Learned Indexing in Proteins: Substituting Complex Distance Calculations with Embedding and Clustering Techniques

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This publication doesn't include Institute of Computer Science. It includes Faculty of Informatics. Official publication website can be found on muni.cz.

OĽHA Jaroslav SLANINÁKOVÁ Terézia GENDIAR Martin ANTOL Matej DOHNAL Vlastislav

Year of publication 2022
Type Article in Proceedings
Conference Similarity Search and Applications, 15th International Conference, SISAP 2022, Bologna, Italy, October 5–7, 2022, Proceedings
MU Faculty or unit

Faculty of Informatics

Web https://link.springer.com/chapter/10.1007/978-3-031-17849-8_22
Doi http://dx.doi.org/10.1007/978-3-031-17849-8_22
Keywords Protein database;Embedding non-vector data;Learned metric index;Similarity search;Machine learning for indexing
Description Despite the constant evolution of similarity searching research, it continues to face challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions. Various machine learning techniques have proven capable of replacing elaborate mathematical models with simple linear functions, often gaining speed and simplicity at the cost of formal guarantees of accuracy and correctness of querying. The authors explore the potential of this research trend by presenting a lightweight solution for the complex problem of 3D protein structure search. The solution consists of three steps – (i) transformation of 3D protein structural information into very compact vectors, (ii) use of a probabilistic model to group these vectors and respond to queries by returning a given number of similar objects, and (iii) a final filtering step which applies basic vector distance functions to refine the result.
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