scholarly journals A parallel data clustering algorithm for Intel MIC accelerators

2019 ◽  
pp. 104-115
Author(s):  
Т.В. Речкалов ◽  
М.Л. Цымблер
Keyword(s):  
Dna Microarrays ◽  
Clustering Algorithm ◽  
Real Data ◽  
Data Sets ◽  
Data Layout ◽  
Partitioning Around Medoids ◽  
Wide Range ◽  
Input Dataset ◽  
Intel Mic ◽  
Many Integrated Core

Алгоритм PAM (Partitioning Around Medoids) представляет собой разделительный алгоритм кластеризации, в котором в качестве центров кластеров выбираются только кластеризуемые объекты (медоиды). Кластеризация на основе техники медоидов применяется в широком спектре приложений: сегментирование медицинских и спутниковых изображений, анализ ДНК-микрочипов и текстов и др. На сегодня имеются параллельные реализации PAM для систем GPU и FPGA, но отсутствуют таковые для многоядерных ускорителей архитектуры Intel Many Integrated Core (MIC). В настоящей статье предлагается новый параллельный алгоритм кластеризации PhiPAM для ускорителей Intel MIC. Вычисления распараллеливаются с помощью технологии OpenMP. Алгоритм предполагает использование специализированной компоновки данных в памяти и техники тайлинга, позволяющих эффективно векторизовать вычисления на системах Intel MIC. Эксперименты, проведенные на реальных наборах данных, показали хорошую масштабируемость алгоритма. The PAM (Partitioning Around Medoids) is a partitioning clustering algorithm where each cluster is represented by an object from the input dataset (called a medoid). The medoid-based clustering is used in a wide range of applications: the segmentation of medical and satellite images, the analysis of DNA microarrays and texts, etc. Currently, there are parallel implementations of PAM for GPU and FPGA systems, but not for Intel Many Integrated Core (MIC) accelerators. In this paper, we propose a novel parallel PhiPAM clustering algorithm for Intel MIC systems. Computations are parallelized by the OpenMP technology. The algorithm exploits a sophisticated memory data layout and loop tiling technique, which allows one to efficiently vectorize computations with Intel MIC. Experiments performed on real data sets show a good scalability of the algorithm.

scholarly journals Self-Adaptive K-Means Based on a Covering Algorithm

Complexity ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-16 ◽  
Author(s):  
Yiwen Zhang ◽  
Yuanyuan Zhou ◽  
Xing Guo ◽  
Jintao Wu ◽  
Qiang He ◽  
...  
Keyword(s):  
Large Scale ◽  
Clustering Algorithm ◽  
Real Data ◽  
Second Phase ◽  
Data Sets ◽  
Number Of Clusters ◽  
Large Scale Data ◽  
Long Time ◽  
Two Phases ◽  
Selection Of

The K-means algorithm is one of the ten classic algorithms in the area of data mining and has been studied by researchers in numerous fields for a long time. However, the value of the clustering number k in the K-means algorithm is not always easy to be determined, and the selection of the initial centers is vulnerable to outliers. This paper proposes an improved K-means clustering algorithm called the covering K-means algorithm (C-K-means). The C-K-means algorithm can not only acquire efficient and accurate clustering results but also self-adaptively provide a reasonable numbers of clusters based on the data features. It includes two phases: the initialization of the covering algorithm (CA) and the Lloyd iteration of the K-means. The first phase executes the CA. CA self-organizes and recognizes the number of clusters k based on the similarities in the data, and it requires neither the number of clusters to be prespecified nor the initial centers to be manually selected. Therefore, it has a “blind” feature, that is, k is not preselected. The second phase performs the Lloyd iteration based on the results of the first phase. The C-K-means algorithm combines the advantages of CA and K-means. Experiments are carried out on the Spark platform, and the results verify the good scalability of the C-K-means algorithm. This algorithm can effectively solve the problem of large-scale data clustering. Extensive experiments on real data sets show that the accuracy and efficiency of the C-K-means algorithm outperforms the existing algorithms under both sequential and parallel conditions.

