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Added tybalt info to readme
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norberz committed May 16, 2023
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Expand Up @@ -45,7 +45,31 @@ example usage of CLI train.py:

### Tybalt WaveNet VAE

T.B.D.
A alteration on the [Tybalt VAE model](https://github.com/greenelab/tybalt) by [Way et al.](https://www.biorxiv.org/content/10.1101/174474v2).
I gave it one extra linear layer to help reducing the data to a smaller latent space.

![Tybalt VAE Diagram](https://github.com/WouterBesse/Sonified-Latent-Data/blob/main/media/Tybalt.svg?raw=true)

#### Training and model

My model is downloadable from 'n.b.t.', it's trained on the TCGA dataset. You can train your own model using `train.py` from the WaveNetVAE folder or by using the `WaveVaePlayground.ipynb` jupyter notebook.
The acquisition and preprocessing scripts are available in the original [Tybalt GitHub](https://github.com/greenelab/tybalt).

example usage of CLI train.py:

`python3 train.py -tp "./traindatasetfolder/" -vp "./validationdatasetfolder/" -ep 100`
| **Short Flag** | **Long Flag** | **Description** |
|----------------|---------------------|---------------------------------------------------------------------------------------|
| `-dp` | `--data_path` | Path of folder where training data is stored, validation split is made automatically. |
| `-ep` | `--epochs` | Amount of epochs to train |
| `-ex` | `--export_path` | Path of folder to export model files to |
| `-bs` | `--batch_size` | Batch size |
| `-lr` | `--learning_rate` | Learning rate, I recommend 0.00001 |
| `-kla` | `--kl_anneal` | How much the kl rate multiplier is increased after every log step |
| `-mkl` | `--max_kl` | What the maximum kl rate multiplier will be |
| `-lpe` | `--logs_per_epoch` | How often a tensorboard log is stored per epoch |
| `-d` | `--device` | What device to train on, e.g. `cuda:0`, `cpu` |
| `-mf` | `--max_files` | The maximum amount of files to use in the train dataset |

### Mocap WaveNet VAE

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