Simrec: a similarity measure recommendation system for mixed data clustering algorithms

Clustering algorithm for mixed datasets using density peaks and Self-Organizing Generative Adversarial Networks

Many scientific works on grouping mixed data have chosen different experimental scenarios to structure their findings, which involve deciding from the programming language to the use of real-world and/or simulated datasets and performance measures, for example. Due to these characteristics directly influence the conclusion of the studies and the way new scientific works are proposed, it would be useful to have a wide map with the main choices that have been done by the authors of high-impact scientific documents so that the community can reflect on the thematic direction, identify best practices, and propose new paths for future research. To the best of our knowledge, such a map does not exist, neither a methodological procedure to build it. Therefore, this paper proposes a systematic methodology to reach such maps and provides a wide and in-depth map of the main choices the authors of high-impact scientific documents on mixed data clustering and surrounding studies have done in their experiments. As a result, 160 documents were systematically selected and classified into one of the six class of data clustering approaches, besides individually tabulated. From the tables for each class, we found, for instance, that real-world datasets are used more frequently than simulated ones, the documents used more external indices, followed by internal and relative ones, it is not common for the authors to inform the programming language they have used, except in the partitional class. We also provided the address of the algorithms’ code when they are made available by the authors.

This article introduces a novel clustering algorithm for dealing with mixed and incomplete data descriptions of instances: the A2FCPAntSA algorithm. Unlike previous proposals, this new algorithm uses groups of instances as initial clusters in an agglomerative clustering scheme. It also merges in a single step, all of the most similar clusters. In addition, the proposal incorporates the use of bio-inspired algorithms to refine the obtained clusters. The numerical experiments carried out over several repository datasets display the superiority of the proposal with respect to other state of the art clustering algorithms, for mixed and incomplete data, by considering several dissimilarity measures and supervised cluster validity indexes.

<span>Clustering is a significant approach in data mining, which seeks to find groups or clusters of data. Both numeric and categorical features are frequently used to define the data in real-world applications. Several different clustering algorithms are proposed for the numerical and categorical datasets. In clustering algorithms, the quality of clustering results is evaluated using cluster validation. This paper proposes an efficient clustering algorithm for mixed numerical and categorical data using re-clustering and cluster validation. Initially, the mixed dataset is clustered with four traditional clustering algorithms like expectation-maximization (EM), hierarchical cluster (HC), k-means (KM), and self-organizing map (SOM). These four algorithms are validated, and the best algorithm is selected for re-clustering. It is an iterative process for improving the quality of cluster results. The incorrectly clustered data is iteratively re-clustered and evaluated based on the cluster validation. The performance of the proposed clustering method is evaluated with a real-time dataset in terms of purity, normalized mutual information, rand index, precision, and recall. The experimental results have shown that the proposed reclust algorithm achieves better performance compared to other clustering algorithms.</span>

The mixed data clustering algorithms have been timidly emerging since the end of the last century. One of the last algorithms proposed for this data-type has been KAMILA (KAy-means for MIxed LArge data) algorithm. While the KAMILA has outperformed the previous mixed data algorithms results, it has some gaps. Among them is the definition of numerical and categorical variable weights, which is a user-defined parameter or, by default, equal to one for all features. Hence, we propose an optimization algorithm called Biased Random-Key Genetic Algorithm for Features Weighting (BRKGAFW) to accomplish the weighting of the numerical and categorical variables in the KAMILA algorithm. The experiment relied on six real-world mixed data sets and two baseline algorithms to perform the comparison, which are the KAMILA with default weight definition, and the KAMILA with weight definition done by the traditional genetic algorithm. The results have revealed the proposed algorithm overperformed the baseline algorithms results in all data sets.

