A novel method for clustering cellular data to improve classification

Many fields,such as neuroscience,are experiencing the vast prolife ration of cellular data,underscoring the need fo r organizing and interpreting large datasets.A popular approach partitions data into manageable subsets via hierarchical clustering,but objective methods to determine the appropriate classification granularity are missing.We recently introduced a technique to systematically identify when to stop subdividing clusters based on the fundamental principle that cells must differ more between than within clusters.Here we present the corresponding protocol to classify cellular datasets by combining datadriven unsupervised hierarchical clustering with statistical testing.These general-purpose functions are applicable to any cellular dataset that can be organized as two-dimensional matrices of numerical values,including molecula r,physiological,and anatomical datasets.We demonstrate the protocol using cellular data from the Janelia MouseLight project to chara cterize morphological aspects of neurons.

A Shared Natural Neighbors Based-Hierarchical Clustering Algorithm for Discovering Arbitrary-Shaped Clusters

In clustering algorithms,the selection of neighbors significantly affects the quality of the final clustering results.While various neighbor relationships exist,such as K-nearest neighbors,natural neighbors,and shared neighbors,most neighbor relationships can only handle single structural relationships,and the identification accuracy is low for datasets with multiple structures.In life,people’s first instinct for complex things is to divide them into multiple parts to complete.Partitioning the dataset into more sub-graphs is a good idea approach to identifying complex structures.Taking inspiration from this,we propose a novel neighbor method:Shared Natural Neighbors(SNaN).To demonstrate the superiority of this neighbor method,we propose a shared natural neighbors-based hierarchical clustering algorithm for discovering arbitrary-shaped clusters(HC-SNaN).Our algorithm excels in identifying both spherical clusters and manifold clusters.Tested on synthetic datasets and real-world datasets,HC-SNaN demonstrates significant advantages over existing clustering algorithms,particularly when dealing with datasets containing arbitrary shapes.

Inertial Entropy and External Validation of Clusterings

Axiomatization of Shannon entropy is a subject that has received lots of attention in the information theory literature.While Shannon entropy is defined on probability distribution,we define a new type of entropy on the set of partitions of finite subsets of metric spaces,which has a rich algebraic structure as a partially ordered set.We propose an axiomatization of an entropy-like measure of partitions of sets of objects located in metric spaces,and we derive an analytic expression of this new type of entropy referred to as inertial entropy.This approach starts with the notion of inertia of a partition and includes a study of the behavior of the sum of square errors of a partition.In this context,we characterize the chain of partitions produced by the Ward hierarchical clustering method.Starting from inertial entropies of partitions,we introduce conditional entropies which,in turn,generate metrics on partitions of finite sets.These metrics are used as external validation tools for clusterings of labeled data sets.The metric generated by inertial entropy can be used to validate data clustering for labeled data sets.This type of validation aims to determine to what extend labeling of the data coincides with the clustering obtained algorithmically,and we obtain a high degree of consistency of the data labeling with the results of several hierarchical clusterings.

Detection of Residual Yarn in Bobbin Based on Odd Partial Gabor Filter and Multi-Color Space Hierarchical Clustering

In an automatic bobbin management system that simultaneously detects bobbin color and residual yarn,a composite texture segmentation and recognition operation based on an odd partial Gabor filter and multi-color space hierarchical clustering are proposed.Firstly,the parameter-optimized odd partial Gabor filter is used to distinguish bobbin and yarn texture,to explore Garbor parameters for yarn bobbins,and to accurately discriminate frequency characteristics of yarns and texture.Secondly,multi-color clustering segmentation using color spaces such as red,green,blue(RGB)and CIELUV(LUV)solves the problems of over-segmentation and segmentation errors,which are caused by the difficulty of accurately representing the complex and variable color information of yarns in a single-color space and the low contrast between the target and background.Finally,the segmented bobbin is combined with the odd partial Gabor’s edge recognition operator to further distinguish bobbin texture from yarn texture and locate the position and size of the residual yarn.Experimental results show that the method is robust in identifying complex texture,damaged and dyed bobbins,and multi-color yarns.Residual yarn identification can distinguish texture features and residual yarns well and it can be transferred to the detection and differentiation of complex texture,which is significantly better than traditional methods.

Hierarchical hesitant fuzzy K-means clustering algorithm

Due to the limitation and hesitation in one＇s knowledge, the membership degree of an element to a given set usually has a few different values, in which the conventional fuzzy sets are invalid. Hesitant fuzzy sets are a powerful tool to treat this case. The present paper focuses on investigating the clustering technique for hesitant fuzzy sets based on the K-means clustering algorithm which takes the results of hierarchical clustering as the initial clusters. Finally, two examples demonstrate the validity of our algorithm.

