neural-lsh

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EXARTeo / Remote-Homology-Search-with-Approximate-Methods-ESM-2

A hybrid C++/Python pipeline for remote protein homology detection, coupling ESM-2 language model embeddings with custom Neural-LSH for scalable approximate nearest neighbor search.

python machine-learning bioinformatics cpp computational-biology lsh nearest-neighbor-search protein-embeddings remote-homology-detection protein-language-models esm-2 neural-lsh

Updated Jan 30, 2026
Python

AlexTuring010 / protein-homolog-search

Star

Bioinformatics capstone of the UoA DI 'Software Development for Algorithmic Problems' trilogy. Protein remote-homolog search on SwissProt-50k via ESM-2 embeddings + 6 ANN methods (brute, LSH, Hypercube, IVF-Flat, IVF-PQ, Neural LSH), benchmarked against BLAST.

bioinformatics university-project nearest-neighbor-search blast swissprot protein-search homolog-detection approximate-nearest-neighbor esm-2 neural-lsh

Updated May 10, 2026
Python

AlexTuring010 / neural-lsh

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Implementation of Neural LSH (Dong et al., ICLR 2020) for ANN search: C++ k-NN graph + KaHIP graph partitioning + PyTorch MLP for learned bucket assignment, with Bayesian HPO via Optuna. Beats HW1's IVF-Flat ~4× at high recall on MNIST.

university-project pytorch nearest-neighbor-search mnist graph-partitioning optuna approximate-nearest-neighbor kahip neural-lsh

Updated May 10, 2026
Python

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