Samuel Sledzieski

icon indicating a website link samsl.io icon indicating an email [email protected]

icon company Massachusetts Institute of Technology icon location Cambridge, MA icon location PhD student @ MIT. Studying computational biology and bioinformatics.

Results 3 issues of Samuel Sledzieski

Running with n_jobs = -1 throttles all CPU on the machine

Current behavior ([here](https://github.com/samsledje/D-SCRIPT/blob/0955991a27180c9ff4f4e8cd2804d77337aa72f1/dscript/utils.py#L72)) by default uses `n_jobs=-1` to load sequence embeddings in parallel. As a result, any other computation running on the same machine slows down drastically. This should be...

bug

Add multi-GPU support for prediction (and embedding?)

A single process splits candidate interactions to the number of allocated GPUs, and all are able to access the same loaded embeddings in memory - currently can't run more than...

enhancement

dscript predict doesn't batch candidates, could be sped up 100s of times

enhancement