Computing and Information Systems - Research Publications
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ItemLightweight Nontermination Inference with CHCs(SPRINGER INTERNATIONAL PUBLISHING AG, 2021)Non-termination is an unwanted program property (considered a bug) for some software systems, and a safety property for other systems. In either case, automated discovery of preconditions for non-termination is of interest. We introduce NtHorn, a fast lightweight non-termination analyser, able to deduce non-trivial sufficient conditions for non-termination. Using Constrained Horn Clauses (CHCs) as a vehicle, we show how established techniques for CHC program transformation and abstract interpretation can be exploited for the purpose of non-termination analysis. NtHorn is comparable in power to the state-of-the-art non-termination analysis tools, as measured on standard competition benchmark suites (consisting of integer manipulating programs), while typically solving problems an order of magnitude faster.
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ItemDisjunctive Interval Analysis(SPRINGER INTERNATIONAL PUBLISHING AG, 2021)We revisit disjunctive interval analysis based on the Boxes abstract domain. We propose the use of what we call range decision diagrams (RDDs) to implement Boxes, and we provide algorithms for the necessary RDD operations. RDDs tend to be more compact than the linear decision diagrams (LDDs) that have traditionally been used for Boxes. Representing information more directly, RDDs also allow for the implementation of more accurate abstract operations. This comes at no cost in terms of analysis efficiency, whether LDDs utilise dynamic variable ordering or not. RDD and LDD implementations are available in the Crab analyzer, and our experiments confirm that RDDs are well suited for disjunctive interval analysis.
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ItemOptimising Automatic Calibration of Electric Muscle Stimulation(ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE, 2021)Electrical Muscle Stimulation (EMS) has become a popular interaction technology in Human-Computer Interaction; allowing the computer to take direct control of the user's body. To date, however, the explorations have been limited to coarse, toy examples, due to the low resolution of achievable control. To increase this resolution, the EMS needs to increase significantly in complexity - using large numbers of electrodes in complex patterns. The calibration of such a system remains an unsolved challenge. We present a new SAT-based black-box calibration method, which requires no spatial information about muscular or electrode positioning. The method encodes domain knowledge and observations in a constraint model, and uses these to prune the space of feasible control signals. In a simulated environment we find this method can scale reliably to large arrays while requiring only a modest number of trials, and preliminary tests on real hardware show we can effectively calibrate an electrode array in a few minutes.
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ItemAbstract Interpretation over Non-Lattice Abstract Domains(Springer, 2013)The classical theoretical framework for static analysis of programs is abstract interpretation. Much of the power and elegance of that framework rests on the assumption that an abstract domain is a lattice. Nonetheless, and for good reason, the literature on program analysis provides many examples of non-lattice domains, including non-convex numeric domains. The lack of domain structure, however, has negative consequences, both for the precision of program analysis and for the termination of standard Kleene iteration. In this paper we explore these consequences and present general remedies.
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ItemAbstract interpretation, symbolic execution and constraints(Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2020)Abstract interpretation is a static analysis framework for sound over-approximation of all possible runtime states of a program. Symbolic execution is a framework for reachability analysis which tries to explore all possible execution paths of a program. A shared feature between abstract interpretation and symbolic execution is that each – implicitly or explicitly – maintains constraints during execution, in the form of invariants or path conditions. We investigate the relations between the worlds of abstract interpretation, symbolic execution and constraint solving, to expose potential synergies.
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ItemSynthesizing Optimal Switching Lattices(Association for Computing Machinery, 2014-11)The use of nanoscale technologies to create electronic devices has revived interest in the use of regular structures for defining complex logic functions. One such structure is the switching lattice, a two-dimensional lattice of four-terminal switches. We show how to directly construct switching lattices of polynomial size from arbitrary logic functions; we also show how to synthesize minimal-sized lattices by translating the problem to the satisfiability problem for a restricted class of quantified Boolean formulas. The synthesis method is an anytime algorithm that uses modern SAT solving technology and dichotomic search. It improves considerably on an earlier proposal for creating switching lattices for arbitrary logic functions.
