Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology

Machine Learning of User Profiles: Representational Issues

As more information becomes available electronically, tools for finding information of interest to users becomes increasingly important. The goal of the research described here is to build a system for generating comprehensible user profiles that accurately capture user interest with minimum user interaction. The research described here focuses on the importance of a suitable generalization hierarchy and representation for learning profiles which are predictively accurate and comprehensible. In our experiments we evaluated both traditional features based on weighted term vectors as well as subject features corresponding to categories which could be drawn from a thesaurus. Our experiments, conducted in the context of a content-based profiling system for on-line newspapers on the World Wide Web (the IDD News Browser), demonstrate the importance of a generalization hierarchy and the promise of combining natural language processing techniques with machine learning (ML) to address an information retrieval (IR) problem.Comment: 6 page

Information Security as Strategic (In)effectivity

Security of information flow is commonly understood as preventing any information leakage, regardless of how grave or harmless consequences the leakage can have. In this work, we suggest that information security is not a goal in itself, but rather a means of preventing potential attackers from compromising the correct behavior of the system. To formalize this, we first show how two information flows can be compared by looking at the adversary's ability to harm the system. Then, we propose that the information flow in a system is effectively information-secure if it does not allow for more harm than its idealized variant based on the classical notion of noninterference

Automated user modeling for personalized digital libraries

Digital libraries (DL) have become one of the most typical ways of accessing any kind of digitalized information. Due to this key role, users welcome any improvements on the services they receive from digital libraries. One trend used to improve digital services is through personalization. Up to now, the most common approach for personalization in digital libraries has been user-driven. Nevertheless, the design of efficient personalized services has to be done, at least in part, in an automatic way. In this context, machine learning techniques automate the process of constructing user models. This paper proposes a new approach to construct digital libraries that satisfy user’s necessity for information: Adaptive Digital Libraries, libraries that automatically learn user preferences and goals and personalize their interaction using this information

Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data

We discuss a cancer hallmark network framework for modelling genome-sequencing data to predict cancer clonal evolution and associated clinical phenotypes. Strategies of using this framework in conjunction with genome sequencing data in an attempt to predict personalized drug targets, drug resistance, and metastasis for a cancer patient, as well as cancer risks for a healthy individual are discussed. Accurate prediction of cancer clonal evolution and clinical phenotypes will have substantial impact on timely diagnosis, personalized management and prevention of cancer.Comment: 5 figs, related papers, visit lab homepage: http://www.cancer-systemsbiology.org, Seminar in Cancer Biology, 201