Evidence Accumulation Clustering Research Articles

A novel member enhancement‐based clustering ensemble algorithm

SummaryClustering ensemble is a popular approach for identifying data clusters that combines the clustering results from multiple base clustering algorithms to produce more accurate and robust data clusters. However, the performance of clustering ensemble algorithms is highly dependent on the quality of clustering members. To address this problem, this paper proposes a member enhancement‐based clustering ensemble (MECE) algorithm that selects the ensemble members by considering their distribution consistency. MECE has two main components, called heterocluster splitting and homocluster merging. The first component estimates two probability density functions (p.d.f.s) estimated on the sample points of an heterocluster and represents them using a Gaussian distribution and a Gaussian mixture model. If the random numbers generated by these two p.d.f.s have different probability distributions, the heterocluster is then split into smaller clusters. The second component merges the clusters that have high neighborhood densities into a homocluster, where the neighborhood density is measured using a novel evaluation criterion. In addition, a co‐association matrix is presented, which serves as a summary for the ensemble of diverse clusters. A series of experiments were conducted to evaluate the feasibility and effectiveness of the proposed ensemble member generation algorithm. Results show that the proposed MECE algorithm can select high quality ensemble members and as a result yield the better clusterings than six state‐of‐the‐art ensemble clustering algorithms, that is, cluster‐based similarity partitioning algorithm (CSPA), meta‐clustering algorithm (MCLA), hybrid bipartite graph formulation (HBGF), evidence accumulation clustering (EAC), locally weighted evidence accumulation (LWEA), and locally weighted graph partition (LWGP). Specifically, MECE algorithm has the nearly 23% higher average NMI, 27% higher average ARI, 15% higher average FMI, and 10% higher average purity than CSPA, MCLA, HBGF, EAC, LWEA, and LWGA algorithms. The experimental results demonstrate that MECE algorithm is a valid approach to deal with the clustering ensemble problems.

Consensus clustering applied to multi-omics disease subtyping

BackgroundFacing the diversity of omics data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce robust results.ResultsHere, we introduce ClustOmics, a generic consensus clustering tool that we use in the context of cancer subtyping. ClustOmics relies on a non-relational graph database, which allows for the simultaneous integration of both multiple omics data and results from various clustering methods. This new tool conciliates input clusterings, regardless of their origin, their number, their size or their shape. ClustOmics implements an intuitive and flexible strategy, based upon the idea of evidence accumulation clustering. ClustOmics computes co-occurrences of pairs of samples in input clusters and uses this score as a similarity measure to reorganize data into consensus clusters.ConclusionWe applied ClustOmics to multi-omics disease subtyping on real TCGA cancer data from ten different cancer types. We showed that ClustOmics is robust to heterogeneous qualities of input partitions, smoothing and reconciling preliminary predictions into high-quality consensus clusters, both from a computational and a biological point of view. The comparison to a state-of-the-art consensus-based integration tool, COCA, further corroborated this statement. However, the main interest of ClustOmics is not to compete with other tools, but rather to make profit from their various predictions when no gold-standard metric is available to assess their significance.AvailabilityThe ClustOmics source code, released under MIT license, and the results obtained on TCGA cancer data are available on GitHub: https://github.com/galadrielbriere/ClustOmics.

Subspace clustering using ensembles of K-subspaces

Abstract Subspace clustering is the unsupervised grouping of points lying near a union of low-dimensional linear subspaces. Algorithms based directly on geometric properties of such data tend to either provide poor empirical performance, lack theoretical guarantees or depend heavily on their initialization. We present a novel geometric approach to the subspace clustering problem that leverages ensembles of the $K$-subspace (KSS) algorithm via the evidence accumulation clustering framework. Our algorithm, referred to as ensemble $K$-subspaces (EKSSs), forms a co-association matrix whose $(i,j)$th entry is the number of times points $i$ and $j$ are clustered together by several runs of KSS with random initializations. We prove general recovery guarantees for any algorithm that forms an affinity matrix with entries close to a monotonic transformation of pairwise absolute inner products. We then show that a specific instance of EKSS results in an affinity matrix with entries of this form, and hence our proposed algorithm can provably recover subspaces under similar conditions to state-of-the-art algorithms. The finding is, to the best of our knowledge, the first recovery guarantee for evidence accumulation clustering and for KSS variants. We show on synthetic data that our method performs well in the traditionally challenging settings of subspaces with large intersection, subspaces with small principal angles and noisy data. Finally, we evaluate our algorithm on six common benchmark datasets and show that unlike existing methods, EKSS achieves excellent empirical performance when there are both a small and large number of points per subspace.

