Datasets:
Upload folder using huggingface_hub
Browse files- README.md +153 -0
- data/stroke_district_hospital.csv +0 -0
- data/stroke_rural_facility.csv +0 -0
- data/stroke_tertiary_hospital.csv +0 -0
- generate_dataset.py +269 -0
- requirements.txt +3 -0
- validate_dataset.py +125 -0
- validation_report.png +3 -0
README.md
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| 1 |
+
---
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| 2 |
+
license: cc-by-4.0
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| 3 |
+
task_categories:
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| 4 |
+
- tabular-classification
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| 5 |
+
language:
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| 6 |
+
- en
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| 7 |
+
tags:
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| 8 |
+
- healthcare
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| 9 |
+
- stroke
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| 10 |
+
- cerebrovascular
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| 11 |
+
- hypertension
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| 12 |
+
- neurology
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| 13 |
+
- thrombolysis
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| 14 |
+
- sub-saharan-africa
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| 15 |
+
- lmic
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| 16 |
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pretty_name: "Stroke & Cerebrovascular Disease (Type, Severity, Treatment, Disability)"
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| 17 |
+
size_categories:
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| 18 |
+
- 10K<n<100K
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| 19 |
+
configs:
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| 20 |
+
- config_name: tertiary_hospital
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| 21 |
+
data_files: data/stroke_tertiary_hospital.csv
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| 22 |
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- config_name: district_hospital
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| 23 |
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data_files: data/stroke_district_hospital.csv
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| 24 |
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default: true
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| 25 |
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- config_name: rural_facility
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| 26 |
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data_files: data/stroke_rural_facility.csv
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| 27 |
+
---
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| 28 |
+
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| 29 |
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# Stroke & Cerebrovascular Disease Dataset
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| 30 |
+
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| 31 |
+
## Abstract
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| 32 |
+
|
| 33 |
+
This dataset provides **30,000 simulated stroke records** (10,000 per scenario) of adults presenting with acute stroke in sub-Saharan Africa. Each record contains 50+ variables including risk factors, stroke type, severity (NIHSS, GCS), imaging, treatment, complications, and outcomes (30-day mortality, mRS). Three settings: tertiary hospital (28% mortality), district hospital (41%), and rural facility (57%).
|
| 34 |
+
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| 35 |
+
## 1. Introduction
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| 36 |
+
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| 37 |
+
Stroke in Africa has an annual incidence up to 316/100K person-years, with 30-day case fatality rates of ~30% (range 18-40%) and 90-day mortality reaching 50% at some centres. Approximately 60% of strokes are ischaemic and 32% haemorrhagic — a higher proportion of haemorrhagic stroke than in HICs. Mean age at onset is ~59 years, 10 years younger than Western populations. Hypertension is the dominant risk factor with BP control rates <10% in many SSA populations. CT scanning and thrombolysis are virtually unavailable outside tertiary centres.
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| 38 |
+
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| 39 |
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**This dataset is entirely simulated. It must not be used for clinical decision-making.**
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| 40 |
+
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| 41 |
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## 2. Methodology
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| 42 |
+
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| 43 |
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### 2.1 Parameterization
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| 44 |
+
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| 45 |
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| Parameter | Value | Source |
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| 46 |
+
| --- | --- | --- |
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| 47 |
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| Incidence (Africa) | Up to 316/100K | Frontiers Stroke 2025 |
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| 48 |
+
| 30-day CFR (SSA pooled) | ~30% | PLOS Glob PH 2024 |
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| 49 |
+
| 90-day mortality | ~50% | Muhimbili 2018 |
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| 50 |
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| Ischaemic / ICH / SAH | 60% / 32% / 8% | Sierra Leone 2021 |
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| 51 |
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| Mean age | 59 years | Sierra Leone 2021 |
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| 52 |
+
| Hypertension prevalence | 75% | PMC 2015 |
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| 53 |
+
| BP control rate | <10% | PMC 2015 |
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| 54 |
+
| Recurrence rate | 9-25% | PMC 2024 |
|
| 55 |
+
|
| 56 |
+
### 2.2 Scenario Design
|
| 57 |
+
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| 58 |
+
| Scenario | CT | Thrombolysis | Stroke Unit | 30-Day Mortality |
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| 59 |
+
| --- | --- | --- | --- | --- |
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| 60 |
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| Tertiary hospital | Yes | Limited | Yes | 28% |
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| 61 |
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| District hospital | No | No | No | 41% |
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| 62 |
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| Rural facility | No | No | No | 57% |
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| 63 |
+
|
| 64 |
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## 3. Schema
|
| 65 |
+
|
| 66 |
+
| Column | Type | Description |
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| 67 |
+
| --- | --- | --- |
|
| 68 |
+
| id | int | Unique identifier |
|
| 69 |
+
| age_years | int | Patient age |
|
| 70 |
+
| sex | categorical | M / F |
|
| 71 |
+
| hypertension | binary | Hypertension |
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| 72 |
+
| systolic_bp | int | Systolic BP (mmHg) |
|
| 73 |
+
| diastolic_bp | int | Diastolic BP (mmHg) |
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| 74 |
+
| diabetes | binary | Diabetes |
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| 75 |
+
| atrial_fibrillation | binary | AF |
|
| 76 |
+
