DENCLUE-IM: A New Approach for Big Data Clustering

AbstractEvery day, a large volume of data is generated by multiple sources, social networks, mobile devices, etc. This variety of data sources produce an heterogeneous data, which are engendered in high frequency. One of the techniques allowing to a better use and exploit this kind of complex data is clustering. Finding a compromise between performance and speed response time present a major challenge to classify this monstrous data. For this purpose, we propose an efficient algorithm which is an improved version of DENCLUE, called DENCLUE-IM. The idea behind is to speed calculation by avoiding the crucial step in DENCLUE which is the Hill Climbing step. Experimental results using large datasets proves the efficiency of our proposed algorithm

Gene-Based Clustering Algorithms: Comparison Between Denclue, Fuzzy-C, and BIRCH

The current study seeks to compare 3 clustering algorithms that can be used in gene-based bioinformatics research to understand disease networks, protein-protein interaction networks, and gene expression data. Denclue, Fuzzy-C, and Balanced Iterative and Clustering using Hierarchies (BIRCH) were the 3 gene-based clustering algorithms selected. These algorithms were explored in relation to the subfield of bioinformatics that analyzes omics data, which include but are not limited to genomics, proteomics, metagenomics, transcriptomics, and metabolomics data. The objective was to compare the efficacy of the 3 algorithms and determine their strength and drawbacks. Result of the review showed that unlike Denclue and Fuzzy-C which are more efficient in handling noisy data, BIRCH can handle data set with outliers and have a better time complexity

A Survey of Some Density Based Clustering Techniques

Density Based Clustering are a type of Clustering methods using in data mining for extracting previously unknown patterns from data sets. There are a number of density based clustering methods such as DBSCAN, OPTICS, DENCLUE, VDBSCAN, DVBSCAN, DBCLASD and ST-DBSCAN. In this paper, a study of these methods is done along with their characteristics, advantages and disadvantages and most importantly, their applicability to different types of data sets to mine useful and appropriate patterns.Comment: 4 pages, 1 figure, conference pape