Evidence accumulation clustering using combinations of features

Evidence accumulation clustering (EAC) is an ensemble clustering algorithm that can cluster data for arbitrary shapes and numbers of clusters. Here, we present a variant of EAC in which we aimed to better cluster data with a large number of features, many of which may be uninformative. Our new method builds on the existing EAC algorithm by populating the clustering ensemble with clusterings based on combinations of fewer features than the original dataset at a time. Our method also calls for prewhitening the recombined data and weighting the influence of each individual clustering by an estimate of its informativeness. We provide code of an example implementation of the algorithm in Matlab and demonstrate its effectiveness compared to ordinary evidence accumulation clustering with synthetic data.•The clustering ensemble is made by clustering on subset combinations of features from the data•The recombined data may be prewhitened•Evidence accumulation can be improved by weighting the evidence with a goodness-of-clustering measure

Safety detection algorithm in sensor network based on ant colony optimization with improved multiple clustering algorithms

The Sensing network attack connection has the characteristics of behavioral variability and complexity. It is not feasible to construct an abnormal intrusion detection model by using behavior mining technology based on traditional clustering. According to the characteristics of Sensing network attack behavior, this paper proposed a Sensing network attack detection algorithm based on improved multi-cluster. Firstly, it used improved spatial clustering algorithm to reduce spatial data feature dimensions and feature computational complexity during attack detection. Secondly, it used improved K-means clustering algorithm to classify spatial datasets. Ant colony optimization algorithm is used to detect whether there is Sinkhole attack in routing and generate alert information of sensor nodes. Finally, it used improved evidence accumulation clustering algorithm to calculate the difference distance between each isolated point and the cluster centroid and it also used matrix clustering algorithm to calculate the detection threshold and determine the attack behavior in the Sensing network. P2P trust model is used to calculate the trust value of each node in the list of suspect nodes, and the node whose trust value is lower than the preset threshold is regarded as the attack node. Through the attack detection experiment based on KDD 99 dataset, the comparison with the detection results of different algorithm s shows that the proposed algorithm has higher detection rate and lower false positive rate.

Clustering ensemble selection considering quality and diversity

It is highly likely that there is a partition that is judged by a stability measure as a bad one while it contains one (or more) high quality cluster(s); and then it is totally neglected. So, inspiring from the evaluation of partitions, researchers turn to define measures for evaluation of clusters. Many stability measures have been proposed such as Normalized Mutual Information to validate a partition. The defined measures are based on Normalized Mutual Information. The drawback of the commonly used approach will be discussed in this paper and a criterion is proposed to assess the association between a cluster and a partition which is called Edited Normalized Mutual Information, ENMI criterion. The ENMI criterion compensates the drawback of the common Normalized Mutual Information (NMI) measure. Also, a clustering ensemble method that is based on aggregating a subset of primary clusters is proposed. The proposed method uses the Average ENMI as fitness measure to select a number of clusters. The clusters that satisfy a predefined threshold of the mentioned measure are selected to participate in the final ensemble. To combine the chosen clusters a set of consensus function methods are employed. One class of the used consensus functions is the co-association based consensus functions. Since the Evidence Accumulation Clustering, EAC, method can’t derive the co-association matrix from a subset of clusters, Extended EAC, EEAC, is employed to construct the co-association matrix from the chosen subset of clusters. The second class of the used consensus functions is based on hyper graph partitioning algorithms. The other class of the used consensus functions considers the chosen clusters as a new feature space and uses a simple clustering algorithm to extract the consensus partitioning. The empirical studies show that the proposed method outperforms other well-known ensembles.

A novel approach to probabilistic characterisation of neural firing patterns

BackgroundThe advances in extracellular neural recording techniques result in big data volumes that necessitate fast, reliable, and automatic identification of statistically similar units. This study proposes a single framework yielding a compact set of probabilistic descriptors that characterise the firing patterns of a single unit. New methodProbabilistic features are estimated from an inter-spike-interval time series, without assumptions about the firing distribution or the stationarity. The first level of proposed firing patterns decomposition divides the inter-spike intervals into bursting, moderate and idle firing modes, yielding a coarse feature set. The second level identifies the successive bursting spikes, or the spiking acceleration/deceleration in the moderate firing mode, yielding a refined feature set. The features are estimated from simulated data and from experimental recordings from the lateral prefrontal cortex in awake, behaving rhesus monkeys. ResultsAn efficient and stable partitioning of neural units is provided by the ensemble evidence accumulation clustering. The possibility of selecting the number of clusters and choosing among coarse and refined feature sets provides an opportunity to explore and compare different data partitions. ConclusionsThe estimation of features, if applied to a single unit, can serve as a tool for the firing analysis, observing either overall spiking activity or the periods of interest in trial-to-trial recordings. If applied to massively parallel recordings, it additionally serves as an input to the clustering procedure, with the potential to compare the functional properties of various brain structures and to link the types of neural cells to the particular behavioural states.

