freddolino-lab / ShapeME

Algorithm to discover structural motifs informative of expression patterns
MIT License
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Implement motif optimization in rust #17

Closed mikewolfe closed 2 years ago

mikewolfe commented 2 years ago

Here we plan to create a custom swarm (https://machinelearningmastery.com/a-gentle-introduction-to-particle-swarm-optimization/) or multi-swarm optimization (https://ieeexplore.ieee.org/document/6256566) algorithm to determine the best motifs.

This will go in its own crate https://github.com/mikewolfe/DNAshape_motif_finder/tree/rust_dev/rust_utils/optim

jwschroeder3 commented 2 years ago

Simulated annealing seems to be working best, but we can do replica exchange and particle swarm if desired. They take longer and don't yield adjusted mutual information values as high as simple simulated annealing on test data, though.