Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity in order to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic and (iv) machine learning methods applied to dissect, quantify and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology towards coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.Comment: 27 pages, 2 figure

Toward sustainable data centers: a comprehensive energy management strategy

Data centers are major contributors to the emission of carbon dioxide to the atmosphere, and this contribution is expected to increase in the following years. This has encouraged the development of techniques to reduce the energy consumption and the environmental footprint of data centers. Whereas some of these techniques have succeeded to reduce the energy consumption of the hardware equipment of data centers (including IT, cooling, and power supply systems), we claim that sustainable data centers will be only possible if the problem is faced by means of a holistic approach that includes not only the aforementioned techniques but also intelligent and unifying solutions that enable a synergistic and energy-aware management of data centers. In this paper, we propose a comprehensive strategy to reduce the carbon footprint of data centers that uses the energy as a driver of their management procedures. In addition, we present a holistic management architecture for sustainable data centers that implements the aforementioned strategy, and we propose design guidelines to accomplish each step of the proposed strategy, referring to related achievements and enumerating the main challenges that must be still solved.Peer ReviewedPostprint (author's final draft

A Survey of Prediction and Classification Techniques in Multicore Processor Systems

In multicore processor systems, being able to accurately predict the future provides new optimization opportunities, which otherwise could not be exploited. For example, an oracle able to predict a certain application\u27s behavior running on a smart phone could direct the power manager to switch to appropriate dynamic voltage and frequency scaling modes that would guarantee minimum levels of desired performance while saving energy consumption and thereby prolonging battery life. Using predictions enables systems to become proactive rather than continue to operate in a reactive manner. This prediction-based proactive approach has become increasingly popular in the design and optimization of integrated circuits and of multicore processor systems. Prediction transforms from simple forecasting to sophisticated machine learning based prediction and classification that learns from existing data, employs data mining, and predicts future behavior. This can be exploited by novel optimization techniques that can span across all layers of the computing stack. In this survey paper, we present a discussion of the most popular techniques on prediction and classification in the general context of computing systems with emphasis on multicore processors. The paper is far from comprehensive, but, it will help the reader interested in employing prediction in optimization of multicore processor systems