Low Size-Complexity Inductive Logic Programming: The East-West Challenge Considered as a Problem in Cost-Sensitive Classification

The Inductive Logic Programming community has considered proof-complexity and model-complexity, but, until recently, size-complexity has received little attention. Recently a challenge was issued "to the international computing community" to discover low size-complexity Prolog programs for classifying trains. The challenge was based on a problem first proposed by Ryszard Michalski, 20 years ago. We interpreted the challenge as a problem in cost-sensitive classification and we applied a recently developed cost-sensitive classifier to the competition. Our algorithm was relatively successful (we won a prize). This paper presents our algorithm and analyzes the results of the competition

Efficient algorithms to discover alterations with complementary functional association in cancer

Recent large cancer studies have measured somatic alterations in an unprecedented number of tumours. These large datasets allow the identification of cancer-related sets of genetic alterations by identifying relevant combinatorial patterns. Among such patterns, mutual exclusivity has been employed by several recent methods that have shown its effectivenes in characterizing gene sets associated to cancer. Mutual exclusivity arises because of the complementarity, at the functional level, of alterations in genes which are part of a group (e.g., a pathway) performing a given function. The availability of quantitative target profiles, from genetic perturbations or from clinical phenotypes, provides additional information that can be leveraged to improve the identification of cancer related gene sets by discovering groups with complementary functional associations with such targets. In this work we study the problem of finding groups of mutually exclusive alterations associated with a quantitative (functional) target. We propose a combinatorial formulation for the problem, and prove that the associated computation problem is computationally hard. We design two algorithms to solve the problem and implement them in our tool UNCOVER. We provide analytic evidence of the effectiveness of UNCOVER in finding high-quality solutions and show experimentally that UNCOVER finds sets of alterations significantly associated with functional targets in a variety of scenarios. In addition, our algorithms are much faster than the state-of-the-art, allowing the analysis of large datasets of thousands of target profiles from cancer cell lines. We show that on one such dataset from project Achilles our methods identify several significant gene sets with complementary functional associations with targets.Comment: Accepted at RECOMB 201

On application of least-delay variation problem in ethernet networks using SDN concept

The goal of this paper is to present an application idea of SDN in Smart Grids, particularly, in the area of L2 multicast as defined by IEC 61850-9-2. Authors propose an Integer Linear Formulation (ILP) dealing with a Least-Delay-Variation multicast forwarding problem that has a potential to utilize Ethernet networks in a new way. The proposed ILP formulation is numerically evaluated on random graph topologies and results are compared to a shortest path tree approach that is traditionally a product of Spanning Tree Protocols. Results confirm the correctness of the ILP formulation and illustrate dependency of a solution quality on the selected graph models, especially, in a case of scale-free topologies

Efficient Haplotype Inference with Pseudo-Boolean Optimization

Abstract. Haplotype inference from genotype data is a key computational problem in bioinformatics, since retrieving directly haplotype information from DNA samples is not feasible using existing technology. One of the methods for solving this problem uses the pure parsimony criterion, an approach known as Haplotype Inference by Pure Parsimony (HIPP). Initial work in this area was based on a number of different Integer Linear Programming (ILP) models and branch and bound algorithms. Recent work has shown that the utilization of a Boolean Satisfiability (SAT) formulation and state of the art SAT solvers represents the most efficient approach for solving the HIPP problem. Motivated by the promising results obtained using SAT techniques, this paper investigates the utilization of modern Pseudo-Boolean Optimization (PBO) algorithms for solving the HIPP problem. The paper starts by applying PBO to existing ILP models. The results are promising, and motivate the development of a new PBO model (RPoly) for the HIPP problem, which has a compact representation and eliminates key symmetries. Experimental results indicate that RPoly outperforms the SAT-based approach on most problem instances, being, in general, significantly more efficient

An Energy-driven Network Function Virtualization for Multi-domain Software Defined Networks

Network Functions Virtualization (NFV) in Software Defined Networks (SDN) emerged as a new technology for creating virtual instances for smooth execution of multiple applications. Their amalgamation provides flexible and programmable platforms to utilize the network resources for providing Quality of Service (QoS) to various applications. In SDN-enabled NFV setups, the underlying network services can be viewed as a series of virtual network functions (VNFs) and their optimal deployment on physical/virtual nodes is considered a challenging task to perform. However, SDNs have evolved from single-domain to multi-domain setups in the recent era. Thus, the complexity of the underlying VNF deployment problem in multi-domain setups has increased manifold. Moreover, the energy utilization aspect is relatively unexplored with respect to an optimal mapping of VNFs across multiple SDN domains. Hence, in this work, the VNF deployment problem in multi-domain SDN setup has been addressed with a primary emphasis on reducing the overall energy consumption for deploying the maximum number of VNFs with guaranteed QoS. The problem in hand is initially formulated as a "Multi-objective Optimization Problem" based on Integer Linear Programming (ILP) to obtain an optimal solution. However, the formulated ILP becomes complex to solve with an increasing number of decision variables and constraints with an increase in the size of the network. Thus, we leverage the benefits of the popular evolutionary optimization algorithms to solve the problem under consideration. In order to deduce the most appropriate evolutionary optimization algorithm to solve the considered problem, it is subjected to different variants of evolutionary algorithms on the widely used MOEA framework (an open source java framework based on multi-objective evolutionary algorithms).Comment: Accepted for publication in IEEE INFOCOM 2019 Workshop on Intelligent Cloud Computing and Networking (ICCN 2019