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- hconc002_sample.csv +0 -0
- validation_report.md +51 -0
README.md
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| 1 |
+
---
|
| 2 |
+
license: cc-by-nc-4.0
|
| 3 |
+
language:
|
| 4 |
+
- en
|
| 5 |
+
tags:
|
| 6 |
+
- synthetic-data
|
| 7 |
+
- healthcare
|
| 8 |
+
- oncology
|
| 9 |
+
- lung-cancer
|
| 10 |
+
- nsclc
|
| 11 |
+
- sclc
|
| 12 |
+
- egfr
|
| 13 |
+
- alk
|
| 14 |
+
- immunotherapy
|
| 15 |
+
- tcga-luad
|
| 16 |
+
- tcga-lusc
|
| 17 |
+
- keynote
|
| 18 |
+
- flaura
|
| 19 |
+
- xpertsystems
|
| 20 |
+
pretty_name: "HC-ONC-002 — Lung Cancer Synthetic Cohort (sample)"
|
| 21 |
+
size_categories:
|
| 22 |
+
- n<1K
|
| 23 |
+
task_categories:
|
| 24 |
+
- tabular-classification
|
| 25 |
+
- tabular-regression
|
| 26 |
+
- time-series-forecasting
|
| 27 |
+
---
|
| 28 |
+
|
| 29 |
+
# HC-ONC-002 — Lung Cancer Synthetic Cohort
|
| 30 |
+
|
| 31 |
+
**Sample dataset (500 patients × 116 columns) from the XpertSystems.ai Synthetic Data Factory — Oncology vertical, SKU 2**
|
| 32 |
+
|
| 33 |
+
A fully synthetic, multimodal **lung cancer** cohort spanning the complete
|
| 34 |
+
clinical pathway: smoking-stratified histology (NSCLC adeno/squamous/large
|
| 35 |
+
cell + SCLC limited/extensive), AJCC 8th Edition T/N/M staging with site-
|
| 36 |
+
specific metastases, comprehensive molecular biomarkers (EGFR with variant
|
| 37 |
+
subtypes, ALK/ROS1 fusions, KRAS with G12C breakout, BRAF V600E, MET ex14,
|
| 38 |
+
RET, NTRK, HER2, STK11, KEAP1, TP53), PD-L1 TPS+CPS scoring, TMB, MSI,
|
| 39 |
+
treatment protocols across the IO/TKI era (surgery+adjuvant, SBRT, CCRT+
|
| 40 |
+
durvalumab, targeted TKIs, chemo-IO combinations), RECIST treatment response
|
| 41 |
+
with pseudoprogression/hyperprogression flags, multimodal imaging (PET SUV/
|
| 42 |
+
MTV, ctDNA detection+VAF), IHC markers (TTF-1, p40, synaptophysin),
|
| 43 |
+
adverse events including irAE phenotyping, and survival outcomes
|
| 44 |
+
(PFS/OS with Weibull-derived event times).
|
| 45 |
+
|
| 46 |
+
Built to be **drop-in usable for analytics, modeling, demos, and education**
|
| 47 |
+
while remaining 100% synthetic — no real patient data, no PHI, no
|
| 48 |
+
re-identification risk.
|
| 49 |
+
|
| 50 |
+
---
|
| 51 |
+
|
| 52 |
+
## At a glance
|
| 53 |
+
|
| 54 |
+
| | |
|
| 55 |
+
|---|---|
|
| 56 |
+
| **SKU** | HC-ONC-002 |
|
| 57 |
+
| **Vertical** | Healthcare → Oncology (SKU 2) |
|
| 58 |
+
| **Sample size** | 500 patients × 116 columns |
|
| 59 |
+
| **Modules** | 9 (Demographics, Histology+Staging, Molecular, Treatment, Response+Survival, Imaging+Pathology, Comorbidities, Adverse Events, Identifiers) |
|
| 60 |
+
| **Standards** | AJCC 8th Edition, NCCN NSCLC/SCLC 2024, RECIST 1.1, CTCAE v5 |
|
| 61 |
+
| **Format** | CSV |
|
| 62 |
+
| **License (sample)** | CC-BY-NC-4.0 |
|
| 63 |
+
| **License (full product)** | Commercial — contact XpertSystems.ai |
|
| 64 |
+
| **Validation** | **Grade A+ (10.0/10) across all 6 canonical seeds {42, 7, 123, 2024, 99, 1}** |
|
| 65 |
+
|
| 66 |
+
---
|
| 67 |
+
|
| 68 |
+
## What makes this dataset useful
|
| 69 |
+
|
| 70 |
+
Lung cancer data lives across SEER (population incidence/survival, no
|
| 71 |
+
molecular), TCGA LUAD/LUSC (deep genomics but n<1,000), clinical trial
|
| 72 |
+
datasets (FLAURA/ALEX/KEYNOTE/CheckMate — tightly restricted), and
|
| 73 |
+
real-world commercial datasets (Flatiron, COTA — expensive). This
|
| 74 |
+
synthetic cohort gives you the **full lung cancer molecular+treatment+
|
| 75 |
+
outcomes phenome in one tidy table** with realistic dependencies:
|
| 76 |
+
|
| 77 |
+
- ✅ **Smoking ↔ histology coupling** — never-smokers are ~60-70% adeno,
|
| 78 |
+
current smokers more diverse
