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

A Survey on Homomorphic Encryption Schemes: Theory and Implementation

Legacy encryption systems depend on sharing a key (public or private) among the peers involved in exchanging an encrypted message. However, this approach poses privacy concerns. Especially with popular cloud services, the control over the privacy of the sensitive data is lost. Even when the keys are not shared, the encrypted material is shared with a third party that does not necessarily need to access the content. Moreover, untrusted servers, providers, and cloud operators can keep identifying elements of users long after users end the relationship with the services. Indeed, Homomorphic Encryption (HE), a special kind of encryption scheme, can address these concerns as it allows any third party to operate on the encrypted data without decrypting it in advance. Although this extremely useful feature of the HE scheme has been known for over 30 years, the first plausible and achievable Fully Homomorphic Encryption (FHE) scheme, which allows any computable function to perform on the encrypted data, was introduced by Craig Gentry in 2009. Even though this was a major achievement, different implementations so far demonstrated that FHE still needs to be improved significantly to be practical on every platform. First, we present the basics of HE and the details of the well-known Partially Homomorphic Encryption (PHE) and Somewhat Homomorphic Encryption (SWHE), which are important pillars of achieving FHE. Then, the main FHE families, which have become the base for the other follow-up FHE schemes are presented. Furthermore, the implementations and recent improvements in Gentry-type FHE schemes are also surveyed. Finally, further research directions are discussed. This survey is intended to give a clear knowledge and foundation to researchers and practitioners interested in knowing, applying, as well as extending the state of the art HE, PHE, SWHE, and FHE systems.Comment: - Updated. (October 6, 2017) - This paper is an early draft of the survey that is being submitted to ACM CSUR and has been uploaded to arXiv for feedback from stakeholder

Distributed Computation of Generalized One-Sided Concept Lattices on Sparse Data Tables

In this paper we present the study on the usage of distributed version of the algorithm for generalized one-sided concept lattices (GOSCL), which provides a special case for fuzzy version of data analysis approach called formal concept analysis (FCA). The methods of this type create the conceptual model of the input data based on the theory of concept lattices and were successfully applied in several domains. GOSCL is able to create one-sided concept lattices for data tables with different attribute types processed as fuzzy sets. One of the problems with the creation of FCA-based models is their computational complexity. In order to reduce the computation times, we have designed the distributed version of the algorithm for GOSCL. The algorithm is able to work well especially for data where the number of newly generated concepts is reduced, i.e., for sparse input data tables which are often used in domains like text-mining and information retrieval. Therefore, we present the experimental results on sparse data tables in order to show the applicability of the algorithm on the generated data and the selected text-mining datasets