Performance comparison of gene family clustering methods with expert curated gene family data set in Arabidopsis thaliana

Planta ◽  
2008 ◽  
Vol 228 (3) ◽  
pp. 439-447 ◽  
Author(s):  
Kuan Yang ◽  
Liqing Zhang
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Performance Comparison ◽  
Family Data ◽  
Clustering Methods ◽  
Data Set

scholarly journals Performance Comparison with Hierarchical and Partitional Clustering Methods

2021 ◽  
Vol 20 ◽  
pp. 177-184
Author(s):  
Ozer Ozdemir ◽  
Simgenur Cerman
Keyword(s):  
Data Mining ◽  
Hierarchical Clustering ◽  
Clustering Algorithms ◽  
Performance Comparison ◽  
Hierarchical Partitioning ◽  
Clustering Methods ◽  
Data Set ◽  
Partitional Clustering ◽  
Statistical Programming ◽  
Using Data

In data mining, one of the commonly-used techniques is the clustering. Clustering can be done by the different algorithms such as hierarchical, partitioning, grid, density and graph based algorithms. In this study first of all the concept of data mining explained, then giving information the aims of using data mining and the areas of using and then clustering and clustering algorithms that used in data mining are explained theoretically. Ultimately within the scope of this study, "Mall Customers" data set that taken from Kaggle database, based partitioned clustering and hierarchical clustering algorithms aimed at the separation of clusters according to their costumers features. In the clusters obtained by the partitional clustering algorithms, the similarity within the cluster is maximum and the similarity between the clusters is minimum. The hierarchical clustering algorithms is based on the gathering of similar features or vice versa. The partitional clustering algorithms used; k-means and PAM, hierarchical clustering algorithms used; AGNES and DIANA are algorithms. In this study, R statistical programming language was used in the application of algorithms. At the end of the study, the data set was run with clustering algorithms and the obtained analysis results were interpreted.

scholarly journals Sequence Characterization of Glutamate Receptor Genes of Rat a Vertebrate and Arabidopsis Thaliana a Plant

2018 ◽  
Author(s):  
Antara Sengupta ◽  
Pabitra Pal Choudhury ◽  
Subhadip Chakraborty
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Phylogenetic Trees ◽  
Chemical Properties ◽  
Protein Sequences ◽  
Data Set ◽  
Sequence Characterization ◽  
Conserved Regions ◽  
Long Course

AbstractiGluR gene family of a vertebrate, Rat and AtGLR gene family of a plant, Arabidopsis thaliana [4] perform some common functionalities in neuro-transmission, which have been compared quantitatively. Our attempt is based on the chemical properties of amino acids [6, 7, 8] comprising the primary protein sequences of the aforesaid genes. 19 AtGLR genes of length varying from 808 amino acid (aa) to 1039 aa and 16 iGluR genes length varying from 902aa to 1482 aa have been taken as data sets. Thus, we detected the commonalities (conserved elements) during the long evolution of plants and animals from a common ancestor [4]. Eight different conserved regions have been found based on individual amino acids. Two different conserved regions are also found, which are based on chemical groups of amino acids. We have tried too to find different possible patterns which are common throughout the data set taken. 9 such patterns have been found with size varying from 2 to 5 amino acids at different regions in each primary protein sequences. Phylogenetic trees of AtGLR and iGluR families have also been constructed. This approach is likely to shed light on the long course of evolution.

scholarly journals Microarchitectural Characterization on a Mobile Workload

2021 ◽  
Vol 11 (3) ◽  
pp. 1225
Author(s):  
Woohyong Lee ◽  
Jiyoung Lee ◽  
Bo Kyung Park ◽  
R. Young Chul Kim
Keyword(s):  
Performance Monitoring ◽  
Performance Metrics ◽  
Performance Comparison ◽  
Instruction Level Parallelism ◽  
Data Set ◽  
Performance Events ◽  
Hardware Performance Counters ◽  
On Chip ◽  
The Comparative Study ◽  
Level Parallelism

