HNSW for biology

[jianshu93]

Dear HNSW author,

This is Jianshu, a bioinformatics phd student at Georgia Tech. I am writing to you to ask your interest to form a new collaboration. Specifically, applying HNSW into genome classification problems, that is to find the closest genome in a big genome database to see the close related ones in the database so that enivronmental microbiologist can tell what taxonomy the query genome is. This will have a very big impact on the field and will definitely have a lot of citations. I want to completely rely on rust for this project without using any other language considering the advantages compared to C++ and python. I am not an expert in rust but have been using it for 2 years. The biology needed and taxonomy related information will be my strong part. I also know all the classification software in this field and have benign using/modifying them for my master and half of my Ph.D I am confident that HNSW in rust will greatly improved the speed of genome classifiers. Hopefully we can come up with a paper in the end. My email is [email protected]

Let me know if you are interest and if something I mentioned above is not clear.

Many thanks,

Jianshu

[vadixidav]

Hey @jianshu93. Typically we communicate over the Rust CV Discord (https://discord.gg/d32jaam). If you still want to use email, I can send one to you, but I would prefer to collaborate on there. You can also find my email on my GitHub profile as well.

I also recommend taking a look at the hgg crate crate, which is a data structure I created more recently roughly based on the HNSW design which is giving me better performance for binary features using hamming distance in computer vision.

Let me know how you want to get in contact and I would love to see how I can help.