On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks

Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed

GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs

We present a prototype of a software tool for exploration of multiple combinatorial optimisation problems in large real-world and synthetic complex networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial Explorer), provides a unified framework for scalable computation and presentation of high-quality suboptimal solutions and bounds for a number of widely studied combinatorial optimisation problems. Efficient representation and applicability to large-scale graphs and complex networks are particularly considered in its design. The problems currently supported include maximum clique, graph colouring, maximum independent set, minimum vertex clique covering, minimum dominating set, as well as the longest simple cycle problem. Suboptimal solutions and intervals for optimal objective values are estimated using scalable heuristics. The tool is designed with extensibility in mind, with the view of further problems and both new fast and high-performance heuristics to be added in the future. GraphCombEx has already been successfully used as a support tool in a number of recent research studies using combinatorial optimisation to analyse complex networks, indicating its promise as a research software tool

Optimised search heuristic combining valid inequalities and tabu search

This paper presents an Optimised Search Heuristic that combines a tabu search method with the verification of violated valid inequalities. The solution delivered by the tabu search is partially destroyed by a randomised greedy procedure, and then the valid inequalities are used to guide the reconstruction of a complete solution. An application of the new method to the Job-Shop Scheduling problem is presented.Optimised Search Heuristic, Tabu Search, GRASP, Valid Inequalities, Job Shop Scheduling

An Order-based Algorithm for Minimum Dominating Set with Application in Graph Mining

Dominating set is a set of vertices of a graph such that all other vertices have a neighbour in the dominating set. We propose a new order-based randomised local search (RLS$_o$) algorithm to solve minimum dominating set problem in large graphs. Experimental evaluation is presented for multiple types of problem instances. These instances include unit disk graphs, which represent a model of wireless networks, random scale-free networks, as well as samples from two social networks and real-world graphs studied in network science. Our experiments indicate that RLS$_o$ performs better than both a classical greedy approximation algorithm and two metaheuristic algorithms based on ant colony optimisation and local search. The order-based algorithm is able to find small dominating sets for graphs with tens of thousands of vertices. In addition, we propose a multi-start variant of RLS$_o$ that is suitable for solving the minimum weight dominating set problem. The application of RLS$_o$ in graph mining is also briefly demonstrated

Framework for sustainable TVET-Teacher Education Program in Malaysia Public Universities

Studies had stated that less attention was given to the education aspect, such as teaching and learning in planning for improving the TVET system. Due to the 21st Century context, the current paradigm of teaching for the TVET educators also has been reported to be fatal and need to be shifted. All these disadvantages reported hindering the country from achieving the 5th strategy in the Strategic Plan for Vocational Education Transformation to transform TVET system as a whole. Therefore, this study aims to develop a framework for sustainable TVET Teacher Education program in Malaysia. This study had adopted an Exploratory Sequential Mix-Method design, which involves a semi-structured interview (phase one) and survey method (phase two). Nine experts had involved in phase one chosen by using Purposive Sampling Technique. As in phase two, 118 TVET-TE program lecturers were selected as the survey sample chosen through random sampling method. After data analysis in phase one (thematic analysis) and phase two (Principal Component Analysis), eight domains and 22 elements have been identified for the framework for sustainable TVET-TE program in Malaysia. This framework was identified to embed the elements of 21st Century Education, thus filling the gap in this research. The research findings also indicate that the developed framework was unidimensional and valid for the development and research regarding TVET-TE program in Malaysia. Lastly, it is in the hope that this research can be a guide for the nations in producing a quality TVET teacher in the future

Satellite downlink scheduling problem: A case study

The synthetic aperture radar (SAR) technology enables satellites to efficiently acquire high quality images of the Earth surface. This generates significant communication traffic from the satellite to the ground stations, and, thus, image downlinking often becomes the bottleneck in the efficiency of the whole system. In this paper we address the downlink scheduling problem for Canada's Earth observing SAR satellite, RADARSAT-2. Being an applied problem, downlink scheduling is characterised with a number of constraints that make it difficult not only to optimise the schedule but even to produce a feasible solution. We propose a fast schedule generation procedure that abstracts the problem specific constraints and provides a simple interface to optimisation algorithms. By comparing empirically several standard meta-heuristics applied to the problem, we select the most suitable one and show that it is clearly superior to the approach currently in use.Comment: 23 page