Generalized roof duality and bisubmodular functions

Consider a convex relaxation $\hat f$ of a pseudo-boolean function $f$. We say that the relaxation is {\em totally half-integral} if $\hat f(x)$ is a polyhedral function with half-integral extreme points $x$, and this property is preserved after adding an arbitrary combination of constraints of the form $x_i=x_j$, $x_i=1-x_j$, and $x_i=\gamma$ where \gamma\in\{0, 1, 1/2} is a constant. A well-known example is the {\em roof duality} relaxation for quadratic pseudo-boolean functions $f$. We argue that total half-integrality is a natural requirement for generalizations of roof duality to arbitrary pseudo-boolean functions. Our contributions are as follows. First, we provide a complete characterization of totally half-integral relaxations $\hat f$ by establishing a one-to-one correspondence with {\em bisubmodular functions}. Second, we give a new characterization of bisubmodular functions. Finally, we show some relationships between general totally half-integral relaxations and relaxations based on the roof duality.Comment: 14 pages. Shorter version to appear in NIPS 201

Safe solutions for walks on graphs

In this thesis we study the concept of “safe solutions” in different problems whose solutions are walks on graphs. A safe solution to a problem X can be understood as a partial solution common to all solutions to problem X. In problems whose solutions are walks on graphs, safe solutions refer to walks common to all walks which are solutions to the problem. In this thesis, we focused on formulating four main graph traversal problems and finding characterizations for those walks contained in all their solutions. We give formulations for these graph traversal problems, we prove some of their combinatorial and structural properties, and we give safe and complete algorithms for finding their safe solutions based on their characterizations. We use the genome assembly problem and its applications as our main motivating example for finding safe solutions in these graph traversal problems. We begin by motivating and exemplifying the notion of safe solutions through a problem on s-t paths in undirected graphs with at least two non-trivial biconnected components S and T and with s ∈ S, t ∈ T . We continue by reviewing similar and related notions in other fields, especially in combinatorial optimization and previous work on the bioinformatics problem of genome assembly. We then proceed to characterize the safe solutions to the Eulerian cycle problem, where one must find a circular walk in a graph G which traverses each edge exactly once. We suggest a characterization for them by improving on (Nagarajan, Pop, JCB 2009) and a polynomial-time algorithm for finding them. We then study edge-covering circular walks in a graph G. We look at the characterization from (Tomescu, Medvedev, JCB 2017) for their safe solutions and their suggested polynomial-time algorithm and we show an optimal O(mn)-time algorithm that we proposed in (Cairo et al. CPM 2017). Finally, we generalize this to edge-covering collections of circular walks. We characterize safe solutions in an edge-covering setting and provide a polynomial-time algorithm for computing them. We suggested these originally in (Obscura et al. ALMOB 2018)

Improving RNA Assembly via Safety and Completeness in Flow Decompositions

Extended version of RECOMB 2022 paperDecomposing a network flow into weighted paths is a problem with numerous applications, ranging from networking, transportation planning, to bioinformatics. In some applications we look for a decomposition that is optimal with respect to some property, such as the number of paths used, robustness to edge deletion, or length of the longest path. However, in many bioinformatic applications, we seek a specific decomposition where the paths correspond to some underlying data that generated the flow. In these cases, no optimization criteria guarantee the identification of the correct decomposition. Therefore, we propose to instead report the safe paths, which are subpaths of at least one path in every flow decomposition. In this work, we give the first local characterization of safe paths for flow decompositions in directed acyclic graphs, leading to a practical algorithm for finding the complete set of safe paths. In addition, we evaluate our algorithm on RNA transcript data sets against a trivial safe algorithm (extended unitigs), the recently proposed safe paths for path covers (TCBB 2021) and the popular heuristic greedy-width. On the one hand, we found that besides maintaining perfect precision, our safe and complete algorithm reports a significantly higher coverage (≈50 compared with the other safe algorithms. On the other hand, the greedy-width algorithm although reporting a better coverage, it also reports a significantly lower precision on complex graphs (for genes expressing a large number of transcripts). Overall, our safe and complete algorithm outperforms (by ≈20 greedy-width on a unified metric (F-score) considering both coverage and precision when the evaluated data set has a significant number of complex graphs. Moreover, it also has a superior time (4−5×) and space performance (1.2−2.2×), resulting in a better and more practical approach for bioinformatic applications of flow decomposition.Peer reviewe