| smoking | binary | Current smoker |
|
| 77 |
+
| alcohol_heavy | binary | Heavy alcohol |
|
| 78 |
+
| prior_stroke | binary | Prior stroke |
|
| 79 |
+
| stroke_type | categorical | ischaemic / intracerebral_haemorrhage / subarachnoid_haemorrhage |
|
| 80 |
+
| ischaemic_subtype | categorical | large_vessel / small_vessel / cardioembolic / undetermined |
|
| 81 |
+
| nihss_score | int | NIHSS (0-42) |
|
| 82 |
+
| gcs_score | int | GCS (3-15) |
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| 83 |
+
| hemiparesis | binary | Hemiparesis |
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| 84 |
+
| aphasia | binary | Aphasia |
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| 85 |
+
| dysphagia | binary | Dysphagia |
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| 86 |
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| onset_to_arrival_hours | int | Time to presentation |
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| 87 |
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| ct_performed | binary | CT scan done |
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| 88 |
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| thrombolysis | binary | Thrombolysis given |
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| 89 |
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| antiplatelet | binary | Antiplatelet |
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| 90 |
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| statin | binary | Statin |
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| 91 |
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| physiotherapy_started | binary | Early physiotherapy |
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| 92 |
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| aspiration_pneumonia | binary | Aspiration pneumonia |
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| 93 |
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| outcome_30_day | categorical | survived / died |
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| 94 |
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| mrs_discharge | int | Modified Rankin Scale (0-5) |
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| 95 |
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| disability | categorical | none / mild / moderate / severe |
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| 96 |
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| hospital_days | int | Hospital stay |
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| 97 |
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| 98 |
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## 4. Validation
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| 99 |
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| 100 |
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<p align="center">
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| 101 |
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<img src="validation_report.png" alt="Validation Report" width="100%">
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| 102 |
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</p>
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| 103 |
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| 104 |
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Key validation checks:
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| 105 |
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| 106 |
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- **Mortality gradient**: 28% → 41% → 57% ✓
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| 107 |
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- **Stroke type**: 60% ischaemic, 32% ICH ✓
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| 108 |
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- **Hypertension**: 75% prevalence ✓
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| 109 |
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- **CT access**: 80% tertiary vs 0% district/rural ✓
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| 110 |
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- **ICH mortality > ischaemic** ✓
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| 111 |
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- **Mean age ~59** ✓
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| 112 |
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| 113 |
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## 5. Usage
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| 114 |
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|
| 115 |
+
```python
|
| 116 |
+
from datasets import load_dataset
|
| 117 |
+
dataset = load_dataset("electricsheepafrica/stroke-cerebrovascular-disease", "district_hospital")
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| 118 |
+
df = dataset["train"].to_pandas()
|
| 119 |
+
```
|
| 120 |
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|
| 121 |
+
## 6. Limitations
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| 122 |
+
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| 123 |
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- **Simulated**: Not from real stroke registries.
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| 124 |
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- **No neuroimaging**: No actual CT/MRI data.
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| 125 |
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- **No longitudinal**: 30-day outcome only, no long-term follow-up.
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| 126 |
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- **No rehabilitation**: Limited rehab outcome data.
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| 127 |
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- **Simplified**: No detailed vascular territory mapping.
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| 128 |
+
|
| 129 |
+
## 7. References
|
| 130 |
+
|
| 131 |
+
1. Frontiers Stroke (2025). Strategic action plan for stroke in Africa.
|
| 132 |
+
2. PLOS Glob Public Health (2024). 30-day stroke CFR in SSA.
|
| 133 |
+
3. PubMed (2021). Stroke register Sierra Leone.
|
| 134 |
+
4. PubMed (2020). Predictors of stroke mortality Uganda.
|
| 135 |
+
5. PubMed (2018). Stroke at Muhimbili Tanzania.
|
| 136 |
+
6. PMC (2015). Burden of stroke in Africa.
|
| 137 |
+
7. PMC (2024). Stroke recurrence in SSA.
|
| 138 |
+
|
| 139 |
+
## Citation
|
| 140 |
+
|
| 141 |
+
```bibtex
|
| 142 |
+
@dataset{esa_stroke_2025,
|
| 143 |
+
title={Stroke and Cerebrovascular Disease Dataset},
|
| 144 |
+
author={Electric Sheep Africa},
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| 145 |
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year={2025},
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| 146 |
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publisher={Hugging Face},
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| 147 |
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url={https://huggingface.co/datasets/electricsheepafrica/stroke-cerebrovascular-disease}
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| 148 |
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}
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| 149 |
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```
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| 150 |
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| 151 |
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## License
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| 152 |
+
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| 153 |
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[CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/)
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data/stroke_district_hospital.csv
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The diff for this file is too large to render.
