Evaluation updated to competing risks #29
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chiragnagpal
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Jan 2, 2021
Closed
chiragnagpal
reviewed
Jan 3, 2021
dsm/dsm_api.py
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| if not(self.fitted): | ||
| raise Exception("The model has not been fitted yet. Please fit the " + | ||
| "model using the `fit` method on some training data " + | ||
| "before calling `eval`.") |
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change eval to _eval_nll
chiragnagpal
reviewed
Jan 3, 2021
dsm/dsm_api.py
Outdated
| @@ -120,6 +121,26 @@ def fit(self, x, t, e, vsize=0.15, | |||
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| return self | |||
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| def _eval_nll(self, x, t, e): | |||
| """ | |||
| Evaluates models with conditional loss | |||
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Add more descriptive docstring: specify what x, t , e requires and what the output is. The docstring should clearly describe that this function outputs the negative log likelihood of the dsm model
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Also specify how NLL is calculated in the presence of multiple competing risks
chiragnagpal
reviewed
Jan 3, 2021
dsm/dsm_api.py
Outdated
| @@ -32,7 +32,8 @@ | |||
| from dsm.dsm_torch import DeepConvolutionalSurvivalMachinesTorch | |||
| from dsm.losses import predict_cdf | |||
| import dsm.losses as losses | |||
| from dsm.utilities import train_dsm, _get_padded_features, _get_padded_targets | |||
| from dsm.utilities import train_dsm, _get_padded_features, _get_padded_targets, \ | |||
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break into 3 separate import statements 1) train_dsm, 2) _get_padded_features, _get_padded_targets and 3) _reshape_tensor_with_nans
chiragnagpal
requested changes
Jan 3, 2021
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@Jeanselme would this work for both simple DSM and Recurrent DSM ? Please check, ideally it should. Also look at the inline comments I have added.
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Yes, it does |
Update followings comments
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LGTM. Merged. |
texchi2
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Jan 23, 2021
* Implemented computation of Negative Log-Likelihood.
texchi2
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Jan 23, 2021
* conv_model * Update .travis.yml * modified: dsm/dsm_torch.py * modified: dsm/dsm_api.py modified: dsm/dsm_torch.py * fixed_syntax_small_bugs * removed_data * Change fit return to match Sklearn format * linting * torch * linting * whitespace * linting * removed_trailing_whitespace * modified: dsm/dsm_api.py modified: dsm/dsm_torch.py modified: examples/conv_example.ipynb modified: dsm/utilities.py modified: examples/conv_example.ipynb modified: examples/pbc_final_experiment.ipynb * Fix validation loss computation * modified: docs/dsm_api.html modified: docs/dsm_torch.html modified: docs/losses.html * Evaluation updated to competing risks (autonlab#29) * Implemented computation of Negative Log-Likelihood. * modified: docs/dsm_api.html modified: dsm/dsm_api.py * modified: requirements.txt * modified: requirements.txt * Update README.md * modified: docs/datasets.html modified: docs/dsm_api.html modified: docs/dsm_torch.html modified: docs/index.html modified: docs/losses.html modified: docs/utilities.html * Change multi risk for irregular length (autonlab#32) * Update README.md * Update README.md * Update README.md Co-authored-by: Chufan Gao <[email protected]> Co-authored-by: Chirag Nagpal <[email protected]> Co-authored-by: Chirag Nagpal <[email protected]> Co-authored-by: Vincent Jeanselme <[email protected]>
texchi2
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Jan 23, 2021
* conv_model * Update .travis.yml * modified: dsm/dsm_torch.py * modified: dsm/dsm_api.py modified: dsm/dsm_torch.py * fixed_syntax_small_bugs * removed_data * Change fit return to match Sklearn format * linting * torch * linting * whitespace * linting * removed_trailing_whitespace * modified: dsm/dsm_api.py modified: dsm/dsm_torch.py modified: examples/conv_example.ipynb modified: dsm/utilities.py modified: examples/conv_example.ipynb modified: examples/pbc_final_experiment.ipynb * Fix validation loss computation * modified: docs/dsm_api.html modified: docs/dsm_torch.html modified: docs/losses.html * Evaluation updated to competing risks (autonlab#29) * Implemented computation of Negative Log-Likelihood. * modified: docs/dsm_api.html modified: dsm/dsm_api.py * modified: requirements.txt * modified: requirements.txt * Update README.md * modified: docs/datasets.html modified: docs/dsm_api.html modified: docs/dsm_torch.html modified: docs/index.html modified: docs/losses.html modified: docs/utilities.html * Change multi risk for irregular length (autonlab#32) * Update README.md * Update README.md * Update README.md Co-authored-by: Chufan Gao <[email protected]> Co-authored-by: Chirag Nagpal <[email protected]> Co-authored-by: Chirag Nagpal <[email protected]> Co-authored-by: Vincent Jeanselme <[email protected]>
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