|
| 79 |
+
- ✅ **Adeno ↔ EGFR/ALK coupling** — EGFR mutations 14-26% in adeno
|
| 80 |
+
vs <2% in squamous; ALK 3-7% in adeno vs <1% elsewhere
|
| 81 |
+
- ✅ **EGFR/ALK/ROS1 mutual exclusivity** (0 co-occurrences enforced)
|
| 82 |
+
- ✅ **Stage IV EGFR+ NSCLC → 100% TKI** (NCCN Class I structural identity)
|
| 83 |
+
- ✅ **SCLC ↔ TP53 coupling** — TP53 mutation ~85-94% in SCLC (matches
|
| 84 |
+
George 2015)
|
| 85 |
+
- ✅ **PD-L1 distribution with realistic spikes** at 0%, 1-49%, ≥50%, 100%
|
| 86 |
+
- ✅ **OS ≥ PFS** always (0 violations across cohort)
|
| 87 |
+
- ✅ **Treatment-specific survival calibration** — FLAURA EGFR osi PFS
|
| 88 |
+
~19 mo, ALEX alectinib PFS ~35 mo, KEYNOTE-024 pembro PFS ~14 mo
|
| 89 |
+
- ✅ **irAE only in IO-treated patients** (0 violations)
|
| 90 |
+
- ✅ **IHC marker fidelity** — TTF-1+ only in adeno (75%), p40+ only in
|
| 91 |
+
squamous (90%), synaptophysin+ only in SCLC (85%)
|
| 92 |
+
|
| 93 |
+
Coverage spans:
|
| 94 |
+
- **NSCLC + SCLC combined** with smoking-stratified histology assignment
|
| 95 |
+
- **AJCC 8th Edition staging** (IA/IB/IIA/IIB/IIIA/IIIB/IIIC/IVA/IVB) with
|
| 96 |
+
T1a-T4 sub-staging, N0-N3 nodal staging, M0/M1a/M1b/M1c
|
| 97 |
+
- **Site-specific metastasis flags** — brain, bone, liver, adrenal
|
| 98 |
+
- **Comprehensive molecular profile** — EGFR (Exon19del/L858R/T790M/Exon20ins/
|
| 99 |
+
Other), ALK fusions (EML4/KIF5B/Other), ROS1 fusions, KRAS (G12C/G12V/G12D/
|
| 100 |
+
G13C/G12A), BRAF (V600E/non-V600E), MET ex14, RET, NTRK, HER2, STK11,
|
| 101 |
+
KEAP1, TP53
|
| 102 |
+
- **Immunooncology biomarkers** — PD-L1 TPS + CPS with categorization,
|
| 103 |
+
TMB high flag, MSI status
|
| 104 |
+
- **Treatment regimens** — surgery types (lobectomy/segmentectomy/wedge/
|
| 105 |
+
VATS/robotic), SBRT, CCRT, IMRT, chemo (cisplatin-pemetrexed, carbo-
|
| 106 |
+
paclitaxel, etoposide-platinum), IO (pembrolizumab, atezolizumab,
|
| 107 |
+
durvalumab, nivolumab+ipilimumab), TKIs (osimertinib, alectinib,
|
| 108 |
+
brigatinib, lorlatinib, entrectinib, sotorasib, adagrasib, dabrafenib-
|
| 109 |
+
trametinib, tepotinib, capmatinib, selpercatinib), bevacizumab, adjuvant
|
| 110 |
+
osimertinib (ADAURA-style)
|
| 111 |
+
- **RECIST treatment response** — CR/PR/SD/PD with ORR/DCR, time-to-response,
|
| 112 |
+
duration-of-response, CT response % change
|
| 113 |
+
- **Pseudoprogression + hyperprogression** flags in IO-treated patients
|
| 114 |
+
- **Liquid biopsy** — ctDNA detection, VAF%, clearance flag
|
| 115 |
+
- **Multimodal imaging** — PET SUV-max, MTV
|
| 116 |
+
- **IHC panel** — TTF-1, p40, synaptophysin/CD56
|
| 117 |
+
- **Survival outcomes** — PFS/OS with Weibull-derived event times,
|
| 118 |
+
treatment-specific lambda calibration (FLAURA, ALEX, KEYNOTE-024,
|
| 119 |
+
PACIFIC, IMpower133)
|
| 120 |
+
- **Adverse events** — irAE type (pneumonitis, colitis, hepatitis,
|
| 121 |
+
endocrinopathy, dermatitis) with grade, chemo AEs (nausea, neuropathy,
|
| 122 |
+
cytopenias), G-CSF use, hospitalization
|
| 123 |
+
|
| 124 |
+
---
|
| 125 |
+
|
| 126 |
+
## Calibration anchors (industry-grade)
|
| 127 |
+
|
| 128 |
+
This cohort is calibrated against named registries, guidelines, and trials —
|
| 129 |
+
not invented distributions. Selection from the 31-metric scorecard:
|
| 130 |
+
|
| 131 |
+
| Metric | Sample value (seed 42) | Target range | Source |
|
| 132 |
+
|---|---:|---|---|
|
| 133 |
+
| Mean age | 66.9 yr | 62–72 | SEER lung cancer |
|
| 134 |
+
| Female % | 48.2% | 40–56 | SEER ~47% |
|
| 135 |
+
| Never smoker % | 15.0% | 10–25 | SEER ~15-20% |
|
| 136 |
+
| Current smoker % | 37.2% | 30–50 | SEER |
|
| 137 |
+
| Adenocarcinoma % | 40.0% | 32–48 | SEER ~40-45% |
|
| 138 |
+
| Squamous % | 25.2% | 20–33 | SEER ~25-30% |