scholarly journals CAMISIM: Simulating metagenomes and microbial communities

2018 ◽  
Author(s):  
Adrian Fritz ◽  
Peter Hofmann ◽  
Stephan Majda ◽  
Eik Dahms ◽  
Johannes Dröge ◽  
...  
Keyword(s):  
Microbial Communities ◽  
De Novo ◽  
Real Data ◽  
Small Data ◽  
Data Sets ◽  
Sequencing Data ◽  
Taxonomic Profiling ◽  
Benchmark Data ◽  
Sequencing Technologies ◽  
Wide Range

Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. Here, we describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series and differential abundance studies, includes real and simulated strain-level diversity, and generates second and third generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT and metaSPAdes, on several thousand small data sets generated with CAMISIM. CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with truth standards for method evaluation. All data sets and the software are freely available at: https://github.com/CAMI-challenge/CAMISIM

A new stochastic gradient descent possibilistic clustering algorithm

2021 ◽  
pp. 1-18
Author(s):  
Angeliki Koutsimpela ◽  
Konstantinos D. Koutroumbas
Keyword(s):  
Cost Function ◽  
Gradient Descent ◽  
Clustering Algorithm ◽  
Clustering Algorithms ◽  
Real Data ◽  
Stochastic Gradient ◽  
Stochastic Gradient Descent ◽  
Data Sets ◽  
Convergence Results ◽  
Possibilistic Clustering

Several well known clustering algorithms have their own online counterparts, in order to deal effectively with the big data issue, as well as with the case where the data become available in a streaming fashion. However, very few of them follow the stochastic gradient descent philosophy, despite the fact that the latter enjoys certain practical advantages (such as the possibility of (a) running faster than their batch processing counterparts and (b) escaping from local minima of the associated cost function), while, in addition, strong theoretical convergence results have been established for it. In this paper a novel stochastic gradient descent possibilistic clustering algorithm, called O- PCM 2 is introduced. The algorithm is presented in detail and it is rigorously proved that the gradient of the associated cost function tends to zero in the L 2 sense, based on general convergence results established for the family of the stochastic gradient descent algorithms. Furthermore, an additional discussion is provided on the nature of the points where the algorithm may converge. Finally, the performance of the proposed algorithm is tested against other related algorithms, on the basis of both synthetic and real data sets.

scholarly journals Endmember Learning with K-Means through SCD Model in Hyperspectral Scene Reconstructions

2019 ◽  
Vol 5 (11) ◽  
pp. 85 ◽  
Author(s):  
Ayan Chatterjee ◽  
Peter W. T. Yuen
Keyword(s):  
Dictionary Learning ◽  
Sparse Coding ◽  
Clustering Algorithm ◽  
Matching Pursuit ◽  
Orthogonal Matching Pursuit ◽  
Scene Reconstruction ◽  
Data Sets ◽  
Practical Applications ◽  
Input Dataset ◽  
Better Than

This paper proposes a simple yet effective method for improving the efficiency of sparse coding dictionary learning (DL) with an implication of enhancing the ultimate usefulness of compressive sensing (CS) technology for practical applications, such as in hyperspectral imaging (HSI) scene reconstruction. CS is the technique which allows sparse signals to be decomposed into a sparse representation “a” of a dictionary D u . The goodness of the learnt dictionary has direct impacts on the quality of the end results, e.g., in the HSI scene reconstructions. This paper proposes the construction of a concise and comprehensive dictionary by using the cluster centres of the input dataset, and then a greedy approach is adopted to learn all elements within this dictionary. The proposed method consists of an unsupervised clustering algorithm (K-Means), and it is then coupled with an advanced sparse coding dictionary (SCD) method such as the basis pursuit algorithm (orthogonal matching pursuit, OMP) for the dictionary learning. The effectiveness of the proposed K-Means Sparse Coding Dictionary (KMSCD) is illustrated through the reconstructions of several publicly available HSI scenes. The results have shown that the proposed KMSCD achieves ~40% greater accuracy, 5 times faster convergence and is twice as robust as that of the classic Spare Coding Dictionary (C-SCD) method that adopts random sampling of data for the dictionary learning. Over the five data sets that have been employed in this study, it is seen that the proposed KMSCD is capable of reconstructing these scenes with mean accuracies of approximately 20–500% better than all competing algorithms adopted in this work. Furthermore, the reconstruction efficiency of trace materials in the scene has been assessed: it is shown that the KMSCD is capable of recovering ~12% better than that of the C-SCD. These results suggest that the proposed DL using a simple clustering method for the construction of the dictionary has been shown to enhance the scene reconstruction substantially. When the proposed KMSCD is incorporated with the Fast non-negative orthogonal matching pursuit (FNNOMP) to constrain the maximum number of materials to coexist in a pixel to four, experiments have shown that it achieves approximately ten times better than that constrained by using the widely employed TMM algorithm. This may suggest that the proposed DL method using KMSCD and together with the FNNOMP will be more suitable to be the material allocation module of HSI scene simulators like the CameoSim package.