Ground truth bias in external cluster validity indices

Mixed data comprises both numeric and categorical features, and mixed datasets occur frequently in many domains, such as health, finance, and marketing. Clustering is often applied to mixed datasets to find structures and to group similar objects for further analysis. However, clustering mixed data is challenging because it is difficult to directly apply mathematical operations, such as summation or averaging, to the feature values of these datasets. In this paper, we present a taxonomy for the study of mixed data clustering algorithms by identifying five major research themes. We then present a state-of-the-art review of the research works within each research theme. We analyze the strengths and weaknesses of these methods with pointers for future research directions. Lastly, we present an in-depth analysis of the overall challenges in this field, highlight open research questions and discuss guidelines to make progress in the field.

Nowadays many applications generate mixed data objects consisting of numerical and categorical attributes. Simultaneously dealing with mixed objects is more challenging and various approaches convert one type to another one to face this issue. But in many cases this leads to information loss. Therefore integrating categorical and numerical attributes sounds reasonable since it keeps the original format of any attribute. In this paper we focus on clustering and especially density-based clustering as one of the well-known clustering approaches well-performed on arbitrary shape clusters. Density-based clustering algorithms require a distance measure to discover dense regions. Therefore we introduce the distance hierarchy as a distance measure appropriate for both categorical and numerical attributes. However setting the parameters regarding any parametric clustering algorithm could be another issue. Therefore we employ minimum description length principle to automate this process.

Mixed datasets consist of both numeric and categorical attributes. Various k-means-based clustering algorithms have been developed for these datasets. Generally, these algorithms use random partition as a starting point, which tends to produce different clustering results for different runs. In this paper, we propose, initKmix, a novel algorithm for finding an initial partition for k-means-based clustering algorithms for mixed datasets. In the initKmix algorithm, a k-means-based clustering algorithm is run many times, and in each run, one of the attributes is used to create initial clusters for that run. The clustering results of various runs are combined to produce the initial partition. This initial partition is then used as a seed to a k-means-based clustering algorithm to cluster mixed data. Experiments with various categorical and mixed datasets showed that initKmix produced accurate and consistent results, and outperformed the random initial partition method and other state-of-the-art initialization methods. Experiments also showed that k-means-based clustering for mixed datasets with initKmix performed similar to or better than many state-of-the-art clustering algorithms for categorical and mixed datasets.

DNA microarray technology is a fundamental tool in gene expression data analysis. The collection of datasets from the technology has underscored the need for quantitative analytical tools to examine such data. Due to the large number of genes and complex gene regulation networks, clustering is a useful exploratory technique for analyzing these data. Many clustering algorithms have been proposed to analyze microarray gene expression data, but very few of them evaluate the quality of the clusters. In this paper, a novel cluster analysis technique has been proposed without considering number of clusters a priori. The method computes a similarity measurement function based on which the clusters are merged and subsequently splits a cluster by computing the degree of separation of the cluster. The process of splitting and merging performs iteratively until the cluster validity index (i.e. DB index) degrades. The experimental result shows that the proposed cluster analysis technique gives comparable results on gene cancer dataset with existing methods. This study may help raise relevant issues in the extraction of meaningful biological information from microarray expression data. Keywords- DNA microarray data, Clustering technique, Cluster validity index, Similarity measurement, Splitting and Merging, Cancer data analysis

Most clustering algorithms have been designed only for pure numerical or pure categorical data sets, while nowadays many applications generate mixed data. It raises the question how to integrate various types of attributes so that one could efficiently group objects without loss of information. It is already well understood that a simple conversion of categorical attributes into a numerical domain is not sufficient since relationships between values such as a certain order are artificially introduced. Leveraging the natural conceptual hierarchy among categorical information, concept trees summarize the categorical attributes. In this paper, we introduce the algorithm ClicoT (CLustering mixed-type data Including COncept Trees) as reported by Behzadi et al. (Advances in Knowledge Discovery and Data Mining, Springer, Cham, 2019) which is based on the minimum description length principle. Profiting of the conceptual hierarchies, ClicoT integrates categorical and numerical attributes by means of a MDL-based objective function. The result of ClicoT is well interpretable since concept trees provide insights into categorical data. Extensive experiments on synthetic and real data sets illustrate that ClicoT is noise-robust and yields well-interpretable results in a short runtime. Moreover, we investigate the impact of concept hierarchies as well as various data characteristics in this paper.

