Identification of Coherent Generators by Support Vector Clustering With an Embedding Strategy

Clustering is a group of unsupervised statistical techniques commonly used in many disciplines. Considering their applications to fish abundance data, many technical details need to be considered to ensure reasonable interpretation. However, the reliability and stability of the clustering methods have rarely been studied in the contexts of fisheries. This study presents an intensive evaluation of three common clustering methods, including hierarchical clustering (HC), K-means (KM), and expectation-maximization (EM) methods, based on fish community surveys in the coastal waters of Shandong, China. We evaluated the performances of these three methods considering different numbers of clusters, data size, and data transformation approaches, focusing on the consistency validation using the index of average proportion of non-overlap (APN). The results indicate that the three methods tend to be inconsistent in the optimal number of clusters. EM showed relatively better performances to avoid unbalanced classification, whereas HC and KM provided more stable clustering results. Data transformation including scaling, square-root, and log-transformation had substantial influences on the clustering results, especially for KM. Moreover, transformation also influenced clustering stability, wherein scaling tended to provide a stable solution at the same number of clusters. The APN values indicated improved stability with increasing data size, and the effect leveled off over 70 samples in general and most quickly in EM. We conclude that the best clustering method can be chosen depending on the aim of the study and the number of clusters. In general, KM is relatively robust in our tests. We also provide recommendations for future application of clustering analyses. This study is helpful to ensure the credibility of the application and interpretation of clustering methods.

A cluster validity measure with a hybrid parameter search method for the support vector clustering algorithm

In this study, clustering based method for activation detection in functional magnetic resonance imaging (fMRI) is employed. Moreover, some features are obtained by fitting two models namely FIR filter and Gamma function, to hemodynamic response function (HRF). After applying clustering methods (that require number of clusters as an input) to feature space, our simulations show that number of clusters can affect activation detection significantly. Therefore a newly proposed clustering algorithm namely evolving neural gas (ENG) that gives optimal number of clusters is exploited. In addition to ENG, the result of four clustering algorithms namely k-means, fuzzy C-means, neural gas, and clara in different number of clusters are evaluated. The results show that the best activation detection is taken place using obtained optimal number of clusters.

With the development of shale gas reservoirs, various fracture propagation models have been developed to predict hydraulic fracture geometry by considering the stress shadow effects. Also, many researchers have been working on development of various production-simulation approaches to simulate production from the complex fracture geometries. The objective of this study is to combine the fracture propagation modeling and reservoir simulation to optimize production in shale gas reservoirs. First, we have developed a semi-analytical model to simulate shale gas production from the complex non-planar fracture geometry with varying fracture width and fracture permeability along fracture length. The important gas transport mechanisms including gas slippage, gas diffusion, and gas desorption are considered. Second, we integrate the semi-analytical model with a three-dimensional fracture propagation model, which fully couples elastic deformation of the rock and fluid flow to simulate complex hydraulic fracture propagation, to optimize fracture treatment design in Marcellus shale gas reservoirs. Specifically, the fracture propagation model is utilized to predict the more-realistic non-planar fracture geometry with varying fracture width and fracture permeability along fracture length. In this study, the effect of varying number of perforation clusters within a given stage ranging from 2 to 5 on the fracture propagation was investigated. Three values of stage spacing were considered including 100 ft, 200 ft, and 300 ft. After predicting the non-planar fracture geometry, the semi-analytical model is employed to simulate production from such fracture geometries. According to the well productivity, the optimal number of clusters per stage for varying stage spacing is discussed and determined. In addition, we compared the well performance with the optimal number of perforation clusters for the stage spacing of 100 ft, 200 ft, and 300 ft under a given horizontal well length of 2,500 ft. Furthermore, we used the integrated approach to analyze a well performance from Marcellus shale gas reservoirs. Through the field case study, the more-realistic non-planar fracture geometry was quantified. Also, the difference between the non-planar fracture geometry and ideal planar fracture geometry with equal fracture width and fracture half-length was compared. Finally, the optimal fracture treatment design for the field well development was recommended. This work can provide new insights into optimization of number of perforation clusters per stage within a given fracture stage and a better understanding of the non-planar fracture geometry in shale gas reservoirs.

The paper presents a new method for identifying coherent generators under various power-system disturbances. A coherency index, which is introduced by using frequency response of the simplified and linearised power-system model, is proposed for evaluating coherent generators. The method is applied to a power system constructed with ten machines and 39 busbars, and the efficiency of the method is investigated under various system disturbances. The results prove that the proposed method is highly effective in the identification of coherent generators under various system disturbances. Moreover, it is also recognised the case in which various regulator actions and flux that the proposed method may be easily applied to decays may be taken into account

