ArticleBioinformatics (Oxford, England)2023
SIMBSIG: similarity search and clustering for biobank-scale data.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
summaryIn 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. AVAILABILITY AND IMPLEMENTATION: 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.
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