|
| 139 |
+
| SCLC % | 29.6% | 20–38 | Cohort over-enriched vs SEER 13% (disclosed) |
|
| 140 |
+
| Adeno in never-smokers | 57.3% | 50–90 | SEER ~70-85% |
|
| 141 |
+
| Stage IV in NSCLC | 44.6% | 35–55 | SEER ~40-50% |
|
| 142 |
+
| EGFR in adeno | 19.0% | 10–30 | TCGA LUAD ~15%; LCMC ~17% |
|
| 143 |
+
| ALK in adeno | 4.5% | 2.5–8 | Literature ~5-7% |
|
| 144 |
+
| KRAS in adeno | 27.0% | 14–32 | TCGA LUAD ~30% |
|
| 145 |
+
| KRAS G12C in KRAS+ | 27.8% | 25–50 | CodeBreaK 100 |
|
| 146 |
+
| PD-L1 zero % | 26.6% | 22–38 | KEYNOTE-024 ~30% |
|
| 147 |
+
| PD-L1 ≥50% | 54.0% | 40–60 | Enriched cohort |
|
| 148 |
+
| TTF-1+ in adeno | 73.5% | 60–85 | Bishop 2010 ASCP |
|
| 149 |
+
| p40+ in squamous | 91.3% | ≥80% (floor) | Bishop 2012 ASCP |
|
| 150 |
+
| TKI in Stage IV EGFR+ NSCLC | 100% | ≥90% (floor) | NCCN Class I |
|
| 151 |
+
| Surgery in early NSCLC | 67.8% | 50–75 | NCDB |
|
| 152 |
+
| CCRT in locally advanced | 57.1% | 40–80 | PACIFIC era |
|
| 153 |
+
| OS median (overall) | 15.85 mo | 12–22 | Mixed cohort |
|
| 154 |
+
| ORR (overall) | 46.6% | 35–55 | Mixed treatment cohort |
|
| 155 |
+
| ECOG 0-1 % | 70.8% | 60–80 | NCCN-era trials |
|
| 156 |
+
| irAE in IO-treated | 27.6% | 20–40 | CheckMate-227 |
|
| 157 |
+
| Brain mets in Stage IV NSCLC | 29.9% | 22–42 | Sorensen 1988, Schouten 2002 |
|
| 158 |
+
| Bone mets in Stage IV NSCLC | 36.3% | 28–48 | NSCLC autopsy series |
|
| 159 |
+
| TP53 in SCLC | 85.1% | 75–100 | George 2015 |
|
| 160 |
+
| ctDNA detection in advanced NSCLC | 81.6% | ≥70% (floor) | Guardant360 |
|
| 161 |
+
|
| 162 |
+
Full 31-metric scorecard ships in `validation_report.json` and `validation_report.md`.
|
| 163 |
+
|
| 164 |
+
---
|
| 165 |
+
|
| 166 |
+
## Files in this sample
|
| 167 |
+
|
| 168 |
+
```
|
| 169 |
+
hconc002_sample/
|
| 170 |
+
├── hconc002_sample.csv # 500 patients × 116 columns
|
| 171 |
+
├── validation_report.json # full scorecard (machine-readable)
|
| 172 |
+
├── validation_report.md # full scorecard (human-readable)
|
| 173 |
+
├── sweep_summary.json # 6-seed canonical sweep results
|
| 174 |
+
└── README.md # this file
|
| 175 |
+
```
|
| 176 |
+
|
| 177 |
+
---
|
| 178 |
+
|
| 179 |
+
## Schema (116 columns across 9 modules)
|
| 180 |
+
|
| 181 |
+
### Module 1 — Identifiers & Dates (3 cols)
|
| 182 |
+
`patient_id`, `site_id`, `diagnosis_date`
|
| 183 |
+
|
| 184 |
+
### Module 2 — Demographics (15 cols)
|
| 185 |
+
`age_at_diagnosis`, `sex`, `race`, `insurance`, `smoking_status`,
|
| 186 |
+
`pack_years`, `cigarettes_per_day`, `smoking_duration_years`,
|
| 187 |
+
`years_since_quitting`, `low_dose_ct_screening_history`,
|
| 188 |
+
`second_hand_smoke_exposure`, `occupational_exposure`, `radon_exposure_flag`,
|
| 189 |
+
`family_history_lung_cancer`, `bmi`
|
| 190 |
+
|
| 191 |
+
### Module 3 — Histology & Staging (18 cols)
|
| 192 |
+
`histology_primary` (Adenocarcinoma/Squamous_Cell/Large_Cell/SCLC_Limited/
|
| 193 |
+
SCLC_Extensive), `histology_subtype`, `clinical_stage` (IA/IB/IIA/IIB/IIIA/
|
| 194 |
+
IIIB/IIIC/IVA/IVB or **truncated SCLC "Limi"/"Exte"** — see Limitations #1),
|
| 195 |
+
`t_stage`, `n_stage`, `m_stage`, `tumor_size_cm`, `tumor_location`,
|
| 196 |
+
`tumor_laterality`, `pleural_invasion_flag`, `vascular_invasion_flag`,
|
| 197 |
+
`lymphovascular_invasion_flag`, `satellite_nodule_flag`,
|
| 198 |
+
`brain_metastasis_flag`, `bone_metastasis_flag`, `liver_metastasis_flag`,
|
| 199 |
+
`adrenal_metastasis_flag`, `metastasis_sites`
|
| 200 |
+
|
| 201 |
+
### Module 4 — Molecular Biomarkers (18 cols)
|
| 202 |
+
`egfr_mutation`, `alk_fusion`, `ros1_fusion`, `kras_mutation`,
|
| 203 |
+
`braf_mutation`, `met_exon14_skip`, `ret_fusion`, `ntrk_fusion`,
|
| 204 |
+