To find an optimal cluster size and number of clusters for a reasonable estimate of the prevalence of cataract blindness in people aged > or = 50 years in 19 rural districts of a state in India. Cluster sampling methodology was used in 19 rural districts of Karnataka State, India. In each district, 15 clusters were randomly selected and 90 people aged > or = 50 years were examined in each cluster. As a result the visual acuity and lens status of a total of 22,218 people were assessed. For each district, the design effect for cluster size ranging from 20 to 90 was calculated and the optimal cluster size and the required number of clusters to achieve an accuracy of 1% errors and 80% confidence was assessed. The age and gender adjusted prevalence of cataract blindness varied from 1.58% to 7.24%, which justifies district level surveys. The design effect is nearly 1.5 for clusters of sizes 30 and 40. With an average prevalence of 4.93% with 1% error and 80% confidence level, the optimal number of clusters is 37 and 28 for a cluster size of 30 and 40 respectively and the average sample size for a district around 1100. Rapid assessments for cataract blindness in those aged > or = 50 years can be conducted at district level in India with existing resources and at affordable costs. These provide reliable data, essential for effective monitoring and planning. Other parameters, for instance, surgical coverage can also be assessed. The availability of standardized software for data entry and analysis and strict adherence to survey procedures is essential.

Unsupervised classification needs no prior knowledge of interested region and has less human interference that is suitable for processing messes of digital images acquired from earth observation satellites. A typical sequence for unsupervised classification might begin with the analyst specifying minimum and maximum numbers of categories to be generated by the classification algorithm. Usually, a larger cluster number is assigned in advance for the initial clustering. Then, several classified clusters are merged into a larger group so that the number of clusters can be reduced. The selection of an appropriate cluster number is up to the analyst's experience. This paper illustrates the convergence of cluster-center optimization and the optimal cluster number varying with the dimension in Minkowski space. One of the simplest and most popular is Euclidean distance while Minkowski distance is measured in two dimensions. The experiment was executed on several digital images by a classifier employing Genetic Algorithm as a searching tool and Davies-Bouldin index as a cluster validity measure. The results show that a smaller dimension, e.g. one-, two-, and infinity dimensions, in Minkowski space derives less clusters, while the assignment of a larger dimension results in a larger cluster number with a more detailed segmentation.

BackgroundCluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing “outliers” among the objects being clustered. Few clustering algorithms currently deal directly with the outlier problem. Furthermore, existing methods for identifying the number of clusters still have some drawbacks. Thus, there is a need for a better algorithm to tackle both challenges.ResultsWe present a new approach, implemented in an R package called Thresher, to cluster objects in general datasets. Thresher combines ideas from principal component analysis, outlier filtering, and von Mises-Fisher mixture models in order to select the optimal number of clusters. We performed a large Monte Carlo simulation study to compare Thresher with other methods for detecting outliers and determining the number of clusters. We found that Thresher had good sensitivity and specificity for detecting and removing outliers. We also found that Thresher is the best method for estimating the optimal number of clusters when the number of objects being clustered is smaller than the number of variables used for clustering. Finally, we applied Thresher and eleven other methods to 25 sets of breast cancer data downloaded from the Gene Expression Omnibus; only Thresher consistently estimated the number of clusters to lie in the range of 4–7 that is consistent with the literature.ConclusionsThresher is effective at automatically detecting and removing outliers. By thus cleaning the data, it produces better estimates of the optimal number of clusters when there are more variables than objects. When we applied Thresher to a variety of breast cancer datasets, it produced estimates that were both self-consistent and consistent with the literature. We expect Thresher to be useful for studying a wide variety of biological datasets.

Past decades have witnessed the advancement of wireless sensor networks (WSNs) in both academic and industrial communities. Clustering is one of the most popular methods to increase the lifespan of WSNs. The optimal number of cluster heads and how to organize the clusters are the most important issues to be addressed in the clustering methods. In this paper, we proposed a novel user-independent and dynamical method to calculate the optimal number of clusters, organize the clusters, and determine the best cluster heads in each round. In this method, efficient energy consumption and link quality were considered to compute the optimal number of clusters. Then, the algorithm began to organize the compact clusters with high energy level cluster heads. We investigated a new fitness function in order to achieve these objectives. A new version of gravitational search algorithm (GSA) was used to solve this optimization problem. In this algorithm, the power distance sums scaling method was applied to calculate the mass values. Then, a fuzzy logic controller is employed to identify the parameter of this algorithm to control the exploitation and exploration abilities of the method during the computational process of the algorithm. Then, the novel version of GSA was applied to reach an appropriate solution for the fitness function, find the optimal number of clusters, and properly organize these clusters. To evaluate the effectiveness of the proposed method, several experiments were performed and the obtained results were compared with the results of other popular clustering methods. The simulation results revealed that the performance of the modified GSA was better than other state-of-the-art meta-heuristic optimization algorithms. Moreover, the proposed method for the clustering problem in WSNs outperformed other popular clustering methods and increased the lifetime of WSNs.

Advances in mass spectrometry-based proteomics have yielded a substantial mapping of the tyrosine phosphoproteome and thus provided an important step toward a systematic analysis of intracellular signaling networks in higher eukaryotes. In this study we decomposed an uncharacterized proteomics data set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid binding.

