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Oufattole / meds-torch

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Enable users to define their own dataset class #125

Open payalchandak opened 2 weeks ago

payalchandak commented 2 weeks ago

Summary by CodeRabbit

Release Notes

coderabbitai[bot] commented 2 weeks ago

Walkthrough

The changes in this pull request involve modifications to several configuration files for the meds_torch project. Key updates include the replacement of task name references from ${data.task_name} to ${data.dataset.task_name} across multiple YAML files, enhancing the specificity of dataset-related configurations. Additionally, new configuration files for dataset management have been introduced, while some existing files have been removed. The PytorchDataset class has undergone structural changes, including enhanced error handling and a simplified initialization process. Overall, these modifications aim to improve the organization and robustness of the dataset management system.

Changes

File Path Change Summary
MIMICIV_TUTORIAL/configs/meds-torch-configs/experiment/eic_mtr.yaml Updated tags entry from ${data.task_name} to ${data.dataset.task_name}.
MIMICIV_TUTORIAL/configs/meds-torch-configs/experiment/text_code_mtr.yaml Updated tags entry from ${data.task_name} to ${data.dataset.task_name}.
MIMICIV_TUTORIAL/configs/meds-torch-configs/experiment/triplet_mtr.yaml Updated tags entry from ${data.task_name} to ${data.dataset.task_name}.
src/meds_torch/configs/data/dataset/multiwindow_pytorch_dataset.yaml Added configuration for MultiWindowPytorchDataset, including defaults, _target_, subject_level_sampling, and raw_windows_fp.
src/meds_torch/configs/data/dataset/pytorch_dataset.yaml Updated _target_ path, added split: train, and modified several path parameters to use ${data.dataset.*}. Removed dataloader section.
src/meds_torch/configs/data/dataset/random_windows_pytorch_dataset.yaml Added new configuration for random window sampling dataset.
src/meds_torch/configs/data/default.yaml Introduced structured setup for dataset management, specifying defaults for training phases.
src/meds_torch/configs/data/multiwindow_pytorch_dataset.yaml Deleted file containing previous multi-window dataset configuration.
src/meds_torch/configs/data/random_windows_pytorch_dataset.yaml Deleted file containing previous random windows dataset configuration.
src/meds_torch/configs/model/backbone/default.yaml Updated vocab_size reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/backbone/eic_transformer_decoder.yaml Updated num_tokens reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/backbone/eic_transformer_encoder.yaml Updated num_tokens reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/backbone/eic_transformer_encoder_attn_avg.yaml Updated num_tokens reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/backbone/triplet_transformer_decoder.yaml Updated num_tokens reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/backbone/triplet_transformer_encoder.yaml Updated num_tokens reference to ${data.dataset.tokenizer}.
src/meds_torch/configs/model/backbone/triplet_transformer_encoder_attn_avg.yaml Updated num_tokens reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/ebcl.yaml Updated _resolved_max_seq_len, vocab_size, and task_name references to data.dataset.*.
src/meds_torch/configs/model/eic_forecasting.yaml Updated _resolved_max_seq_len, vocab_size, and task_name references to data.dataset.*.
src/meds_torch/configs/model/input_encoder/eic_encoder.yaml Updated vocab_size reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/input_encoder/text_code_encoder.yaml Updated several parameters to reference data.dataset.*.
src/meds_torch/configs/model/input_encoder/triplet_encoder.yaml Updated vocab_size reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/input_encoder/triplet_prompt_encoder.yaml Updated vocab_size reference to ${data.dataset.vocab_size}.
src/meds_torch/configs/model/ocp.yaml Updated _resolved_max_seq_len, vocab_size, and task_name references to data.dataset.*.
src/meds_torch/configs/model/supervised.yaml Updated _resolved_max_seq_len, vocab_size, and task_name references to data.dataset.*.
src/meds_torch/configs/model/triplet_forecasting.yaml Updated _resolved_max_seq_len, vocab_size, and task_name references to data.dataset.*.
src/meds_torch/configs/model/value_forecasting.yaml Updated _resolved_max_seq_len, vocab_size, and task_name references to data.dataset.*.
src/meds_torch/configs/train.yaml Updated data from pytorch_dataset to default and model from supervised to triplet_forecasting.
src/meds_torch/data/components/pytorch_dataset.py Updated class to inherit from Module, simplified constructor, and enhanced error handling.
src/meds_torch/data/datamodule.py Removed get_dataset method and simplified dataset initialization in the constructor.

🐇 In the meadow, changes bloom,
Tags now point where datasets loom.
Configs refined, paths align,
For every task, the data will shine.
With each update, the code grows bright,
Hop along, it feels just right! 🌼

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