Density-based algorithms for active and anytime clustering

Data intensive applications like biology, medicine, and neuroscience require effective and efficient data mining technologies. Advanced data acquisition methods produce a constantly increasing volume and complexity. As a consequence, the need of new data mining technologies to deal with complex data has emerged during the last decades. In this thesis, we focus on the data mining task of clustering in which objects are separated in different groups (clusters) such that objects inside a cluster are more similar than objects in different clusters. Particularly, we consider density-based clustering algorithms and their applications in biomedicine. The core idea of the density-based clustering algorithm DBSCAN is that each object within a cluster must have a certain number of other objects inside its neighborhood. Compared with other clustering algorithms, DBSCAN has many attractive benefits, e.g., it can detect clusters with arbitrary shape and is robust to outliers, etc. Thus, DBSCAN has attracted a lot of research interest during the last decades with many extensions and applications. In the first part of this thesis, we aim at developing new algorithms based on the DBSCAN paradigm to deal with the new challenges of complex data, particularly expensive distance measures and incomplete availability of the distance matrix. Like many other clustering algorithms, DBSCAN suffers from poor performance when facing expensive distance measures for complex data. To tackle this problem, we propose a new algorithm based on the DBSCAN paradigm, called Anytime Density-based Clustering (A-DBSCAN), that works in an anytime scheme: in contrast to the original batch scheme of DBSCAN, the algorithm A-DBSCAN first produces a quick approximation of the clustering result and then continuously refines the result during the further run. Experts can interrupt the algorithm, examine the results, and choose between (1) stopping the algorithm at any time whenever they are satisfied with the result to save runtime and (2) continuing the algorithm to achieve better results. Such kind of anytime scheme has been proven in the literature as a very useful technique when dealing with time consuming problems. We also introduced an extended version of A-DBSCAN called A-DBSCAN-XS which is more efficient and effective than A-DBSCAN when dealing with expensive distance measures. Since DBSCAN relies on the cardinality of the neighborhood of objects, it requires the full distance matrix to perform. For complex data, these distances are usually expensive, time consuming or even impossible to acquire due to high cost, high time complexity, noisy and missing data, etc. Motivated by these potential difficulties of acquiring the distances among objects, we propose another approach for DBSCAN, called Active Density-based Clustering (Act-DBSCAN). Given a budget limitation B, Act-DBSCAN is only allowed to use up to B pairwise distances ideally to produce the same result as if it has the entire distance matrix at hand. The general idea of Act-DBSCAN is that it actively selects the most promising pairs of objects to calculate the distances between them and tries to approximate as much as possible the desired clustering result with each distance calculation. This scheme provides an efficient way to reduce the total cost needed to perform the clustering. Thus it limits the potential weakness of DBSCAN when dealing with the distance sparseness problem of complex data. As a fundamental data clustering algorithm, density-based clustering has many applications in diverse fields. In the second part of this thesis, we focus on an application of density-based clustering in neuroscience: the segmentation of the white matter fiber tracts in human brain acquired from Diffusion Tensor Imaging (DTI). We propose a model to evaluate the similarity between two fibers as a combination of structural similarity and connectivity-related similarity of fiber tracts. Various distance measure techniques from fields like time-sequence mining are adapted to calculate the structural similarity of fibers. Density-based clustering is used as the segmentation algorithm. We show how A-DBSCAN and A-DBSCAN-XS are used as novel solutions for the segmentation of massive fiber datasets and provide unique features to assist experts during the fiber segmentation process.Datenintensive Anwendungen wie Biologie, Medizin und Neurowissenschaften erfordern effektive und effiziente Data-Mining-Technologien. Erweiterte Methoden der Datenerfassung erzeugen stetig wachsende Datenmengen und Komplexit\"at. In den letzten Jahrzehnten hat sich daher ein