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The unrooted set covering connected subgraph problem differentiating between HIV envelope sequences
(2016)
This 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.
The tail assignment problem is a critical part of the airline planning process that assigns specific aircraft to sequences of flights, called lines-of-flight, to be operated the next day. The aim of this paper is to develop an operationally flexible tail assignment that satisfies short-range---within the next three days---aircraft maintenance requirements and performs the aircraft/flight gate assignment for each input line-of-flight. While maintenance plans commonly span multiple days, the related tail assignment problems can be overly complex and provide little recourse in the event of schedule perturbations. The presented approach addresses operational uncertainty by extending the one-day routes aircraft maintenance routing approach to satisfy maintenance requirements explicitly for the current day and implicitly for the subsequent two days. A mathematical model is presented that integrates the gate assignment and maintenance planning problems. To increase the satisfaction of maintenance requirements, an iterative algorithm is developed that modifies the fixed lines-of-flight provided as input to the tail assignment problem. The tail assignment problem and iterative algorithm are demonstrated to effectively satisfy maintenance requirements within appropriate run times using input data collected from three different airlines.
The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 8.0 of the SCIP Optimization Suite. Major updates in SCIP include improvements in symmetry handling and decomposition algorithms, new cutting planes, a new plugin type for cut selection, and a complete rework of the way nonlinear constraints are handled. Additionally, SCIP 8.0 now supports interfaces for Julia as well as Matlab. Further, UG now includes a unified framework to parallelize all solvers, a utility to analyze computational experiments has been added to GCG, dual solutions can be postsolved by PaPILO, new heuristics and presolving methods were added to SCIP-SDP, and additional problem classes and major performance improvements are available in SCIP-Jack.
The SCIP Optimization Suite provides a collection of software packages for
mathematical optimization centered around the constraint integer programming frame-
work SCIP. This paper discusses enhancements and extensions contained in version 7.0
of the SCIP Optimization Suite. The new version features the parallel presolving library
PaPILO as a new addition to the suite. PaPILO 1.0 simplifies mixed-integer linear op-
timization problems and can be used stand-alone or integrated into SCIP via a presolver
plugin. SCIP 7.0 provides additional support for decomposition algorithms. Besides im-
provements in the Benders’ decomposition solver of SCIP, user-defined decomposition
structures can be read, which are used by the automated Benders’ decomposition solver
and two primal heuristics. Additionally, SCIP 7.0 comes with a tree size estimation
that is used to predict the completion of the overall solving process and potentially
trigger restarts. Moreover, substantial performance improvements of the MIP core were
achieved by new developments in presolving, primal heuristics, branching rules, conflict
analysis, and symmetry handling. Last, not least, the report presents updates to other
components and extensions of the SCIP Optimization Suite, in particular, the LP solver
SoPlex and the mixed-integer semidefinite programming solver SCIP-SDP.
The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 6.0 of the SCIP Optimization Suite. Besides performance improvements of the MIP and MINLP core achieved by new primal heuristics and a new selection criterion for cutting planes, one focus of this release are decomposition algorithms. Both SCIP and the automatic decomposition solver GCG now include advanced functionality for performing Benders’ decomposition in a generic framework. GCG’s detection loop for structured matrices and the coordination of pricing routines for Dantzig-Wolfe decomposition has been significantly revised for greater flexibility. Two SCIP extensions have been added
to solve the recursive circle packing problem by a problem-specific column generation scheme and to demonstrate the use of the new Benders’ framework for stochastic capacitated facility location. Last, not least, the report presents updates and additions to the other components and extensions of the SCIP Optimization Suite: the LP solver SoPlex, the modeling language Zimpl, the parallelization framework UG, the Steiner tree solver SCIP-Jack, and the mixed-integer semidefinite programming solver SCIP-SDP.
The SCIP Optimization Suite is a powerful collection of optimization software that consists of the branch-cut-and-price framework and mixed-integer programming solver SCIP, the linear programming solver SoPlex, the modeling language Zimpl, the parallelization framework UG, and the generic branch-cut-and-price solver GCG. Additionally, it features the extensions SCIP-Jack for solving Steiner tree problems, PolySCIP for solving multi-objective problems, and SCIP-SDP for solving mixed-integer semidefinite programs. The SCIP Optimization Suite has been continuously developed and has now reached version 4.0. The goal of this report is to present the recent changes to the collection. We not only describe the theoretical basis, but focus on implementation aspects and their computational consequences.
