NEMESYS: Enhanced Network Security for Seamless Service Provisioning in the Smart Mobile Ecosystem

As a consequence of the growing popularity of smart mobile devices, mobile malware is clearly on the rise, with attackers targeting valuable user information and exploiting vulnerabilities of the mobile ecosystems. With the emergence of large-scale mobile botnets, smartphones can also be used to launch attacks on mobile networks. The NEMESYS project will develop novel security technologies for seamless service provisioning in the smart mobile ecosystem, and improve mobile network security through better understanding of the threat landscape. NEMESYS will gather and analyze information about the nature of cyber-attacks targeting mobile users and the mobile network so that appropriate counter-measures can be taken. We will develop a data collection infrastructure that incorporates virtualized mobile honeypots and a honeyclient, to gather, detect and provide early warning of mobile attacks and better understand the modus operandi of cyber-criminals that target mobile devices. By correlating the extracted information with the known patterns of attacks from wireline networks, we will reveal and identify trends in the way that cyber-criminals launch attacks against mobile devices.Comment: Accepted for publication in Proceedings of the 28th International Symposium on Computer and Information Sciences (ISCIS'13); 9 pages; 1 figur

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Machine Learning at the Edge: A Data-Driven Architecture with Applications to 5G Cellular Networks

The fifth generation of cellular networks (5G) will rely on edge cloud deployments to satisfy the ultra-low latency demand of future applications. In this paper, we argue that such deployments can also be used to enable advanced data-driven and Machine Learning (ML) applications in mobile networks. We propose an edge-controller-based architecture for cellular networks and evaluate its performance with real data from hundreds of base stations of a major U.S. operator. In this regard, we will provide insights on how to dynamically cluster and associate base stations and controllers, according to the global mobility patterns of the users. Then, we will describe how the controllers can be used to run ML algorithms to predict the number of users in each base station, and a use case in which these predictions are exploited by a higher-layer application to route vehicular traffic according to network Key Performance Indicators (KPIs). We show that the prediction accuracy improves when based on machine learning algorithms that rely on the controllers' view and, consequently, on the spatial correlation introduced by the user mobility, with respect to when the prediction is based only on the local data of each single base station.Comment: 15 pages, 10 figures, 5 tables. IEEE Transactions on Mobile Computin

Pathway and network analysis in proteomics

Proteomics is inherently a systems science that studies not only measured protein and their expressions in a cell, but also the interplay of proteins, protein complexes, signaling pathways, and network modules. There is a rapid accumulation of Proteomics data in recent years. However, Proteomics data are highly variable, with results sensitive to data preparation methods, sample condition, instrument types, and analytical methods. To address the challenge in Proteomics data analysis, we review current tools being developed to incorporate biological function and network topological information. We categorize these tools into four types: tools with basic functional information and little topological features (e.g., GO category analysis), tools with rich functional information and little topological features (e.g., GSEA), tools with basic functional information and rich topological features (e.g., Cytoscape), and tools with rich functional information and rich topological features (e.g., PathwayExpress). We first review the potential application of these tools to Proteomics; then we review tools that can achieve automated learning of pathway modules and features, and tools that help perform integrated network visual analytics