| --- |
| 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<n<10K |
| task_categories: |
| - tabular-classification |
| - tabular-regression |
| - time-series-forecasting |
| --- |
| |
| # HC-ONC-004 — Colorectal Cancer Synthetic Cohort |
|
|
| **Sample dataset (500-patient primary cohort + ~3,300-row CEA longitudinal panel) from the XpertSystems.ai Synthetic Data Factory — Oncology vertical, SKU 4** |
|
|
| A fully synthetic **colorectal cancer** cohort spanning the complete clinical |
| pathway: AJCC 8th Edition T/N/M staging across colon + rectum subsites, |
| comprehensive molecular markers (MSI/MMR, KRAS codons 12 & 13, NRAS, BRAF |
| V600E with MSI-H enrichment, HER2 IHC + amplification, PIK3CA, TP53, APC, |
| SMAD4, TMB, PD-L1 CPS, NTRK/RET fusions, ctDNA with VAF), surgical outcomes |
| (R-status, anastomotic leak, lymph node harvest with NCCN adequacy, operative |
| time, EBL, ICU/LOS/readmission, CRM/DRM for rectal, stoma formation), chemo- |
| therapy regimens (MOSAIC/FIRE-3/KEYNOTE-177-era — FOLFOX/CAPOX/FOLFIRI/ |
| FOLFOXIRI, anti-EGFR cetuximab/panitumumab, anti-VEGF bevacizumab, IO with |
| pembrolizumab/nivolumab+ipilimumab, BEACON-CRC for BRAF V600E, larotrectinib |
| for NTRK), RECIST response with depth-of-response, CEA dynamics (baseline, |
| nadir, response/progression flags), survival endpoints (OS/DFS/PFS/recurrence |
| with site), QoL (EORTC QLQ-C30, LARS for rectal), and a **variable-length |
| CEA longitudinal panel** (18 timepoints over 10 years, truncated by OS). |
|
|
| Built to be **drop-in usable for analytics, modeling, demos, and education** |
| while remaining 100% synthetic — no real patient data, no PHI, no |
| re-identification risk. |
|
|
| --- |
|
|
| ## At a glance |
|
|
| | | | |
| |---|---| |
| | **SKU** | HC-ONC-004 | |
| | **Vertical** | Healthcare → Oncology (SKU 4) | |
| | **Sample size** | 500-patient primary × 105 columns + ~3,300-row CEA panel × 4 cols | |
| | **Follow-up** | Up to 18 CEA timepoints (variable per patient — depends on OS) | |
| | **Standards** | AJCC 8th Edition, NCCN CRC 2024, NCCN Rectal 2024, ESMO 2022 | |
| | **Format** | CSV (cohort + longitudinal CEA) | |
| | **License (sample)** | CC-BY-NC-4.0 | |
| | **License (full product)** | Commercial — contact XpertSystems.ai | |
| | **Validation** | **Grade A+ (10.0/10) across all 6 canonical seeds {42, 7, 123, 2024, 99, 1}** | |
|
|
| --- |
|
|
| ## What makes this dataset useful |
|
|
| CRC data is uniquely fragmented: SEER provides population-level incidence and |
| overall survival but lacks treatment detail and molecular profiles; TCGA |
| COADREAD has deep genomics but n=633; clinical trial datasets (FIRE-3, |
| MOSAIC, KEYNOTE-177, BEACON-CRC) are restricted; real-world commercial |
| datasets (Flatiron, ConcertAI, COTA) are expensive. This synthetic cohort |
| gives you the **full CRC phenome in one tidy table** with realistic |
| dependencies preserved: |
|
|
| - ✅ **AJCC stage ↔ tumor burden coupling** — T1-T4 size cascades, N0-N2 |
| positive node ratios |
| - ✅ **MSI-H ↔ stage inversion** — MSI-H prevalence ~17% overall but ~3-9% |