Epithelium and Stroma Identification in Histopathological Images Using Unsupervised and Semi-Supervised Superpixel-Based Segmentation

We present superpixel-based segmentation frameworks for unsupervised and semi-supervised epithelium-stroma identification in histopathological images or oropharyngeal tissue micro arrays. A superpixel segmentation algorithm is initially used to split-up the image into binary regions (superpixels) and their colour features are extracted and fed into several base clustering algorithms with various parameter initializations. Two Consensus Clustering (CC) formulations are then used: the Evidence Accumulation Clustering (EAC) and the voting-based consensus function. These combine the base clustering outcomes to obtain a more robust detection of tissue compartments than the base clustering methods on their own. For the voting-based function, a technique is introduced to generate consistent labellings across the base clustering results. The obtained CC result is then utilized to build a self-training Semi-Supervised Classification (SSC) model. Unlike supervised segmentations, which rely on large number of labelled training images, our SSC approach performs a quality segmentation while relying on few labelled samples. Experiments conducted on forty-five hand-annotated images of oropharyngeal cancer tissue microarrays show that (a) the CC algorithm generates more accurate and stable results than individual clustering algorithms; (b) the clustering performance of the voting-based function outperforms the existing EAC; and (c) the proposed SSC algorithm outperforms the supervised methods, which is trained with only a few labelled instances.

WoCE: A framework for Clustering Ensemble by Exploiting the Wisdom of Crowds Theory.

The wisdom of crowds (WOCs), as a theory in the social science, gets a new paradigm in computer science. The WOC theory explains that the aggregate decision made by a group is often better than those of its individual members if specific conditions are satisfied. This paper presents a novel framework for unsupervised and semisupervised cluster ensemble by exploiting the WOC theory. We employ four conditions in the WOC theory, i.e., diversity, independency, decentralization, and aggregation, to guide both constructing of individual clustering results and final combination for clustering ensemble. First, independency criterion, as a novel mapping system on the raw data set, removes the correlation between features on our proposed method. Then, decentralization as a novel mechanism generates high quality individual clustering results. Next, uniformity as a new diversity metric evaluates the generated clustering results. Further, weighted evidence accumulation clustering method is proposed for the final aggregation without using thresholding procedure. Experimental study on varied data sets demonstrates that the proposed approach achieves superior performance to state-of-the-art methods.

Evidence Accumulation Clustering with Possibilitic Fuzzy C-Means base clustering approach to disease diagnosis

Traditionally, supervised machine learning methods are the first choice for tasks involving classification of data. This study provides a non-conventional hybrid alternative technique (pEAC) that blends the Possibilistic Fuzzy C- Means (PFCM) as base cluster generating algorithm into the ‘standard’ Evidence Accumulation Clustering (EAC) clustering method. The PFCM coalesces the separate properties of the Possibilistic C-Means (PCM) and Fuzzy C-Means (FCM) algorithms into a sophisticated clustering algorithm. Notwithstanding the tremendous capabilities offered by this hybrid technique, in terms of structure, it resembles the hEAC and fEAC ensemble clustering techniques that are realised by integrating the K-Means and FCM clustering algorithms into the EAC technique. To validate the new technique's effectiveness, its performance on both synthetic and real medical datasets was evaluated alongside individual runs of well-known clustering methods, other unsupervised ensemble clustering techniques and some supervised machine learning methods. Our results show that the proposed pEAC technique outperformed the individual runs of the clustering methods and other unsupervised ensemble techniques in terms accuracy for the diagnosis of hepatitis, cardiovascular, breast cancer, and diabetes ailments that were used in the experiments. Remarkably, compared alongside selected supervised machine learning classification models, our proposed pEAC ensemble technique exhibits better diagnosing accuracy for the two breast cancer datasets that were used, which suggests that even at the cost of none labelling of data, the proposed technique offers efficient medical data classification.

Combining multiple clusterings via crowd agreement estimation and multi-granularity link analysis

The clustering ensemble technique aims to combine multiple clusterings into a probably better and more robust clustering and has been receiving an increasing attention in recent years. There are mainly two aspects of limitations in the existing clustering ensemble approaches. Firstly, many approaches lack the ability to weight the base clusterings without access to the original data and can be affected significantly by the low-quality, or even ill clusterings. Secondly, they generally focus on the instance level or cluster level in the ensemble system and fail to integrate multi-granularity cues into a unified model. To address these two limitations, this paper proposes to solve the clustering ensemble problem via crowd agreement estimation and multi-granularity link analysis. We present the normalized crowd agreement index (NCAI) to evaluate the quality of base clusterings in an unsupervised manner and thus weight the base clusterings in accordance with their clustering validity. To explore the relationship between clusters, the source aware connected triple (SACT) similarity is introduced with regard to their common neighbors and the source reliability. Based on NCAI and multi-granularity information collected among base clusterings, clusters, and data instances, we further propose two novel consensus functions, termed weighted evidence accumulation clustering (WEAC) and graph partitioning with multi-granularity link analysis (GP-MGLA) respectively. The experiments are conducted on eight real-world datasets. The experimental results demonstrate the effectiveness and robustness of the proposed methods.