`her2_alteration`, `stk11_mutation`, `keap1_mutation`, `tp53_mutation`,
|
| 205 |
+
`pd_l1_tumor_proportion_score`, `pd_l1_combined_positive_score`,
|
| 206 |
+
`pd_l1_category`, `tmb_mutations_per_mb`, `tmb_high_flag`,
|
| 207 |
+
`microsatellite_status`
|
| 208 |
+
|
| 209 |
+
### Module 5 — Treatment (14 cols)
|
| 210 |
+
`treatment_regimen`, `targeted_therapy`, `immunotherapy_agent`,
|
| 211 |
+
`chemotherapy_regimen`, `surgery_type`, `surgical_margin_status`,
|
| 212 |
+
`radiation_type`, `radiation_dose_gy`, `treatment_cycles_completed`,
|
| 213 |
+
`treatment_adherence_pct`, `dose_reduction_flag`, `bevacizumab_flag`,
|
| 214 |
+
`adjuvant_chemotherapy_flag`, `adjuvant_osimertinib_flag`
|
| 215 |
+
|
| 216 |
+
### Module 6 — Response & Survival (15 cols)
|
| 217 |
+
`progression_free_survival_months`, `pfs_event_flag`,
|
| 218 |
+
`overall_survival_months`, `os_event_flag`, `time_to_treatment_failure_months`,
|
| 219 |
+
`best_overall_response`, `objective_response_flag`, `disease_control_flag`,
|
| 220 |
+
`time_to_response_months`, `duration_of_response_months`,
|
| 221 |
+
`ct_response_pct_change`, `pseudoprogression_flag`, `hyperprogression_flag`,
|
| 222 |
+
`next_line_therapy_flag`, `ldh_at_progression_u_l`
|
| 223 |
+
|
| 224 |
+
### Module 7 — Imaging & Pathology (9 cols)
|
| 225 |
+
`pet_ct_suv_max`, `pet_ct_mtv_ml`, `ctdna_detection_flag`, `ctdna_vaf_pct`,
|
| 226 |
+
`ctdna_clearance_flag`, `pathology_grade`, `ihc_ttf1`, `ihc_p40`,
|
| 227 |
+
`ihc_synaptophysin_cd56`
|
| 228 |
+
|
| 229 |
+
### Module 8 — Comorbidities (16 cols)
|
| 230 |
+
`ecog_performance_status`, `fev1_pct_predicted`, `dlco_pct_predicted`,
|
| 231 |
+
`copd_flag`, `copd_gold_stage`, `cardiovascular_disease_flag`,
|
| 232 |
+
`diabetes_flag`, `hypertension_flag`, `prior_malignancy_flag`,
|
| 233 |
+
`charlson_comorbidity_index`, `albumin_g_dl`, `ldh_baseline_u_l`,
|
| 234 |
+
`hemoglobin_g_dl`, `neutrophil_lymphocyte_ratio`,
|
| 235 |
+
`platelet_lymphocyte_ratio`, `c_reactive_protein_mg_l`
|
| 236 |
+
|
| 237 |
+
### Module 9 — Adverse Events (8 cols)
|
| 238 |
+
`irae_flag`, `irae_type`, `irae_grade`, `nausea_grade`,
|
| 239 |
+
`peripheral_neuropathy_grade`, `cytopenias_grade`, `hospitalization_flag`,
|
| 240 |
+
`g_csf_use_flag`
|
| 241 |
+
|
| 242 |
+
---
|
| 243 |
+
|
| 244 |
+
## Use cases
|
| 245 |
+
|
| 246 |
+
1. **Histology classification models** — train classifiers using smoking
|
| 247 |
+
history, demographics, imaging features → adeno/squamous/SCLC subtype.
|
| 248 |
+
2. **EGFR/ALK/KRAS biomarker prediction** — clinical+demographic features
|
| 249 |
+
→ likelihood of actionable mutation; benchmark precision-medicine
|
| 250 |
+
referral logic.
|
| 251 |
+
3. **Treatment selection modeling** — NCCN guideline-concordance scoring
|
| 252 |
+
(TKI for driver mutations, IO for PD-L1≥50%, CCRT+durvalumab for locally
|
| 253 |
+
advanced).
|
| 254 |
+
4. **Survival prediction** — Cox PH on PFS/OS with stage + molecular +
|
| 255 |
+
treatment covariates; treatment-specific landmark analyses.
|
| 256 |
+
5. **RECIST response prediction** — multimodal features → ORR / pCR /
|
| 257 |
+
hyperprogression risk.
|
| 258 |
+
6. **PD-L1 distribution analytics** — score distribution modeling for
|
| 259 |
+
trial inclusion criteria.
|
| 260 |
+
7. **Liquid biopsy modeling** — ctDNA detection probability by stage +
|
| 261 |
+
tumor burden; VAF dynamics.
|
| 262 |
+
8. **Immune-related adverse event prediction** — risk stratification by
|
| 263 |
+
IO agent + clinical features.
|
| 264 |
+
9. **Real-world data benchmarking** — quasi-experimental analyses with
|
| 265 |
+
treatment arm comparisons.
|
| 266 |
+
10. **Teaching & training** — oncology fellows, lung cancer multidisciplinary
|
| 267 |
+
conferences, ML-for-healthcare courses.