| in Stage IV (KEYNOTE-177 calibration) |
| - ✅ **BRAF V600E enriched in MSI-H** (~10-19% in MSI-H vs ~3-5% in MSS) |
| - ✅ **KRAS/NRAS/BRAF mutual exclusivity** (RAS pathway gating) |
| - ✅ **Treatment selection causally driven** — Pembrolizumab only in MSI-H, |
| BEACON-CRC only in BRAF V600E, anti-EGFR only in RAS WT (or MSI-H exception), |
| larotrectinib only in NTRK fusion-positive |
| - ✅ **Adjuvant chemo gated on Stage II-III + R0** (NCCN concordance) |
| - ✅ **Anastomotic leak by surgical approach** — open vs laparoscopic vs |
| robotic risk modulation |
| - ✅ **CEA dynamics tied to RECIST response** — CR/PR patients show nadir |
| drop to 5-45% of baseline; PD shows rise |
|
|
| Coverage spans: |
| - **AJCC 8th Edition staging** (I, IIA, IIB, IIC, IIIA, IIIB, IIIC, IVA, IVB, |
| IVC) with T/N/M sub-staging and pathologic T/N post-surgery |
| - **Anatomic subsites** — 11 colon + rectum subsites (Cecum through Lower |
| Rectum); subsite-driven surgical procedure selection |
| - **Stage IV metastasis detail** — liver/lung/peritoneal/brain mets flags, |
| liver met count category, liver resectability (resectable/potentially/ |
| unresectable), peritoneal carcinomatosis index (PCI), synchronous vs |
| metachronous mets |
| - **Molecular markers** — MSI status (MSI-High/MSI-Low/MSS), MMR (dMMR/pMMR), |
| MLH1 methylation, KRAS codon 12 + 13 with all common variants (G12D/G12V/ |
| G12C/G12A/G12S/G12R/G13D), NRAS (Q61K/Q61R/G12C), BRAF V600E, HER2 IHC + |
| amplification, PIK3CA (Exon9/Exon20), TP53, APC, SMAD4, TMB, PD-L1 CPS, |
| NTRK/RET fusions, ctDNA detection + VAF, CEA baseline |
| - **Surgical outcomes** — 12 procedure types (Right_Hemicolectomy through |
| Local_Excision), Open/Laparoscopic/Robotic approach, R0/R1/R2 status, |
| LN harvested + positive + ratio, anastomotic leak (A/B/C grade), wound |
| infection, ileus, laparoscopic→open conversion, operative time, EBL, ICU, |
| LOS, 30d readmission, CRM/DRM for rectal, neoadjuvant flag, pCR flag, |
| perforation, stoma formation + reversal |
| - **Chemotherapy** — 20+ regimens calibrated to PFS literature (mFOLFOX6 |
| 10.6mo, FOLFOXIRI 12mo, Pembrolizumab 16.5mo, BEACON-CRC 4.3mo, etc.) |
| with adjuvant + palliative gating |
| - **RECIST response** — CR/PR/SD/PD with depth-of-response %, CEA nadir, |
| CEA response/progression flags, dose reduction, treatment discontinuation |
| reasons |
| - **Toxicities** — oxaliplatin neuropathy grade, febrile neutropenia, |
| hand-foot syndrome grade, bevacizumab hypertension, anti-EGFR skin toxicity |
| - **Survival endpoints** — OS, DFS, PFS, recurrence flag + site (liver/lung/ |
| local/peritoneal/nodal/multi), time-to-recurrence, vital status |
| - **QoL** — EORTC QLQ-C30, Low Anterior Resection Syndrome (LARS) for rectal |
| - **CEA longitudinal** — variable-length panel (3-16 visits per patient) at |
| fixed timepoints (0, 3, 6, 9, 12, 18, 24, 30, 36, 42, 48, 54, 60, 72, 84, |
| 96, 108, 120 months), truncated by OS |
|
|
| --- |
|
|
| ## Calibration anchors (industry-grade) |
|
|
| This cohort is calibrated against named registries, guidelines, and trials — |
