100,075 research outputs found

    Which fMRI clustering gives good brain parcellations?

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    International audienceAnalysis and interpretation of neuroimaging data often require one to divide the brain into a number of regions, or parcels, with homogeneous characteristics, be these regions defined in the brain volume or on on the cortical surface. While predefined brain atlases do not adapt to the signal in the individual subjects images, parcellation approaches use brain activity (e.g. found in some functional contrasts of interest) and clustering techniques to define regions with some degree of signal homogeneity. In this work, we address the question of which clustering technique is appropriate and how to optimize the corresponding model. We use two principled criteria: goodness of fit (accuracy), and reproducibility of the parcellation across bootstrap samples. We study these criteria on both simulated and two task-based functional Magnetic Resonance Imaging datasets for the Ward, spectral and K-means clustering algorithms. We show that in general Ward's clustering performs better than alternative methods with regard to reproducibility and accuracy and that the two criteria diverge regarding the preferred models (reproducibility leading to more conservative solutions), thus deferring the practical decision to a higher level alternative, namely the choice of a trade-off between accuracy and stability

    SMART: Unique splitting-while-merging framework for gene clustering

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    Copyright @ 2014 Fa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named “splitting merging awareness tactics” (SMART), which does not require any a priori knowledge of either the number of clusters or even the possible range of this number. Unlike existing self-splitting algorithms, which over-cluster the dataset to a large number of clusters and then merge some similar clusters, our framework has the ability to split and merge clusters automatically during the process and produces the the most reliable clustering results, by intrinsically integrating many clustering techniques and tasks. The SMART framework is implemented with two distinct clustering paradigms in two algorithms: competitive learning and finite mixture model. Nevertheless, within the proposed SMART framework, many other algorithms can be derived for different clustering paradigms. The minimum message length algorithm is integrated into the framework as the clustering selection criterion. The usefulness of the SMART framework and its algorithms is tested in demonstration datasets and simulated gene expression datasets. Moreover, two real microarray gene expression datasets are studied using this approach. Based on the performance of many metrics, all numerical results show that SMART is superior to compared existing self-splitting algorithms and traditional algorithms. Three main properties of the proposed SMART framework are summarized as: (1) needing no parameters dependent on the respective dataset or a priori knowledge about the datasets, (2) extendible to many different applications, (3) offering superior performance compared with counterpart algorithms.National Institute for Health Researc

    Improved approximation of arbitrary shapes in dem simulations with multi-spheres

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    DEM simulations are originally made for spherical particles only. But most of real particles are anything but not spherical. Due to this problem, the multi-sphere method was invented. It provides the possibility to clump several spheres together to create complex shape structures. The proposed algorithm oïŹ€ers a novel method to create multi-sphere clumps for the given arbitrary shapes. Especially the use of modern clustering algorithms, from the ïŹeld of computational intelligence, achieve satisfactory results. The clustering is embedded into an optimisation algorithm which uses a pre-deïŹned criterion. A mostly unaided algorithm with only a few input and hyperparameters is able to approximate arbitrary shapes

    Fuzzy clustering with volume prototypes and adaptive cluster merging

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    Two extensions to the objective function-based fuzzy clustering are proposed. First, the (point) prototypes are extended to hypervolumes, whose size can be fixed or can be determined automatically from the data being clustered. It is shown that clustering with hypervolume prototypes can be formulated as the minimization of an objective function. Second, a heuristic cluster merging step is introduced where the similarity among the clusters is assessed during optimization. Starting with an overestimation of the number of clusters in the data, similar clusters are merged in order to obtain a suitable partitioning. An adaptive threshold for merging is proposed. The extensions proposed are applied to Gustafson–Kessel and fuzzy c-means algorithms, and the resulting extended algorithm is given. The properties of the new algorithm are illustrated by various examples

    Clustering as an example of optimizing arbitrarily chosen objective functions

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    This paper is a reflection upon a common practice of solving various types of learning problems by optimizing arbitrarily chosen criteria in the hope that they are well correlated with the criterion actually used for assessment of the results. This issue has been investigated using clustering as an example, hence a unified view of clustering as an optimization problem is first proposed, stemming from the belief that typical design choices in clustering, like the number of clusters or similarity measure can be, and often are suboptimal, also from the point of view of clustering quality measures later used for algorithm comparison and ranking. In order to illustrate our point we propose a generalized clustering framework and provide a proof-of-concept using standard benchmark datasets and two popular clustering methods for comparison
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