See raw diff
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data/stroke_rural_facility.csv
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The diff for this file is too large to render.
See raw diff
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data/stroke_tertiary_hospital.csv
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The diff for this file is too large to render.
See raw diff
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generate_dataset.py
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| 1 |
+
#!/usr/bin/env python3
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| 2 |
+
"""
|
| 3 |
+
Literature-Informed Stroke & Cerebrovascular Disease Dataset
|
| 4 |
+
==============================================================
|
| 5 |
+
|
| 6 |
+
Generates realistic synthetic records of stroke patients in
|
| 7 |
+
sub-Saharan Africa, including risk factors, stroke type, severity,
|
| 8 |
+
imaging, treatment, and outcomes.
|
| 9 |
+
|
| 10 |
+
Target population: Adults presenting with acute stroke to SSA
|
| 11 |
+
health facilities.
|
| 12 |
+
|
| 13 |
+
References (web-searched):
|
| 14 |
+
-----------
|
| 15 |
+
[1] Frontiers Stroke 2025. Africa stroke incidence up to
|
| 16 |
+
316/100K person-years. 3-year fatality rate reaching 84%.
|
| 17 |
+
[2] PLOS Glob Public Health 2024. 30-day in-hospital stroke
|
| 18 |
+
CFR in SSA: pooled ~30% (range 18-40%).
|
| 19 |
+
[3] Sierra Leone stroke register 2021. 60% ischaemic, 22%
|
| 20 |
+
ICH, 3% SAH, 15% undetermined. Mean age 59.
|
| 21 |
+
[4] Uganda cohort 2020. Low consciousness at admission,
|
| 22 |
+
severity, haemorrhagic type predict 30/90-day mortality.
|
| 23 |
+
[5] Muhimbili Tanzania 2018. 90-day mortality 50%.
|
| 24 |
+
Thrombolysis virtually unavailable in SSA.
|
| 25 |
+
[6] PMC 2015. Hypertension is #1 risk factor. BP control
|
| 26 |
+
rates <10% in many SSA populations.
|
| 27 |
+
[7] Stroke recurrence SSA 2024. Recurrence 9.4-25%.
|
| 28 |
+
Hypertension, alcohol, prior stroke main risk factors.
|
| 29 |
+
"""
|
| 30 |
+
|
| 31 |
+
import numpy as np
|
| 32 |
+
import pandas as pd
|
| 33 |
+
import argparse
|
| 34 |
+
import os
|
| 35 |
+
|
| 36 |
+
SCENARIOS = {
|
| 37 |
+
'tertiary_hospital': {
|
| 38 |
+
'description': 'Tertiary hospital with CT/MRI, stroke unit, '
|
| 39 |
+
'physiotherapy, some thrombolysis capability '
|
| 40 |
+
'(e.g., Muhimbili Tanzania, UCH Ibadan, KBTH Ghana)',
|
| 41 |
+
'ct_available': True,
|
| 42 |
+
'mri_available': True,
|
| 43 |
+
'thrombolysis_available': True,
|
| 44 |
+
'stroke_unit': True,
|
| 45 |
+
'physiotherapy': True,
|
| 46 |
+
'mortality_mod': 0.7,
|
| 47 |
+
},
|
| 48 |
+
'district_hospital': {
|
| 49 |
+
'description': 'District hospital, no CT, clinical diagnosis, '
|
| 50 |
+
'basic BP management, no stroke unit '
|
| 51 |
+
'(e.g., district hospitals Malawi, Uganda)',
|
| 52 |
+
'ct_available': False,
|
| 53 |
+
'mri_available': False,
|
| 54 |
+
'thrombolysis_available': False,
|
| 55 |
+
'stroke_unit': False,
|
| 56 |
+
'physiotherapy': False,
|
| 57 |
+
'mortality_mod': 1.0,
|
| 58 |
+
},
|
| 59 |
+
'rural_facility': {
|
| 60 |
+
'description': 'Rural facility, no imaging, delayed referral, '
|
| 61 |
+
'minimal management '
|
| 62 |
+
'(e.g., rural DRC, Chad, South Sudan)',
|
| 63 |
+
'ct_available': False,
|
| 64 |
+
