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README.md ADDED
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1
+ ---
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+ license: cc-by-nc-4.0
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+ language:
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+ - en
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+ tags:
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+ - synthetic-data
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+ - healthcare
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+ - oncology
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+ - lung-cancer
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+ - nsclc
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+ - sclc
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+ - egfr
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+ - alk
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+ - immunotherapy
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+ - tcga-luad
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+ - tcga-lusc
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+ - keynote
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+ - flaura
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+ - xpertsystems
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+ pretty_name: "HC-ONC-002 — Lung Cancer Synthetic Cohort (sample)"
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+ size_categories:
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+ - n<1K
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+ task_categories:
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+ - tabular-classification
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+ - tabular-regression
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+ - time-series-forecasting
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+ ---
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+
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+ # HC-ONC-002 — Lung Cancer Synthetic Cohort
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+
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+ **Sample dataset (500 patients × 116 columns) from the XpertSystems.ai Synthetic Data Factory — Oncology vertical, SKU 2**
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+
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+ A fully synthetic, multimodal **lung cancer** cohort spanning the complete
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+ clinical pathway: smoking-stratified histology (NSCLC adeno/squamous/large
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+ cell + SCLC limited/extensive), AJCC 8th Edition T/N/M staging with site-
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+ specific metastases, comprehensive molecular biomarkers (EGFR with variant
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+ subtypes, ALK/ROS1 fusions, KRAS with G12C breakout, BRAF V600E, MET ex14,
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+ RET, NTRK, HER2, STK11, KEAP1, TP53), PD-L1 TPS+CPS scoring, TMB, MSI,
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+ treatment protocols across the IO/TKI era (surgery+adjuvant, SBRT, CCRT+
40
+ durvalumab, targeted TKIs, chemo-IO combinations), RECIST treatment response
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+ with pseudoprogression/hyperprogression flags, multimodal imaging (PET SUV/
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+ MTV, ctDNA detection+VAF), IHC markers (TTF-1, p40, synaptophysin),
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+ adverse events including irAE phenotyping, and survival outcomes
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+ (PFS/OS with Weibull-derived event times).
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+
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+ Built to be **drop-in usable for analytics, modeling, demos, and education**
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+ while remaining 100% synthetic — no real patient data, no PHI, no
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+ re-identification risk.
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+
50
+ ---
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+
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+ ## At a glance
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+
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+ | | |
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+ |---|---|
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+ | **SKU** | HC-ONC-002 |
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+ | **Vertical** | Healthcare → Oncology (SKU 2) |
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+ | **Sample size** | 500 patients × 116 columns |
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+ | **Modules** | 9 (Demographics, Histology+Staging, Molecular, Treatment, Response+Survival, Imaging+Pathology, Comorbidities, Adverse Events, Identifiers) |
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+ | **Standards** | AJCC 8th Edition, NCCN NSCLC/SCLC 2024, RECIST 1.1, CTCAE v5 |
61
+ | **Format** | CSV |
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+ | **License (sample)** | CC-BY-NC-4.0 |
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+ | **License (full product)** | Commercial — contact XpertSystems.ai |
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+ | **Validation** | **Grade A+ (10.0/10) across all 6 canonical seeds {42, 7, 123, 2024, 99, 1}** |
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+
66
+ ---
67
+
68
+ ## What makes this dataset useful
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+
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+ Lung cancer data lives across SEER (population incidence/survival, no
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+ molecular), TCGA LUAD/LUSC (deep genomics but n<1,000), clinical trial
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+ datasets (FLAURA/ALEX/KEYNOTE/CheckMate — tightly restricted), and
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+ real-world commercial datasets (Flatiron, COTA — expensive). This
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+ synthetic cohort gives you the **full lung cancer molecular+treatment+
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+ outcomes phenome in one tidy table** with realistic dependencies:
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+
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+ - ✅ **Smoking ↔ histology coupling** — never-smokers are ~60-70% adeno,
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+ current smokers more diverse
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+ - ✅ **Adeno ↔ EGFR/ALK coupling** — EGFR mutations 14-26% in adeno
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+ vs <2% in squamous; ALK 3-7% in adeno vs <1% elsewhere
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+ - ✅ **EGFR/ALK/ROS1 mutual exclusivity** (0 co-occurrences enforced)
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+ - ✅ **Stage IV EGFR+ NSCLC → 100% TKI** (NCCN Class I structural identity)
83
+ - ✅ **SCLC ↔ TP53 coupling** — TP53 mutation ~85-94% in SCLC (matches
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+ 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 ADDED
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validation_report.md ADDED
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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.