Intuitionistic fuzzy hierarchical clustering algorithms

Intuitionistic fuzzy set （IFS） is a set of 2-tuple arguments, each of which is characterized by a membership degree and a nonmembership degree. The generalized form of IFS is interval-valued intuitionistic fuzzy set （IVIFS）, whose components are intervals rather than exact numbers. IFSs and IVIFSs have been found to be very useful to describe vagueness and uncertainty. However, it seems that little attention has been focused on the clustering analysis of IFSs and IVIFSs. An intuitionistic fuzzy hierarchical algorithm is introduced for clustering IFSs, which is based on the traditional hierarchical clustering procedure, the intuitionistic fuzzy aggregation operator, and the basic distance measures between IFSs： the Hamming distance, normalized Hamming, weighted Hamming, the Euclidean distance, the normalized Euclidean distance, and the weighted Euclidean distance. Subsequently, the algorithm is extended for clustering IVIFSs. Finally the algorithm and its extended form are applied to the classifications of building materials and enterprises respectively.

Quality of Service Improvement with Optimal Software-Defined Networking Controller and Control Plane Clustering

The controller is indispensable in software-defined networking(SDN).With several features,controllers monitor the network and respond promptly to dynamic changes.Their performance affects the quality-of-service(QoS)in SDN.Every controller supports a set of features.However,the support of the features may be more prominent in one controller.Moreover,a single controller leads to performance,single-point-of-failure(SPOF),and scalability problems.To overcome this,a controller with an optimum feature set must be available for SDN.Furthermore,a cluster of optimum feature set controllers will overcome an SPOF and improve the QoS in SDN.Herein,leveraging an analytical network process(ANP),we rank SDN controllers regarding their supporting features and create a hierarchical control plane based cluster(HCPC)of the highly ranked controller computed using the ANP,evaluating their performance for the OS3E topology.The results demonstrated in Mininet reveal that a HCPC environment with an optimum controller achieves an improved QoS.Moreover,the experimental results validated in Mininet show that our proposed approach surpasses the existing distributed controller clustering(DCC)schemes in terms of several performance metrics i.e.,delay,jitter,throughput,load balancing,scalability and CPU(central processing unit)utilization.

Hierarchical Stream Clustering Based NEWS Summarization System

News feed is one of the potential information providing sources which give updates on various topics of different domains.These updates on various topics need to be collected since the domain specific interested users are in need of important updates in their domains with organized data from various sources.In this paper,the news summarization system is proposed for the news data streams from RSS feeds and Google news.Since news stream analysis requires live content,the news data are continuously collected for our experimentation.Themajor contributions of thiswork involve domain corpus based news collection,news content extraction,hierarchical clustering of the news and summarization of news.Many of the existing news summarization systems lack in providing dynamic content with domain wise representation.This is alleviated in our proposed systemby tagging the news feed with domain corpuses and organizing the news streams with the hierarchical structure with topic wise representation.Further,the news streams are summarized for the users with a novel summarization algorithm.The proposed summarization system generates topic wise summaries effectively for the user and no system in the literature has handled the news summarization by collecting the data dynamically and organizing the content hierarchically.The proposed system is compared with existing systems and achieves better results in generating news summaries.The Online news content editors are highly benefitted by this system for instantly getting the news summaries of their domain interest.

CLUSTERING OF DOA DATA IN RADAR PULSE BASED ON SOFM AND CDBW

Clustering is the main method of deinterleaving of radar pulse using multi-parameter.However,the problem in clustering of radar pulses lies in finding the right number of clusters.To solve this problem,a method is proposed based on Self-Organizing Feature Maps(SOFM) and Composed Density between and within clusters(CDbw).This method firstly extracts the feature of Direction Of Arrival(DOA) data by SOFM using the characteristic of DOA parameter,and then cluster of SOFM.Through computing the cluster validity index CDbw,the right number of clusters is found.The results of simulation show that the method is effective in sorting the data of DOA.

Combined Density-based and Constraint-based Algorithm for Clustering

We propose a new clustering algorithm that assists the researchers to quickly and accurately analyze data. We call this algorithm Combined Density-based and Constraint-based Algorithm (CDC). CDC consists of two phases. In the first phase, CDC employs the idea of density-based clustering algorithm to split the original data into a number of fragmented clusters. At the same time, CDC cuts off the noises and outliers. In the second phase, CDC employs the concept of K-means clustering algorithm to select a greater cluster to be the center. Then, the greater cluster merges some smaller clusters which satisfy some constraint rules. Due to the merged clusters around the center cluster, the clustering results show high accuracy. Moreover, CDC reduces the calculations and speeds up the clustering process. In this paper, the accuracy of CDC is evaluated and compared with those of K-means, hierarchical clustering, and the genetic clustering algorithm (GCA) proposed in 2004. Experimental results show that CDC has better performance.

