EVALUATION OF THE CLUSTERING PERFORMANCE OF AFFINITY PROPAGATION ALGORITHM CONSIDERING THE INFLUENCE OF PREFERENCE PARAMETER AND DAMPING FACTOR

The identification of significant underlying data patterns such as image composition and spatial arrangements is fundamental in remote sensing tasks. Therefore, the development of an effective approach for information extraction is crucial to achieve this goal. Affinity propagation (AP) algorithm is a novel powerful technique with the ability of handling with unusual data, containing both categorical and numerical attributes. However, AP has some limitations related to the choice of initial preference parameter, occurrence of oscillations and processing of large data sets. This paper evaluates the clustering performance of AP algorithm taking into account the influence of preference parameter and damping factor. The study was conducted considering the AP algorithm, the adaptive AP and partition AP. According to the experiments, the choice of preference and damping greatly influences on the quality and the final number of clusters

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

<p>Abstract</p> <p>Background</p> <p>In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present <it>clusterMaker</it>, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. <it>clusterMaker </it>is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL.</p> <p>Results</p> <p>Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast <it>Saccharomyces cerevisiae</it>; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section.</p> <p>Conclusions</p> <p>The Cytoscape plugin <it>clusterMaker </it>provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the <it>clusterMaker </it>plugin. <it>clusterMaker </it>is available via the Cytoscape plugin manager.</p

Scalable and Efficient Clustering for Fingerprint-Based Positioning

Indoor Positioning based on wifi fingerprinting needs a reference dataset, also known as a radio map, in order to match the incoming fingerprint in the operational phase with the most similar fingerprint in the dataset and then estimate the device position indoors. Scalability problems may arise when the radio map is large, e.g., providing positioning in large geographical areas or involving crowdsourced data collection. Some researchers divide the radio map into smaller independent clusters, such that the search area is reduced to less dense groups than the initial database with similar features. Thus, the computational load in the operational stage is reduced both at the user devices and on servers. Nevertheless, the clustering models are machine-learning algorithms without specific domain knowledge on indoor positioning or signal propagation. This work proposes several clustering variants to optimize the coarse and fine-grained search and evaluates them over different clustering models and datasets. Moreover, we provide guidelines to obtain efficient and accurate positioning depending on the dataset features. Finally, we show that the proposed new clustering variants reduce the execution time by half and the positioning error by ≈7% with respect to fingerprinting with the traditional clustering models.publishedVersionPeer reviewe

State-Of-The-Art In Image Clustering Based On Affinity Propagation

Proclivity spread (AP) is a productive unsupervised grouping technique, which display a quick execution speed and discover bunches in a low mistake rate. AP calculation takes as info a similitude network that comprise of genuine esteemed likenesses between information focuses. The strategy iteratively trades genuine esteemed messages between sets of information focuses until a decent arrangement of models developed. The development of the comparability network dependent on the Euclidean separation is a significant stage during the time spent AP. Appropriately, the conventional Euclidean separation which is the summation of the pixel-wise force contrasts perform beneath normal when connected for picture grouping, as it endures of being reasonable to exceptions and even to little misshapening in pictures. Studies should be done on different methodologies from existing investigations especially in the field of picture grouping with different datasets. In this way, a sensible picture closeness metric will be researched to suite with datasets in the picture clustering field. As an end, changing the comparability lattice will prompt a superior clustering results

Effective Graph-Based Content--Based Image Retrieval Systems for Large-Scale and Small-Scale Image Databases

This dissertation proposes two novel manifold graph-based ranking systems for Content-Based Image Retrieval (CBIR). The two proposed systems exploit the synergism between relevance feedback-based transductive short-term learning and semantic feature-based long-term learning to improve retrieval performance. Proposed systems first apply the active learning mechanism to construct users\u27 relevance feedback log and extract high-level semantic features for each image. These systems then create manifold graphs by incorporating both the low-level visual similarity and the high-level semantic similarity to achieve more meaningful structures for the image space. Finally, asymmetric relevance vectors are created to propagate relevance scores of labeled images to unlabeled images via manifold graphs. The extensive experimental results demonstrate two proposed systems outperform the other state-of-the-art CBIR systems in the context of both correct and erroneous users\u27 feedback

Functional and structural MRI image analysis for brain glial tumors treatment

Cotutela con il Dipartimento di Biotecnologie e Scienze della Vita, Universiità degli Studi dell'Insubria.openThis Ph.D Thesis is the outcome of a close collaboration between the Center for Research in Image Analysis and Medical Informatics (CRAIIM) of the Insubria University and the Operative Unit of Neurosurgery, Neuroradiology and Health Physics of the University Hospital ”Circolo Fondazione Macchi”, Varese. The project aim is to investigate new methodologies by means of whose, develop an integrated framework able to enhance the use of Magnetic Resonance Images, in order to support clinical experts in the treatment of patients with brain Glial tumor. Both the most common uses of MRI technology for non-invasive brain inspection were analyzed. From the Functional point of view, the goal has been to provide tools for an objective reliable and non-presumptive assessment of the brain’s areas locations, to preserve them as much as possible at surgery. From the Structural point of view, methodologies for fully automatic brain segmentation and recognition of the tumoral areas, for evaluating the tumor volume, the spatial distribution and to be able to infer correlation with other clinical data or trace growth trend, have been studied. Each of the proposed methods has been thoroughly assessed both qualitatively and quantitatively. All the Medical Imaging and Pattern Recognition algorithmic solutions studied for this Ph.D. Thesis have been integrated in GliCInE: Glioma Computerized Inspection Environment, which is a MATLAB prototype of an integrated analysis environment that offers, in addition to all the functionality specifically described in this Thesis, a set of tools needed to manage Functional and Structural Magnetic Resonance Volumes and ancillary data related to the acquisition and the patient.openInformaticaPedoia, ValentinaPedoia, Valentin

Overlapping Community Detection in Networks: the State of the Art and Comparative Study

This paper reviews the state of the art in overlapping community detection algorithms, quality measures, and benchmarks. A thorough comparison of different algorithms (a total of fourteen) is provided. In addition to community level evaluation, we propose a framework for evaluating algorithms' ability to detect overlapping nodes, which helps to assess over-detection and under-detection. After considering community level detection performance measured by Normalized Mutual Information, the Omega index, and node level detection performance measured by F-score, we reached the following conclusions. For low overlapping density networks, SLPA, OSLOM, Game and COPRA offer better performance than the other tested algorithms. For networks with high overlapping density and high overlapping diversity, both SLPA and Game provide relatively stable performance. However, test results also suggest that the detection in such networks is still not yet fully resolved. A common feature observed by various algorithms in real-world networks is the relatively small fraction of overlapping nodes (typically less than 30%), each of which belongs to only 2 or 3 communities.Comment: This paper (final version) is accepted in 2012. ACM Computing Surveys, vol. 45, no. 4, 2013 (In press) Contact: [email protected]