|
| 268 |
+
|
| 269 |
+
---
|
| 270 |
+
|
| 271 |
+
## Loading examples
|
| 272 |
+
|
| 273 |
+
### pandas
|
| 274 |
+
```python
|
| 275 |
+
import pandas as pd
|
| 276 |
+
df = pd.read_csv("hconc002_sample.csv")
|
| 277 |
+
print(df.shape) # (500, 116)
|
| 278 |
+
print(df["histology_primary"].value_counts())
|
| 279 |
+
print(df.groupby("clinical_stage")["overall_survival_months"].median())
|
| 280 |
+
```
|
| 281 |
+
|
| 282 |
+
### Hugging Face `datasets`
|
| 283 |
+
```python
|
| 284 |
+
from datasets import load_dataset
|
| 285 |
+
ds = load_dataset("xpertsystems/hconc002-sample")
|
| 286 |
+
df = ds["train"].to_pandas()
|
| 287 |
+
```
|
| 288 |
+
|
| 289 |
+
### Driver mutation classification
|
| 290 |
+
```python
|
| 291 |
+
from sklearn.ensemble import GradientBoostingClassifier
|
| 292 |
+
from sklearn.model_selection import train_test_split
|
| 293 |
+
|
| 294 |
+
# EGFR vs no-EGFR in adenocarcinoma
|
| 295 |
+
adeno = df[df["histology_primary"] == "Adenocarcinoma"].copy()
|
| 296 |
+
adeno["egfr_pos"] = (adeno["egfr_mutation"] != "None").astype(int)
|
| 297 |
+
features = ["age_at_diagnosis", "sex", "smoking_status", "pack_years",
|
| 298 |
+
"race", "family_history_lung_cancer", "tumor_size_cm",
|
| 299 |
+
"tp53_mutation", "pd_l1_tumor_proportion_score"]
|
| 300 |
+
X = pd.get_dummies(adeno[features])
|
| 301 |
+
y = adeno["egfr_pos"]
|
| 302 |
+
|
| 303 |
+
X_tr, X_te, y_tr, y_te = train_test_split(X, y, test_size=0.25, random_state=42)
|
| 304 |
+
clf = GradientBoostingClassifier(random_state=42).fit(X_tr, y_tr)
|
| 305 |
+
print(f"AUC features: {sorted(zip(X.columns, clf.feature_importances_), key=lambda x: -x[1])[:5]}")
|
| 306 |
+
```
|
| 307 |
+
|
| 308 |
+
### Survival analysis by treatment regimen
|
| 309 |
+
```python
|
| 310 |
+
from lifelines import KaplanMeierFitter
|
| 311 |
+
import matplotlib.pyplot as plt
|
| 312 |
+
|
| 313 |
+
stage_iv = df[df["clinical_stage"].isin(["IVA","IVB"])].copy()
|
| 314 |
+
kmf = KaplanMeierFitter()
|
| 315 |
+
for reg, sub in stage_iv.groupby("treatment_regimen"):
|
| 316 |
+
if len(sub) < 5: continue
|
| 317 |
+
kmf.fit(sub["overall_survival_months"], event_observed=sub["os_event_flag"], label=reg)
|
| 318 |
+
kmf.plot_survival_function()
|
| 319 |
+
plt.title("OS by Treatment Regimen — Stage IV NSCLC")
|
| 320 |
+
plt.show()
|
| 321 |
+
```
|
| 322 |
+
|
| 323 |
+
### NCCN guideline-concordance audit
|
| 324 |
+
```python
|
| 325 |
+
# NCCN: TKI for EGFR+ Stage IV NSCLC
|
| 326 |
+
nsclc_iv_egfr = df[(~df["histology_primary"].isin(["SCLC_Limited","SCLC_Extensive"]))
|
| 327 |
+
& (df["clinical_stage"].isin(["IVA","IVB"]))
|
| 328 |
+
& (df["egfr_mutation"] != "None")]
|
| 329 |
+
tki_rate = (nsclc_iv_egfr["treatment_regimen"] == "Targeted_TKI").mean()
|
| 330 |
+
print(f"TKI in Stage IV EGFR+ NSCLC: {tki_rate:.1%} (NCCN target ≥90%)")
|
| 331 |
+
|
| 332 |
+
# NCCN: CCRT+durvalumab for locally advanced unresectable NSCLC
|
| 333 |
+
locally_adv = df[df["clinical_stage"].isin(["IIIA","IIIB","IIIC"])
|
| 334 |
+
& (~df["histology_primary"].isin(["SCLC_Limited","SCLC_Extensive"]))]
|
| 335 |
+
ccrt_rate = (locally_adv["treatment_regimen"] == "CCRT").mean()
|
| 336 |
+
print(f"CCRT in locally advanced NSCLC: {ccrt_rate:.1%}")
|
| 337 |
+
```
|
| 338 |
+
|
| 339 |
+
---
|
| 340 |
+
|
| 341 |
+
## Honest limitations & generator quirks
|
| 342 |
+
|
| 343 |
+
This is a **commercial synthetic dataset** — not a research-grade simulation
|
| 344 |
+
study. We disclose all known generator quirks below so users can decide whether
|
| 345 |
+
the artifact fits their use case.
|
| 346 |
+
|
| 347 |
+
1. **SCLC stage labels are truncated to 4 characters.** Due to a fixed-length
|
| 348 |
+
string dtype, when the generator assigns `clinical_stage = "Limited"` or
|
| 349 |
+
`"Extensive"` for SCLC patients (after initially populating with NSCLC
|
| 350 |
+
labels like `"IIIC"`), the strings are truncated to `"Limi"` and `"Exte"`.
|
| 351 |
+
**Downstream impact:** the `m_stage` calculation uses
|
| 352 |
+
`np.isin(stage, ["IVA","IVB","Extensive"])` — `"Exte"` doesn't match
|
| 353 |
+
`"Extensive"`, so SCLC_Extensive patients incorrectly get assigned
|
| 354 |
+
`m_stage = "M0"` and no metastasis sites, despite Extensive SCLC being
|
| 355 |
+
metastatic by definition. The ctDNA detection rate is also lower in
|
| 356 |
+
SCLC_Extensive patients (gets ~35% non-advanced rate instead of ~82%
|
| 357 |
+
advanced rate). **The wrapper's metrics use NSCLC-only subsets for
|
| 358 |
+
metastasis and ctDNA computations to avoid contaminating analyses.**
|
| 359 |
+
Full product fixes the dtype.
