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millanp95 / DeLUCS

This repository contains all the source files required to run DeLUCS, a deep learning clustering algorithm for DNA sequences.
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How to know which specific sequence contributed to the classification? #6

Open zddzxxsmile opened 2 years ago

zddzxxsmile commented 2 years ago

Dear authors,

Your work is very valuable. I am a doctor worked in a hospital, not very familiar to the code. Here is a question, how to know which specific sequence contributed to the classification?

Thanks very much.

millanp95 commented 2 years ago

Hi,

Thank you for your question. In principle, all sequences should contribute the same to the final values of the network parameters. One thing you can do to check this is to monitor each layer's activations with your sequence of interest.

After training, the networks operate as if they were trained using supervised learning, so all the interpretability methodologies should apply. I would recommend a tool called SHAP used by doctors in explainable AI (https://github.com/slundberg/shap)