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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
Visualizing and Interacting with Concept Hierarchies
Concept Hierarchies and Formal Concept Analysis are theoretically well
grounded and largely experimented methods. They rely on line diagrams called
Galois lattices for visualizing and analysing object-attribute sets. Galois
lattices are visually seducing and conceptually rich for experts. However they
present important drawbacks due to their concept oriented overall structure:
analysing what they show is difficult for non experts, navigation is
cumbersome, interaction is poor, and scalability is a deep bottleneck for
visual interpretation even for experts. In this paper we introduce semantic
probes as a means to overcome many of these problems and extend usability and
application possibilities of traditional FCA visualization methods. Semantic
probes are visual user centred objects which extract and organize reduced
Galois sub-hierarchies. They are simpler, clearer, and they provide a better
navigation support through a rich set of interaction possibilities. Since probe
driven sub-hierarchies are limited to users focus, scalability is under control
and interpretation is facilitated. After some successful experiments, several
applications are being developed with the remaining problem of finding a
compromise between simplicity and conceptual expressivity
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