Update README.md
Browse files
README.md
CHANGED
|
@@ -131,8 +131,8 @@ LuMamba experiments are categorized by two Hydra configurations, in `BioFoundati
|
|
| 131 |
|
| 132 |
0. **Install & read data prep**: clone the [BioFoundation repo](https://github.com/pulp-bio/BioFoundation), set up the environment as described there, then open `make_datasets/README.md` for dataset-specific notes (naming, expected folder layout, and common pitfalls).
|
| 133 |
1. **Point to weights**: set `pretrained_safetensors_path: /path/to/LuMamba_*.safetensors` in the experiment YAML.
|
| 134 |
-
2. **Preprocess data**: acquire fine-tuning dataset and follow preprocessing protocol (in `/make_datasets/README.md`
|
| 135 |
-
3. **Update data module**:
|
| 136 |
- **TUH datasets (TUAB/TUSL/TUAR)** → change `_target_` in `/data_module:` to `datasets.tuh_dataset.TUH_Dataset`.
|
| 137 |
- **Other** → change `/data_module:_target_` to corresponding dataset.py file in `BioFoundation/datasets` (e.g., for TDBrain dataset use `_target_:datasets.tdbrain_dataset.TDBrain_Dataset`)
|
| 138 |
- **HDF5 file location** → change `/data_module:hdf5_file` for `train`, `test`, and `val` with the path to the corresponding HDF5 data split file.
|
|
|
|
| 131 |
|
| 132 |
0. **Install & read data prep**: clone the [BioFoundation repo](https://github.com/pulp-bio/BioFoundation), set up the environment as described there, then open `make_datasets/README.md` for dataset-specific notes (naming, expected folder layout, and common pitfalls).
|
| 133 |
1. **Point to weights**: set `pretrained_safetensors_path: /path/to/LuMamba_*.safetensors` in the experiment YAML.
|
| 134 |
+
2. **Preprocess data**: acquire fine-tuning dataset and follow preprocessing protocol (see guide in `/make_datasets/README.md`) to generate `train/test/val.h5` files.
|
| 135 |
+
3. **Update data module of `LuMamba_finetune.yaml` config**:
|
| 136 |
- **TUH datasets (TUAB/TUSL/TUAR)** → change `_target_` in `/data_module:` to `datasets.tuh_dataset.TUH_Dataset`.
|
| 137 |
- **Other** → change `/data_module:_target_` to corresponding dataset.py file in `BioFoundation/datasets` (e.g., for TDBrain dataset use `_target_:datasets.tdbrain_dataset.TDBrain_Dataset`)
|
| 138 |
- **HDF5 file location** → change `/data_module:hdf5_file` for `train`, `test`, and `val` with the path to the corresponding HDF5 data split file.
|