A density-based similarity matrix construction for spectral clustering

In the first part of this paper, we present a method to build affinity matrices for spectral clustering from a density estimator relying on K-means with subbagging procedure. The approach is anchored in the theoretical works of Wong (1980, 1982a, b) [13–15] on the asymptotic properties of K-means as a density estimation method. The subbagging procedure is introduced to improve the density estimate accuracy. The behavior of the proposed method is analyzed on diverse data sets and two new mechanisms are suggested to improve clustering results on non-convex data. In the second part of the paper, we establish a link between the presented method and the evidence accumulation clustering (EAC) approach by showing that a normalized version of the density-based similarity matrix is approximately equal to a normalized version of the co-association matrix. The co-association matrix provides the co-occurrence probability of data pairs assigned to a same cluster over multiple K-means clustering partitions. Experimental results on artificial and real data demonstrate the effectiveness of the method and provide empirical support for the established link.

Cluster ensemble selection based on a new cluster stability measure1

Many stability measures, such as Normalized Mutual Information NMI, have been proposed to validate a set of partitionings. It is highly possible that a set of partitionings may contain one or more high quality clusters but is still adjudged a bad cluster by a stability measure, and as a result, is completely neglected. Inspired by evaluation approaches measuring the efficacy of a set of partitionings, researchers have tried to define new measures for evaluating a cluster. Thus far, the measures defined for assessing a cluster are mostly based on the well-known NMI measure. The drawback of this commonly used approach is discussed in this paper, after which a new asymmetric criterion, called the Alizadeh--Parvin--Moshki--Minaei criterion APMM, is proposed to assess the association between a cluster and a set of partitionings. We show that the APMM criterion overcomes the deficiency in the conventional NMI measure. We also propose a clustering ensemble framework that incorporates the APMM's capabilities in order to find the best performing clusters. The framework uses Average APMM AAPMM as a fitness measure to select a number of clusters instead of using all of the results. Any cluster that satisfies a predefined threshold of the mentioned measure is selected to participate in an elite ensemble. To combine the chosen clusters, a co-association matrix-based consensus function by which the set of resultant partitionings are obtained is used. Because Evidence Accumulation Clustering EAC can not derive the co-association matrix from a subset of clusters appropriately, a new EAC-based method, called Extended EAC EEAC, is employed to construct the co-association matrix from the chosen subset of clusters. Empirical studies show that our proposed approach outperforms other cluster ensemble approaches.

Probabilistic consensus clustering using evidence accumulation

Clustering ensemble methods produce a consensus partition of a set of data points by combining the results of a collection of base clustering algorithms. In the evidence accumulation clustering (EAC) paradigm, the clustering ensemble is transformed into a pairwise co-association matrix, thus avoiding the label correspondence problem, which is intrinsic to other clustering ensemble schemes. In this paper, we propose a consensus clustering approach based on the EAC paradigm, which is not limited to crisp partitions and fully exploits the nature of the co-association matrix. Our solution determines probabilistic assignments of data points to clusters by minimizing a Bregman divergence between the observed co-association frequencies and the corresponding co-occurrence probabilities expressed as functions of the unknown assignments. We additionally propose an optimization algorithm to find a solution under any double-convex Bregman divergence. Experiments on both synthetic and real benchmark data show the effectiveness of the proposed approach.

Automated unsupervised authorship analysis using evidence accumulation clustering

AbstractAuthorship Analysis aims to extract information about the authorship of documents from features within those documents. Typically, this is performed as a classification task with the aim of identifying the author of a document, given a set of documents of known authorship. Alternatively, unsupervised methods have been developed primarily as visualisation tools to assist the manual discovery of clusters of authorship within a corpus by analysts. However, there is a need in many fields for more sophisticated unsupervised methods to automate the discovery, profiling and organisation of related information through clustering of documents by authorship. An automated and unsupervised methodology for clustering documents by authorship is proposed in this paper. The methodology is named NUANCE, forn-gram Unsupervised Automated Natural Cluster Ensemble. Testing indicates that the derived clusters have a strong correlation to the true authorship of unseen documents.