In the field of pattern recognition, the study of the gene expression profiles for different tissue samples over different experimental conditions has became feasible with the arrival of micro-array based technology. In cancer research, classification of tissue samples is necessary for cancer diagnosis, which can be done with the help of micro-array technology. In this article we have presented a multi-objective optimization ( MOO ) based clustering technique utilizing AMOSA ( Archived Multi-Objective Simulated Annealing ) as the underlying optimization strategy for classification of tissue samples from cancer data sets. As objective functions three cluster validity indices namely, XB, PBM, and FCM indices are optimized simultaneously to form more accurate clusters of tissue samples. The presented clustering technique is evaluated for two open source benchmark cancer data sets, which are Brain tumor data set and Adult Malignancy data set. In order to evaluate the quality or goodness of produced clusters two cluster quality measures viz, Adjusted Rand Index ( ARI ) and Classification Accuracy ( %CoA ) are calculated for each data set. Comparative results of the presented clustering algorithm with 10 state-of-the-art existing single-objective, multi-objective based clustering algorithms are shown for two benchmark data sets.

In this work, the agglomerative hierarchical clustering and K-means clustering algorithms are implemented on small datasets. Considering that the selection of the similarity measure is a vital factor in data clustering, two measures are used in this study - cosine similarity measure and Euclidean distance - along with two evaluation metrics - entropy and purity - to assess the clustering quality. The datasets used in this work are taken from UCI machine learning depository. The experimental results indicate that k-means clustering outperformed hierarchical clustering in terms of entropy and purity using cosine similarity measure. However, hierarchical clustering outperformed k-means clustering using Euclidean distance. It is noted that performance of clustering algorithm is highly dependent on the similarity measure. Moreover, as the number of clusters gets reasonably increased, the clustering algorithms’ performance gets higher.

The existence of large volumes of time series data in many applications has motivated data miners to investigate specialized methods for mining time series data. Clustering is a popular data mining method due to its powerful exploratory nature and its usefulness as a preprocessing step for other data mining techniques. This article develops two novel clustering algorithms for time series data that are extensions of a crisp c-shapes algorithm. The two new algorithms are heuristic derivatives of fuzzy c-means (FCM). Fuzzy c-Shapes plus (FCS+) replaces the inner product norm in the FCM model with a shape-based distance function. Fuzzy c-Shapes double plus (FCS++) uses the shape-based distance, and also replaces the FCM cluster centers with shape-extracted prototypes. Numerical experiments on 48 real time series data sets show that the two new algorithms outperform state-of-the-art shape-based clustering algorithms in terms of accuracy and efficiency. Four external cluster validity indices (the Rand index, Adjusted Rand Index, Variation of Information, and Normalized Mutual Information) are used to match candidate partitions generated by each of the studied algorithms. All four indices agree that for these finite waveform data sets, FCS++ gives a small improvement over FCS+, and in turn, FCS+ is better than the original crisp c-shapes method. Finally, we apply two tests of statistical significance to the three algorithms. The Wilcoxon and Friedman statistics both rank the three algorithms in exactly the same way as the four cluster validity indices.

A novel similarity measure based on spatial overlapping relation is proposed in this paper, which calculates the similarity between a pair of data points by using the mutual overlapping relation between them in a multi-dimensional space. A spatial overlapping based hierarchical clustering method SOHC was also developed and implemented aimed to justify the effectiveness of the proposed similarity measure. SOHC works well both in low-dimensional and high-dimensional datasets, and is able to cluster arbitrary shape of clusters. Moreover, it can work for both numerical and categorical attributes in a uniform way. Experimental results carried out on some public datasets collected from the UCI machine learning repository and predictive toxicology domain show that SOHC is a promising clustering method in data mining.