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ItemBetaSearch: a new method for querying β-residue motifs.(Springer Science and Business Media LLC, 2012-07-30)BACKGROUND: Searching for structural motifs across known protein structures can be useful for identifying unrelated proteins with similar function and characterising secondary structures such as β-sheets. This is infeasible using conventional sequence alignment because linear protein sequences do not contain spatial information. β-residue motifs are β-sheet substructures that can be represented as graphs and queried using existing graph indexing methods, however, these approaches are designed for general graphs that do not incorporate the inherent structural constraints of β-sheets and require computationally-expensive filtering and verification procedures. 3D substructure search methods, on the other hand, allow β-residue motifs to be queried in a three-dimensional context but at significant computational costs. FINDINGS: We developed a new method for querying β-residue motifs, called BetaSearch, which leverages the natural planar constraints of β-sheets by indexing them as 2D matrices, thus avoiding much of the computational complexities involved with structural and graph querying. BetaSearch exhibits faster filtering, verification, and overall query time than existing graph indexing approaches whilst producing comparable index sizes. Compared to 3D substructure search methods, BetaSearch achieves 33 and 240 times speedups over index-based and pairwise alignment-based approaches, respectively. Furthermore, we have presented case-studies to demonstrate its capability of motif matching in sequentially dissimilar proteins and described a method for using BetaSearch to predict β-strand pairing. CONCLUSIONS: We have demonstrated that BetaSearch is a fast method for querying substructure motifs. The improvements in speed over existing approaches make it useful for efficiently performing high-volume exploratory querying of possible protein substructural motifs or conformations. BetaSearch was used to identify a nearly identical β-residue motif between an entirely synthetic (Top7) and a naturally-occurring protein (Charcot-Leyden crystal protein), as well as identifying structural similarities between biotin-binding domains of avidin, streptavidin and the lipocalin gamma subunit of human C8.
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ItemDashed Strings and the Replace(-all) Constraint(Springer International Publishing, 2020)Dashed strings are a formalism for modelling the domain of string variables when solving combinatorial problems with string constraints. In this work we focus on (variants of) the Replace constraint, which aims to find the first occurrence of a query string in a target string, and (possibly) replaces it with a new string. We define a Replace propagator which can also handle Replace-Last (for replacing the last occurrence) and Replace-All (for replacing all the occurrences). Empirical results clearly show that string constraint solving can draw great benefit from this approach.
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ItemDashed strings for string constraint solving(Elsevier, 2020-12-01)String processing is ubiquitous across computer science, and arguably more so in web programming — where it is also a critical part of security issues such as injection attacks. In recent years, a number of string solvers have been developed to solve combinatorial problems involving string variables and constraints. We examine the dashed string approach to string constraint solving, which represents an unknown string as a sequence of blocks of characters with bounds on their cardinalities. The solving approach relies on propagation of information about the blocks of characters that arise from reasoning about the constraints in which they occur. This approach shows promising performance on many benchmarks involving constraints like string length, equality, concatenation, and regular expression membership. In this paper, we formally review the definition, the properties and the use of dashed strings for string constraint solving, and we provide an empirical validation that confirms the effectiveness of this approach.
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ItemA complete refinement procedure for regular separability of context-free languages(ELSEVIER SCIENCE BV, 2016-04-25)Often, when analyzing the behaviour of systems modelled as context-free languages, we wish to know if two languages overlap. To this end, we present a class of semi-decision procedures for regular separability of context-free languages, based on counter-example guided abstraction refinement. We propose two effective instances of this approach, one that is complete but relatively expensive, and one that is inexpensive and sound, but for which we do not have a completeness proof. The complete method will prove disjointness whenever the input languages are regularly separable. Both methods will terminate whenever the input languages overlap. We provide an experimental evaluation of these procedures, and demonstrate their practicality on a range of verification and language-theoretic instances.