'mri_available': False,
|
| 65 |
+
'thrombolysis_available': False,
|
| 66 |
+
'stroke_unit': False,
|
| 67 |
+
'physiotherapy': False,
|
| 68 |
+
'mortality_mod': 1.5,
|
| 69 |
+
},
|
| 70 |
+
}
|
| 71 |
+
|
| 72 |
+
|
| 73 |
+
def generate_dataset(n=10000, seed=42, scenario='district_hospital'):
|
| 74 |
+
rng = np.random.default_rng(seed)
|
| 75 |
+
sc = SCENARIOS[scenario]
|
| 76 |
+
|
| 77 |
+
records = []
|
| 78 |
+
|
| 79 |
+
for idx in range(n):
|
| 80 |
+
rec = {'id': idx + 1}
|
| 81 |
+
|
| 82 |
+
# ── 1. Demographics [3] ──
|
| 83 |
+
rec['age_years'] = max(18, min(95, int(rng.normal(59, 14))))
|
| 84 |
+
rec['sex'] = rng.choice(['M', 'F'], p=[0.52, 0.48])
|
| 85 |
+
rec['rural'] = 1 if rng.random() < 0.60 else 0
|
| 86 |
+
|
| 87 |
+
# ── 2. Risk factors [6][7] ──
|
| 88 |
+
rec['hypertension'] = 1 if rng.random() < 0.75 else 0
|
| 89 |
+
rec['bp_on_treatment'] = 0
|
| 90 |
+
if rec['hypertension']:
|
| 91 |
+
rec['bp_on_treatment'] = 1 if rng.random() < 0.30 else 0
|
| 92 |
+
rec['bp_controlled'] = 0
|
| 93 |
+
if rec['bp_on_treatment']:
|
| 94 |
+
rec['bp_controlled'] = 1 if rng.random() < 0.25 else 0
|
| 95 |
+
|
| 96 |
+
rec['systolic_bp'] = max(90, min(260, int(rng.normal(
|
| 97 |
+
160 if rec['hypertension'] and not rec['bp_controlled'] else 130, 25))))
|
| 98 |
+
rec['diastolic_bp'] = max(50, min(150, int(rng.normal(
|
| 99 |
+
95 if rec['hypertension'] and not rec['bp_controlled'] else 80, 15))))
|
| 100 |
+
|
| 101 |
+
rec['diabetes'] = 1 if rng.random() < 0.20 else 0
|
| 102 |
+
rec['atrial_fibrillation'] = 1 if rng.random() < 0.08 else 0
|
| 103 |
+
rec['smoking'] = 1 if rng.random() < 0.15 else 0
|
| 104 |
+
rec['alcohol_heavy'] = 1 if rng.random() < 0.20 else 0
|
| 105 |
+
rec['hiv_positive'] = 1 if rng.random() < 0.08 else 0
|
| 106 |
+
rec['bmi'] = round(max(15, min(45, rng.normal(26, 5))), 1)
|
| 107 |
+
rec['prior_stroke'] = 1 if rng.random() < 0.12 else 0
|
| 108 |
+
rec['prior_tia'] = 1 if rng.random() < 0.05 else 0
|
| 109 |
+
rec['sickle_cell'] = 1 if rng.random() < 0.03 else 0
|
| 110 |
+
|
| 111 |
+
# ── 3. Stroke characteristics [3] ──
|
| 112 |
+
rec['stroke_type'] = rng.choice(
|
| 113 |
+
['ischaemic', 'intracerebral_haemorrhage', 'subarachnoid_haemorrhage'],
|
| 114 |
+
p=[0.60, 0.32, 0.08])
|
| 115 |
+
|
| 116 |
+
if rec['stroke_type'] == 'ischaemic':
|
| 117 |
+
rec['ischaemic_subtype'] = rng.choice(
|
| 118 |
+
['large_vessel', 'small_vessel', 'cardioembolic', 'undetermined'],
|
| 119 |
+
p=[0.30, 0.25, 0.15, 0.30])
|
| 120 |
+
else:
|
| 121 |
+
rec['ischaemic_subtype'] = 'n/a'
|
| 122 |
+
|
| 123 |
+
rec['nihss_score'] = max(0, min(42, int(rng.exponential(8))))
|
| 124 |
+
rec['gcs_score'] = max(3, min(15, int(rng.normal(
|
| 125 |
+
12 if rec['nihss_score'] < 15 else 8, 3))))
|
| 126 |
+
|
| 127 |
+
rec['hemiparesis'] = 1 if rng.random() < 0.75 else 0
|
| 128 |
+
rec['aphasia'] = 1 if rng.random() < 0.30 else 0
|
| 129 |
+
rec['dysphagia'] = 1 if rng.random() < 0.35 else 0
|
| 130 |
+
rec['visual_field_defect'] = 1 if rng.random() < 0.15 else 0
|
| 131 |
+
rec['neglect'] = 1 if rng.random() < 0.10 else 0
|
| 132 |
+
|
| 133 |
+
rec['onset_to_arrival_hours'] = max(1, int(rng.exponential(
|
| 134 |
+
24 if scenario == 'rural_facility' else 12)))
|
| 135 |
+
|
| 136 |
+
# ── 4. Diagnosis ──
|
| 137 |
+
rec['ct_performed'] = 0
|
| 138 |
+