Geekbench is one of the most referenced cross-platform benchmarks in the mobile world. Most of its workloads are synthetic but some of them aim to simulate real-world behavior. In the mobile world, its microarchitectural behavior has been reported rarely since the hardware profiling features are limited to the public. As a popular mobile performance workload, it is hard to find Geekbench’s microarchitecture characteristics in mobile devices. In this paper, a thorough experimental study of Geekbench performance characterization is reported with detailed performance metrics. This study also identifies mobile system on chip (SoC) microarchitecture impacts, such as the cache subsystem, instruction-level parallelism, and branch performance. After the study, we could understand the bottleneck of workloads, especially in the cache sub-system. This means that the change of data set size directly impacts performance score significantly in some systems and will ruin the fairness of the CPU benchmark. In the experiment, Samsung’s Exynos9820-based platform was used as the tested device with Android Native Development Kit (NDK) built binaries. The Exynos9820 is a superscalar processor capable of dual issuing some instructions. To help performance analysis, we enable the capability to collect performance events with performance monitoring unit (PMU) registers. The PMU is a set of hardware performance counters which are built into microprocessors to store the counts of hardware-related activities. Throughout the experiment, functional and microarchitectural performance profiles were fully studied. This paper describes the details of the mobile performance studies above. In our experiment, the ARM DS5 tool was used for collecting runtime PMU profiles including OS-level performance data. After the comparative study is completed, users will understand more about the mobile architecture behavior, and this will help to evaluate which benchmark is preferable for fair performance comparison.

SEMIPARAMETRIC CLUSTERING METHOD FOR MICROARRAY DATA ANALYSIS

2008 ◽  
Vol 06 (02) ◽  
pp. 261-282 ◽  
Author(s):  
AO YUAN ◽  
WENQING HE
Keyword(s):  
Data Analysis ◽  
Microarray Data ◽  
Mixture Distribution ◽  
Information Criterion ◽  
Optimal Number ◽  
Microarray Data Analysis ◽  
Parametric Methods ◽  
Clustering Methods ◽  
Microarray Gene Expression ◽  
Data Set

Clustering is a major tool for microarray gene expression data analysis. The existing clustering methods fall mainly into two categories: parametric and nonparametric. The parametric methods generally assume a mixture of parametric subdistributions. When the mixture distribution approximately fits the true data generating mechanism, the parametric methods perform well, but not so when there is nonnegligible deviation between them. On the other hand, the nonparametric methods, which usually do not make distributional assumptions, are robust but pay the price for efficiency loss. In an attempt to utilize the known mixture form to increase efficiency, and to free assumptions about the unknown subdistributions to enhance robustness, we propose a semiparametric method for clustering. The proposed approach possesses the form of parametric mixture, with no assumptions to the subdistributions. The subdistributions are estimated nonparametrically, with constraints just being imposed on the modes. An expectation-maximization (EM) algorithm along with a classification step is invoked to cluster the data, and a modified Bayesian information criterion (BIC) is employed to guide the determination of the optimal number of clusters. Simulation studies are conducted to assess the performance and the robustness of the proposed method. The results show that the proposed method yields reasonable partition of the data. As an illustration, the proposed method is applied to a real microarray data set to cluster genes.

scholarly journals A simple clustering technique to extract subsets of data for function approximation

2015 ◽  
Vol 17 (5) ◽  
pp. 719-732
Author(s):  
Dulakshi Santhusitha Kumari Karunasingha ◽  
Shie-Yui Liong
Keyword(s):  
Function Approximation ◽  
Prediction Models ◽  
Data Extraction ◽  
Single Parameter ◽  
Subtractive Clustering ◽  
Data Sets ◽  
Clustering Methods ◽  
Clustering Method ◽  
Data Set ◽  
Functional Relationships

A simple clustering method is proposed for extracting representative subsets from lengthy data sets. The main purpose of the extracted subset of data is to use it to build prediction models (of the form of approximating functional relationships) instead of using the entire large data set. Such smaller subsets of data are often required in exploratory analysis stages of studies that involve resource consuming investigations. A few recent studies have used a subtractive clustering method (SCM) for such data extraction, in the absence of clustering methods for function approximation. SCM, however, requires several parameters to be specified. This study proposes a clustering method, which requires only a single parameter to be specified, yet it is shown to be as effective as the SCM. A method to find suitable values for the parameter is also proposed. Due to having only a single parameter, using the proposed clustering method is shown to be orders of magnitudes more efficient than using SCM. The effectiveness of the proposed method is demonstrated on phase space prediction of three univariate time series and prediction of two multivariate data sets. Some drawbacks of SCM when applied for data extraction are identified, and the proposed method is shown to be a solution for them.

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