The unrooted set covering connected subgraph problem differentiating between HIV envelope sequences

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordThis paper presents a novel application of operations research techniques to the analysis of HIV Env gene sequences, aiming to identify key features that are possible vaccine targets. These targets are identified as being critical to the transmission of HIV by being present in early transmitted (founder) sequences and absent in later chronic sequences. Identifying the key features of Env involves two steps: first, calculating the covariance of amino acid combinations and positions to form a network of related and compensatory mutations; and second, developing an integer program to identify the smallest connected subgraph of the constructed covariance network that exhibits a set covering property. The integer program developed for this analysis, labelled the unrooted set covering connected subgraph problem (USCCSP), integrates a set covering problem and connectivity evaluation, the latter formulated as a network flow problem. The resulting integer program is very large and complex, requiring the use of Benders’ decomposition to develop an efficient solution approach. The results will demonstrate the necessity of applying acceleration techniques to the Benders’ decomposition solution approach and the effectiveness of these techniques and heuristic approaches for solving the USCCSP

Approximating Minimum Cost Connectivity Orientation and Augmentation

We investigate problems addressing combined connectivity augmentation and orientations settings. We give a polynomial-time 6-approximation algorithm for finding a minimum cost subgraph of an undirected graph $G$ that admits an orientation covering a nonnegative crossing $G$-supermodular demand function, as defined by Frank. An important example is $(k,\ell)$-edge-connectivity, a common generalization of global and rooted edge-connectivity. Our algorithm is based on a non-standard application of the iterative rounding method. We observe that the standard linear program with cut constraints is not amenable and use an alternative linear program with partition and co-partition constraints instead. The proof requires a new type of uncrossing technique on partitions and co-partitions. We also consider the problem setting when the cost of an edge can be different for the two possible orientations. The problem becomes substantially more difficult already for the simpler requirement of $k$-edge-connectivity. Khanna, Naor, and Shepherd showed that the integrality gap of the natural linear program is at most $4$ when $k=1$ and conjectured that it is constant for all fixed $k$. We disprove this conjecture by showing an $\Omega(|V|)$ integrality gap even when $k=2$

From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data

Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically derive knowledge of a cellular signaling system at a conceptual level from systematic perturbation-response data. In this study, we explored a framework that unifies knowledge mining and data mining approaches towards the goal. The framework consists of the following automated processes: 1) applying an ontology-driven knowledge mining approach to identify functional modules among the genes responding to a perturbation in order to reveal potential signals affected by the perturbation; 2) applying a graph-based data mining approach to search for perturbations that affect a common signal with respect to a functional module, and 3) revealing the architecture of a signaling system organize signaling units into a hierarchy based on their relationships. Applying this framework to a compendium of yeast perturbation-response data, we have successfully recovered many well-known signal transduction pathways; in addition, our analysis have led to many hypotheses regarding the yeast signal transduction system; finally, our analysis automatically organized perturbed genes as a graph reflecting the architect of the yeast signaling system. Importantly, this framework transformed molecular findings from a gene level to a conceptual level, which readily can be translated into computable knowledge in the form of rules regarding the yeast signaling system, such as "if genes involved in MAPK signaling are perturbed, genes involved in pheromone responses will be differentially expressed"

Approximating Minimum-Cost k-Node Connected Subgraphs via Independence-Free Graphs

We present a 6-approximation algorithm for the minimum-cost $k$-node connected spanning subgraph problem, assuming that the number of nodes is at least $k^3(k-1)+k$. We apply a combinatorial preprocessing, based on the Frank-Tardos algorithm for $k$-outconnectivity, to transform any input into an instance such that the iterative rounding method gives a 2-approximation guarantee. This is the first constant-factor approximation algorithm even in the asymptotic setting of the problem, that is, the restriction to instances where the number of nodes is lower bounded by a function of $k$.Comment: 20 pages, 1 figure, 28 reference

Discrete and fuzzy dynamical genetic programming in the XCSF learning classifier system

A number of representation schemes have been presented for use within learning classifier systems, ranging from binary encodings to neural networks. This paper presents results from an investigation into using discrete and fuzzy dynamical system representations within the XCSF learning classifier system. In particular, asynchronous random Boolean networks are used to represent the traditional condition-action production system rules in the discrete case and asynchronous fuzzy logic networks in the continuous-valued case. It is shown possible to use self-adaptive, open-ended evolution to design an ensemble of such dynamical systems within XCSF to solve a number of well-known test problems

Planning UAV Activities for Efficient User Coverage in Disaster Areas

Climate changes brought about by global warming as well as man-made environmental changes are often the cause of sever natural disasters. ICT, which is itself responsible for global warming due to its high carbon footprint, can play a role in alleviating the consequences of such hazards by providing reliable, resilient means of communication during a disaster crisis. In this paper, we explore the provision of wireless coverage through UAVs (Unmanned Aerial Vehicles) to complement, or replace, the traditional communication infrastructure. The use of UAVs is indeed crucial in emergency scenarios, as they allow for the quick and easy deployment of micro and pico cellular base stations where needed. We characterize the movements of UAVs and define an optimization problem to determine the best UAV coverage that maximizes the user throughput, while maintaining fairness across the different parts of the geographical area that has been affected by the disaster. To evaluate our strategy, we simulate a flooding in San Francisco and the car traffic resulting from people seeking safety on higher ground

Robustness: a New Form of Heredity Motivated by Dynamic Networks

We investigate a special case of hereditary property in graphs, referred to as {\em robustness}. A property (or structure) is called robust in a graph $G$ if it is inherited by all the connected spanning subgraphs of $G$. We motivate this definition using two different settings of dynamic networks. The first corresponds to networks of low dynamicity, where some links may be permanently removed so long as the network remains connected. The second corresponds to highly-dynamic networks, where communication links appear and disappear arbitrarily often, subject only to the requirement that the entities are temporally connected in a recurrent fashion ({\it i.e.} they can always reach each other through temporal paths). Each context induces a different interpretation of the notion of robustness. We start by motivating the definition and discussing the two interpretations, after what we consider the notion independently from its interpretation, taking as our focus the robustness of {\em maximal independent sets} (MIS). A graph may or may not admit a robust MIS. We characterize the set of graphs \forallMIS in which {\em all} MISs are robust. Then, we turn our attention to the graphs that {\em admit} a robust MIS (\existsMIS). This class has a more complex structure; we give a partial characterization in terms of elementary graph properties, then a complete characterization by means of a (polynomial time) decision algorithm that accepts if and only if a robust MIS exists. This algorithm can be adapted to construct such a solution if one exists