Reasoning about Complex Networks: A Logic Programming Approach

Reasoning about complex networks has in recent years become an important topic of study due to its many applications: the adoption of commercial products, spread of disease, the diffusion of an idea, etc. In this paper, we present the MANCaLog language, a formalism based on logic programming that satisfies a set of desiderata proposed in previous work as recommendations for the development of approaches to reasoning in complex networks. To the best of our knowledge, this is the first formalism that satisfies all such criteria. We first focus on algorithms for finding minimal models (on which multi-attribute analysis can be done), and then on how this formalism can be applied in certain real world scenarios. Towards this end, we study the problem of deciding group membership in social networks: given a social network and a set of groups where group membership of only some of the individuals in the network is known, we wish to determine a degree of membership for the remaining group-individual pairs. We develop a prototype implementation that we use to obtain experimental results on two real world datasets, including a current social network of criminal gangs in a major U.S.\ city. We then show how the assignment of degree of membership to nodes in this case allows for a better understanding of the criminal gang problem when combined with other social network mining techniques -- including detection of sub-groups and identification of core group members -- which would not be possible without further identification of additional group members.Comment: arXiv admin note: substantial text overlap with arXiv:1301.030

Cdk1 Targets Srs2 to Complete Synthesis-Dependent Strand Annealing and to Promote Recombinational Repair

Cdk1 kinase phosphorylates budding yeast Srs2, a member of UvrD protein family, displays both DNA translocation and DNA unwinding activities in vitro. Srs2 prevents homologous recombination by dismantling Rad51 filaments and is also required for double-strand break (DSB) repair. Here we examine the biological significance of Cdk1-dependent phosphorylation of Srs2, using mutants that constitutively express the phosphorylated or unphosphorylated protein isoforms. We found that Cdk1 targets Srs2 to repair DSB and, in particular, to complete synthesis-dependent strand annealing, likely controlling the disassembly of a D-loop intermediate. Cdk1-dependent phosphorylation controls turnover of Srs2 at the invading strand; and, in absence of this modification, the turnover of Rad51 is not affected. Further analysis of the recombination phenotypes of the srs2 phospho-mutants showed that Srs2 phosphorylation is not required for the removal of toxic Rad51 nucleofilaments, although it is essential for cell survival, when DNA breaks are channeled into homologous recombinational repair. Cdk1-targeted Srs2 displays a PCNA–independent role and appears to have an attenuated ability to inhibit recombination. Finally, the recombination defects of unphosphorylatable Srs2 are primarily due to unscheduled accumulation of the Srs2 protein in a sumoylated form. Thus, the Srs2 anti-recombination function in removing toxic Rad51 filaments is genetically separable from its role in promoting recombinational repair, which depends exclusively on Cdk1-dependent phosphorylation. We suggest that Cdk1 kinase counteracts unscheduled sumoylation of Srs2 and targets Srs2 to dismantle specific DNA structures, such as the D-loops, in a helicase-dependent manner during homologous recombinational repair

Dynamic Network Configurations for Functionality and Security

Networks are designed with functionality, security, performance, and cost in mind. Flows should be served while controlling risk due to attackers. Configuration is time intensive and largely static until a major new vulnerability or service requirement forces change. We address this problem with an autonomous framework consisting of Observe, Orient, Decide and Act phases and look to optimization techniques for solutions to the Orient and Decide phases. Our first solution explores opportunities to improve network Quality of Service by combining a single flow routing solutions with a global multi-flow solution in a hybrid manner. In order to evaluate the quality of our solutions we implement an autonomous framework which generates the routing solution in a software defined network. We then explore two additional solutions that address both functional and security requirements and explore the trade-off of modeling and implementation choices for this problem. These two solutions innovate in modeling security risk in a way that is amenable to optimization and in the evaluation of the quality of the resulting configurations. Our framework allows an enterprise to automatically reconfigure their network upon a change in functionality (shift in user demand) or security (publication or patching of a vulnerability). The primary contributions of this work are two-fold: 1) the formulation and integrations of methods to address network Quality of Service and security in an autonomous framework and 2) detailed evaluation of these methods combining both emulation and simulation

Dynamic Network Configurations for Functionality and Security

Networks are designed with functionality, security, performance, and cost in mind. Flows should be served while controlling risk due to attackers. Configuration is time intensive and largely static until a major new vulnerability or service requirement forces change. We address this problem with an autonomous framework consisting of Observe, Orient, Decide and Act phases and look to optimization techniques for solutions to the Orient and Decide phases. Our first solution explores opportunities to improve network Quality of Service by combining a single flow routing solutions with a global multi-flow solution in a hybrid manner. In order to evaluate the quality of our solutions we implement an autonomous framework which generates the routing solution in a software defined network. We then explore two additional solutions that address both functional and security requirements and explore the trade-off of modeling and implementation choices for this problem. These two solutions innovate in modeling security risk in a way that is amenable to optimization and in the evaluation of the quality of the resulting configurations. Our framework allows an enterprise to automatically reconfigure their network upon a change in functionality (shift in user demand) or security (publication or patching of a vulnerability). The primary contributions of this work are two-fold: 1) the formulation and integrations of methods to address network Quality of Service and security in an autonomous framework and 2) detailed evaluation of these methods combining both emulation and simulation