Complete agglomerative hierarchy document’s clustering based on fuzzy luhn’s gibbs latent dirichlet allocation

Agglomerative hierarchical is a bottom up clustering method, where the distances between documents can be retrieved by extracting feature values using a topic-based latent dirichlet allocation method. To reduce the number of features, term selection can be done using Luhn’s Idea. Those methods can be used to build the better clusters for document. But, there is less research discusses it. Therefore, in this research, the term weighting calculation uses Luhn’s Idea to select the terms by defining upper and lower cut-off, and then extracts the feature of terms using gibbs sampling latent dirichlet allocation combined with term frequency and fuzzy Sugeno method. The feature values used to be the distance between documents, and clustered with single, complete and average link algorithm. The evaluations show the feature extraction with and without lower cut-off have less difference. But, the topic determination of each term based on term frequency and fuzzy Sugeno method is better than Tsukamoto method in finding more relevant documents. The used of lower cut-off and fuzzy Sugeno gibbs latent dirichlet allocation for complete agglomerative hierarchical clustering have consistent metric values. This clustering method suggested as a better method in clustering documents that is more relevant to its gold standard

Feature-based clustering of stomach cancer gene expression data

This report presents the results of using a probabilistic clustering technique in the analysis of microRNAseq and RNAseq data from gastric cancer tumor samples deposited at TCGA (The Cancer Genome Atlas). Using the method of Hoff, who has proposed a Dirichlet process unsupervised clustering framework with feature selection, it is possible to reveal interesting structure in gastric cancer gene expression data that relates to Epstein-Barr virus (EBV) microRNA levels. This structure is not as readily identified by a typical hierarchical clustering method, and the results of this analysis contribute to an understanding of the role of EBV viral microRNAs in gastric cancer tumors.Statistic

ENHANCEMENT OF DECISION TREE METHOD BASED ON HIERARCHICAL CLUSTERING AND DISPERSION RATIO

The classification process using a decision tree is a classification method that has a feature selection process. Decision tree classifications using information gain have a disadvantage when the dataset has unique attributes for each imbalanced class record and distribution. The data used for decision tree classification has 2 types, numerical and nominal. The numerical data type is carried out a discretization process so that it gets data intervals. Weaknesses in the information gain method can be reduced by using a dispersion ratio method that does not depend on the class distribution, but on the frequency distribution. Numeric type data will be dis-criticized using the hierarchical clustering method to obtain a balanced data cluster. The data used in this study were taken from the UCI machine learning repository, which has two types of numeric and nominal data. There are two stages in this research namely, first the numeric type data will be discretized using hierarchical clustering with 3 methods, namely single link, complete link, and average link. Second, the results of discretization will be merged again then the formation of trees with splitting attributes using dispersion ratio and evaluated with cross-validation k-fold 7. The results obtained show that the discretization of data with hierarchical clustering can increase predictions by 14.6% compared with data without discretization. The attribute splitting process with the dispersion ratio of the data resulting from the discretization of hierarchical clustering can increase the prediction by 6.51%

A supervised clustering approach for fMRI-based inference of brain states

We propose a method that combines signals from many brain regions observed in functional Magnetic Resonance Imaging (fMRI) to predict the subject's behavior during a scanning session. Such predictions suffer from the huge number of brain regions sampled on the voxel grid of standard fMRI data sets: the curse of dimensionality. Dimensionality reduction is thus needed, but it is often performed using a univariate feature selection procedure, that handles neither the spatial structure of the images, nor the multivariate nature of the signal. By introducing a hierarchical clustering of the brain volume that incorporates connectivity constraints, we reduce the span of the possible spatial configurations to a single tree of nested regions tailored to the signal. We then prune the tree in a supervised setting, hence the name supervised clustering, in order to extract a parcellation (division of the volume) such that parcel-based signal averages best predict the target information. Dimensionality reduction is thus achieved by feature agglomeration, and the constructed features now provide a multi-scale representation of the signal. Comparisons with reference methods on both simulated and real data show that our approach yields higher prediction accuracy than standard voxel-based approaches. Moreover, the method infers an explicit weighting of the regions involved in the regression or classification task

Feature selection by multi-objective optimization: application to network anomaly detection by hierarchical self-organizing maps.

