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robogast authored Sep 23, 2021
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# 2D-VQ-AE-2
2D Vector-Quantized Auto-Encoder for compression of Whole-Slide Images in Histopathology

# How to run
## Locally
## How to run
### Locally
set `CAMELYON16_PATH` and run `train.py`:
```bash
CAMELYON16_PATH=<camelyon-path> python train.py
```
## Lisa
### Lisa
set `CAMELYON16_PATH`, and append `--multirun` to automatically submit a `sbatch` job through `submitit`, which copies CAMELYON16 to `$SCRATCH` of the allocated node.
```bash
CAMELYON16_PATH=<camelyon-path> python train.py --multirun
```

Change node type by overwriting the node config, e.g.:
```bash
CAMELYON16_PATH=<camelyon-path> python train.py hydra/launcher/node@hydra.launcher=gpu_titanrtx --multirun
```

## WIP results
Top: original, bottom: reconstruction.
Input dimensionality: `256×256×3`, latent dimensionality: `32×32` (i.e. `99.47%` compression).

![image](https://user-images.githubusercontent.com/5969044/134488209-4c1696d3-6478-41d0-a7bf-e7e99544382b.png)



## Research
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