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README.md CHANGED
@@ -5,19 +5,21 @@ colorFrom: red
5
  colorTo: gray
6
  sdk: docker
7
  pinned: false
8
- license: apache-2.0
9
  short_description: Tox21 TabPFN Classifier for Tox21
10
  ---
11
 
12
  # Tox21 TabPFN Classifier
13
 
14
- This repository hosts a Hugging Face Space that provides an examplary API for submitting models to the [Tox21 Leaderboard](https://huggingface.co/spaces/tschouis/tox21_leaderboard).
15
 
16
  In this example, we train a TabPFN classifier on the Tox21 targets and save the trained model in the `assets/` folder.
17
 
18
  **Important:** For leaderboard submission, your Space needs to implement inference in the `predict()` function inside `predict.py`. The `predict()` function must keep the provided skeleton: it should take a list of SMILES strings as input and return a prediction dictionary as output, with SMILES and targets as keys. Therefore, any preprocessing of SMILES strings must be executed on-the-fly during inference.
19
 
20
  # Repository Structure
 
 
21
  - `predict.py` - Defines the `predict()` function required by the leaderboard (entry point for inference).
22
  - `app.py` - FastAPI application wrapper (can be used as-is).
23
 
@@ -53,6 +55,14 @@ conda activate tox21_tabpfn_cls
53
  pip install -r requirements.txt
54
  ```
55
 
 
 
 
 
 
 
 
 
56
  # Training
57
 
58
  To fit the TabPFN model for the Tox21 dataset:
 
5
  colorTo: gray
6
  sdk: docker
7
  pinned: false
8
+ license: cc-by-nc-4.0
9
  short_description: Tox21 TabPFN Classifier for Tox21
10
  ---
11
 
12
  # Tox21 TabPFN Classifier
13
 
14
+ This repository hosts a Hugging Face Space that provides an examplary API for submitting models to the [Tox21 Leaderboard](https://huggingface.co/spaces/tschouis/tox21_leaderboard). Built with PriorLabs-TabPFN
15
 
16
  In this example, we train a TabPFN classifier on the Tox21 targets and save the trained model in the `assets/` folder.
17
 
18
  **Important:** For leaderboard submission, your Space needs to implement inference in the `predict()` function inside `predict.py`. The `predict()` function must keep the provided skeleton: it should take a list of SMILES strings as input and return a prediction dictionary as output, with SMILES and targets as keys. Therefore, any preprocessing of SMILES strings must be executed on-the-fly during inference.
19
 
20
  # Repository Structure
21
+ - `preprocess.py` - Preprocessing pipeline
22
+ - `train.py` - Training script
23
  - `predict.py` - Defines the `predict()` function required by the leaderboard (entry point for inference).
24
  - `app.py` - FastAPI application wrapper (can be used as-is).
25
 
 
55
  pip install -r requirements.txt
56
  ```
57
 
58
+ # Preprocessing
59
+ To preprocess the data, execute the following code:
60
+
61
+ ```bash
62
+ wget -P ./data http://bioinf.jku.at/research/DeepTox/tox21_compoundData.csv
63
+ python preprocess.py
64
+ ```
65
+
66
  # Training
67
 
68
  To fit the TabPFN model for the Tox21 dataset: