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arXiv · 2403.19718

A Python library for efficient computation of molecular fingerprints

Michał Szafarczyk·Piotr Ludynia·Przemysław Kukla
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Abstract

Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for vectorizing chemical molecules as a part of preprocessing in this kind of solution. However, despite their popularity, there are no libraries that implement them efficiently for large datasets, utilizing modern, multicore architectures. On top of that, most of them do not provide the user with an intuitive interface, or one that would be compatible with other machine learning tools. In this project, we created a Python library that computes molecular fingerprints efficiently and delivers an interface that is comprehensive and enables the user to easily incorporate the library into their existing machine learning workflow. The library enables the user to perform computation on large datasets using parallelism. Because of that, it is possible to perform such tasks as hyperparameter tuning in a reasonable time. We describe tools used in implementation of the library and asses its time performance on example benchmark datasets. Additionally, we show that using molecular fingerprints we can achieve results comparable to state-of-the-art ML solutions even with very simple models.

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Michał Szafarczyk, Piotr Ludynia, Przemysław Kukla. 2024-03-27. A Python library for efficient computation of molecular fingerprints. https://arxiv.org/abs/2403.19718

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