songlab-cal/gpn

Benefits of using S4D?

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Hi! Very nice paper, congratulations :) I was just wandering - I saw you had S4D implemented in your repo but I couldn't find any related results in the paper. Do you have any insight whether this model has benefits for modelling DNA or not necessarily?

Thank you very much!

Hello, thank you for your interest in our paper!

We did a very quick try of S4D but without really evaluating different hyperparameter choices, which seem to be important. It was doing a bit worse than our ConvNet so we didn't pursue further.

My guess would be that choosing the right training dataset will have a much bigger impact than the specific model architecture. Also, 512 context size might be too small for S4D to shine.