Update help menus, fix typos (in documentation and variable names), add more explanation of day offsets

[alisoncallahan]

2. CLMBR Pre-training.ipynb

--clmbr_create_info

• rename --extract_dir to --input_data_dir (or something similar), and explain what it is in the help menu - right now the description in help is the name of the command ('Extract dir') which isn't very informative

--clmbr_train_model

• complete the help menu descriptions, i.e. add English language descriptions of all the options
• make the required options actually required (the help menu indicates that they are all optional arguments, but then the notebook says there are two required arguments)
• the description of --model_dir is kind of confusing - 'override' implies that there's a default output location, but then the notebook says this option is required, and that it can't already exist (what if I want to overwrite the content of an existing folder? I have to delete the folder first? sure, the benefit is that it is a stopgap to prevent accidental overwriting, but also one extra step)
• also, it seems like the logic for the directory overwriting is just in the next cell, not actually built into the clmbr_train_model function, which isn't consistent with the documentation of the notebook

3a. Model Training with Custom Labeler.ipynb

• "Set up the labeler for the downstream task we're interested in"

  • the comment for the DiabetesLabeler class could use a little more detail - the description below this cell makes it sound like the labeler is labeling patient days based on whether there is a diabetes code present on that day or not. But the comment talks about a prediction task with a time horizon (also, how does one specify the time point that the horizon is relative to?).

  • why do timelines have dictionaries? need documentation in timeline.pyi

  • "this randomly selects on label per patient " should be "this randomly selects one label per patient"

  • for output of ehr_ml.clmbr.featurize_patients_w_labels (features, labels, patient_ids, day_offsets) -- what is day_offsets relative to? DOB of patient?

• "Using the trained model"

  • in the first cell, I think patient_indices should be day_offsets (based on featurize_patients_w_labels in https://github.com/som-shahlab/ehr_ml/blob/245dd3436a5dcddada41222611e8129be96cd85b/ehr_ml/clmbr/__init__.py)

3b. Model Training with Patient List.ipynb

• explanation of day offsets could include more information, for truly new users - e.g. is this date the date that a prediction should be made? Is this date somehow used as a cutoff for generating features? The notebook seems to assume a lot of knowledge/intution about the day offsets that users may not have.

[woffett]

Update to reflect changes in the newest PR:

2. CLMBR Pre-training

• clmbr_create_info
  • the flag has been renamed to --input_data_dir
• clmbr_train_model
  • help menu descriptions have been added for all options
  • the required options have been specified as positional arguments instead of optional arguments
  • description of --model_dir has been updated
  • the logic in the cell exists to prevent folks from overwriting the existing sample documents; it is redundant, as a check also exists in the code for the command, but this makes it clear for people who are just running the notebook and don't need to look at the code
  • the typo has been fixed

3a. Model Training with Custom Labeler

• This first point is still open and is to be addressed.
• I think this comment refers to the line in the labeler class diabetes_code = timelines.get_dictionary().map("ICD10CM/E11.9"). I'm not too sure myself, @lalaland do you have any clarification on this?
• My understanding was that day_offsets indexes into an array of all days where a patient observation is recorded in the dataset. TODO: the documentation still needs to be updated to reflect this, once it's updated we can link to it in the notebook for clarity.
• the variable should be renamed in the next PR

3b. Model Training with Patient List

• That's a good point. TODO: add explanation in 3b. about what convert_patient_data is doing