Efficient Pattern Matching in Python

Pattern matching is a powerful tool for symbolic computations. Applications include term rewriting systems, as well as the manipulation of symbolic expressions, abstract syntax trees, and XML and JSON data. It also allows for an intuitive description of algorithms in the form of rewrite rules. We present the open source Python module MatchPy, which offers functionality and expressiveness similar to the pattern matching in Mathematica. In particular, it includes syntactic pattern matching, as well as matching for commutative and/or associative functions, sequence variables, and matching with constraints. MatchPy uses new and improved algorithms to efficiently find matches for large pattern sets by exploiting similarities between patterns. The performance of MatchPy is investigated on several real-world problems

The N-end rule pathway controls multiple functions during Arabidopsis shoot and leaf development

The ubiquitin-dependent N-end rule pathway relates the in vivo half-life of a protein to the identity of its N-terminal residue. This proteolytic system is present in all organisms examined and has been shown to have a multitude of functions in animals and fungi. In plants, however, the functional understanding of the N-end rule pathway is only beginning. The N-end rule has a hierarchic structure. Destabilizing activity of N-terminal Asp, Glu, and (oxidized) Cys requires their conjugation to Arg by an arginyl–tRNA–protein transferase (R-transferase). The resulting N-terminal Arg is recognized by the pathway's E3 ubiquitin ligases, called “N-recognins.” Here, we show that the Arabidopsis R-transferases AtATE1 and AtATE2 regulate various aspects of leaf and shoot development. We also show that the previously identified N-recognin PROTEOLYSIS6 (PRT6) mediates these R-transferase-dependent activities. We further demonstrate that the arginylation branch of the N-end rule pathway plays a role in repressing the meristem-promoting BREVIPEDICELLUS (BP) gene in developing leaves. BP expression is known to be excluded from Arabidopsis leaves by the activities of the ASYMMETRIC LEAVES1 (AS1) transcription factor complex and the phytohormone auxin. Our results suggest that AtATE1 and AtATE2 act redundantly with AS1, but independently of auxin, in the control of leaf development

Hierarchic Superposition Revisited

Many applications of automated deduction require reasoning in first-order logic modulo background theories, in particular some form of integer arithmetic. A major unsolved research challenge is to design theorem provers that are "reasonably complete" even in the presence of free function symbols ranging into a background theory sort. The hierarchic superposition calculus of Bachmair, Ganzinger, and Waldmann already supports such symbols, but, as we demonstrate, not optimally. This paper aims to rectify the situation by introducing a novel form of clause abstraction, a core component in the hierarchic superposition calculus for transforming clauses into a form needed for internal operation. We argue for the benefits of the resulting calculus and provide two new completeness results: one for the fragment where all background-sorted terms are ground and another one for a special case of linear (integer or rational) arithmetic as a background theory

Synthesis for Polynomial Lasso Programs

We present a method for the synthesis of polynomial lasso programs. These programs consist of a program stem, a set of transitions, and an exit condition, all in the form of algebraic assertions (conjunctions of polynomial equalities). Central to this approach is the discovery of non-linear (algebraic) loop invariants. We extend Sankaranarayanan, Sipma, and Manna's template-based approach and prove a completeness criterion. We perform program synthesis by generating a constraint whose solution is a synthesized program together with a loop invariant that proves the program's correctness. This constraint is non-linear and is passed to an SMT solver. Moreover, we can enforce the termination of the synthesized program with the support of test cases.Comment: Paper at VMCAI'14, including appendi

Efficient Encodings of First-Order Horn Formulas in Equational Logic

We present several translations from first-order Horn formulas to equational logic. The goal of these translations is to allow equational theorem provers to efficiently reason about non-equational problems. Using these translations we were able to solve 37 problems of rating 1.0 (i.e. which had not previously been automatically solved) from the TPTP

Incompressible strips in dissipative Hall bars as origin of quantized Hall plateaus

We study the current and charge distribution in a two dimensional electron system, under the conditions of the integer quantized Hall effect, on the basis of a quasi-local transport model, that includes non-linear screening effects on the conductivity via the self-consistently calculated density profile. The existence of ``incompressible strips'' with integer Landau level filling factor is investigated within a Hartree-type approximation, and non-local effects on the conductivity along those strips are simulated by a suitable averaging procedure. This allows us to calculate the Hall and the longitudinal resistance as continuous functions of the magnetic field B, with plateaus of finite widths and the well-known, exactly quantized values. We emphasize the close relation between these plateaus and the existence of incompressible strips, and we show that for B values within these plateaus the potential variation across the Hall bar is very different from that for B values between adjacent plateaus, in agreement with recent experiments.Comment: 13 pages, 11 figures, All color onlin