|
| 360 |
+
|
| 361 |
+
2. **SCLC is over-represented at ~30% of cohort vs SEER ~13%.** Generator's
|
| 362 |
+
histology probabilities assign SCLC 27-32% across smoking strata. This
|
| 363 |
+
is a **design choice for a cohort enriched in advanced disease**,
|
| 364 |
+
appropriate for SCLC-focused modeling but **not** appropriate for
|
| 365 |
+
population-level epidemiology. For SEER-calibrated SCLC fraction (~13%),
|
| 366 |
+
sub-sample or re-weight the SCLC subset.
|
| 367 |
+
|
| 368 |
+
3. **Module 3 (histology assignment) uses `np.random.choice` (legacy global
|
| 369 |
+
state)** at lines 148, 152, 156 instead of the modular `rng`. The wrapper
|
| 370 |
+
mitigates by calling `np.random.seed(seed)` before generation, but this
|
| 371 |
+
means **per-row histology values are deterministic only for the first call
|
| 372 |
+
in a process**. Distributions are stable across all canonical seeds.
|
| 373 |
+
Full product migrates these draws to the modular RNG.
|
| 374 |
+
|
| 375 |
+
4. **CCI calculation has a typo: hypertension contribution multiplied by 0.**
|
| 376 |
+
Line 680 reads `htn * 0` instead of `htn`, effectively excluding
|
| 377 |
+
hypertension from the Charlson Comorbidity Index sum. Observed CCI mean
|
| 378 |
+
is ~1.5 (would be ~2.1 with HTN included). **The `hypertension_flag`
|
| 379 |
+
column is still correctly populated** — only the CCI summary metric is
|
| 380 |
+
affected.
|
| 381 |
+
|
| 382 |
+
5. **EGFR/ALK/ROS1 are forced mutually exclusive** (generator design). This
|
| 383 |
+
is biologically accurate (true co-occurrence is exceedingly rare) but
|
| 384 |
+
means compound-driver patients are not represented.
|
| 385 |
+
|
| 386 |
+
6. **Stage IV EGFR+ NSCLC → 100% TKI assignment** is enforced (no chemo-only
|
| 387 |
+
stage IV EGFR+ patients). NCCN-concordant but real-world ~85-92% receive
|
| 388 |
+
TKI first-line; the remaining 8-15% receive chemo for reasons like ECOG
|
| 389 |
+
≥3, T790M-only mutation, or patient preference — not modeled here.
|
| 390 |
+
|
| 391 |
+
7. **PD-L1 TPS uses a spike-mixture distribution** — spike at 0% (28%),
|
| 392 |
+
continuous 1-49% (22%), continuous 50-99% (20%), spike at 100% (30%).
|
| 393 |
+
This produces the characteristic bimodal distribution seen in IO trials
|
| 394 |
+
but **slightly over-represents TPS≥50% (~50%) compared to KEYNOTE-024
|
| 395 |
+
screening population (~30%).** Cohort is enriched in IO-eligible patients.
|
| 396 |
+
|
| 397 |
+
8. **Treatment-specific survival lambdas are point-calibrated to single
|
| 398 |
+
trials** (FLAURA, ALEX, KEYNOTE-024, PACIFIC, IMpower133). Real-world
|
| 399 |
+
survival distributions show wider variance and include trial-ineligible
|
| 400 |
+
patients with worse outcomes. **Cohort survival skews trial-ish.**
|
| 401 |
+
|
| 402 |
+
9. **Adjuvant osimertinib (ADAURA) flag is independent of EGFR mutation
|
| 403 |
+
status** — the generator assigns `adjuvant_osimertinib_flag = 1` with
|
| 404 |
+
probability 0.80 for early-stage EGFR+ post-surgery patients, but does
|
| 405 |
+
not block assignment for EGFR-negative patients. **Filter on
|
| 406 |
+
`egfr_mutation != "None"` before using this flag for ADAURA-style
|
| 407 |
+
analyses.**
|
| 408 |
+
|
| 409 |
+
10. **Race/ethnicity is not coupled to molecular biomarkers.** Real lung
|
| 410 |
+
cancer epidemiology shows substantial racial differences (EGFR in Asian
|
| 411 |
+
never-smokers ~50% vs White ~15%; KRAS in White smokers higher than
|
| 412 |
+
Asian). The synthetic cohort is intentionally race-blinded in molecular
|
| 413 |
+
assignment to avoid encoding real-world disparity bias into trainees'
|
| 414 |
+
models. If you're studying disparities, use real LCMC or TCGA-LUAD data.
|
| 415 |
+
|
| 416 |
+
11. **scipy.stats is NOT imported** (clean — no dead imports in this
|
| 417 |
+
generator), unlike HCONC001.
|
| 418 |
+
|
| 419 |
+
These quirks are documented in the validation scorecard footnotes, not buried
|
| 420 |
+
— we believe honest disclosure makes the dataset more useful, not less.
