Quadratic Binary Programming Models in Computational Biology

In this paper we formulate four problems in computational molecular biology as 0-1 quadratic programs. These problems are all NP-hard and the current solution methods used in practice consist of heuristics or approximation algorithms tailored to each problem. Using test problems from scientific databases, we address the question, “Can a general-purpose solver obtain good answers in reasonable time?” In addition, we use the latest heuristics as incumbent solutions to address the question, “Can a general-purpose solver confirm optimality or find an improved solution in reasonable time?” Our computational experiments compare four different reformulation methods: three forms of linearization and one form of quadratic convexification

Branching strategies for mixed-integer programs containing logical constraints and decomposable structure

Decision-making optimisation problems can include discrete selections, e.g. selecting a route, arranging non-overlapping items or designing a network of items. Branch-and-bound (B&B), a widely applied divide-and-conquer framework, often solves such problems by considering a continuous approximation, e.g. replacing discrete variable domains by a continuous superset. Such approximations weaken the logical relations, e.g. for discrete variables corresponding to Boolean variables. Branching in B&B reintroduces logical relations by dividing the search space. This thesis studies designing B&B branching strategies, i.e. how to divide the search space, for optimisation problems that contain both a logical and a continuous structure. We begin our study with a large-scale, industrially-relevant optimisation problem where the objective consists of machine-learnt gradient-boosted trees (GBTs) and convex penalty functions. GBT functions contain if-then queries which introduces a logical structure to this problem. We propose decomposition-based rigorous bounding strategies and an iterative heuristic that can be embedded into a B&B algorithm. We approach branching with two strategies: a pseudocost initialisation and strong branching that target the structure of GBT and convex penalty aspects of the optimisation objective, respectively. Computational tests show that our B&B approach outperforms state-of-the-art solvers in deriving rigorous bounds on optimality. Our second project investigates how satisfiability modulo theories (SMT) derived unsatisfiable cores may be utilised in a B&B context. Unsatisfiable cores are subsets of constraints that explain an infeasible result. We study two-dimensional bin packing (2BP) and develop a B&B algorithm that branches on SMT unsatisfiable cores. We use the unsatisfiable cores to derive cuts that break 2BP symmetries. Computational results show that our B&B algorithm solves 20% more instances when compared with commercial solvers on the tested instances. Finally, we study convex generalized disjunctive programming (GDP), a framework that supports logical variables and operators. Convex GDP includes disjunctions of mathematical constraints, which motivate branching by partitioning the disjunctions. We investigate separation by branching, i.e. eliminating solutions that prevent rigorous bound improvement, and propose a greedy algorithm for building the branches. We propose three scoring methods for selecting the next branching disjunction. We also analyse how to leverage infeasibility to expedite the B&B search. Computational results show that our scoring methods can reduce the number of explored B&B nodes by an order of magnitude when compared with scoring methods proposed in literature. Our infeasibility analysis further reduces the number of explored nodes.Open Acces

Learning Discriminative Bayesian Networks from High-dimensional Continuous Neuroimaging Data

Due to its causal semantics, Bayesian networks (BN) have been widely employed to discover the underlying data relationship in exploratory studies, such as brain research. Despite its success in modeling the probability distribution of variables, BN is naturally a generative model, which is not necessarily discriminative. This may cause the ignorance of subtle but critical network changes that are of investigation values across populations. In this paper, we propose to improve the discriminative power of BN models for continuous variables from two different perspectives. This brings two general discriminative learning frameworks for Gaussian Bayesian networks (GBN). In the first framework, we employ Fisher kernel to bridge the generative models of GBN and the discriminative classifiers of SVMs, and convert the GBN parameter learning to Fisher kernel learning via minimizing a generalization error bound of SVMs. In the second framework, we employ the max-margin criterion and build it directly upon GBN models to explicitly optimize the classification performance of the GBNs. The advantages and disadvantages of the two frameworks are discussed and experimentally compared. Both of them demonstrate strong power in learning discriminative parameters of GBNs for neuroimaging based brain network analysis, as well as maintaining reasonable representation capacity. The contributions of this paper also include a new Directed Acyclic Graph (DAG) constraint with theoretical guarantee to ensure the graph validity of GBN.Comment: 16 pages and 5 figures for the article (excluding appendix

A parallel tabu search for the unconstrained binary quadratic programming problem

International audienceAlthough several sequential heuristics have been proposed for dealing with the Unconstrained Binary Quadratic Programming (UBQP), very little effort has been made for designing parallel algorithms for the UBQP. This paper propose a novel decentralized parallel search algorithm, called Parallel Elite Biased Tabu Search (PEBTS). It is based on D2TS, a state-of-the-art sequential UBQP metaheuristic. The key strategies in the PEBTS algorithm include: (i) a lazy distributed cooperation procedure to maintain diversity among different search processes and (ii) finely tuned bit-flip operators which can help the search escape local optima efficiently. Our experiments on the Tianhe-2 supercomputer with up to 24 computing cores show the accuracy of the efficiency of PEBTS compared with a straightforward parallel algorithm running multiple independent and non-cooperating D2TS processes

Exploiting Structures in Mixed-Integer Second-Order Cone Optimization Problems for Branch-and-Conic-Cut Algorithms

This thesis studies computational approaches for mixed-integer second-order cone optimization (MISOCO) problems. MISOCO models appear in many real-world applications, so MISOCO has gained significant interest in recent years. However, despite recent advancements, there is a gap between the theoretical developments and computational practice. Three chapters of this thesis address three areas of computational methodology for an efficient branch-and-conic-cut (BCC) algorithm to solve MISOCO problems faster in practice. These chapters include a detailed discussion on practical work on adding cuts in a BCC algorithm, novel methodologies for warm-starting second-order cone optimization (SOCO) subproblems, and heuristics for MISOCO problems.The first part of this thesis concerns the development of a novel warm-starting method of interior-point methods (IPM) for SOCO problems. The method exploits the Jordan frames of an original instance and solves two auxiliary linear optimization problems. The solutions obtained from these problems are used to identify an ideal initial point of the IPM. Numerical results on public test sets indicate that the warm-start method works well in practice and reduces the number of iterations required to solve related SOCO problems by around 30-40%.The second part of this thesis presents novel heuristics for MISOCO problems. These heuristics use the Jordan frames from both continuous relaxations and penalty problems and present a way of finding feasible solutions for MISOCO problems. Numerical results on conic and quadratic test sets show significant performance in terms of finding a solution that has a small gap to optimality.The last part of this thesis presents application of disjunctive conic cuts (DCC) and disjunctive cylindrical cuts (DCyC) to asset allocation problems (AAP). To maximize the benefit from these powerful cuts, several decisions regarding the addition of these cuts are inspected in a practical setting. The analysis in this chapter gives insight about how these cuts can be added in case-specific settings