Searching for network modules

When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a novel type of objective function for graph clustering, in the form of a multilinear polynomial whose coefficients are determined by network topology. It may be thought of as a potential function, to be maximized, taking its values on fuzzy clusterings or families of fuzzy subsets of nodes over which every node distributes a unit membership. When suitably parametrized, this potential is shown to attain its maximum when every node concentrates its all unit membership on some module. The output thus is a partition, while the original discrete optimization problem is turned into a continuous version allowing to conceive alternative search strategies. The instance of the problem being a pseudo-Boolean function assigning real-valued cluster scores to node subsets, modularity maximization is employed to exemplify a so-called quadratic form, in that the scores of singletons and pairs also fully determine the scores of larger clusters, while the resulting multilinear polynomial potential function has degree 2. After considering further quadratic instances, different from modularity and obtained by interpreting network topology in alternative manners, a greedy local-search strategy for the continuous framework is analytically compared with an existing greedy agglomerative procedure for the discrete case. Overlapping is finally discussed in terms of multiple runs, i.e. several local searches with different initializations.Comment: 10 page

A Survey on Soft Subspace Clustering

Subspace clustering (SC) is a promising clustering technology to identify clusters based on their associations with subspaces in high dimensional spaces. SC can be classified into hard subspace clustering (HSC) and soft subspace clustering (SSC). While HSC algorithms have been extensively studied and well accepted by the scientific community, SSC algorithms are relatively new but gaining more attention in recent years due to better adaptability. In the paper, a comprehensive survey on existing SSC algorithms and the recent development are presented. The SSC algorithms are classified systematically into three main categories, namely, conventional SSC (CSSC), independent SSC (ISSC) and extended SSC (XSSC). The characteristics of these algorithms are highlighted and the potential future development of SSC is also discussed.Comment: This paper has been published in Information Sciences Journal in 201

Techniques for clustering gene expression data

Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered

Segmentation of articular cartilage and early osteoarthritis based on the fuzzy soft thresholding approach driven by modified evolutionary ABC optimization and local statistical aggregation

Articular cartilage assessment, with the aim of the cartilage loss identification, is a crucial task for the clinical practice of orthopedics. Conventional software (SW) instruments allow for just a visualization of the knee structure, without post processing, offering objective cartilage modeling. In this paper, we propose the multiregional segmentation method, having ambitions to bring a mathematical model reflecting the physiological cartilage morphological structure and spots, corresponding with the early cartilage loss, which is poorly recognizable by the naked eye from magnetic resonance imaging (MRI). The proposed segmentation model is composed from two pixel's classification parts. Firstly, the image histogram is decomposed by using a sequence of the triangular fuzzy membership functions, when their localization is driven by the modified artificial bee colony (ABC) optimization algorithm, utilizing a random sequence of considered solutions based on the real cartilage features. In the second part of the segmentation model, the original pixel's membership in a respective segmentation class may be modified by using the local statistical aggregation, taking into account the spatial relationships regarding adjacent pixels. By this way, the image noise and artefacts, which are commonly presented in the MR images, may be identified and eliminated. This fact makes the model robust and sensitive with regards to distorting signals. We analyzed the proposed model on the 2D spatial MR image records. We show different MR clinical cases for the articular cartilage segmentation, with identification of the cartilage loss. In the final part of the analysis, we compared our model performance against the selected conventional methods in application on the MR image records being corrupted by additive image noise.Web of Science117art. no. 86

Blind separation of underdetermined mixtures with additive white and pink noises

This paper presents an approach for underdetermined blind source separation in the case of additive Gaussian white noise and pink noise. Likewise, the proposed approach is applicable in the case of separating I + 3 sources from I mixtures with additive two kinds of noises. This situation is more challenging and suitable to practical real world problems. Moreover, unlike to some conventional approaches, the sparsity conditions are not imposed. Firstly, the mixing matrix is estimated based on an algorithm that combines short time Fourier transform and rough-fuzzy clustering. Then, the mixed signals are normalized and the source signals are recovered using modified Gradient descent Local Hierarchical Alternating Least Squares Algorithm exploiting the mixing matrix obtained from the previous step as an input and initialized by multiplicative algorithm for matrix factorization based on alpha divergence. The experiments and simulation results show that the proposed approach can separate I + 3 source signals from I mixed signals, and it has superior evaluation performance compared to some conventional approaches

Underdetermined blind source separation based on Fuzzy C-Means and Semi-Nonnegative Matrix Factorization

Conventional blind source separation is based on over-determined with more sensors than sources but the underdetermined is a challenging case and more convenient to actual situation. Non-negative Matrix Factorization (NMF) has been widely applied to Blind Source Separation (BSS) problems. However, the separation results are sensitive to the initialization of parameters of NMF. Avoiding the subjectivity of choosing parameters, we used the Fuzzy C-Means (FCM) clustering technique to estimate the mixing matrix and to reduce the requirement for sparsity. Also, decreasing the constraints is regarded in this paper by using Semi-NMF. In this paper we propose a new two-step algorithm in order to solve the underdetermined blind source separation. We show how to combine the FCM clustering technique with the gradient-based NMF with the multi-layer technique. The simulation results show that our proposed algorithm can separate the source signals with high signal-to-noise ratio and quite low cost time compared with some algorithms