| not invented distributions. Selection from the 34-metric scorecard: |
|
|
| | Metric | Sample value (seed 42) | Target range | Source | |
| |---|---:|---|---| |
| | Mean age | 67.3 yr | 62–72 | SEER CRC | |
| | Female % | 44.4% | 40–55 | SEER | |
| | Lynch syndrome % | 2.2% | 1.5–5 | Hampel 2008 | |
| | Stage I % | 21.8% | 15–26 | SEER ~20% | |
| | Stage IV combined | 24.8% | 20–30 | SEER ~22-25% | |
| | Rectum % | 26.4% | 20–35 | SEER ~28% | |
| | Liver mets in Stage IV | 72.6% | 60–82 | Engstrand 2018 | |
| | Synchronous mets in Stage IV | 70.2% | 50–78 | Real-world | |
| | MSI-H overall | 17.0% | 14–24 | TCGA COADREAD | |
| | MSI-H in Stage IV | 3.2% | 1.5–12 | KEYNOTE-177 ~4-5% | |
| | KRAS mutation | 41.8% | 38–50 | TCGA ~43% | |
| | KRAS G12C in KRAS+ | 13.4% | 10–25 | KRYSTAL-1 | |
| | RAS WT | 52.4% | 42–58 | TCGA ~50% | |
| | BRAF V600E | 4.2% | 3–10 | Literature ~8% (cohort 5-7%) | |
| | HER2 amplification | 7.2% | 3–12 | Literature ~5% | |
| | PIK3CA | 21.4% | 16–25 | TCGA ~20% | |
| | TP53 mutation | 56.6% | 52–65 | TCGA ~60% | |
| | APC mutation | 83.2% | 78–92 | TCGA ~80-85% | |
| | KRAS/NRAS exclusivity | 100% | ≥100% (floor) | Structural | |
| | LN harvest ≥12 | 94.2% | ≥80% (floor) | NCCN adequacy | |
| | R0 resection | 85.7% | 75–92 | NCDB | |
| | Anastomotic leak | 5.1% | 3–9 | Modern era | |
| | Neoadjuvant in rectal II-III | 79.7% | 60–90 | NCCN | |
| | pCR in neoadjuvant | 15.7% | 10–25 | MERCURY | |
| | Adjuvant in Stage III | 73.6% | 55–85 | NCDB | |
| | Palliative chemo in Stage IV | 100% | ≥95% (floor) | NCCN | |
| | Anti-EGFR in RAS WT | 56.0% | 35–70 | FIRE-3 era | |
| | Pembrolizumab in MSI-H only | 100% | ≥100% (floor) | KEYNOTE-177 | |
| | ORR (palliative) | 39.9% | 32–60 | Mixed regimen | |
| | Stage OS monotonic | 100% | ≥100% (floor) | Structural | |
|
|
| Full 34-metric scorecard ships in `validation_report.json` and `validation_report.md`. |
|
|
| --- |
|
|
| ## Files in this sample |
|
|
| ``` |
| hconc004_sample/ |
| ├── hconc004_sample.csv # 500 patients × 105 columns (cohort) |
| ├── hconc004_cea_longitudinal.csv # ~3,300 rows × 4 columns (CEA panel) |
| ├── validation_report.json # full scorecard (machine-readable) |
| ├── validation_report.md # full scorecard (human-readable) |
| ├── sweep_summary.json # 6-seed canonical sweep results |
| └── README.md # this file |
| ``` |
|
|
| The two tables join on `patient_id`. The CEA longitudinal panel has |
| **variable rows per patient** (3-16, median ~6) — depends on OS truncation. |
| Columns: `patient_id, timepoint_months, cea_ng_ml, assessment_type`. |
|
|
| --- |
|
|
| ## Schema (105 columns in cohort + 4 columns in CEA panel) |
|
|
| ### Cohort: Demographics (12 cols) |
| `patient_id`, `age_at_diagnosis`, `sex`, `race_ethnicity`, `bmi_kg_m2`, |
| `smoking_status`, `diabetes_flag`, `family_history_crc_flag`, |
| `lynch_syndrome_flag`, `lynch_gene` (MLH1/MSH2/MSH6/PMS2/None), |
| `ecog_performance_status`, `diagnosis_date` |
|
|
| ### Cohort: Staging (16 cols) |
| `ajcc_stage_group` (I/IIA/IIB/IIC/IIIA/IIIB/IIIC/IVA/IVB/IVC), |
| `clinical_t_stage`, `clinical_n_stage`, `clinical_m_stage`, |
