To efficiently solve exact discrete optimization problems, branch and bound algorithms require tight bounds. In constraint programming, for optimization, soft arc consistencies typically derive much stronger bounds than those offered by domain or bound consistencies applied to a cost variable. The reason is that soft local consistencies exchange marginal cost information between variables whereas domain consistencies rely only on shrinking domains, which is less informative. However, CP solvers equipped with soft arc consistencies have so far offered limited support for efficient processing of global constraints. In this work, we show how we can efficiently enforce soft local consistency over the AllDifferent constraint, relying on algorithms for the Linear Assignment Problem (LAP). We implement this propagator in toulbar2, the state-of-the-art weighted CP solver exploiting soft local consistencies for bounding. We show that, equipped with this new propagator, toulbar2 outperforms state-of-the-art domain consistency-based CP as well as integer programming solvers for the Quadratic Assignment Problem and shows better performance for miniCOP instances of the 2024 XCSP competition with AllDifferent constraints.

Applied combinatorial optimization has witnessed a revolution in performance since the turn of the millennium, but the complexity of modern solvers is making bugs an ever more serious concern. The most promising remedy is to make solvers certifying, so that they use proof logging to generate machine-verifiable proofs of correctness. We present the first example of state-of-the-art certified graph colouring by equipping the solver ZykovColor with VeriPB proof logging. Combined with the formally verified CakePB checker, this provides end-to-end formally certified results. An experimental evaluation shows excellent results with only moderate overhead for proof logging and checking.

The optimal allocation of crops to different parcels of land is a problem of paramount practical importance, not only to improve food and feed production, but also to address the challenges posed by climate change. However, this optimization problem is inherently complex due to the large number of agricultural sites available which generates a vast search space that renders traditional optimization techniques impractical. Moreover, as maximizing average production may generate solutions characterized by high year-by-year instability and lead to large and unrealistic cultivated areas, it is necessary to optimize crop allocation considering several objectives at the same time. In order to tackle this complex optimization problem, we propose a multi-objective approach, simultaneously maximizing the average production, minimizing the year-on-year production variance, and minimizing the total cultivated surface. The approach relies on an established multi-objective evolutionary algorithm, and employs a machine learning model able to predict crop production from weather and irrigation conditions, trained on historical data, making it possible to tackle allocation problems of large size. The proposed approach is compared to a quadratic programming algorithm tailored to the target problem. A case study focusing on the allocation of soybean crops in the European continent for the years 2000–2023 shows that the proposed methodology is able to identify informative tradeoffs between the three conflicting objectives considered, and identify realistic and meaningful crop allocations for supporting stakeholders’ decisions.

In Constraint Programming, solving discrete minimization problems with hard and soft constraints can be done either using (i) soft global constraints, (ii) a reformulation into a linear program, or (iii) a reformulation into local cost functions. Approach (i) benefits from a vast catalog of constraints. Each soft constraint propagator communicates with other soft constraints only through the variable domains, resulting in weak lower bounds. Conversely, the approach (ii) provides a global view with strong bounds, but the size of the reformulation can be problematic. We focus on approach (iii) in which soft arc consistency (SAC) algorithms produce bounds of intermediate quality. Recently, the introduction of linear constraints as local cost functions increases their modeling expressiveness. We adapt an existing SAC algorithm to handle linear constraints. We show that our algorithm significantly improves the lower bounds compared to the original algorithm on several benchmarks, reducing solving time in some cases.

Many current complete MaxSAT algorithms fall into two categories: core-guided or implicit hitting set. The two kinds of algorithms seem to have complementary strengths in practice, so that each kind of solver is better able to handle different families of instances. This suggests that a hybrid might match and outperform either, but the techniques used seem incompatible. In this paper, we focus on PMRES and OLL, two core-guided algorithms based on max resolution and soft cardinality constraints, respectively. We show that these algorithms implicitly discover cores of the original formula, as has been previously shown for PM1. Moreover, we show that in some cases, including unweighted instances, they compute the optimum hitting set of these cores at each iteration. We also give compact integer linear programs for each which encode this hitting set problem. Importantly, their continuous relaxation has an optimum that matches the bound computed by the respective algorithms. This goes some way towards resolving the incompatibility of implicit hitting set and core-guided algorithms, since solvers based on the implicit hitting set algorithm typically solve the problem by encoding it as a linear program.