if sc['ct_available']:
|
| 139 |
+
rec['ct_performed'] = 1 if rng.random() < 0.80 else 0
|
| 140 |
+
|
| 141 |
+
rec['mri_performed'] = 0
|
| 142 |
+
if sc['mri_available'] and rec['ct_performed']:
|
| 143 |
+
rec['mri_performed'] = 1 if rng.random() < 0.20 else 0
|
| 144 |
+
|
| 145 |
+
rec['ecg_done'] = 1 if rng.random() < (0.70 if sc['stroke_unit'] else 0.30) else 0
|
| 146 |
+
rec['echo_done'] = 1 if rng.random() < (0.30 if sc['ct_available'] else 0.05) else 0
|
| 147 |
+
rec['clinical_diagnosis_only'] = 1 if not rec['ct_performed'] else 0
|
| 148 |
+
|
| 149 |
+
# ── 5. Treatment [5] ──
|
| 150 |
+
rec['thrombolysis'] = 0
|
| 151 |
+
if (sc['thrombolysis_available'] and rec['stroke_type'] == 'ischaemic'
|
| 152 |
+
and rec['onset_to_arrival_hours'] <= 4.5):
|
| 153 |
+
rec['thrombolysis'] = 1 if rng.random() < 0.10 else 0
|
| 154 |
+
|
| 155 |
+
rec['antiplatelet'] = 0
|
| 156 |
+
if rec['stroke_type'] == 'ischaemic':
|
| 157 |
+
rec['antiplatelet'] = 1 if rng.random() < (0.75 if sc['ct_available'] else 0.40) else 0
|
| 158 |
+
|
| 159 |
+
rec['anticoagulant'] = 0
|
| 160 |
+
if rec['atrial_fibrillation'] and rec['stroke_type'] == 'ischaemic':
|
| 161 |
+
rec['anticoagulant'] = 1 if rng.random() < 0.20 else 0
|
| 162 |
+
|
| 163 |
+
rec['antihypertensive_acute'] = 1 if rec['systolic_bp'] > 180 and rng.random() < 0.60 else 0
|
| 164 |
+
rec['statin'] = 1 if rng.random() < (0.40 if sc['stroke_unit'] else 0.10) else 0
|
| 165 |
+
rec['surgical_evacuation'] = 0
|
| 166 |
+
if rec['stroke_type'] == 'intracerebral_haemorrhage' and sc['ct_available']:
|
| 167 |
+
rec['surgical_evacuation'] = 1 if rng.random() < 0.05 else 0
|
| 168 |
+
|
| 169 |
+
rec['nasogastric_feeding'] = 0
|
| 170 |
+
if rec['dysphagia']:
|
| 171 |
+
rec['nasogastric_feeding'] = 1 if rng.random() < (0.50 if sc['stroke_unit'] else 0.15) else 0
|
| 172 |
+
|
| 173 |
+
rec['physiotherapy_started'] = 0
|
| 174 |
+
if sc['physiotherapy']:
|
| 175 |
+
rec['physiotherapy_started'] = 1 if rng.random() < 0.50 else 0
|
| 176 |
+
|
| 177 |
+
rec['dvt_prophylaxis'] = 1 if rng.random() < (0.40 if sc['stroke_unit'] else 0.05) else 0
|
| 178 |
+
|
| 179 |
+
# ── 6. Complications ──
|
| 180 |
+
rec['aspiration_pneumonia'] = 0
|
| 181 |
+
if rec['dysphagia'] and not rec['nasogastric_feeding']:
|
| 182 |
+
rec['aspiration_pneumonia'] = 1 if rng.random() < 0.25 else 0
|
| 183 |
+
|
| 184 |
+
rec['dvt_pe'] = 1 if rng.random() < (0.03 if rec['dvt_prophylaxis'] else 0.08) else 0
|
| 185 |
+
rec['pressure_ulcer'] = 1 if rng.random() < 0.10 else 0
|
| 186 |
+
rec['seizure'] = 1 if rng.random() < 0.08 else 0
|
| 187 |
+
rec['haemorrhagic_transformation'] = 0
|
| 188 |
+
if rec['stroke_type'] == 'ischaemic':
|
| 189 |
+
rec['haemorrhagic_transformation'] = 1 if rng.random() < 0.05 else 0
|
| 190 |
+
|
| 191 |
+
# ── 7. Outcome [2][4][5] ──
|
| 192 |
+
base_mort = 0.25
|
| 193 |
+
if rec['stroke_type'] == 'intracerebral_haemorrhage':
|
| 194 |
+
base_mort = 0.40
|
| 195 |
+
elif rec['stroke_type'] == 'subarachnoid_haemorrhage':
|
| 196 |
+
base_mort = 0.45
|
| 197 |
+
|
| 198 |
+
mort = base_mort * sc['mortality_mod']
|
| 199 |
+
if rec['gcs_score'] <= 8:
|
| 200 |
+
mort *= 1.8
|
| 201 |
+
if rec['nihss_score'] > 20:
|
| 202 |
+
mort *= 1.5
|
| 203 |
+
if rec['thrombolysis']:
|
| 204 |
+
mort *= 0.6
|
| 205 |
+
if rec['aspiration_pneumonia']:
|
| 206 |
+
mort *= 1.5
|
| 207 |
+
if rec['age_years'] > 75:
|
| 208 |
+
mort *= 1.3
|
| 209 |
+
|
| 210 |
+
rec['outcome_30_day'] = 'died' if rng.random() < min(mort, 0.80) else 'survived'
|
| 211 |
+
|
| 212 |
+
rec['mrs_discharge'] = 5
|
| 213 |
+
if rec['outcome_30_day'] == 'survived':
|
| 214 |
+
if rec['nihss_score'] < 5:
|
| 215 |
+
rec['mrs_discharge'] = rng.choice([0, 1, 2, 3], p=[0.10, 0.25, 0.35, 0.30])
|
| 216 |
+
elif rec['nihss_score'] < 15:
|
| 217 |
+
rec['mrs_discharge'] = rng.choice([2, 3, 4], p=[0.20, 0.45, 0.35])
|
| 218 |
+
else:
|
| 219 |
+
rec['mrs_discharge'] = rng.choice([3, 4, 5], p=[0.15, 0.45, 0.40])
|
| 220 |
+
|
| 221 |
+
rec['disability'] = 'none' if rec['mrs_discharge'] <= 1 else (
|
| 222 |
+
'mild' if rec['mrs_discharge'] == 2 else (
|
| 223 |
+
'moderate' if rec['mrs_discharge'] == 3 else 'severe'))
|
| 224 |
+
|
| 225 |
+
rec['hospital_days'] = max(1, min(60, int(rng.exponential(10))))
|
| 226 |
+
if rec['outcome_30_day'] == 'died':
|
| 227 |
+
rec['hospital_days'] = max(1, min(30, int(rng.exponential(5))))
|
| 228 |
+
|
| 229 |
+
records.append(rec)
|
| 230 |
+
|
| 231 |
+
df = pd.DataFrame(records)
|
| 232 |
+
|
| 233 |
+
print(f"\n{'='*65}")
|
| 234 |
+
print(f"Stroke — {scenario} (n={n}, seed={seed})")
|
| 235 |
+
print(f"{'='*65}")
|
| 236 |
+
print(f"\n Ischaemic: {(df['stroke_type']=='ischaemic').mean()*100:.1f}%")
|
| 237 |
+
print(f" Haemorrhagic: {(df['stroke_type']=='intracerebral_haemorrhage').mean()*100:.1f}%")
|
| 238 |
+
print(f" Hypertension: {df['hypertension'].mean()*100:.1f}%")
|
| 239 |
+
print(f" CT performed: {df['ct_performed'].mean()*100:.1f}%")
|
| 240 |
+
died = (df['outcome_30_day']=='died').mean()*100
|
| 241 |
+
print(f" 30-day mortality: {died:.1f}%")
|
| 242 |
+
|
| 243 |
+
return df
|
| 244 |
+
|
| 245 |
+
|
| 246 |
+
if __name__ == '__main__':
|
| 247 |
+
parser = argparse.ArgumentParser(
|
| 248 |
+
description='Generate stroke dataset')
|
| 249 |
+
parser.add_argument('--scenario', type=str, default='district_hospital',
|
| 250 |
+
choices=list(SCENARIOS.keys()))
|
| 251 |
+
parser.add_argument('--n', type=int, default=10000)
|
| 252 |
+
parser.add_argument('--seed', type=int, default=42)
|
| 253 |
+
parser.add_argument('--output', type=str, default=None)
|
| 254 |
+
parser.add_argument('--all-scenarios', action='store_true')
|
| 255 |
+
args = parser.parse_args()
|
| 256 |
+
|
| 257 |
+
os.makedirs('data', exist_ok=True)
|
| 258 |
+
|
| 259 |
+
if args.all_scenarios:
|
| 260 |
+
for sc_name in SCENARIOS:
|
| 261 |
+
df = generate_dataset(n=args.n, seed=args.seed, scenario=sc_name)
|
| 262 |
+
out = os.path.join('data', f'stroke_{sc_name}.csv')
|
| 263 |
+
df.to_csv(out, index=False)
|
| 264 |
+
print(f" → Saved to {out}\n")
|
| 265 |
+
else:
|
| 266 |
+
df = generate_dataset(n=args.n, seed=args.seed, scenario=args.scenario)
|
| 267 |
+
out = args.output or os.path.join('data', f'stroke_{args.scenario}.csv')
|
| 268 |
+
df.to_csv(out, index=False)
|
| 269 |
+
print(f" → Saved to {out}")
|
requirements.txt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
numpy>=1.24
|
| 2 |
+
pandas>=2.0
|
| 3 |
+
matplotlib>=3.7
|
validate_dataset.py
ADDED
|
@@ -0,0 +1,125 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
#!/usr/bin/env python3
|
| 2 |
+
"""Validation & Diagnostic Visualization for Stroke Dataset."""