A Hierarchical Clustering and Fixed-Layer Local Learning Based Support Vector Machine Algorithm for Large Scale Classification Problems

It is a challenging topic to develop an efficient algorithm for large scale classification problems in many applications of machine learning. In this paper, a hierarchical clustering and fixed- layer local learning （HCFLL） based support vector machine（SVM） algorithm is proposed to deal with this problem. Firstly, HCFLL hierarchically dusters a given dataset into a modified clustering feature tree based on the ideas of unsupervised clustering and supervised clustering. Then it locally trains SVM on each labeled subtree at a fixed-layer of the tree. The experimental results show that compared with the existing popular algorithms such as core vector machine and decision.tree support vector machine, HCFLL can significantly improve the training and testing speeds with comparable testing accuracy.

Quantum Hierarchical Agglomerative Clustering Based on One Dimension Discrete Quantum Walk with Single-Point Phase Defects

As an important branch of machine learning,clustering analysis is widely used in some fields,e.g.,image pattern recognition,social network analysis,information security,and so on.In this paper,we consider the designing of clustering algorithm in quantum scenario,and propose a quantum hierarchical agglomerative clustering algorithm,which is based on one dimension discrete quantum walk with single-point phase defects.In the proposed algorithm,two nonclassical characters of this kind of quantum walk,localization and ballistic effects,are exploited.At first,each data point is viewed as a particle and performed this kind of quantum walk with a parameter,which is determined by its neighbors.After that,the particles are measured in a calculation basis.In terms of the measurement result,every attribute value of the corresponding data point is modified appropriately.In this way,each data point interacts with its neighbors and moves toward a certain center point.At last,this process is repeated several times until similar data points cluster together and form distinct classes.Simulation experiments on the synthetic and real world data demonstrate the effectiveness of the presented algorithm.Compared with some classical algorithms,the proposed algorithm achieves better clustering results.Moreover,combining quantum cluster assignment method,the presented algorithm can speed up the calculating velocity.

Resizable, Rescalable and Free-Style Visualization of Hierarchical Clustering and Bioinformatics Analysis

Graphical representation of hierarchical clustering results is of final importance in hierarchical cluster analysis of data. Unfortunately, almost all mathematical or statistical software may have a weak capability of showcasing such clustering results. Particularly, most of clustering results or trees drawn cannot be represented in a dendrogram with a resizable, rescalable and free-style fashion. With the “dynamic” drawing instead of “static” one, this research works around these weak functionalities that restrict visualization of clustering results in an arbitrary manner. It introduces an algorithmic solution to these functionalities, which adopts seamless pixel rearrangements to be able to resize and rescale dendrograms or tree diagrams. The results showed that the algorithm developed makes clustering outcome representation a really free visualization of hierarchical clustering and bioinformatics analysis. Especially, it possesses features of selectively visualizing and/or saving results in a specific size, scale and style (different views).

AVLINK： Robust Clustering Algorithm based on Average Link Applied to Protein Sequence Analysis

Robust Clustering methods are aimed at avoiding unsatisfactory results resulting from the presence of certain amount of outlying observations in the input data of many practical applications such as biological sequences analysis or gene expressions analysis. This paper presents a fuzzy clustering algorithm based on average link and possibilistic clustering paradigm termed as AVLINK. It minimizes the average dissimilarity between pairs of patterns within the same cluster and at the same time the size of a cluster is maximized by computing the zeros of the derivative of proposed objective function. AVLINK along with the proposed initialization procedure show a high outliers rejection capability as it makes their membership very low furthermore it does not requires the number of clusters to be known in advance and it can discover clusters of non convex shape. The effectiveness and robustness of the proposed algorithms have been demonstrated on different types of protein data sets.

