v0.1.0 Add model and experiments (Simulation & Histopathology) (#3)

- Add model
- Add simulation and histopathology experiments
- Push package to pypi

.gitignore

@@ -158,3 +158,7 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+.DS_Store
+data
+*.out

README.md

@@ -1,2 +1,40 @@
 # MixMIL
-Code coming soon.
+Code for the paper: [Attention-based Multi-instance Mixed Models](https://arxiv.org/abs/2311.02455)
+
+Please raise an issue for questions and bug-reports.
+## Installation
+Install with:
+```
+pip install mixmil
+```
+or if you want to adapt the code:
+```
+git clone https://github.com/AIH-SGML/mixmil.git
+cd mixmil
+pip install -e .
+```
+To enable computations on GPU please follow the installation instructions of [PyTorch](https://pytorch.org/) and [PyTorch Scatter](https://github.com/rusty1s/pytorch_scatter).
+MixMIL works e.g. with PyTorch 2.1.
+## Experiments
+See the notebooks in the `experiments` folder for examples on how to run the simulation and histopathology experiments.
+
+### Histopathology
+Install `anndata` (`pip install anndata`) to run the notebook. 
+
+#### Download Data
+To download the embeddings provided by the DSMIL authors, either:
+- Full embeddings: `python scripts/dsmil_data_download.py`
+- PCA reduced embeddings: [Google Drive](https://drive.google.com/drive/folders/1X9ho1_W5ixyHSw_2hCfQsBb5nzkjMviA?usp=sharing)
+
+
+## Citation
+```
+@misc{engelmann2023attentionbased,
+      title={Attention-based Multi-instance Mixed Models}, 
+      author={Jan P. Engelmann and Alessandro Palma and Jakub M. Tomczak and Fabian J Theis and Francesco Paolo Casale},
+      year={2023},
+      eprint={2311.02455},
+      archivePrefix={arXiv},
+      primaryClass={cs.LG}
+}
+```