Semantic distillation: a method for clustering objects by their contextual specificity

Techniques for data-mining, latent semantic analysis, contextual search of databases, etc. have long ago been developed by computer scientists working on information retrieval (IR). Experimental scientists, from all disciplines, having to analyse large collections of raw experimental data (astronomical, physical, biological, etc.) have developed powerful methods for their statistical analysis and for clustering, categorising, and classifying objects. Finally, physicists have developed a theory of quantum measurement, unifying the logical, algebraic, and probabilistic aspects of queries into a single formalism. The purpose of this paper is twofold: first to show that when formulated at an abstract level, problems from IR, from statistical data analysis, and from physical measurement theories are very similar and hence can profitably be cross-fertilised, and, secondly, to propose a novel method of fuzzy hierarchical clustering, termed \textit{semantic distillation} -- strongly inspired from the theory of quantum measurement --, we developed to analyse raw data coming from various types of experiments on DNA arrays. We illustrate the method by analysing DNA arrays experiments and clustering the genes of the array according to their specificity.Comment: Accepted for publication in Studies in Computational Intelligence, Springer-Verla

A comparative evaluation of interactive segmentation algorithms

In this paper we present a comparative evaluation of four popular interactive segmentation algorithms. The evaluation was carried out as a series of user-experiments, in which participants were tasked with extracting 100 objects from a common dataset: 25 with each algorithm, constrained within a time limit of 2 min for each object. To facilitate the experiments, a “scribble-driven” segmentation tool was developed to enable interactive image segmentation by simply marking areas of foreground and background with the mouse. As the participants refined and improved their respective segmentations, the corresponding updated segmentation mask was stored along with the elapsed time. We then collected and evaluated each recorded mask against a manually segmented ground truth, thus allowing us to gauge segmentation accuracy over time. Two benchmarks were used for the evaluation: the well-known Jaccard index for measuring object accuracy, and a new fuzzy metric, proposed in this paper, designed for measuring boundary accuracy. Analysis of the experimental results demonstrates the effectiveness of the suggested measures and provides valuable insights into the performance and characteristics of the evaluated algorithms

On morphological hierarchical representations for image processing and spatial data clustering

Hierarchical data representations in the context of classi cation and data clustering were put forward during the fties. Recently, hierarchical image representations have gained renewed interest for segmentation purposes. In this paper, we briefly survey fundamental results on hierarchical clustering and then detail recent paradigms developed for the hierarchical representation of images in the framework of mathematical morphology: constrained connectivity and ultrametric watersheds. Constrained connectivity can be viewed as a way to constrain an initial hierarchy in such a way that a set of desired constraints are satis ed. The framework of ultrametric watersheds provides a generic scheme for computing any hierarchical connected clustering, in particular when such a hierarchy is constrained. The suitability of this framework for solving practical problems is illustrated with applications in remote sensing

Optimum graph cuts for pruning binary partition trees of polarimetric SAR images

This paper investigates several optimum graph-cut techniques for pruning binary partition trees (BPTs) and their usefulness for the low-level processing of polarimetric synthetic aperture radar (PolSAR) images. BPTs group pixels to form homogeneous regions, which are hierarchically structured by inclusion in a binary tree. They provide multiple resolutions of description and easy access to subsets of regions. Once constructed, BPTs can be used for a large number of applications. Many of these applications consist in populating the tree with a specific feature and in applying a graph cut called pruning to extract a partition of the space. In this paper, different pruning examples involving the optimization of a global criterion are discussed and analyzed in the context of PolSAR images for segmentation. Through the objective evaluation of the resulting partitions by means of precision-and-recall-for-boundaries curves, the best pruning technique is identified, and the influence of the tree construction on the performances is assessed.Peer ReviewedPostprint (author's final draft

Spark solutions for discovering fuzzy association rules in Big Data

The research reported in this paper was partially supported the COPKIT project from the 8th Programme Framework (H2020) research and innovation programme (grant agreement No 786687) and from the BIGDATAMED projects with references B-TIC-145-UGR18 and P18-RT-2947.The high computational impact when mining fuzzy association rules grows significantly when managing very large data sets, triggering in many cases a memory overflow error and leading to the experiment failure without its conclusion. It is in these cases when the application of Big Data techniques can help to achieve the experiment completion. Therefore, in this paper several Spark algorithms are proposed to handle with massive fuzzy data and discover interesting association rules. For that, we based on a decomposition of interestingness measures in terms of α-cuts, and we experimentally demonstrate that it is sufficient to consider only 10equidistributed α-cuts in order to mine all significant fuzzy association rules. Additionally, all the proposals are compared and analysed in terms of efficiency and speed up, in several datasets, including a real dataset comprised of sensor measurements from an office building.COPKIT project from the 8th Programme Framework (H2020) research and innovation programme 786687BIGDATAMED projects B-TIC-145-UGR18 P18-RT-294

Adaptive Double Self-Organizing Map for Clustering Gene Expression Data

This thesis presents a novel clustering technique known as adaptive double self- organizing map (ADSOM) that addresses the issue of identifying the correct number of clusters. ADSOM has a flexible topology and performs clustering and cluster visualization simultaneously, thereby requiring no a priori knowledge about the number of clusters. ADSOM combines features of the popular self-organizing map with two- dimensional position vectors, which serve as a visualization tool to decide the number of clusters. It updates its free parameters during training and it allows convergence of its position vectors to a fairly consistent number of clusters provided that its initial number of nodes is greater than the expected number of clusters. A novel index is introduced based on hierarchical clustering of the final locations of position vectors. The index allows automated detection of the number of clusters, thereby reducing human error that could be incurred from counting clusters visually. The reliance of ADSOM in identifying the number of clusters is proven by applying it to publicly available gene expression data from multiple biological systems such as yeast, human, mouse, and bacteria

Automatic Detection of Critical Dermoscopy Features for Malignant Melanoma Diagnosis

Improved methods for computer-aided analysis of identifying features of skin lesions from digital images of the lesions are provided. Improved preprocessing of the image that 1) eliminates artifacts that occlude or distort skin lesion features and 2) identifies groups of pixels within the skin lesion that represent features and/or facilitate the quantification of features are provided including improved digital hair removal algorithms. Improved methods for analyzing lesion features are also provided

A graph-based mathematical morphology reader

This survey paper aims at providing a "literary" anthology of mathematical morphology on graphs. It describes in the English language many ideas stemming from a large number of different papers, hence providing a unified view of an active and diverse field of research