In this paper, we extend a Burer-Monteiro style method to compute low rank Semi-Definite Programming (SDP) bounds for the MAP problem on discrete graphical models with an arbitrary number of states and arbitrary pairwise potentials. We consider both a penalized constraint approach and a dedicated Block Coordinate Descent (BCD) approach which avoids large penalty coefficients in the cost matrix. We show our algorithm is decreasing. Experiments show that the BCD approach compares favorably to the penalized approach and to usual linear bounds relying on convergent message passing approaches.

MOTIVATION: Inferring gene regulatory networks in non-independent genetically related panels is a methodological challenge. This hampers evolutionary and biological studies using heterozygote individuals such as in wild sunflower populations or cultivated hybrids. RESULTS: First, we simulated 100 datasets of gene expressions and polymorphisms, displaying the same gene expression distributions, heterozygosities and heritabilities as in our dataset including 173 genes and 353 genotypes measured in sunflower hybrids. Secondly, we performed a meta-analysis based on six inference methods [least absolute shrinkage and selection operator (Lasso), Random Forests, Bayesian Networks, Markov Random Fields, Ordinary Least Square and fast inference of networks from directed regulation (Findr)] and selected the minimal density networks for better accuracy with 64 edges connecting 79 genes and 0.35 area under precision and recall (AUPR) score on average. We identified that triangles and mutual edges are prone to errors in the inferred networks. Applied on classical datasets without heterozygotes, our strategy produced a 0.65 AUPR score for one dataset of the DREAM5 Systems Genetics Challenge. Finally, we applied our method to an experimental dataset from sunflower hybrids. We successfully inferred a network composed of 105 genes connected by 106 putative regulations with a major connected component. AVAILABILITY AND IMPLEMENTATION: Our inference methodology dedicated to genomic and transcriptomic data is available at https://forgemia.inra.fr/sunrise/inference_methods. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bayesian networks are probabilistic graphical models with a wide range of application areas including gene regulatory networks inference, risk analysis and image processing. Learning the structure of a Bayesian network (BNSL) from discrete data is known to be an NP-hard task with a superexponential search space of directed acyclic graphs. In this work, we propose a new polynomial time algorithm for discovering a subset of all possible cluster cuts, a greedy algorithm for approximately solving the resulting linear program, and a generalized arc consistency algorithm for the acyclicity constraint. We embed these in the constraint programming-based branch-and-bound solver CPBayes and show that, despite being suboptimal, they improve performance by orders of magnitude. The resulting solver also compares favorably with GOBNILP, a state-of-the-art solver for the BNSL problem which solves an NP-hard problem to discover each cut and solves the linear program exactly.

The goal of constraint acquisition is to learn exactly a constraint network given access to an oracle that answers truthfully certain types of queries. In this paper we focus on partial membership queries and initiate a systematic investigation of the learning complexity of constraint languages. First, we use the notion of chain length to show that a wide class of languages can be learned with as few as O(n log(n)) queries. Then, we combine this result with generic lower bounds to derive a dichotomy in the learning complexity of binary languages. Finally, we identify a class of ternary languages that eludes our framework and hints at new research directions.

Graph coloring is an important problem in combinatorial optimization and a major component of numerous allocation and scheduling problems. In this paper we introduce a hybrid CP/SAT approach to graph coloring based on the addition-contraction recurrence of Zykov. Decisions correspond to either adding an edge between two non-adjacent vertices or contracting these two vertices, hence enforcing inequality or equality, respectively. This scheme yields a symmetry-free tree and makes learnt clauses stronger by not committing to a particular color. We introduce a new lower bound for this problem based on Mycielskian graphs; a method to produce a clausal explanation of this bound for use in a CDCL algorithm; a branching heuristic emulating Br´elaz’ heuristic on the Zykov tree; and dedicated pruning techniques relying on marginal costs with respect to the bound and on reasoning about transitivity when unit propagating learnt clauses. The combination of these techniques in both a branch-and-bound and in a bottom-up search outperforms other SAT-based approaches and Dsatur on standard benchmarks both for finding upper bounds and for proving lower bounds.

