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

An Incremental Learning Method to Support the Annotation of Workflows with Data-to-Data Relations

Workflow formalisations are often focused on the representation of a process with the primary objective to support execution. However, there are scenarios where what needs to be represented is the effect of the process on the data artefacts involved, for example when reasoning over the corresponding data policies. This can be achieved by annotating the workflow with the semantic relations that occur between these data artefacts. However, manually producing such annotations is difficult and time consuming. In this paper we introduce a method based on recommendations to support users in this task. Our approach is centred on an incremental rule association mining technique that allows to compensate the cold start problem due to the lack of a training set of annotated workflows. We discuss the implementation of a tool relying on this approach and how its application on an existing repository of workflows effectively enable the generation of such annotations

Mining Complex Hydrobiological Data with Galois Lattices

We have used Galois lattices for mining hydrobiological data. These data are about macrophytes, that are macroscopic plants living in water bodies. These plants are characterized by several biological traits, that own several modalities. Our aim is to cluster the plants according to their common traits and modalities and to find out the relations between traits. Galois lattices are efficient methods for such an aim, but apply on binary data. In this article, we detail a few approaches we used to transform complex hydrobiological data into binary data and compare the first results obtained thanks to Galois lattices