A Reduction-Preserving Completion for Proving Confluence of Non-Terminating Term Rewriting Systems

We give a method to prove confluence of term rewriting systems that contain non-terminating rewrite rules such as commutativity and associativity. Usually, confluence of term rewriting systems containing such rules is proved by treating them as equational term rewriting systems and considering E-critical pairs and/or termination modulo E. In contrast, our method is based solely on usual critical pairs and it also (partially) works even if the system is not terminating modulo E. We first present confluence criteria for term rewriting systems whose rewrite rules can be partitioned into a terminating part and a possibly non-terminating part. We then give a reduction-preserving completion procedure so that the applicability of the criteria is enhanced. In contrast to the well-known Knuth-Bendix completion procedure which preserves the equivalence relation of the system, our completion procedure preserves the reduction relation of the system, by which confluence of the original system is inferred from that of the completed system

Automatic Generation of Invariants for Circular Derivations in {SUP(LA)} 1

The hierarchic combination of linear arithmetic and firstorder logic with free function symbols, FOL(LA), results in a strictly more expressive logic than its two parts. The SUP(LA) calculus can be turned into a decision procedure for interesting fragments of FOL(LA). For example, reachability problems for timed automata can be decided by SUP(LA) using an appropriate translation into FOL(LA). In this paper, we extend the SUP(LA) calculus with an additional inference rule, automatically generating inductive invariants from partial SUP(LA) derivations. The rule enables decidability of more expressive fragments, including reachability for timed automata with unbounded integer variables. We have implemented the rule in the SPASS(LA) theorem prover with promising results, showing that it can considerably speed up proof search and enable termination of saturation for practically relevant problems

BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition

BIG/DARK OVEREXPRESSION OF CAB1/TRANSPORT INHIBITOR RESPONSE3 is a 0.5-MDa protein associated with multiple functions in Arabidopsis (Arabidopsis thaliana) signalling and development. However, the biochemical functions of BIG are unknown. We investigated a role for BIG in the Arg/N-degron pathways, in which substrate protein fate is influenced by the N-terminal (Nt) residue. We crossed a big loss-of-function allele to two N-degron pathway E3 ligase mutants, proteolysis6 (prt6) and prt1, and examined the stability of protein substrates. Stability of model substrates was enhanced in prt6-1 big-2 and prt1-1 big-2 relative to the respective single mutants and the abundance of the PRT6 physiological substrates, HYPOXIA-RESPONSIVE ERF2 (HRE2) and VERNALIZATION2 (VRN2) was similarly increased in prt6 big double mutants. Hypoxia marker expression was enhanced in prt6 big double mutants; this constitutive response required arginyltransferase activity and RAP-type ERFVII transcription factors. Transcriptomic analysis of roots not only demonstrated increased expression of multiple hypoxia-responsive genes in the double mutant relative to prt6, but also revealed other roles for PRT6 and BIG, including regulation of suberin deposition through both ERFVII-dependent and independent mechanisms, respectively. Our results show that BIG acts together with PRT6 to regulate the hypoxia response and broader processes in Arabidopsis

Quantifier-Free Interpolation of a Theory of Arrays

The use of interpolants in model checking is becoming an enabling technology to allow fast and robust verification of hardware and software. The application of encodings based on the theory of arrays, however, is limited by the impossibility of deriving quantifier- free interpolants in general. In this paper, we show that it is possible to obtain quantifier-free interpolants for a Skolemized version of the extensional theory of arrays. We prove this in two ways: (1) non-constructively, by using the model theoretic notion of amalgamation, which is known to be equivalent to admit quantifier-free interpolation for universal theories; and (2) constructively, by designing an interpolating procedure, based on solving equations between array updates. (Interestingly, rewriting techniques are used in the key steps of the solver and its proof of correctness.) To the best of our knowledge, this is the first successful attempt of computing quantifier- free interpolants for a variant of the theory of arrays with extensionality