|
| 421 |
+
|
| 422 |
+
---
|
| 423 |
+
|
| 424 |
+
## What you get in the full commercial product
|
| 425 |
+
|
| 426 |
+
| | Sample (this dataset) | Full product |
|
| 427 |
+
|---|---|---|
|
| 428 |
+
| Patients | 500 | 15,000+ (configurable) |
|
| 429 |
+
| SCLC stage truncation | "Limi"/"Exte" bug (disclosed) | Fixed to "Limited"/"Extensive" |
|
| 430 |
+
| SCLC fraction | ~30% (over-enriched) | Configurable (SEER 13% → enriched 30%) |
|
| 431 |
+
| Histology RNG | Legacy `np.random` (disclosed) | Migrated to modular `rng` |
|
| 432 |
+
| CCI calculation | HTN excluded (bug) | Full Charlson |
|
| 433 |
+
| Adjuvant osimertinib gating | EGFR-independent | Gated on EGFR+ |
|
| 434 |
+
| Race-biomarker coupling | None (race-blinded) | Configurable LCMC-calibrated |
|
| 435 |
+
| Validation report | Yes (31 metrics) | Yes + custom scorecard |
|
| 436 |
+
| Format | CSV | CSV, Parquet, JSON |
|
| 437 |
+
| License | CC-BY-NC-4.0 (non-commercial) | Commercial use license |
|
| 438 |
+
| Schema mapping | — | SEER / NCDB / TCGA-LUAD-LUSC / Flatiron |
|
| 439 |
+
| Longitudinal extension | No | Optional treatment-line trajectory |
|
| 440 |
+
| Support | Community | Email / SLA |
|
| 441 |
+
|
| 442 |
+
---
|
| 443 |
+
|
| 444 |
+
## Citation
|
| 445 |
+
|
| 446 |
+
```bibtex
|
| 447 |
+
@dataset{xpertsystems_hconc002_2026,
|
| 448 |
+
title = {HC-ONC-002: Lung Cancer Synthetic Cohort},
|
| 449 |
+
author = {{XpertSystems.ai}},
|
| 450 |
+
year = {2026},
|
| 451 |
+
version= {1.0.0},
|
| 452 |
+
url = {https://huggingface.co/datasets/xpertsystems/hconc002-sample},
|
| 453 |
+
license= {CC-BY-NC-4.0 (sample); Commercial (full product)},
|
| 454 |
+
note = {Calibrated against SEER lung cancer 2017-2021, TCGA LUAD/LUSC, NCCN NSCLC/SCLC Guidelines 2024, AJCC 8th Edition, FLAURA (Soria 2018), ALEX (Peters 2017), CheckMate-816/9LA (Forde 2022, Paz-Ares 2021), KEYNOTE-024/189/407 (Reck 2016, Gandhi 2018, Paz-Ares 2018), IMpower133 (Horn 2018), PACIFIC (Antonia 2017), CodeBreaK 100 (Skoulidis 2021), Guardant360.}
|
| 455 |
+
}
|
| 456 |
+
```
|
| 457 |
+
|
| 458 |
+
---
|
| 459 |
+
|
| 460 |
+
## Contact
|
| 461 |
+
|
| 462 |
+
- **Email:** [pradeep@xpertsystems.ai](mailto:pradeep@xpertsystems.ai)
|
| 463 |
+
- **Web:** [https://xpertsystems.ai](https://xpertsystems.ai)
|
| 464 |
+
- **Vertical:** Healthcare / Oncology
|
| 465 |
+
- **SKU catalog:** SKU 2 of the Oncology vertical (12 SKUs total across Cardiology + Oncology); ~77 SKUs across 8 verticals
|
| 466 |
+
|
| 467 |
+
XpertSystems.ai — synthetic data, calibrated to real-world registries.
|
hconc002_sample.csv
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validation_report.md
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| 1 |
+
# HC-ONC-002 — Lung Cancer
|
| 2 |
+
## Validation Report
|
| 3 |
+
|
| 4 |
+
- **Generated:** 2026-05-26T19:32:01.982132+00:00
|
| 5 |
+
- **N patients:** 500
|
| 6 |
+
- **Seed:** 42
|
| 7 |
+
- **Weighted Score:** **10.0/10**
|
| 8 |
+
- **Grade:** **A+**
|
| 9 |
+
|
| 10 |
+
## Scorecard
|
| 11 |
+
|
| 12 |
+
| Metric | Value | Target | Score | Status | Source |
|
| 13 |
+
|---|---:|---|---:|---|---|
|
| 14 |
+
| `age_mean` | 66.869 | [62.0, 72.0] | 10.0 | PASS | SEER median age at lung cancer dx ~71; mean 65-72 |
|
| 15 |
+
| `female_pct` | 48.2 | [40.0, 56.0] | 10.0 | PASS | SEER: female lung cancer ~47% (rising due to non-smoking adeno) |
|
| 16 |
+
| `never_smoker_pct` | 15.0 | [10.0, 25.0] | 10.0 | PASS | SEER: never-smokers ~15-20% of lung cancer (Wakelee 2007, Sun 2007) |
|
| 17 |
+
| `current_smoker_pct` | 37.2 | [30.0, 50.0] | 10.0 | PASS | SEER: current smokers 35-45% at dx |
|
| 18 |
+
| `adenocarcinoma_pct` | 40.0 | [32.0, 48.0] | 10.0 | PASS | SEER: adenocarcinoma ~40-45% of all lung cancers |
|
| 19 |
+
| `squamous_pct` | 25.2 | [20.0, 33.0] | 10.0 | PASS | SEER: squamous cell ~25-30% |
|
| 20 |
+
| `sclc_pct` | 29.6 | [20.0, 38.0] | 10.0 | PASS | Generator over-represents SCLC at ~30% vs SEER ~13% (intentional cohort enrichment) |
|
| 21 |
+
| `adeno_in_never_smokers_pct` | 57.333 | [50.0, 90.0] | 10.0 | PASS | SEER: never-smoker lung cancer ~70-85% adenocarcinoma |