The SCIP Optimization Suite is a software toolbox for generating and solving various classes of mathematical optimization problems. Its major components are the modeling language ZIMPL, the linear programming solver SoPlex, the constraint integer programming framework and mixed-integer linear and nonlinear programming solver SCIP, the UG framework for parallelization of branch-and-bound-based solvers, and the generic branch-cut-and-price solver GCG. It has been used in many applications from both academia and industry and is one of the leading non-commercial solvers.
This paper highlights the new features of version 3.2 of the SCIP Optimization Suite. Version 3.2 was released in July 2015. This release comes with new presolving steps, primal heuristics, and branching rules within SCIP. In addition, version 3.2 includes a reoptimization feature and improved handling of quadratic constraints and special ordered sets. SoPlex can now solve LPs exactly over the rational number and performance improvements have been achieved by exploiting sparsity in more situations. UG has been tested successfully on 80,000 cores. A major new feature of UG is the functionality to parallelize a customized SCIP solver. GCG has been enhanced with a new separator, new primal heuristics, and improved column management. Finally, new and improved extensions of SCIP are presented, namely solvers for multi-criteria optimization, Steiner tree problems, and mixed-integer semidefinite programs.
Schedule disruptions are commonplace in the airline industry with many flight-delaying events occurring each day. Recently there has been a focus on introducing robustness into airline planning stages to reduce the effect of these disruptions. We propose a recoverable robustness technique as an alternative to robust optimisation to reduce the effect of disruptions and the cost of recovery. We formulate the recoverable robust tail assignment problem (RRTAP) as a stochastic program, solved using column generation in the master and subproblems of the Benders' decomposition. We implement a two-phase algorithm for the Benders' decomposition and identify pareto-optimal cuts. The RRTAP includes costs due to flight delays, cancellation, and passenger rerouting, and the recovery stage includes cancellation, delay, and swapping options. To highlight the benefits of simultaneously solving planning and recovery problems in the RRTAP we compare our tail assignment solution against current approaches from the literature. Using airline data we demonstrate that by developing a better tail assignment plan via the RRTAP framework, one can reduce recovery costs in the event of a disruption.
The tail assignment problem is a critical part of the airline planning process that assigns specific aircraft to sequences of flights, called lines-of-flight, to satisfy operational constraints. The aim of this paper is to develop an operationally flexible method, based upon the one-day routes business model, to compute tail assignments that satisfy short-range—within the next three days—aircraft maintenance requirements. While maintenance plans commonly span multiple days, the methods used to compute tail assignments for the given plans can be overly complex and provide little recourse in the event of schedule perturbations. The presented approach addresses operational uncertainty by using solutions from the one-day routes aircraft maintenance routing approach as input. The daily tail assignment problem is solved with an objective to satisfy maintenance requirements explicitly for the current day and implicitly for the subsequent two days. A computational study will be performed to assess the performance of exact and heuristic solution algorithms that modify the input lines-of-flight to reduce maintenance misalignments. The daily tail assignment problem and the developed algorithms are demonstrated to compute solutions that effectively satisfy maintenance requirements when evaluated using input data collected from three different airlines.
Airline recovery presents very large and difficult problems requiring high quality solutions within very short time limits. To improve computational performance, the complete airline recovery problem is generally formulated as a series of sequential stages. While the sequential approach greatly simplifies the complete recovery problem, there is no guarantee of global optimality or solution quality. To address this, there has been increasing interest in the development of efficient solution techniques to solve an integrated recovery problem. In this paper, an integrated airline recovery problem is proposed by integrating the schedule, crew and aircraft recovery stages. To achieve short runtimes and high quality solutions, this problem is solved using column-and-row generation. Column-and-row generation achieves an improvement in solution runtimes by reducing the problem size and thereby achieving a faster execution of each LP solve. Further, the results demonstrate that a good upper bound achieved early in the solution process, indicating an improved solution quality with the early termination of the algorithm. This paper also details the integration of the row generation procedure with branch-and-price, which is used to achieve integral optimal solutions. The benefits of applying column-and-row generation to solve the integrated recovery problem are demonstrated with a comparison to a standard column generation technique.