Ontology-Based Quality Evaluation of Value Generalization Hierarchies for Data Anonymization

In privacy-preserving data publishing, approaches using Value Generalization Hierarchies (VGHs) form an important class of anonymization algorithms. VGHs play a key role in the utility of published datasets as they dictate how the anonymization of the data occurs. For categorical attributes, it is imperative to preserve the semantics of the original data in order to achieve a higher utility. Despite this, semantics have not being formally considered in the specification of VGHs. Moreover, there are no methods that allow the users to assess the quality of their VGH. In this paper, we propose a measurement scheme, based on ontologies, to quantitatively evaluate the quality of VGHs, in terms of semantic consistency and taxonomic organization, with the aim of producing higher-quality anonymizations. We demonstrate, through a case study, how our evaluation scheme can be used to compare the quality of multiple VGHs and can help to identify faulty VGHs.Comment: 18 pages, 7 figures, presented in the Privacy in Statistical Databases Conference 2014 (Ibiza, Spain

Pathway relevance ranking for tumor samples through network-based data integration

The study of cancer, a highly heterogeneous disease with different causes and clinical outcomes, requires a multi-angle approach and the collection of large multi-omics datasets that, ideally, should be analyzed simultaneously. We present a new pathway relevance ranking method that is able to prioritize pathways according to the information contained in any combination of tumor related omics datasets. Key to the method is the conversion of all available data into a single comprehensive network representation containing not only genes but also individual patient samples. Additionally, all data are linked through a network of previously identified molecular interactions. We demonstrate the performance of the new method by applying it to breast and ovarian cancer datasets from The Cancer Genome Atlas. By integrating gene expression, copy number, mutation and methylation data, the method's potential to identify key pathways involved in breast cancer development shared by different molecular subtypes is illustrated. Interestingly, certain pathways were ranked equally important for different subtypes, even when the underlying (epi)-genetic disturbances were diverse. Next to prioritizing universally high-scoring pathways, the pathway ranking method was able to identify subtype-specific pathways. Often the score of a pathway could not be motivated by a single mutation, copy number or methylation alteration, but rather by a combination of genetic and epi-genetic disturbances, stressing the need for a network-based data integration approach. The analysis of ovarian tumors, as a function of survival-based subtypes, demonstrated the method's ability to correctly identify key pathways, irrespective of tumor subtype. A differential analysis of survival-based subtypes revealed several pathways with higher importance for the bad-outcome patient group than for the good-outcome patient group. Many of the pathways exhibiting higher importance for the bad-outcome patient group could be related to ovarian tumor proliferation and survival

Neural Networks for Complex Data

Artificial neural networks are simple and efficient machine learning tools. Defined originally in the traditional setting of simple vector data, neural network models have evolved to address more and more difficulties of complex real world problems, ranging from time evolving data to sophisticated data structures such as graphs and functions. This paper summarizes advances on those themes from the last decade, with a focus on results obtained by members of the SAMM team of Universit\'e Paris