Bedarf an neuen Data-Mining-Technologien f\"ur komplexe Daten ergeben. In dieser Arbeit konzentrieren wir uns auf die Data-Mining-Aufgabe des Clusterings, in der Objekte in verschiedenen Gruppen (Cluster) getrennt werden, so dass Objekte in einem Cluster untereinander viel \"ahnlicher sind als Objekte in verschiedenen Clustern. Insbesondere betrachten wir dichtebasierte Clustering-Algorithmen und ihre Anwendungen in der Biomedizin. Der Kerngedanke des dichtebasierten Clustering-Algorithmus DBSCAN ist, dass jedes Objekt in einem Cluster eine bestimmte Anzahl von anderen Objekten in seiner Nachbarschaft haben muss. Im Vergleich mit anderen Clustering-Algorithmen hat DBSCAN viele attraktive Vorteile, zum Beispiel kann es Cluster mit beliebiger Form erkennen und ist robust gegen\"uber Ausrei{\ss}ern. So hat DBSCAN in den letzten Jahrzehnten gro{\ss}es Forschungsinteresse mit vielen Erweiterungen und Anwendungen auf sich gezogen. Im ersten Teil dieser Arbeit wollen wir auf die Entwicklung neuer Algorithmen eingehen, die auf dem DBSCAN Paradigma basieren, um mit den neuen Herausforderungen der komplexen Daten, insbesondere teurer Abstandsma{\ss}e und unvollst\"andiger Verf\"ugbarkeit der Distanzmatrix umzugehen. Wie viele andere Clustering-Algorithmen leidet DBSCAN an schlechter Per- formanz, wenn es teuren Abstandsma{\ss}en f\"ur komplexe Daten gegen\"uber steht. Um dieses Problem zu l\"osen, schlagen wir einen neuen Algorithmus vor, der auf dem DBSCAN Paradigma basiert, genannt Anytime Density-based Clustering (A-DBSCAN), der mit einem Anytime Schema funktioniert. Im Gegensatz zu dem urspr\"unglichen Schema DBSCAN, erzeugt der Algorithmus A-DBSCAN zuerst eine schnelle Ann\"aherung des Clusterings-Ergebnisses und verfeinert dann kontinuierlich das Ergebnis im weiteren Verlauf. Experten k\"onnen den Algorithmus unterbrechen, die Ergebnisse pr\"ufen und w\"ahlen zwischen (1) Anhalten des Algorithmus zu jeder Zeit, wann immer sie mit dem Ergebnis zufrieden sind, um Laufzeit sparen und (2) Fortsetzen des Algorithmus, um bessere Ergebnisse zu erzielen. Eine solche Art eines "Anytime Schemas" ist in der Literatur als eine sehr n\"utzliche Technik erprobt, wenn zeitaufwendige Problemen anfallen. Wir stellen auch eine erweiterte Version von A-DBSCAN als A-DBSCAN-XS vor, die effizienter und effektiver als A-DBSCAN beim Umgang mit teuren Abstandsma{\ss}en ist. Da DBSCAN auf der Kardinalit\"at der Nachbarschaftsobjekte beruht, ist es notwendig, die volle Distanzmatrix auszurechen. F\"ur komplexe Daten sind diese Distanzen in der Regel teuer, zeitaufwendig oder sogar unm\"oglich zu errechnen, aufgrund der hohen Kosten, einer hohen Zeitkomplexit\"at oder verrauschten und fehlende Daten. Motiviert durch diese m\"oglichen Schwierigkeiten der Berechnung von Entfernungen zwischen Objekten, schlagen wir einen anderen Ansatz f\"ur DBSCAN vor, namentlich Active Density-based Clustering (Act-DBSCAN). Bei einer Budgetbegrenzung B, darf Act-DBSCAN nur bis zu B ideale paarweise Distanzen verwenden, um das gleiche Ergebnis zu produzieren, wie wenn es die gesamte Distanzmatrix zur Hand h\"atte. Die allgemeine Idee von Act-DBSCAN ist, dass es aktiv die erfolgversprechendsten Paare von Objekten w\"ahlt, um die Abst\"ande zwischen ihnen zu berechnen, und versucht, sich so viel wie m\"oglich dem gew\"unschten Clustering mit jeder Abstandsberechnung zu n\"ahern. Dieses Schema bietet eine effiziente M\"oglichkeit, die Gesamtkosten der Durchf\"uhrung des Clusterings zu reduzieren. So schr\"ankt sie die potenzielle Schw\"ache des DBSCAN beim Umgang mit dem Distance Sparseness Problem von komplexen Daten ein. Als fundamentaler Clustering-Algorithmus, hat dichte-basiertes Clustering viele Anwendungen in den unterschiedlichen Bereichen. Im zweiten Teil dieser Arbeit konzentrieren wir uns auf eine Anwendung des dichte-basierten Clusterings in den Neurowissenschaften: Die Segmentierung der wei{\ss}en Substanz bei Faserbahnen im menschlichen Gehirn, die vom Diffusion Tensor Imaging (DTI) erfasst werden. Wir schlagen ein Modell vor, um die \"Ahnlichkeit zwischen zwei Fasern als einer Kombination von struktureller und konnektivit\"atsbezogener \"Ahnlichkeit von Faserbahnen zu beurteilen. Verschiedene Abstandsma{\ss}e aus Bereichen wie dem Time-Sequence Mining werden angepasst, um die strukturelle \"Ahnlichkeit von Fasern zu berechnen. Dichte-basiertes Clustering wird als Segmentierungsalgorithmus verwendet. Wir zeigen, wie A-DBSCAN und A-DBSCAN-XS als neuartige L\"osungen f\"ur die Segmentierung von sehr gro{\ss}en Faserdatens\"atzen verwendet werden, und bieten innovative Funktionen, um Experten w\"ahrend des Fasersegmentierungsprozesses zu unterst\"utzen