An efficient trajectory-clustering algorithm based on an index tree

2011 ◽  
Vol 34 (7) ◽  
pp. 850-861 ◽  
Author(s):  
Guan Yuan ◽  
Shixiong Xia ◽  
Lei Zhang ◽  
Yong Zhou ◽  
Cheng Ji
Keyword(s):  
Radio Frequency Identification ◽  
Clustering Algorithm ◽  
Real Data ◽  
Structural Similarity ◽  
Location Based Services ◽  
Similarity Function ◽  
Data Sets ◽  
Trajectory Clustering ◽  
Trajectory Data ◽  
Index Tree

With the development of location-based services, such as the Global Positioning System and Radio Frequency Identification, a great deal of trajectory data can be collected. Therefore, how to mine knowledge from these data has become an attractive topic. In this paper, we propose an efficient trajectory-clustering algorithm based on an index tree. Firstly, an index tree is proposed to store trajectories and their similarity matrix, with which trajectories can be retrieved efficiently; secondly, a new conception of trajectory structure is introduced to analyse both the internal and external features of trajectories; then, trajectories are partitioned into trajectory segments according to their corners; furthermore, the similarity between every trajectory segment pairs is compared by presenting the structural similarity function; finally, trajectory segments are grouped into different clusters according to their location in the different levels of the index tree. Experimental results on real data sets demonstrate not only the efficiency and effectiveness of our algorithm, but also the great flexibility that feature sensitivity can be adjusted by different parameters, and the cluster results are more practically significant.

scholarly journals Algorithm to forming a rule base for a fuzzy classifier designed on the basis of the K-means clustering algorithm and the whale optimization algorithm

2021 ◽  
Vol 24 (1) ◽  
pp. 42-47
Author(s):  
N. P. Koryshev ◽  
◽  
I. A. Hodashinsky ◽  
Keyword(s):  
Data Clustering ◽  
Clustering Algorithm ◽  
Performance Testing ◽  
Real Data ◽  
Rule Base ◽  
Data Sets ◽  
Fuzzy Classifier ◽  
Whale Optimization ◽  
Clustering Quality ◽  
Using Data

The article presents a description of the algorithm for generating fuzzy rules for a fuzzy classifier using data clustering, metaheuristic, and the clustering quality index, as well as the results of performance testing on real data sets.

scholarly journals A new approach to the fuzzy c-means clustering algorithm by automatic weights and local clustering

2021 ◽  
Vol 3 (1) ◽  
pp. 1-7
Author(s):  
Yadgar Sirwan Abdulrahman
Keyword(s):  
Clustering Algorithm ◽  
Similarity Criterion ◽  
Real Data ◽  
Well Being ◽  
Classical Solutions ◽  
Data Sets ◽  
Data Set ◽  
New Approach ◽  
Fuzzy C Means Clustering ◽  
Global And Local

Clustering is one of the essential strategies in data analysis. In classical solutions, all features are assumed to contribute equally to the data clustering. Of course, some features are more important than others in real data sets. As a result, essential features will have a more significant impact on identifying optimal clusters than other features. In this article, a fuzzy clustering algorithm with local automatic weighting is presented. The proposed algorithm has many advantages such as: 1) the weights perform features locally, meaning that each cluster's weight is different from the rest. 2) calculating the distance between the samples using a non-euclidian similarity criterion to reduce the noise effect. 3) the weight of the features is obtained comparatively during the learning process. In this study, mathematical analyzes were done to obtain the clustering centers well-being and the features' weights. Experiments were done on the data set range to represent the progressive algorithm's efficiency compared to other proposed algorithms with global and local features

