SIMBSIG: similarity search and clustering for biobank-scale data.

Abstract

In many modern bioinformatics applications, such as statistical genetics, or single-cell analysis, one frequently encounters datasets which are orders of magnitude too large for conventional in-memory analysis. To tackle this challenge, we introduce SIMBSIG (SIMmilarity Batched Search Integrated GPU), a highly scalable Python package which provides a scikit-learn-like interface for out-of-core, GPU-enabled similarity searches, principal component analysis and clustering. Due to the PyTorch backend, it is highly modular and particularly tailored to many data types with a particular focus on biobank data analysis. SIMBSIG is freely available from PyPI and its source code and documentation can be found on GitHub (https://github.com/BorgwardtLab/simbsig) under a BSD-3 license.