Two-level Hierarchical Clustering Analysis and Application

Hierarchical clustering analysis based on statistic s is one of the most important mining algorithms, but the traditionary hierarchica l clustering method is based on global comparing, which only takes in Q clusteri ng while ignoring R clustering in practice, so it has some limitation especially when the number of sample and index is very large. Furthermore, because of igno ring the association between the different indexes, the clustering result is not good & true. In this paper, we present the model and the algorithm of two-level hierarchi cal clustering which integrates Q clustering with R clustering. Moreover, becaus e two-level hierarchical clustering is based on the respective clustering resul t of each class, the classification of the indexes directly effects on the a ccuracy of the final clustering result, how to appropriately classify the inde xes is the chief and difficult problem we must handle in advance. Although some literatures also have referred to the issue of the classificati on of the indexes, but the articles classify the indexes only according to their superficial signification, which is unscientific. The reasons are as follow s: First, the superficial signification of some indexes usually takes on different meanings and it is easy to be misapprehended by different person. Furthermore, t his classification method seldom make use of history data, the classification re sult is not so objective. Second, for some indexes, its superficial signification didn’t show any mean ings, so simply from the superficial signification, we can’t classify them to c ertain classes. Third, this classification method need the users have higher level knowledge of this field, otherwise it is difficult for the users to understand the signifi cation of some indexes, which sometimes is not available. So in this paper, to this question, we first use R clustering method to cluste ring indexes, dividing p dimension indexes into q classes, then adopt two-level clustering method to get the final result. Obviously, the classification result is more objective and accurate. Moreover, after the first step, we can get the relation of the different indexes and their interaction. We can also know under a certain class indexes, which samples can be clustering to a class. (These semi finished results sometimes are very useful.) The experiments also indicates the effective and accurate of the algorithms. And, the result of R clustering ca n be easily used for the later practice.

Performances of Clustering Methods Considering Data Transformation and Sample Size: An Evaluation with Fisheries Survey Data

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.

Concept Association and Hierarchical Hamming Clustering Model in Text Classification

We propose two models in this paper. The concept of association model is put forward to obtain the co-occurrence relationships among keywords in the documents and the hierarchical Hamming clustering model is used to reduce the dimensionality of the category feature vector space which can solve the problem of the extremely high dimensionality of the documents' feature space. The results of experiment indicate that it can obtain the co-occurrence relations among key-words in the documents which promote the recall of classification system effectively. The hierarchical Hamming clustering model can reduce the dimensionality of the category feature vector efficiently, the size of the vector space is only about 10% of the primary dimensionality. Key words text classification - concept association - hierarchical clustering - hamming clustering CLC number TN 915. 08 Foundation item: Supporteded by the National 863 Project of China (2001AA142160, 2002AA145090)Biography: Su Gui-yang (1974-), male, Ph. D candidate, research direction: information filter and text classification.

Fair hierarchical clustering of substations based on Gini coefficient

For the load modeling of a large power grid,the large number of substations covered by it must be segregated into several categories and,thereafter,a load model built for each type.To address the problem of skewed clustering tree in the classical hierarchical clustering method used for categorizing substations,a fair hierarchical clustering method is proposed in this paper.First,the fairness index is defined based on the Gini coefficient.Thereafter,a hierarchical clustering method is proposed based on the fairness index.Finally,the clustering results are evaluated using the contour coefficient and the t-SNE two-dimensional plane map.The substations clustering example of a real large power grid considered in this paper illustrates that the proposed fair hierarchical clustering method can effectively address the problem of the skewed clustering tree with high accuracy.

ADC-DL:Communication-Efficient Distributed Learning with Hierarchical Clustering and Adaptive Dataset Condensation

The rapid growth of modern mobile devices leads to a large number of distributed data,which is extremely valuable for learning models.Unfortunately,model training by collecting all these original data to a centralized cloud server is not applicable due to data privacy and communication costs concerns,hindering artificial intelligence from empowering mobile devices.Moreover,these data are not identically and independently distributed(Non-IID)caused by their different context,which will deteriorate the performance of the model.To address these issues,we propose a novel Distributed Learning algorithm based on hierarchical clustering and Adaptive Dataset Condensation,named ADC-DL,which learns a shared model by collecting the synthetic samples generated on each device.To tackle the heterogeneity of data distribution,we propose an entropy topsis comprehensive tiering model for hierarchical clustering,which distinguishes clients in terms of their data characteristics.Subsequently,synthetic dummy samples are generated based on the hierarchical structure utilizing adaptive dataset condensation.The procedure of dataset condensation can be adjusted adaptively according to the tier of the client.Extensive experiments demonstrate that the performance of our ADC-DL is more outstanding in prediction accuracy and communication costs compared with existing algorithms.

Unicast Network Topology Inference Algorithm Based on Hierarchical Clustering

Network topology inference is one of the important applications of network tomography.Traditional network topology inference may impact network normal operation due to its generation of huge data traffic.A unicast network topology inference is proposed to use time to live(TTL)for layering and classify nodes layer by layer based on the similarity of node pairs.Finally,the method infers logical network topology effectively with self-adaptive combination of previous results.Simulation results show that the proposed method holds a high accuracy of topology inference while decreasing network measuring flow,thus improves measurement efficiency.