In many applications of constraint programming, it is often impossible to capture all the relevant information in one numerical criterion. In this case, it is useful to produce a set of high quality yet diverse solutions. In this paper, motivated by a Computational Protein Design application, we consider the general problem of producing a diverse set of high-quality solutions of a given Weighted Constraint Satisfaction Problem, with guarantees both on solution quality and diversity. We use weighted automata decomposed in functions of bounded arity, incremental CFN solving, a simple form of predictive bounding and compressed representations of distance constraints for improved efficiency. We show that this approach can be successfully applied to a variety of problems that include both Protein Design Problems but also large Bayesian networks represented as Cost Function Networks. We also show that our approach has the capacity to enumerate so-called local delta-modes and that it does provide improved protein designs.

Graph coloring is a major component of numerous allocation and scheduling problems. We introduce a hybrid CP/SAT approach to graph coloring based on exploring Zykov’s tree: for two non-neighbors, either they take a different color and there might as well be an edge between them, or they take the same color and we might as well merge them. Branching on whether two neighbors get the same color yields a symmetry-free tree with complete graphs as leaves, which correspond to colorings of the original graph. We introduce a new lower bound for this problem based on Mycielskian graphs; a method to produce a clausal explanation of this bound for use in a CDCL algorithm; and a branching heuristic emulating Brelaz on the Zykov tree. The combination of these techniques in a branch- and-bound search outperforms Dsatur and other SAT-based approaches on standard benchmarks both for finding upper bounds and for proving lower bounds.

The maximum clique and minimum vertex cover problems are among Karp's 21 NP-complete problems, and have numerous applications: in combinatorial auctions, for computing phylogenetic trees, to predict the structure of proteins, to analyse social networks, and so forth. Currently, the best complete methods are branch & bound algorithms and rely largely on graph colouring to compute a bound. We introduce a new approach based on SAT and on the "Conflict-Driven Clause Learning" (CDCL) algorithm. We propose an efficient implementation of Babel's bound and pruning rule, as well as a novel dominance rule. Moreover, we show how to compute concise explanations for this inference. Our experimental results show that this approach is competitive and often outperforms the state of the art for finding cliques of maximum weight.

A number of problems involve managing a set of optional clauses. For example, the soft clauses in a MAXSAT formula are optional—they can be falsified for a cost. Similarly, when computing a Minimum Correction Set for an unsatisfiable formula, all clauses are optional—some can be falsified in order to satisfy the remaining. In both of these cases the task is to find a subset of the optional clauses that achieves some criteria, and whose removal leaves a satisfiable formula. Relaxation search is a simple method of using a standard SAT solver to solve this task. Relaxation search is easy to implement, sometimes requiring only a simple modification of the variable selection heuristic in the SAT solver; it offers considerable flexibility and control over the order in which subsets of optional clauses are examined; and it automatically exploits clause learning to exchange information between the two phases of finding a suitable subset of optional clauses and checking if their removal yields satisfiability. We demonstrate how relaxation search can be used to solve MAXSAT and to compute Minimum Correction Sets. In both cases relaxation search is able to achieve state-of-the-art performance and solve some instances other solvers are not able to solve.

Recent attempts to create versions of Satisfiability (SAT) solversthat exploit parallel hardware and information sharing have met withlimited success. In fact,the most successful parallel solvers in recent competitions were basedon portfolio approaches with little to no exchange of informationbetween processors. This experience contradicts the apparentparallelizability of exploring a combinatorial search space. Wepresent evidence that this discrepancy can be explained by studyingSAT solvers through a proof complexity lens, as resolution refutationengines. Starting with theobservation that a recently studied measure of resolution proofs,namely depth, provides a (weak) upper bound to the best possiblespeedup achievable by such solvers, we empirically show the existenceof bottlenecks to parallelizability that resolution proofs typicallygenerated by SAT solvers exhibit. Further, we propose a new measureof parallelizability based on the best-case makespan of an offlineresource constrained scheduling problem. This measureexplicitly accounts for a bounded number of parallel processors andappears to empirically correlate with parallel speedups observed inpractice. Our findings suggest that efficient parallelization of SATsolvers is not simply a matter of designing the right clause sharingheuristics; even in the best case, it can be --- and indeed is ---hindered by the structure of the resolution proofs current SAT solverstypically produce.

