A conceptual approach to gene expression analysis enhanced by visual analytics

The analysis of gene expression data is a complex task for biologists wishing to understand the role of genes in the formation of diseases such as cancer. Biologists need greater support when trying to discover, and comprehend, new relationships within their data. In this paper, we describe an approach to the analysis of gene expression data where overlapping groupings are generated by Formal Concept Analysis and interactively analyzed in a tool called CUBIST. The CUBIST workflow involves querying a semantic database and converting the result into a formal context, which can be simplified to make it manageable, before it is visualized as a concept lattice and associated charts

Detecting self-similarity in surface microstructures

The relative configurational entropy per cell as a function of length scale is a sensitive detector of spatial self-similarity. For Sierpinski carpets the equally separated peaks of the above function appear at the length scales that depend on the kind of the carpet. These peaks point to the presence of self-similarity even for randomly perturbed initial fractal sets. This is also demonstrated for the model population of particles diffusing over the surface considered by Van Siclen, Phys. Rev. E 56 (1997) 5211. These results allow the subtle self-similarity traces to be explored.Comment: 9 pages, 4 figures, presented at ECOSS18 (Vienna) Sept. 199

On mining complex sequential data by means of FCA and pattern structures

Nowadays data sets are available in very complex and heterogeneous ways. Mining of such data collections is essential to support many real-world applications ranging from healthcare to marketing. In this work, we focus on the analysis of "complex" sequential data by means of interesting sequential patterns. We approach the problem using the elegant mathematical framework of Formal Concept Analysis (FCA) and its extension based on "pattern structures". Pattern structures are used for mining complex data (such as sequences or graphs) and are based on a subsumption operation, which in our case is defined with respect to the partial order on sequences. We show how pattern structures along with projections (i.e., a data reduction of sequential structures), are able to enumerate more meaningful patterns and increase the computing efficiency of the approach. Finally, we show the applicability of the presented method for discovering and analyzing interesting patient patterns from a French healthcare data set on cancer. The quantitative and qualitative results (with annotations and analysis from a physician) are reported in this use case which is the main motivation for this work. Keywords: data mining; formal concept analysis; pattern structures; projections; sequences; sequential data.Comment: An accepted publication in International Journal of General Systems. The paper is created in the wake of the conference on Concept Lattice and their Applications (CLA'2013). 27 pages, 9 figures, 3 table

Self-Similarities and Invariant Densities for Model Sets

Model sets (also called cut and project sets) are generalizations of lattices. Here we show how the self-similarities of model sets are a natural replacement for the group of translations of a lattice. This leads us to the concept of averaging operators and invariant densities on model sets. We prove that invariant densities exist and that they produce absolutely continuous invariant measures in internal space. We study the invariant densities and their relationships to diffraction, continuous refinement operators, and Hutchinson measures.Comment: 15 pages, 2 figures, to appear in: Algebraic Methods and Theoretical Physics (ed. Y. St. Aubin

Consensus image method for unknown noise removal

Noise removal has been, and it is nowadays, an important task in computer vision. Usually, it is a previous task preceding other tasks, as segmentation or reconstruction. However, for most existing denoising algorithms the noise model has to be known in advance. In this paper, we introduce a new approach based on consensus to deal with unknown noise models. To do this, different filtered images are obtained, then combined using multifuzzy sets and averaging aggregation functions. The final decision is made by using a penalty function to deliver the compromised image. Results show that this approach is consistent and provides a good compromise between filters.This work is supported by the European Commission under Contract No. 238819 (MIBISOC Marie Curie ITN). H. Bustince was supported by Project TIN 2010-15055 of the Spanish Ministry of Science

The State-of-the-Art of Set Visualization

Sets comprise a generic data model that has been used in a variety of data analysis problems. Such problems involve analysing and visualizing set relations between multiple sets defined over the same collection of elements. However, visualizing sets is a non-trivial problem due to the large number of possible relations between them. We provide a systematic overview of state-of-the-art techniques for visualizing different kinds of set relations. We classify these techniques into six main categories according to the visual representations they use and the tasks they support. We compare the categories to provide guidance for choosing an appropriate technique for a given problem. Finally, we identify challenges in this area that need further research and propose possible directions to address these challenges. Further resources on set visualization are available at http://www.setviz.net