Feature selection is an important and active issue in clustering and classification problems. By choosing an adequate feature subset, a dataset dimensionality reduction is allowed, thus contributing to decreasing the classification computational complexity, and to improving the classifier performance by avoiding redundant or irrelevant features. Although feature selection can be formally defined as an optimisation problem with only one objective, that is, the classification accuracy obtained by using the selected feature subset, in recent years, some multi-objective approaches to this problem have been proposed. These either select features that not only improve the classification accuracy, but also the generalisation capability in case of supervised classifiers, or counterbalance the bias toward lower or higher numbers of features that present some methods used to validate the clustering/classification in case of unsupervised classifiers. The main contribution of this paper is a multi-objective approach for feature selection and its application to an unsupervised clustering procedure based on Growing Hierarchical Self-Organizing Maps (GHSOM) that includes a new method for unit labelling and efficient determination of the winning unit. In the network anomaly detection problem here considered, this multi-objective approach makes it possible not only to differentiate between normal and anomalous traffic but also among different anomalies. The efficiency of our proposals has been evaluated by using the well-known DARPA/NSL-KDD datasets that contain extracted features and labeled attacks from around 2 million connections. The selected feature sets computed in our experiments provide detection rates up to 99.8% with normal traffic and up to 99.6% with anomalous traffic, as well as accuracy values up to 99.12%.This work has been funded by FEDER funds and the Ministerio de Ciencia e Innovación of the Spanish Government under Project No. TIN2012-32039

Comparison Between Supervised and Unsupervised Classifications of Neuronal Cell Types: A Case Study

In the study of neural circuits, it becomes essential to discern the different neuronal cell types that build the circuit. Traditionally, neuronal cell types have been classified using qualitative descriptors. More recently, several attempts have been made to classify neurons quantitatively, using unsupervised clustering methods. While useful, these algorithms do not take advantage of previous information known to the investigator, which could improve the classification task. For neocortical GABAergic interneurons, the problem to discern among different cell types is particularly difficult and better methods are needed to perform objective classifications. Here we explore the use of supervised classification algorithms to classify neurons based on their morphological features, using a database of 128 pyramidal cells and 199 interneurons from mouse neocortex. To evaluate the performance of different algorithms we used, as a “benchmark,” the test to automatically distinguish between pyramidal cells and interneurons, defining “ground truth” by the presence or absence of an apical dendrite. We compared hierarchical clustering with a battery of different supervised classification algorithms, finding that supervised classifications outperformed hierarchical clustering. In addition, the selection of subsets of distinguishing features enhanced the classification accuracy for both sets of algorithms. The analysis of selected variables indicates that dendritic features were most useful to distinguish pyramidal cells from interneurons when compared with somatic and axonal morphological variables. We conclude that supervised classification algorithms are better matched to the general problem of distinguishing neuronal cell types when some information on these cell groups, in our case being pyramidal or interneuron, is known a priori. As a spin-off of this methodological study, we provide several methods to automatically distinguish neocortical pyramidal cells from interneurons, based on their morphologies

What are the Best Hierarchical Descriptors for Complex Networks?

This work reviews several hierarchical measurements of the topology of complex networks and then applies feature selection concepts and methods in order to quantify the relative importance of each measurement with respect to the discrimination between four representative theoretical network models, namely Erd\"{o}s-R\'enyi, Barab\'asi-Albert, Watts-Strogatz as well as a geographical type of network. The obtained results confirmed that the four models can be well-separated by using a combination of measurements. In addition, the relative contribution of each considered feature for the overall discrimination of the models was quantified in terms of the respective weights in the canonical projection into two dimensions, with the traditional clustering coefficient, hierarchical clustering coefficient and neighborhood clustering coefficient resulting particularly effective. Interestingly, the average shortest path length and hierarchical node degrees contributed little for the separation of the four network models.Comment: 9 pages, 4 figure