14 SKUs total across Cardiology + Oncology); ~79 SKUs across 8 verticals XpertSystems.ai — synthetic data, calibrated to real-world registries.