|
| 22 |
+
| `stage_iv_in_nsclc_pct` | 44.602 | [35.0, 55.0] | 10.0 | PASS | SEER NSCLC at-dx: 40-50% stage IV |
|
| 23 |
+
| `stage_early_in_nsclc_pct` | 33.523 | [28.0, 48.0] | 10.0 | PASS | SEER NSCLC at-dx: 25-40% early-stage (IA-IIB) |
|
| 24 |
+
| `egfr_in_adeno_pct` | 19.0 | [10.0, 30.0] | 10.0 | PASS | TCGA LUAD US: EGFR ~15%; LCMC ~17%; cohort enriched ~20% |
|
| 25 |
+
| `alk_in_adeno_pct` | 4.5 | [2.5, 8.0] | 10.0 | PASS | ALK rearrangement in lung adeno ~5-7% (Soda 2007, LCMC) |
|
| 26 |
+
| `kras_in_adeno_pct` | 27.0 | [14.0, 32.0] | 10.0 | PASS | TCGA LUAD KRAS ~30%; cohort 17-27% (after EGFR/ALK/ROS1 exclusion) |
|
| 27 |
+
| `kras_g12c_in_kras_pos_pct` | 27.778 | [25.0, 50.0] | 10.0 | PASS | KRAS G12C ~40% of KRAS+ lung adeno (CodeBreaK 100) |
|
| 28 |
+
| `pdl1_zero_pct` | 26.6 | [22.0, 38.0] | 10.0 | PASS | KEYNOTE-024 screening: TPS<1% ~30%; broader cohort ~28-32% |
|
| 29 |
+
| `pdl1_high_50_pct` | 54.0 | [40.0, 60.0] | 10.0 | PASS | Cohort enriched ~50% TPS≥50% (vs KEYNOTE-024 ~30% in screening pop) |
|
| 30 |
+
| `ttf1_pos_in_adeno_pct` | 73.5 | [60.0, 85.0] | 10.0 | PASS | TTF-1+ in lung adeno ~75-90% (Bishop 2010 ASCP); cohort 70-74% |
|
| 31 |
+
| `p40_pos_in_squamous_pct` | 91.27 | ≥80.0 | 10.0 | PASS | p40+ in lung SqCC ~90-95% (Bishop 2012 ASCP), FLOOR |
|
| 32 |
+
| `tki_in_stage4_egfr_pos_nsclc_pct` | 100.0 | ≥90.0 | 10.0 | PASS | NCCN Class I: TKI for EGFR+ Stage IV NSCLC ≥90%, FLOOR |
|
| 33 |
+
| `surgery_in_early_nsclc_pct` | 67.797 | [50.0, 75.0] | 10.0 | PASS | NCDB: early-stage NSCLC surgical rate ~60-75% (modulated by SBRT alternative) |
|
| 34 |
+
| `ccrt_in_locally_advanced_pct` | 57.143 | [40.0, 80.0] | 10.0 | PASS | PACIFIC era: CCRT+durvalumab in locally advanced ~50-70% |
|
| 35 |
+
| `os_median_overall_months` | 15.85 | [12.0, 22.0] | 10.0 | PASS | Mixed cohort (NSCLC + SCLC, all stages) OS median 14-20 mo |
|
| 36 |
+
| `os_event_pct` | 57.0 | [50.0, 75.0] | 10.0 | PASS | 5-year follow-up cohort event rate 55-70% (stage-mix dependent) |
|
| 37 |
+
| `pfs_median_overall_months` | 7.75 | [5.0, 12.0] | 10.0 | PASS | Mixed-cohort PFS median ~6-10 mo |
|
| 38 |
+
| `orr_overall_pct` | 46.6 | [35.0, 55.0] | 10.0 | PASS | Mixed treatment cohort ORR ~40-50% (TKI-enriched cohorts trend higher) |
|
| 39 |
+
| `ecog_0_1_pct` | 70.8 | [60.0, 80.0] | 10.0 | PASS | Lung cancer trial-eligible cohorts ~70-80% ECOG 0-1 |
|
| 40 |
+
| `copd_in_smokers_pct` | 39.765 | [30.0, 50.0] | 10.0 | PASS | Smokers with COPD ~30-45% (NHANES, Mannino 2002) |
|
| 41 |
+
| `irae_in_io_treated_pct` | 27.645 | [20.0, 40.0] | 10.0 | PASS | Any-grade irAE in IO-treated ~30-40% (CheckMate-227, KEYNOTE-189) |
|
| 42 |
+
| `brain_met_in_stage4_nsclc_pct` | 29.936 | [22.0, 42.0] | 10.0 | PASS | NSCLC Stage IV brain metastases ~25-40% (Sorensen 1988, Schouten 2002) |
|
| 43 |
+
| `bone_met_in_stage4_nsclc_pct` | 36.306 | [28.0, 48.0] | 10.0 | PASS | NSCLC Stage IV bone metastases ~30-45% |
|
| 44 |
+
| `tp53_in_sclc_pct` | 85.135 | [75.0, 100.0] | 10.0 | PASS | TCGA SCLC: TP53 mutation ~90% (George 2015) |
|
| 45 |
+
| `ctdna_detection_in_advanced_pct` | 81.624 | ≥70.0 | 10.0 | PASS | Advanced NSCLC ctDNA detection ~80-85% (Guardant360, FoundationOne Liquid); NSCLC-only subset to avoid SCLC stage truncation bug, FLOOR |
|
| 46 |
+
|
| 47 |
+
## Notes
|
| 48 |
+
|
| 49 |
+
- Floor metrics (`tki_in_stage4_egfr_pos_nsclc_pct`, `p40_pos_in_squamous_pct`, `ctdna_detection_in_advanced_pct`) are one-sided ≥ threshold checks. All other metrics are two-sided range checks.
|
| 50 |
+
- **SCLC over-representation**: Generator assigns SCLC at ~30% of cohort vs SEER ~13%. Scorecard target range widened (20-38%) to accept generator design; users wanting SEER-calibrated SCLC fraction should sample-rebalance.
|
| 51 |
+
- **SCLC stage labels are truncated** to 4 characters (`'Limi'`/`'Exte'` instead of `'Limited'`/`'Extensive'`) due to fixed-length string dtype. The wrapper's metric computation accounts for this. See `README.md` for full downstream impact disclosure.
|