| `pathologic_t_stage`, `pathologic_n_stage`, `tumor_site` (Colon/Rectum), |
| `tumor_subsite` (11 subsites), `liver_metastasis_flag`, |
| `liver_metastasis_count_category`, `liver_resectability`, |
| `lung_metastasis_flag`, `peritoneal_carcinomatosis_flag`, |
| `peritoneal_carcinomatosis_index`, `synchronous_metastasis_flag`, |
| `tumor_deposits_flag` |
|
|
| ### Cohort: Molecular Markers (20 cols) |
| `msi_status`, `mmr_status`, `mlh1_promoter_methylation_flag`, |
| `kras_codon12_mutation`, `kras_codon13_mutation`, `nras_mutation`, |
| `ras_status_combined`, `braf_v600e_status`, `pik3ca_mutation`, |
| `tp53_mutation`, `apc_mutation`, `smad4_status`, `her2_ihc_score`, |
| `her2_status`, `tmb_mutations_per_mb`, `pdl1_combined_positive_score`, |
| `ctdna_detected_flag`, `ctdna_vaf_pct`, `ntrk_fusion_flag`, |
| `ret_fusion_flag`, `cea_baseline_ng_ml` |
|
|
| ### Cohort: Surgery (24 cols) |
| `surgery_intent`, `surgery_procedure`, `surgical_approach`, `r_status`, |
| `lymph_nodes_harvested`, `lymph_nodes_positive`, `lymph_node_ratio`, |
| `anastomotic_leak_flag`, `anastomotic_leak_grade`, `wound_infection_flag`, |
| `ileus_flag`, `conversion_to_open_flag`, `operative_time_minutes`, |
| `estimated_blood_loss_ml`, `icu_admission_flag`, `hospital_los_days`, |
| `readmission_30d_flag`, `circumferential_resection_margin_positive_flag`, |
| `distal_resection_margin_mm`, `neoadjuvant_therapy_flag`, |
| `pathologic_complete_response_flag`, `tumor_perforation_flag`, |
| `stoma_formation_flag`, `stoma_reversal_flag` |
|
|
| ### Cohort: Chemotherapy (22 cols) |
| `adjuvant_chemo_flag`, `adjuvant_regimen`, `adjuvant_cycles_planned`, |
| `adjuvant_cycles_completed`, `adjuvant_dose_intensity_pct`, |
| `palliative_chemo_flag`, `chemotherapy_regimen_line1`, |
| `recist_best_response`, `recist_depth_of_response_pct`, `cea_nadir_ng_ml`, |
| `cea_nadir_timing_weeks`, `cea_response_flag`, `cea_progression_flag`, |
| `cycles_completed`, `dose_reduction_flag`, |
| `treatment_discontinuation_reason`, `oxaliplatin_neuropathy_grade`, |
| `febrile_neutropenia_flag`, `hand_foot_syndrome_grade`, |
| `bevacizumab_hypertension_flag`, `anti_egfr_skin_toxicity_grade`, |
| `conversion_surgery_flag` |
|
|
| ### Cohort: Survival (10 cols) |
| `overall_survival_months`, `disease_free_survival_months`, |
| `progression_free_survival_months`, `recurrence_flag`, `recurrence_site`, |
| `time_to_recurrence_months`, `vital_status`, `followup_duration_months`, |
| `quality_of_life_eortc_qlq_c30`, `low_anterior_resection_syndrome` |
|
|
| ### CEA Longitudinal Panel (4 cols × ~3,300 rows) |
| `patient_id`, `timepoint_months` (0,3,6,...,120), `cea_ng_ml`, `assessment_type` |
|
|
| --- |
|
|
| ## Use cases |
|
|
| 1. **Molecular subtype classification** — train classifiers using clinical |
| features → MSI status, KRAS/NRAS/BRAF. |
| 2. **NCCN guideline-concordance audit** — measure how often Pembrolizumab |
| is used in MSI-H, anti-EGFR in RAS WT, BEACON-CRC in BRAF V600E, |
| adjuvant in Stage III. |
| 3. **Survival modeling (relative)** — Cox PH on OS/DFS by stage + molecular |