scholarly journals GRAPH BASED CLUSTERING WITH CONSTRAINTS AND ACTIVE LEARNING

2021 ◽  
Vol 37 (1) ◽  
pp. 71-89
Author(s):  
Vu-Tuan Dang ◽  
Viet-Vu Vu ◽  
Hong-Quan Do ◽  
Thi Kieu Oanh Le
Keyword(s):  
Active Learning ◽  
Clustering Algorithm ◽  
Side Information ◽  
Clustering Algorithms ◽  
Real Data ◽  
Data Sets ◽  
Data Set ◽  
Supervised Clustering ◽  
Class Labels ◽  
Graph Based Clustering

During the past few years, semi-supervised clustering has emerged as a new interesting direction in machine learning research. In a semi-supervised clustering algorithm, the clustering results can be significantly improved by using side information, which is available or collected from users. There are two main kinds of side information that can be learned in semi-supervised clustering algorithms: the class labels - called seeds or the pairwise constraints. The first semi-supervised clustering was introduced in 2000, and since that, many algorithms have been presented in literature. However, it is not easy to use both types of side information in the same algorithm. To address the problem, this paper proposes a semi-supervised graph based clustering algorithm that tries to use seeds and constraints in the clustering process, called MCSSGC. Moreover, we introduces a simple but efficient active learning method to collect the constraints that can boost the performance of MCSSGC, named KMMFFQS. In order to verify effectiveness of the proposed algorithm, we conducted a series of experiments not only on real data sets from UCI, but also on a document data set applied in an Information Extraction of Vietnamese documents. These obtained results show that the proposed algorithm can significantly improve the clustering process compared to some recent algorithms.

scholarly journals Clusterdv, a simple density-based clustering method that is robust, general and automatic

2017 ◽  
Author(s):  
João C. Marques ◽  
Michael B. Orger
Keyword(s):  
Clustering Algorithm ◽  
Underlying Structure ◽  
Data Sets ◽  
Natural Phenomena ◽  
Cluster Number ◽  
Data Set ◽  
Density Peaks ◽  
Wide Range ◽  
Cluster Shape ◽  
Fully Automatic

AbstractHow to partition a data set into a set of distinct clusters is a ubiquitous and challenging problem. The fact that data varies widely in features such as cluster shape, cluster number, density distribution, background noise, outliers and degree of overlap, makes it difficult to find a single algorithm that can be broadly applied. One recent method, clusterdp, based on search of density peaks, can be applied successfully to cluster many kinds of data, but it is not fully automatic, and fails on some simple data distributions. We propose an alternative approach, clusterdv, which estimates density dips between points, and allows robust determination of cluster number and distribution across a wide range of data, without any manual parameter adjustment. We show that this method is able to solve a range of synthetic and experimental data sets, where the underlying structure is known, and identifies consistent and meaningful clusters in new behavioral data.Author summarIt is common that natural phenomena produce groupings, or clusters, in data, that can reveal the underlying processes. However, the form of these clusters can vary arbitrarily, making it challenging to find a single algorithm that identifies their structure correctly, without prior knowledge of the number of groupings or their distribution. We describe a simple clustering algorithm that is fully automatic and is able to correctly identify the number and shape of groupings in data of many types. We expect this algorithm to be useful in finding unknown natural phenomena present in data from a wide range of scientific fields.

scholarly journals A Global-Relationship Dissimilarity Measure for thek-Modes Clustering Algorithm

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Hongfang Zhou ◽  
Yihui Zhang ◽  
Yibin Liu
Keyword(s):  
Categorical Data ◽  
Clustering Algorithm ◽  
Real Data ◽  
Dissimilarity Measure ◽  
Data Sets ◽  
Dissimilarity Measures

Thek-modes clustering algorithm has been widely used to cluster categorical data. In this paper, we firstly analyzed thek-modes algorithm and its dissimilarity measure. Based on this, we then proposed a novel dissimilarity measure, which is named as GRD. GRD considers not only the relationships between the object and all cluster modes but also the differences of different attributes. Finally the experiments were made on four real data sets from UCI. And the corresponding results show that GRD achieves better performance than two existing dissimilarity measures used ink-modes and Cao’s algorithms.

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