Abstract. The paper discusses a generalization of the nearest centroid hierarchical clustering algorithm. A first extension deals with the incorporation of generic distance-based penalty minimizers instead of the classical aggregation by means of centroids. Due to that the presented algorithm can be applied in spaces equipped with an arbitrary dissimilarity measure (images, DNA sequences, etc.). Secondly, a correction preventing the formation of clusters of too highly unbalanced sizes is applied: just like in the recently introduced Genie approach, which extends the single linkage scheme, the new method averts a chosen inequity measure (e.g., the Gini-, de Vergottini-, or Bonferroni-index) of cluster sizes from raising above a predefined threshold. Numerous benchmarks indicate that the introduction of such a correction increases the quality of the resulting clusterings.
stringiis among the top 10 most downloaded
Rpackages, providing various string processing facilities. A new release comes with a few bugfixes and new features.
* [BUGFIX] #214: allow a regex pattern like `.*` to match an empty string. * [BUGFIX] #210: `stri_replace_all_fixed(c("1", "NULL"), "NULL", NA)` now results in `c("1", NA)`. * [NEW FEATURE] #199: `stri_sub<-` now allows for ignoring `NA` locations (a new `omit_na` argument added). * [NEW FEATURE] #207: `stri_sub<-` now allows for substring insertions (via `length=0`). * [NEW FUNCTION] #124: `stri_subset<-` functions added. * [NEW FEATURE] #216: `stri_detect`, `stri_subset`, `stri_subset<-` gained a `negate` argument. * [NEW FUNCTION] #175: `stri_join_list` concatenates all strings in a list of character vectors. Useful with, e.g., `stri_extract_all_regex`, `stri_extract_all_words` etc.
R. The article has been assigned DOI of 10.1016/j.ins.2016.05.003.
Abstract. The time needed to apply a hierarchical clustering algorithm is most often dominated by the number of computations of a pairwise dissimilarity measure. Such a constraint, for larger data sets, puts at a disadvantage the use of all the classical linkage criteria but the single linkage one. However, it is known that the single linkage clustering algorithm is very sensitive to outliers, produces highly skewed dendrograms, and therefore usually does not reflect the true underlying data structure – unless the clusters are well-separated. To overcome its limitations, we propose a new hierarchical clustering linkage criterion called Genie. Namely, our algorithm links two clusters in such a way that a chosen economic inequity measure (e.g., the Gini- or Bonferroni-index) of the cluster sizes does not increase drastically above a given threshold. The presented benchmarks indicate a high practical usefulness of the introduced method: it most often outperforms the Ward or average linkage in terms of the clustering quality while retaining the single linkage speed. The Genie algorithm is easily parallelizable and thus may be run on multiple threads to speed up its execution further on. Its memory overhead is small: there is no need to precompute the complete distance matrix to perform the computations in order to obtain a desired clustering. It can be applied on arbitrary spaces equipped with a dissimilarity measure, e.g., on real vectors, DNA or protein sequences, images, rankings, informetric data, etc. A reference implementation of the algorithm has been included in the open source genie package for R.
Abstract. The use of supervised learning techniques for fitting weights and/or generator functions of weighted quasi-arithmetic means – a special class of idempotent and nondecreasing aggregation functions – to empirical data has already been considered in a number of papers. Nevertheless, there are still some important issues that have not been discussed in the literature yet. In the first part of this two-part contribution we deal with the concept of regularization, a quite standard technique from machine learning applied so as to increase the fit quality on test and validation data samples. Due to the constraints on the weighting vector, it turns out that quite different methods can be used in the current framework, as compared to regression models. Moreover, it is worth noting that so far fitting weighted quasi-arithmetic means to empirical data has only been performed approximately, via the so-called linearization technique. In this paper we consider exact solutions to such special optimization tasks and indicate cases where linearization leads to much worse solutions.
Keywords. Aggregation functions, weighted quasi-arithmetic means, least squares fitting, regularization, linearization
Abstract. The use of supervised learning techniques for fitting weights and/or generator functions of weighted quasi-arithmetic means – a special class of idempotent and nondecreasing aggregation functions – to empirical data has already been considered in a number of papers. Nevertheless, there are still some important issues that have not been discussed in the literature yet. In the second part of this two-part contribution we deal with a quite common situation in which we have inputs coming from different sources, describing a similar phenomenon, but which have not been properly normalized. In such a case, idempotent and nondecreasing functions cannot be used to aggregate them unless proper pre-processing is performed. The proposed idempotization method, based on the notion of B-splines, allows for an automatic calibration of independent variables. The introduced technique is applied in an R source code plagiarism detection system.
Keywords. Aggregation functions, weighted quasi-arithmetic means, least squares fitting, idempotence
Abstract. We discuss a generalization of the fuzzy (weighted) k-means clustering procedure and point out its relationships with data aggregation in spaces equipped with arbitrary dissimilarity measures. In the proposed setting, a data set partitioning is performed based on the notion of points' proximity to generic distance-based penalty minimizers. Moreover, a new data classification algorithm, resembling the k-nearest neighbors scheme but less computationally and memory demanding, is introduced. Rich examples in complex data domains indicate the usability of the methods and aggregation theory in general.
Keywords. fuzzy k-means algorithm, clustering, classification, fusion functions, penalty minimizers
geniepackage for R (co-authors: Maciej Bartoszuk and Anna Cena). A detailed description of the algorithm will be available in a forthcoming paper of ours.
Abstract: The famous Hirsch index has been introduced just ca. 10 years ago. Despite that, it is already widely used in many decision making tasks, like in evaluation of individual scientists, research grant allocation, or even production planning. It is known that the h-index is related to the discrete Sugeno integral and the Ky Fan metric introduced in 1940s. The aim of this paper is to propose a few modifications of this index as well as other fuzzy integrals -- also on bounded chains -- that lead to better discrimination of some types of data that are to be aggregated. All of the suggested compensation methods try to retain the simplicity of the original measure.
Abstract: The Hirsch's h-index is perhaps the most popular citation-based measure of the scientific excellence. In 2013 G. Ionescu and B. Chopard proposed an agent-based model for this index to describe a publications and citations generation process in an abstract scientific community. With such an approach one can simulate a single scientist's activity, and by extension investigate the whole community of researchers. Even though this approach predicts quite well the h-index from bibliometric data, only a solution based on simulations was given. In this paper, we complete their results with exact, analytic formulas. What is more, due to our exact solution we are able to simplify the Ionescu-Chopard model which allows us to obtain a compact formula for h-index. Moreover, a simulation study designed to compare both, approximated and exact, solutions is included. The last part of this paper presents evaluation of the obtained results on a real-word data set.