|
| 3 |
+
|
| 4 |
+
import pandas as pd
|
| 5 |
+
import numpy as np
|
| 6 |
+
import matplotlib.pyplot as plt
|
| 7 |
+
import os
|
| 8 |
+
|
| 9 |
+
SCENARIOS = ['tertiary_hospital', 'district_hospital', 'rural_facility']
|
| 10 |
+
|
| 11 |
+
|
| 12 |
+
def load_scenarios(data_dir='data'):
|
| 13 |
+
dfs = {}
|
| 14 |
+
for sc in SCENARIOS:
|
| 15 |
+
path = os.path.join(data_dir, f'stroke_{sc}.csv')
|
| 16 |
+
if os.path.exists(path):
|
| 17 |
+
dfs[sc] = pd.read_csv(path)
|
| 18 |
+
return dfs
|
| 19 |
+
|
| 20 |
+
|
| 21 |
+
def make_report(dfs, output='validation_report.png'):
|
| 22 |
+
fig, axes = plt.subplots(4, 2, figsize=(16, 22))
|
| 23 |
+
fig.suptitle('Stroke & Cerebrovascular Disease — Validation Report',
|
| 24 |
+
fontsize=16, fontweight='bold', y=0.98)
|
| 25 |
+
df = dfs.get('district_hospital', list(dfs.values())[0])
|
| 26 |
+
colors = ['#2ecc71', '#f39c12', '#e74c3c']
|
| 27 |
+
|
| 28 |
+
ax = axes[0, 0]
|
| 29 |
+
x = np.arange(len(SCENARIOS))
|
| 30 |
+
mort = [(dfs[sc]['outcome_30_day'] == 'died').mean() * 100 for sc in SCENARIOS if sc in dfs]
|
| 31 |
+
ax.bar(x, mort, color=colors, alpha=0.8)
|
| 32 |
+
ax.set_xticks(x)
|
| 33 |
+
ax.set_xticklabels(['Tertiary', 'District', 'Rural'], fontsize=9)
|
| 34 |
+
for i, v in enumerate(mort):
|
| 35 |
+
ax.text(i, v + 0.5, f'{v:.1f}%', ha='center', fontsize=10)
|
| 36 |
+
ax.set_ylabel('30-Day Mortality (%)')
|
| 37 |
+
ax.set_title('30-Day Mortality (SSA pooled ~30%)')
|
| 38 |
+
|
| 39 |
+
ax = axes[0, 1]
|
| 40 |
+
types = ['ischaemic', 'intracerebral_haemorrhage', 'subarachnoid_haemorrhage']
|
| 41 |
+
t_labels = ['Ischaemic', 'ICH', 'SAH']
|
| 42 |
+
vals = [(df['stroke_type'] == t).mean() * 100 for t in types]
|
| 43 |
+
t_colors = ['#3498db', '#e74c3c', '#f39c12']
|
| 44 |
+
ax.pie(vals, labels=t_labels, autopct='%1.0f%%', colors=t_colors,
|
| 45 |
+
startangle=90, textprops={'fontsize': 10})
|
| 46 |
+
ax.set_title('Stroke Type (60% ischaemic, 32% ICH)')
|
| 47 |
+
|
| 48 |
+
ax = axes[1, 0]
|
| 49 |
+
risks = ['hypertension', 'diabetes', 'atrial_fibrillation', 'smoking',
|
| 50 |
+
'alcohol_heavy', 'prior_stroke', 'hiv_positive']
|
| 51 |
+
r_labels = ['HTN', 'DM', 'AF', 'Smoking', 'Alcohol', 'Prior Stroke', 'HIV']
|
| 52 |
+
vals = [df[r].mean() * 100 for r in risks]
|
| 53 |
+
ax.barh(range(7), vals, color='#e74c3c', alpha=0.7)
|
| 54 |
+
ax.set_yticks(range(7))
|
| 55 |
+
ax.set_yticklabels(r_labels, fontsize=8)
|
| 56 |
+
for i, v in enumerate(vals):
|
| 57 |
+
ax.text(v + 0.3, i, f'{v:.0f}%', va='center', fontsize=8)
|
| 58 |
+
ax.set_xlabel('Prevalence (%)')
|
| 59 |
+
ax.set_title('Risk Factors (HTN #1)')
|
| 60 |
+
|
| 61 |
+
ax = axes[1, 1]
|
| 62 |
+
for t, col, lab in [('ischaemic', '#3498db', 'Ischaemic'),
|
| 63 |
+
('intracerebral_haemorrhage', '#e74c3c', 'ICH')]:
|
| 64 |
+
sub = df[df['stroke_type'] == t]
|
| 65 |
+