MOTIVATION: The main challenge for structure-based computational protein design (CPD) remains the combinatorial nature of the search space. Even in its simplest fixed-backbone formulation, CPD encompasses a computationally difficult NP-hard problem that prevents the exact exploration of complex systems defining large sequence-conformation spaces. RESULTS: We present here a CPD framework, based on cost function network (CFN) solving, a recent exact combinatorial optimization technique, to efficiently handle highly complex combinatorial spaces encountered in various protein design problems. We show that the CFN-based approach is able to solve optimality a variety of complex designs that could often not be solved using a usual CPD-dedicated tool or state-of-the-art exact operations research tools. Beyond the identification of the optimal solution, the global minimum-energy conformation, the CFN-based method is also able to quickly enumerate large ensembles of suboptimal solutions of interest to rationally build experimental enzyme mutant libraries. AVAILABILITY: The combined pipeline used to generate energetic models (based on a patched version of the open source solver Osprey 2.0), the conversion to CFN models (based on Perl scripts) and CFN solving (based on the open source solver toulbar2) are all available at http://genoweb.toulouse.inra.fr/~tschiex/CPD

We prove that it is NP-hard for a coalition of two manipulators to compute how to manipulate the Borda voting rule. This resolves one of the last open problems in the computational complexity of manipulating common voting rules. Because of this NP-hardness, we treat computing a manipulation as an approximation problem where we try to minimize the number of manipulators. Based on ideas from bin packing and multiprocessor scheduling, we propose two new approximation methods to compute manipulations of the Borda rule. Experiments show that these methods significantly outperform the previous best known approximation method. We are able to find optimal manipulations in almost all the randomly generated elections tested. Our results suggest that, whilst computing a manipulation of the Borda rule by a coalition is NP-hard, computational complexity may provide only a weak barrier against manipulation in practice.

Bound propagation is an important Artificial Intelligence technique used in Constraint Programming tools to deal with numerical constraints. It is typically embedded within a search procedure (”branch and prune”) and used at every node of the search tree to narrow down the search space, so it is critical that it be fast. The procedure invokes constraint propagators until a common fixpoint is reached, but the known algorithms for this have a pseudo-polynomial worst-case time complexity: they are fast indeed when the variables have a small numerical range, but they have the well-known problem of being prohibitively slow when these ranges are large. An important question is therefore whether strongly-polynomial algorithms exist that compute the common bound consistent fixpoint of a set of constraints. This paper answers this question. In particular we show that this fixpoint computation is in fact NP-complete, even when restricted to binary linear constraints.

Modern complete SAT solvers almost uniformly implement variations of the clause learning framework introduced by Grasp and Chaff. The success of these solvers has been theoretically explained by showing that the clause learning framework is an implementation of a proof system which is as poweful as resolution. However, exponential lower bounds are known for resolution, which suggests that significant advances in SAT solving must come from implementations of more powerful proof systems. We present a clause learning SAT solver that uses extended resolution. It is based on a restriction of the application of the extension rule. This solver outperforms existing solvers on application instances from recent SAT competitions as well as on instances that are provably hard for resolution.

We study propagation algorithms for the conjunction of two AllDifferent constraints. Solutions of an AllDifferent constraint can be seen as perfect matchings on the variable/value bipartite graph. Therefore, we investigate the problem of finding simultaneous bipartite matchings. We present an extension of the famous Hall theorem which characterizes when simultaneous bipartite matchings exists. Unfortunately, finding such matchings is NP-hard in general. However, we prove a surprising result that finding a simultaneous matching on a convex bipartite graph takes just polynomial time. Based on this theoretical result, we provide the first polynomial time bound consistency algorithm for the conjunction of two AllDifferent constraints. We identify a pathological problem on which this propagator is exponentially faster compared to existing propagators. Our experiments show that this new propagator can offer significant benefits over existing methods.

Symmetry is an important feature of many constraint programs. We show that any problem symmetry acting on a set of symmetry breaking constraints can be used to break symmetry. Different symmetries pick out different solutions in each symmetry class. This simple but powerful idea can be used in a number of different ways. We describe one application within model restarts, a search technique designed to reduce the conflict between symmetry breaking and the branching heuristic. In model restarts, we restart search periodically with a random symmetry of the symmetry breaking constraints. Experimental results show that this symmetry breaking technique is effective in practice on some standard benchmark problems.