Lynx: A Programmatic SAT Solver for the RNA-folding Problem

15th International Conference, Trento, Italy, June 17-20, 2012. ProceedingsThis paper introduces Lynx, an incremental programmatic SAT solver that allows non-expert users to introduce domain-specific code into modern conflict-driven clause-learning (CDCL) SAT solvers, thus enabling users to guide the behavior of the solver. The key idea of Lynx is a callback interface that enables non-expert users to specialize the SAT solver to a class of Boolean instances. The user writes specialized code for a class of Boolean formulas, which is periodically called by Lynx’s search routine in its inner loop through the callback interface. The user-provided code is allowed to examine partial solutions generated by the solver during its search, and to respond by adding CNF clauses back to the solver dynamically and incrementally. Thus, the user-provided code can specialize and influence the solver’s search in a highly targeted fashion. While the power of incremental SAT solvers has been amply demonstrated in the SAT literature and in the context of DPLL(T), it has not been previously made available as a programmatic API that is easy to use for non-expert users. Lynx’s callback interface is a simple yet very effective strategy that addresses this need. We demonstrate the benefits of Lynx through a case-study from computational biology, namely, the RNA secondary structure prediction problem. The constraints that make up this problem fall into two categories: structural constraints, which describe properties of the biological structure of the solution, and energetic constraints, which encode quantitative requirements that the solution must satisfy. We show that by introducing structural constraints on-demand through user provided code we can achieve, in comparison with standard SAT approaches, upto 30x reduction in memory usage and upto 100x reduction in time

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

Proceedings of the 22nd Conference on Formal Methods in Computer-Aided Design – FMCAD 2022

The Conference on Formal Methods in Computer-Aided Design (FMCAD) is an annual conference on the theory and applications of formal methods in hardware and system verification. FMCAD provides a leading forum to researchers in academia and industry for presenting and discussing groundbreaking methods, technologies, theoretical results, and tools for reasoning formally about computing systems. FMCAD covers formal aspects of computer-aided system design including verification, specification, synthesis, and testing

Tools and Algorithms for the Construction and Analysis of Systems

This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

Computer Aided Verification

This open access two-volume set LNCS 13371 and 13372 constitutes the refereed proceedings of the 34rd International Conference on Computer Aided Verification, CAV 2022, which was held in Haifa, Israel, in August 2022. The 40 full papers presented together with 9 tool papers and 2 case studies were carefully reviewed and selected from 209 submissions. The papers were organized in the following topical sections: Part I: Invited papers; formal methods for probabilistic programs; formal methods for neural networks; software Verification and model checking; hyperproperties and security; formal methods for hardware, cyber-physical, and hybrid systems. Part II: Probabilistic techniques; automata and logic; deductive verification and decision procedures; machine learning; synthesis and concurrency. This is an open access book

Tools and Algorithms for the Construction and Analysis of Systems

This open access two-volume set constitutes the proceedings of the 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2021, which was held during March 27 – April 1, 2021, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2021. The conference was planned to take place in Luxembourg and changed to an online format due to the COVID-19 pandemic. The total of 41 full papers presented in the proceedings was carefully reviewed and selected from 141 submissions. The volume also contains 7 tool papers; 6 Tool Demo papers, 9 SV-Comp Competition Papers. The papers are organized in topical sections as follows: Part I: Game Theory; SMT Verification; Probabilities; Timed Systems; Neural Networks; Analysis of Network Communication. Part II: Verification Techniques (not SMT); Case Studies; Proof Generation/Validation; Tool Papers; Tool Demo Papers; SV-Comp Tool Competition Papers