Topic models are widely used unsupervised models capable of learning topics – weighted lists of words and documents – from large collections of text documents. When topic models are used for discovery of topics in text collections, a question that arises naturally is how well the model-induced topics correspond to topics of interest to the analyst. In this paper we revisit and extend a so far neglected approach to topic model evaluation based on measuring topic coverage – computationally matching model topics with a set of reference topics that models are expected to uncover. The approach is well suited for analyzing models’ performance in topic discovery and for large-scale analysis of both topic models and measures of model quality. We propose new measures of coverage and evaluate, in a series of experiments, different types of topic models on two distinct text domains for which interest for topic discovery exists. The experiments include evaluation of model quality, analysis of coverage of distinct topic categories, and the analysis of the relationship between coverage and other methods of topic model evaluation. The paper contributes a new supervised measure of coverage, and the first unsupervised measure of coverage. The supervised measure achieves topic matching accuracy close to human agreement. The unsupervised measure correlates highly with the supervised one (Spearman’s $\rho \geq 0.95$ ). Other contributions include insights into both topic models and different methods of model evaluation, and the datasets and code for facilitating future research on topic coverage.

Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis. We present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations. MaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/magellan .