kundajelab / basepairmodels

MIT License
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shap scores for multi-task #28

Open nzhang89 opened 2 years ago

nzhang89 commented 2 years ago

Thank you for developing this fantastic package and the very recent update. I have not tried it yet, but I guess the predict step will be much faster.

I have some questions regarding to multi-task shap score generation.

  1. For profile shap scores: in line 286 of shap_scores.py, the option stranded=True is hard-coded. I think it will work fine for single-task (whether it is stranded or not). But for multi-tasks (unstranded), will it pick up the wrong task? For example, I have 2 tasks (unstranded). Based on the code, task 0 will use output[0:2] (0 and 1) and task 1 will use [2:4] (2 and 3, which will be out of bounds since there are only 2 outputs).

  2. For counts shap scores: in line 280 of shap_scores.py, it seems to use all count outputs. Again this is fine for single task. But for multi-tasks, will it make all tasks having the same scores?

Thank you for your time. Let me know if you have any questions or comments.