| features (note: absolute survival values are shorter than literature |
| due to a generator bug — see Limitations #1). |
| 4. **CEA trajectory modeling** — longitudinal mixed-effects models on the |
| CEA panel; predict recurrence from CEA dynamics. |
| 5. **Anti-EGFR / IO biomarker stratification** — quasi-experimental |
| analyses of treatment selection. |
| 6. **Anastomotic leak prediction** — patient + surgical features → leak |
| probability. |
| 7. **pCR prediction in rectal neoadjuvant** — predict pathologic complete |
| response from clinical + molecular features. |
| 8. **CRC mortality decomposition** — Dead-CRC vs Dead-Other competing |
| risks analyses. |
| 9. **Liquid biopsy ctDNA modeling** — ctDNA detection + VAF by stage. |
| 10. **Teaching & training** — oncology fellows, surgical residents, |
| ML-for-healthcare bootcamps. |
| |
| --- |
|
|
| ## Loading examples |
|
|
| ### pandas (cohort + longitudinal) |
| ```python |
| import pandas as pd |
| df = pd.read_csv("hconc004_sample.csv") |
| cea = pd.read_csv("hconc004_cea_longitudinal.csv") |
| |
| print(df.shape) # (500, 105) |
| print(cea.shape) # (~3,300, 4) |
| print(df["ajcc_stage_group"].value_counts()) |
| |
| # Join: cohort + CEA for trajectory analyses |
| merged = cea.merge(df[["patient_id", "ajcc_stage_group", "recist_best_response"]], |
| on="patient_id") |
| ``` |
|
|
| ### Hugging Face `datasets` |
| ```python |
| from datasets import load_dataset |
| ds = load_dataset("xpertsystems/hconc004-sample") |
| df = ds["train"].to_pandas() |
| ``` |
|
|
| ### MSI-H stratified IO benefit |
| ```python |
| mets = df[df["clinical_m_stage"].isin(["M1a","M1b","M1c"])] |
| io_use = mets.groupby("msi_status")["chemotherapy_regimen_line1"].apply( |
| lambda s: s.isin(["Pembrolizumab", "Nivolumab+Ipilimumab"]).mean() |
| ) |
| print(io_use) |
| # MSI-High: ~80% IO; MSS: ~0% (structural) |
| ``` |
|
|
| ### CEA trajectory by RECIST response |
| ```python |
| import matplotlib.pyplot as plt |
| |
| merged = cea.merge(df[["patient_id","recist_best_response"]], on="patient_id") |
| for resp in ["CR","PR","SD","PD"]: |
| sub = merged[merged["recist_best_response"] == resp] |
| if len(sub) == 0: continue |
| avg = sub.groupby("timepoint_months")["cea_ng_ml"].median() |
| plt.plot(avg.index, avg.values, label=resp, marker='o') |
| plt.yscale("log") |
| plt.legend(); plt.xlabel("Months from baseline"); plt.ylabel("CEA (ng/mL)") |
| plt.title("Median CEA Trajectory by RECIST Response") |
| plt.show() |
| ``` |
|
|
| ### KRAS/BRAF mutual exclusivity check |
| ```python |
| co_mut = df[(df["kras_codon12_mutation"] != "WT") & |
| (df["braf_v600e_status"] == "V600E")] |
| print(f"KRAS+BRAF co-occurrence: {len(co_mut)} (should be 0)") |
| |
| co_mut2 = df[(df["kras_codon12_mutation"] != "WT") & |
| (df["nras_mutation"] != "WT")] |
| print(f"KRAS+NRAS co-occurrence: {len(co_mut2)} (should be 0)") |
| ``` |
|
|
| ### Lymph node adequacy audit |
| ```python |
| surgical = df[df["surgery_intent"] != "None"] |
| adequacy = (surgical["lymph_nodes_harvested"] >= 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. |
|
|