Semantic Based Information Retrieval System Using Modified Inverse Document Frequency

Today, Information Retrieval (IR) provides users with documents that will satisfy their information need. Word sense ambiguity is a cause of poor performance in IR system. IR performance will be increased if ambiguous words can be correctly disambiguated. Word Sense disambiguation (WSD) is the task to assign the correct meaning to such ambiguous words based on the surrounding context. Various senses provided by WSD process have been used as semantics for indexing the documents to aid the information retrieval system. K-Nearest Neighbour (KNN) is used for effective text classification in WSD process and the Vector Space Model (VSM) is used for IR process. The cosine similarity method is used in both KNN and VSM to calculate the similarity in which term frequency and inverse document frequency (TF-IDF) scheme is used to calculate the weight of each word. There is a challenge that the original TF-IDF scheme eliminates the related senses although there is a related sense. This paper thus proposes the modified TF-IDF method, so called TF-MIDF, to solve the no-relevant problem by modifying the IDF equation to improve the accuracy of IR performance. By comparing the performance between the original IDF scheme and the MIDF scheme, the average precision results of the original TF-IDF method is 71% and the average precision results of the TF-MIDF is 80%. Therefore, the proposed methodology is more precise than the original method while retrieving the relevant documents of the required information

Improved pattern extraction scheme for clustering multidimensional data

Multidimensional data refers to data that contains at least three attributes or dimensions. The availability of huge amount of multidimensional data that has been collected over the years has greatly challenged the ability to digest the data and to gain useful knowledge that would otherwise be lost. Clustering technique has enabled the manipulation of this knowledge to gain an interesting pattern analysis that could benefit the relevant parties. In this study, three crucial challenges in extracting the pattern of the multidimensional data are highlighted: the dimension of huge multidimensional data requires efficient exploration method for the pattern extraction, the need for better mechanisms to test and validate clustering results and the need for more informative visualization to interpret the “best” clusters. Densitybased clustering algorithms such as density-based spatial clustering application with noise (DBSCAN), density clustering (DENCLUE) and kernel fuzzy C-means (KFCM) that use probabilistic similarity function have been introduced by previous works to determine the number of clusters automatically. However, they have difficulties in dealing with clusters of different densities, shapes and size. In addition, they require many parameter inputs that are difficult to determine. Kernel-nearestneighbor (KNN)-density-based clustering including kernel-nearest-neighbor-based clustering (KNNClust) has been proposed to solve the problems of determining smoothing parameters for multidimensional data and to discover cluster with arbitrary shape and densities. However, KNNClust faces problem on clustering data with different size. Therefore, this research proposed a new pattern extraction scheme integrating triangular kernel function and local average density technique called TKC to improve KNN-density-based clustering algorithm. The improved scheme has been validated experimentally with two scenarios: using real multidimensional spatio-temporal data and using various classification datasets. Four different measurements were used to validate the clustering results; Dunn and Silhouette index to assess the quality, F-measure to evaluate the performance of approach in terms of accuracy, ANOVA test to analyze the cluster distribution, and processing time to measure the efficiency. The proposed scheme was benchmarked with other well-known clustering methods including KNNClust, Iterative Local Gaussian Clustering (ILGC), basic k-means, KFCM, DBSCAN and DENCLUE. The results on the classification dataset demonstrated that TKC produced clusters with higher accuracy and more efficient than other clustering methods. In addition, the analysis of the results showed that the proposed TKC scheme is capable of handling multidimensional data, validated by Silhouette and Dunn index which was close to one, indicating reliable results

Density propagation based adaptive multi-density clustering algorithm

This research was supported by the Science & Technology Development Foundation of Jilin Province (Grants Nos. 20160101259JC, 20180201045GX), the National Natural Science Foundation of China (Grants No. 61772227) and the Natural Science Foundation of Xinjiang Province (Grants No. 2015211C127). This resarch is also supported by the Engineering and Physical Sciences Research Council (EPSRC) funded project on New Industrial Systems: Manufacturing Immortality (EP/R020957/1).Peer reviewedPublisher PD