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Paper #26

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2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ If you have a bug report to make or a feature request for something you would li
If you have general __questions__, meaning you are unsure about the usage of `sparsesurv`, or have other questions about the package that do not seem like a bug or feature request, please use [Github discussions](https://github.com/BoevaLab/sparsesurv/discussions/).

## Documentation and user guides
Documentation and user guides are available on [Github pages](TODO ADD LINK).
Documentation and user guides are available on [Github pages](https://boevalab.github.io/sparsesurv).

## Contributing
We always welcome new contributors to `sparsesurv`. If you're interested in contributing, get in touch with us (see Contact) or have a look at the open issues.
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2 changes: 1 addition & 1 deletion paper/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ bash reproduce.sh
```

### Results
All of our results, including preprocessed data, computed performance metrics and predicted survival functions for all models and experiments are available on [Zenodo](https://zenodo.org/record/8280015).
All of our results, including preprocessed data, computed performance metrics and predicted survival functions for all models and experiments are available on [Zenodo](https://zenodo.org/records/11058330).

## Questions
In case of any questions, please reach out to [email protected] or open an issue in this repo.
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53 changes: 50 additions & 3 deletions paper/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,61 @@
"OV",
"STAD"
],
"datasets_last": ["LUSC"],
"datasets_lel": ["BLCA"],
"n_outer_splits": 5,
"n_outer_repetitions": 5,
"n_outer_repetitions": 25,
"pc_n_components": 16,
"l1_ratio": 0.9,
"eps": 0.01,
"n_alphas": 100,
"n_inner_cv": 5,
"stratify_cv": true,
"seed": 42,
"shuffle_cv": true
}
"shuffle_cv": true,
"timing_reps": 5,
"l1_ratio_tuned": [0.1, 0.5, 0.7, 0.9, 0.95, 0.99, 1],
"pc_n_components_tuned": [
8,
16,
32,
64
],
"n_jobs": 12,
"max_epochs": 100,
"validation_set_neural": 0.2,
"early_stopping_patience": 10,
"tune_lr": [
0.0005,
0.0008,
0.001,
0.005,
0.01
],
"tune_weight_decay": [
0.0005,
0.005,
0.05,
0.1
],
"tune_modality_hidden_layer_size": [
32,
64,
128,
256,
512
],
"tune_modality_hidden_layers": [
1,
2
],
"tune_p_dropout": [
0,
0.2,
0.4,
0.6
],
"tune_batch_size": [1024],
"random_search_n_iter": 50,
"error_score": 100
}
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