A heuristic approach to determine an appropriate number of topics in topic modeling

BMC Bioinformatics

Proceedings

Zhichao Liu¹  Yijun Ding¹  Weigong Ge¹  James J Chen¹  Roger Perkins¹  Wen Zou¹  Weizhong Zhao² 

[1] Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 72079, Jefferson, AR, USA;Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 72079, Jefferson, AR, USA;College of Information Engineering, Xiangtan University, Xiangtan, Hunan Province, China;

关键词: Rate of perplexity change (RPC);    perplexity;    topic number;    latent Dirichlet allocation (LDA);   

DOI  :  10.1186/1471-2105-16-S13-S8

来源: Springer

【 摘 要 】

BackgroundTopic modelling is an active research field in machine learning. While mainly used to build models from unstructured textual data, it offers an effective means of data mining where samples represent documents, and different biological endpoints or omics data represent words. Latent Dirichlet Allocation (LDA) is the most commonly used topic modelling method across a wide number of technical fields. However, model development can be arduous and tedious, and requires burdensome and systematic sensitivity studies in order to find the best set of model parameters. Often, time-consuming subjective evaluations are needed to compare models. Currently, research has yielded no easy way to choose the proper number of topics in a model beyond a major iterative approach.Methods and resultsBased on analysis of variation of statistical perplexity during topic modelling, a heuristic approach is proposed in this study to estimate the most appropriate number of topics. Specifically, the rate of perplexity change (RPC) as a function of numbers of topics is proposed as a suitable selector. We test the stability and effectiveness of the proposed method for three markedly different types of grounded-truth datasets: Salmonella next generation sequencing, pharmacological side effects, and textual abstracts on computational biology and bioinformatics (TCBB) from PubMed.ConclusionThe proposed RPC-based method is demonstrated to choose the best number of topics in three numerical experiments of widely different data types, and for databases of very different sizes. The work required was markedly less arduous than if full systematic sensitivity studies had been carried out with number of topics as a parameter. We understand that additional investigation is needed to substantiate the method's theoretical basis, and to establish its generalizability in terms of dataset characteristics.

【 授权许可】

Unknown   
© Zhao et al. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.