微调扩展相似性指数的替代加权方案

IF 2.3 4区 化学 Q1 SOCIAL WORK Journal of Chemometrics Pub Date : 2024-05-11 DOI:10.1002/cem.3558
Kenneth López Pérez, Anita Rácz, Dávid Bajusz, Camila Gonzalez, Károly Héberger, Ramón Alain Miranda-Quintana
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引用次数: 0

摘要

扩展的相似性指数(即成对相似性的广义化)因其简单、计算速度快以及在多样性挑选等任务中的优越性,近来越来越受到重视。然而,它们在运行时需要优化几个元参数。之前,我们将二元相似性指数扩展到了 "离散非二元 "和 "连续 "数据;现在,我们继续引入并比较多重加权函数。作为一项案例研究,我们通过基于二维描述符、MACCS 和摩根指纹的扩展相似性对 CYP 酶抑制剂(经整理后有 4016 个分子)的相似性进行了表征。为找到最佳加权函数,采用了基于排序差异总和(SRD)和方差分析(ANOVA)的统计工作流程。总体而言,最佳加权函数是分数("frac"),它符合简约原则。我们还找到了最佳扩展相似性指数,并揭示了它们在不同数据集上的差异。我们希望这项工作能为扩展相似性指数的用户提供有关各种权重选项的指导。计算的源代码见 https://github.com/mqcomplab/MultipleComparisons。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Alternative weighting schemes for fine-tuned extended similarity indices

Extended similarity indices (i.e., generalization of pairwise similarity) have recently gained importance because of their simplicity, fast computation, and superiority in tasks like diversity picking. However, they operate with several meta parameters that should be optimized. Earlier, we extended the binary similarity indices to “discrete non-binary” and “continuous” data; now we continue with introducing and comparing multiple weighting functions. As a case study, the similarity of CYP enzyme inhibitors (4016 molecules after curation) was characterized by their extended similarities, based on 2D descriptors, MACCS and Morgan fingerprints. A statistical workflow based on sum of ranking differences (SRD) and analysis of variance (ANOVA) was used for finding the optimal weight function(s). Overall, the best weighting function is the fraction (“frac”), which corresponds to the principle of parsimony. Optimal extended similarity indices were also found, and their differences are revealed across different data sets. We intend this work to be a guideline for users of extended similarity indices regarding the various weighting options available. Source code for the calculations is available at https://github.com/mqcomplab/MultipleComparisons.

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来源期刊
Journal of Chemometrics
Journal of Chemometrics 化学-分析化学
CiteScore
5.20
自引率
8.30%
发文量
78
审稿时长
2 months
期刊介绍: The Journal of Chemometrics is devoted to the rapid publication of original scientific papers, reviews and short communications on fundamental and applied aspects of chemometrics. It also provides a forum for the exchange of information on meetings and other news relevant to the growing community of scientists who are interested in chemometrics and its applications. Short, critical review papers are a particularly important feature of the journal, in view of the multidisciplinary readership at which it is aimed.
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