The use of mixed suspension mixed product removal (MSMPR) system in the pharmaceutical industry to produce active pharmaceutical ingredients is well known. In industrial settings, the MSMPR system is subject to lot of process uncertainty which, if ignored, might result in poor product quality. In this work, the process uncertainty involved in MSMPR is targeted during the process optimization stage to find robust optimal operating conditions. The temperature and the residence time inside each cascaded MSMPR unit, altogether six, are considered as uncertain parameters. A sampled set of uncertain data points for such six different uncertain parameters are clustered using a novel support vector clustering (SVC) based algorithm. The uniqueness of this algorithm lies in its ability to fine‐tune the hyper‐parameters of SVC while intelligently clustering the uncertain data points into optimal number of clusters. Such identified clusters are helpful to generate more samples from the intended regions rather than generating them randomly to avoid proposing conservative solutions. Both best‐case and worst‐case scenarios for robust oOptimization (RO) are considered with , and samples. As the model has to be evaluated for a large number of samples and the MSMPR models are time‐consuming to evaluate, a surrogate model of the MSMPR process is developed to perform optimization under uncertainty. Performance metrics are used to quantitatively establish the superiority of the SVC based RO over the box‐sampling based RO.

A fundamental problem in data clustering is how to determine the correct number of clusters. The k-adaptive medoid set ant colony optimization (ACO) clustering (METACOC-K) algorithm is superior in solving clustering problems. However, METACOC-K does not guarantee in finding the best number of clusters. It assumed the number of clusters based on an adaptive parameter strategy that lacks feedback learning. This has restrained the algorithm in producing compact clusters and the optimal number of clusters. In this paper, a self-adaptive ACO clustering (S-ACOC) algorithm is proposed to produce the optimal number of clusters by incorporating a self-adaptive parameter strategy. The S-ACOC algorithm is a centroid-based algorithm that automatically adjusts the number of clusters during the algorithm run. The selection of the number of clusters is based on a construction graph that reflects the influence of a pheromone in algorithm learning. Experiments were conducted on real-world datasets to evaluate the performance of the proposed algorithm. The external evaluation metrics (purity, F-measure, and entropy) were used to compare the results of the proposed algorithm with other swarm clustering algorithms, including a genetic algorithm (GA), particle swarm optimization (PSO), and METACOC-K. Results showed that S-ACOC provides higher purity (50%) and lower entropy (40%) than GA, PSO, and METACOC-K. Experiments were also performed on several predefined clusters, and results demonstrate that the S-ACOC algorithm is superior to GA, PSO, and METACOC-K. Based on the superior performance, S-ACOC can be used to solve clustering problems in various application domains.

This paper proposes a method of determining the optimal number of clusters dividing the multiple transformations for the purpose of the efficient processing of query against the results of applying the transformations to time series. In this paper, the moving average is used as a transformation for simplicity. The model of query time to the number of clusters is constructed for determining the optimal number of clusters. As the query time could be represented with the concave function of the number of clusters, it is shown that the optimal number of clusters for the best query time can be obtained. The verification experiment confirms the validity of the model constructed. It is revealed that the optimal number of clusters could be determined by the times obtained from a single query execution.

Averaging amplitudes over consecutive time samples (i.e., time window) is widely used to calculate the peak amplitude of event-related potentials (ERPs). Cluster analysis of the spatio-temporal ERP data is a promising tool to determine the time window of an ERP of interest. However, determining an appropriate number of clusters to optimally represent ERPs is still challenging. Here, we develop a new method to estimate the optimal number of clusters utilizing consensus clustering. Various polarity dependent clustering methods, namely, k-means, hierarchical clustering, fuzzy c-means, self-organizing map, spectral clustering, and Gaussian mixture model, are used to configure consensus clustering after assessing them individually. When a range of clusters is applied many times, the optimal number of clusters should correspond to the expectation, which is the average of the obtained mean inner-similarities of estimated time windows across all conditions and groups converge in the satisfactory thresholds. In order to assess our method, the proposed method has been applied to simulated data and prospective memory experiment ERP data aimed to qualify N2 and P3, and N300 and prospective positivity components, respectively. The results of determining the optimal number of clusters meet at six cluster maps for both ERP data. In addition, our results revealed that the proposed method could be reliably applied to ERP data to determine the appropriate time window for the ERP of interest when the measurement interval is not accurately defined.

Conventional clustering methods such as k-means or subtractive clustering need some information include the optimal number of clusters, otherwise, they lead to the poor results. However in many practical situations it is often so difficult to determine the best number of clusters. On the other hand, there are other clustering algorithms such as Rival Penalized Competitive Learning (RPCL) or ISODATA which find the number of clusters automatically. But these clustering methods have a problem in locating the cluster centers appropriately. In this paper, a novel hybrid structure is proposed which uses these two types of clustering algorithms as complementary to improve clustering performance. Moreover, a new weighted version of RPCL algorithm which is called here WRPCL is suggested. This structure not only outperforms the choice of the optimal number of clusters but also improves the performance of the overall clustering result.