Upload README.md with huggingface_hub
Browse files
README.md
CHANGED
|
@@ -14,8 +14,7 @@ Predicts which of 40 target conditions are **newly** diagnosed in the five
|
|
| 14 |
years after a patient's anchor date, from structured Synthea EHR events
|
| 15 |
recorded strictly before it.
|
| 16 |
|
| 17 |
-
Trained for the M31 research-intern take-home
|
| 18 |
-
clinical device, and not usable for any decision about a real person.**
|
| 19 |
|
| 20 |
## Model
|
| 21 |
|
|
@@ -74,20 +73,19 @@ shift. Every fitted statistic — vocabulary, quantile edges, scalers — is fit
|
|
| 74 |
on training patients only. 152 automated checks cover this, including a grep
|
| 75 |
test that no module outside the time utility parses a timestamp.
|
| 76 |
|
| 77 |
-
## Limitations
|
| 78 |
-
|
| 79 |
-
Synthea is not real EHR data. A discriminator separates it from MIMIC at
|
| 80 |
-
AUC 0.999, and across 19 health datasets the winning classifier agreed between
|
| 81 |
-
real- and synthetic-trained models in only 21–26% of cases. **Whichever model
|
| 82 |
-
wins here, that ranking should not be assumed to transfer.**
|
| 83 |
-
|
| 84 |
## Reproducing
|
| 85 |
|
| 86 |
-
``
|
| 87 |
-
|
| 88 |
-
|
| 89 |
-
|
| 90 |
-
|
| 91 |
-
``
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 92 |
|
| 93 |
Retraining everything from scratch is described in the GitHub README.
|
|
|
|
| 14 |
years after a patient's anchor date, from structured Synthea EHR events
|
| 15 |
recorded strictly before it.
|
| 16 |
|
| 17 |
+
Trained for the M31 research-intern take-home, on synthetic data only.
|
|
|
|
| 18 |
|
| 19 |
## Model
|
| 20 |
|
|
|
|
| 73 |
on training patients only. 152 automated checks cover this, including a grep
|
| 74 |
test that no module outside the time utility parses a timestamp.
|
| 75 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 76 |
## Reproducing
|
| 77 |
|
| 78 |
+
The data is not included here. Rebuilding `predictions.csv` from the files in
|
| 79 |
+
this repository, without any training:
|
| 80 |
+
|
| 81 |
+
1. Clone the code and install it:
|
| 82 |
+
`git clone https://github.com/Sallamsaka/M31-Coding-Test`, then
|
| 83 |
+
`pip install -r requirements.txt` inside it.
|
| 84 |
+
2. Copy the provided data into the repository root: the folders `train_val/` and
|
| 85 |
+
`test/`, and the files `patient_splits.csv`, `target_conditions.csv` and
|
| 86 |
+
`test_anchors.csv`.
|
| 87 |
+
3. Run `python -m src.reproduce --from-hub sallamsaka/M31-Coding-Test`. It downloads
|
| 88 |
+
these model files, predicts every test patient, and checks the result against
|
| 89 |
+
the submitted `predictions.csv`.
|
| 90 |
|
| 91 |
Retraining everything from scratch is described in the GitHub README.
|