Experimental Evaluation of Parameterized Algorithms for Feedback Vertex Set

Feedback Vertex Set is a classic combinatorial optimization problem that asks for a minimum set of vertices in a given graph whose deletion makes the graph acyclic. From the point of view of parameterized algorithms and fixed-parameter tractability, Feedback Vertex Set is one of the landmark problems: a long line of study resulted in multiple algorithmic approaches and deep understanding of the combinatorics of the problem. Because of its central role in parameterized complexity, the first edition of the Parameterized Algorithms and Computational Experiments Challenge (PACE) in 2016 featured Feedback Vertex Set as the problem of choice in one of its tracks. The results of PACE 2016 on one hand showed large discrepancy between performance of different classic approaches to the problem, and on the other hand indicated a new approach based on half-integral relaxations of the problem as probably the most efficient approach to the problem. In this paper we provide an exhaustive experimental evaluation of fixed-parameter and branching algorithms for Feedback Vertex Set

Algorithmic and game-theoretic perspectives on scheduling

This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Thesis (Ph. D.)--Massachusetts Institute of Technology, Sloan School of Management, Operations Research Center, 2008.Includes bibliographical references (p. 103-110).(cont.) Second, for almost all 0-1 bipartite instances, we give a lower bound on the integrality gap of various linear programming relaxations of this problem. Finally, we show that for almost all 0-1 bipartite instances, all feasible schedules are arbitrarily close to optimal. Finally, we consider the problem of minimizing the sum of weighted completion times in a concurrent open shop environment. We present some interesting properties of various linear programming relaxations for this problem, and give a combinatorial primal-dual 2-approximation algorithm.In this thesis, we study three problems related to various algorithmic and game-theoretic aspects of scheduling. First, we apply ideas from cooperative game theory to study situations in which a set of agents faces super modular costs. These situations appear in a variety of scheduling contexts, as well as in some settings related to facility location and network design. Although cooperation is unlikely when costs are super modular, in some situations, the failure to cooperate may give rise to negative externalities. We study the least core value of a cooperative game -- the minimum penalty we need to charge a coalition for acting independently that ensures the existence of an efficient and stable cost allocation -- as a means of encouraging cooperation. We show that computing the least core value of supermodular cost cooperative games is strongly NP-hard, and design an approximation framework for this problem that in the end, yields a (3 + [epsilon])-approximation algorithm. We also apply our approximation framework to obtain better results for two special cases of supermodular cost cooperative games that arise from scheduling and matroid optimization. Second, we focus on the classic precedence- constrained single-machine scheduling problem with the weighted sum of completion times objective. We focus on so-called 0-1 bipartite instances of this problem, a deceptively simple class of instances that has virtually the same approximability behavior as arbitrary instances. In the hope of improving our understanding of these instances, we use models from random graph theory to look at these instances with a probabilistic lens. First, we show that for almost all 0-1 bipartite instances, the decomposition technique of Sidney (1975) does not yield a non-trivial decomposition.by Nelson A. Uhan.Ph.D

Discrete graphical models -- an optimization perspective

This monograph is about discrete energy minimization for discrete graphical models. It considers graphical models, or, more precisely, maximum a posteriori inference for graphical models, purely as a combinatorial optimization problem. Modeling, applications, probabilistic interpretations and many other aspects are either ignored here or find their place in examples and remarks only. It covers the integer linear programming formulation of the problem as well as its linear programming, Lagrange and Lagrange decomposition-based relaxations. In particular, it provides a detailed analysis of the polynomially solvable acyclic and submodular problems, along with the corresponding exact optimization methods. Major approximate methods, such as message passing and graph cut techniques are also described and analyzed comprehensively. The monograph can be useful for undergraduate and graduate students studying optimization or graphical models, as well as for experts in optimization who want to have a look into graphical models. To make the monograph suitable for both categories of readers we explicitly separate the mathematical optimization background chapters from those specific to graphical models.Comment: 270 page