m = (sub['outcome_30_day'] == 'died').mean() * 100 if len(sub) > 0 else 0
|
| 66 |
+
ax.bar(lab, m, color=col, alpha=0.8)
|
| 67 |
+
ax.text(lab, m + 0.5, f'{m:.0f}%', ha='center', fontsize=10)
|
| 68 |
+
ax.set_ylabel('30-Day Mortality (%)')
|
| 69 |
+
ax.set_title('Mortality by Stroke Type (ICH > Ischaemic)')
|
| 70 |
+
|
| 71 |
+
ax = axes[2, 0]
|
| 72 |
+
for sc_name, col in zip(SCENARIOS, colors):
|
| 73 |
+
if sc_name in dfs:
|
| 74 |
+
d = dfs[sc_name]
|
| 75 |
+
ax.hist(d['onset_to_arrival_hours'].clip(upper=72), bins=20,
|
| 76 |
+
alpha=0.4, color=col,
|
| 77 |
+
label=sc_name.replace('_', ' ').title()[:10], edgecolor='white')
|
| 78 |
+
ax.set_xlabel('Hours from Onset to Arrival')
|
| 79 |
+
ax.set_title('Presentation Delay')
|
| 80 |
+
ax.legend(fontsize=7)
|
| 81 |
+
|
| 82 |
+
ax = axes[2, 1]
|
| 83 |
+
cascade = ['CT Scan', 'Antiplatelet', 'Thrombolysis', 'Statin', 'Physio']
|
| 84 |
+
for i, sc_name in enumerate(SCENARIOS):
|
| 85 |
+
if sc_name in dfs:
|
| 86 |
+
d = dfs[sc_name]
|
| 87 |
+
vals = [d['ct_performed'].mean()*100, d['antiplatelet'].mean()*100,
|
| 88 |
+
d['thrombolysis'].mean()*100, d['statin'].mean()*100,
|
| 89 |
+
d['physiotherapy_started'].mean()*100]
|
| 90 |
+
ax.plot(range(5), vals, 'o-', label=sc_name.replace('_', ' ').title()[:10],
|
| 91 |
+
color=colors[i], linewidth=2, markersize=6)
|
| 92 |
+
ax.set_xticks(range(5))
|
| 93 |
+
ax.set_xticklabels(cascade, fontsize=8)
|
| 94 |
+
ax.set_ylabel('Rate (%)')
|
| 95 |
+
ax.set_title('Treatment Cascade (thrombolysis near-zero SSA)')
|
| 96 |
+
ax.legend(fontsize=7)
|
| 97 |
+
|
| 98 |
+
ax = axes[3, 0]
|
| 99 |
+
survived = df[df['outcome_30_day'] == 'survived']
|
| 100 |
+
if len(survived) > 0:
|
| 101 |
+
mrs = survived['mrs_discharge'].value_counts().sort_index()
|
| 102 |
+
ax.bar(mrs.index.astype(str), mrs.values, color='#3498db', alpha=0.8)
|
| 103 |
+
ax.set_xlabel('Modified Rankin Scale')
|
| 104 |
+
ax.set_ylabel('Count')
|
| 105 |
+
ax.set_title('Disability at Discharge (mRS)')
|
| 106 |
+
|
| 107 |
+
ax = axes[3, 1]
|
| 108 |
+
died = df[df['outcome_30_day'] == 'died']['age_years']
|
| 109 |
+
surv = df[df['outcome_30_day'] == 'survived']['age_years']
|
| 110 |
+
ax.hist(surv, bins=20, alpha=0.5, color='#2ecc71', label='Survived', edgecolor='white')
|
| 111 |
+
ax.hist(died, bins=20, alpha=0.7, color='#e74c3c', label='Died', edgecolor='white')
|
| 112 |
+
ax.set_xlabel('Age (years)')
|
| 113 |
+
ax.set_title('Age Distribution (mean ~59, younger than HICs)')
|
| 114 |
+
ax.legend(fontsize=8)
|
| 115 |
+
|
| 116 |
+
plt.tight_layout(rect=[0, 0, 1, 0.97])
|
| 117 |
+
plt.savefig(output, dpi=150, bbox_inches='tight')
|
| 118 |
+
print(f'Saved validation report to {output}')
|
| 119 |
+
plt.close()
|
| 120 |
+
|
| 121 |
+
|
| 122 |
+
if __name__ == '__main__':
|
| 123 |
+
dfs = load_scenarios()
|
| 124 |
+
if dfs:
|
| 125 |
+
make_report(dfs)
|
validation_report.png
ADDED
|
Git LFS Details
|