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Preliminary Notes on Termination and Non-Termination Reasoning  [PDF]
Ton Chanh Le
Computer Science , 2013,
Abstract: In this preliminary note, we will illustrate our ideas on automated mechanisms for termination and non-termination reasoning.
Equilibrium and Termination
Vincent Danos,Nicolas Oury
Electronic Proceedings in Theoretical Computer Science , 2010, DOI: 10.4204/eptcs.26.7
Abstract: We present a reduction of the termination problem for a Turing machine (in the simplified form of the Post correspondence problem) to the problem of determining whether a continuous-time Markov chain presented as a set of Kappa graph-rewriting rules has an equilibrium. It follows that the problem of whether a computable CTMC is dissipative (ie does not have an equilibrium) is undecidable.
Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies
Moara Machado, Wagner CS Magalh?es, Allan Sene, Bruno Araújo, Alessandra C Faria-Campos, Stephen J Chanock, Leandro Scott, Guilherme Oliveira, Eduardo Tarazona-Santos, Maira R Rodrigues
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-3
Abstract: In order to assist with these intermediate tasks, we developed a pipeline that facilitates data handling typical of re-sequencing studies. Our pipeline: (1) consolidates different outputs produced by distinct Phred-Phrap-Consed contigs sharing a reference sequence; (2) checks for genotyping inconsistencies; (3) reformats genotyping data produced by Polyphred into a matrix of genotypes with individuals as rows and segregating sites as columns; (4) prepares input files for haplotype inferences using the popular software PHASE; and (5) handles PHASE output files that contain only polymorphic sites to reconstruct the inferred haplotypes including polymorphic and monomorphic sites as required by population genetics software for re-sequencing data such as DNAsp.We tested the pipeline in re-sequencing studies of haploid and diploid data in humans, plants, animals and microorganisms and observed that it allowed a substantial decrease in the time required for sequencing analyses, as well as being a more controlled process that eliminates several classes of error that may occur when handling datasets. The pipeline is also useful for investigators using other tools for sequencing and population genetics analyses.Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows screening of variation in a way that is unbiased in respect to the allele frequency spectrum and because it is suitable for a wide variety of living organisms. Although there is a plethora of new opportunities from next-generation sequencing (NGS) technologies [1], re-sequencing studies are traditionally performed using Sanger DNA sequencing. This is due, in part, to the widespread availability of automatic sequencers based on capillary electrophoresis and also to the fact that Sanger sequencing is still less prone to base-calling errors [2], which is critical in population genetics studies for which the accurate identification of substitution
Certification extends Termination Techniques  [PDF]
Christian Sternagel,René Thiemann
Computer Science , 2012,
Abstract: There are termination proofs that are produced by termination tools for which certifiers are not powerful enough. However, a similar situation also occurs in the other direction. We have formalized termination techniques in a more general setting as they have been introduced. Hence, we can certify proofs using techniques that no termination tool supports so far. In this paper we shortly present two of these formalizations: Polynomial orders with negative constants and Arctic termination.
The Professional Medical Journal , 2009,
Abstract: Objective: To compare the efficacy of vaginal misoprostal with that of sublingual misoprostol in 2nd trimester of pregnancy by comparing the induction-expulsion interval between two groups of patients induced with vaginal and sublingual misoprostol. Study design: Interventional, quasi experimental study. Settings: Obstetrics & Gynaecology Unit 1, Sir Ganga Ram Hospital, Lahore. Duration of study: Thirteen months from October 2006 to November 2007. Subjects and Methods: Sixty women at 12-26 weeks of gestation which were selected for termination of pregnancy were assigned into two groups. Thirty women received sublingual misoprostol and thirty women received vaginal misoprostol. Dosage regimen was tablet Misoprostol 200μg 4 hours apart till expulsion of fetus (maximum 5 doses). Main outcome measures were: 1. Induction-expulsion intervals 2. Maternal side effects 3. Fever 4. Nausea/vomiting 5.Diarrhea. Results: Mean induction-expulsion interval in vaginal group was 11.8±8.3 hours and in the sublingual group was 12.8±8.5 hours. Percentage of complete expulsion was 53.3% in both groups. Cases of failed induction in vaginal group were 10% and in sublingual group were 13.3%. One case ( 3.3%) of fever and two cases (6.6%) of vomiting were observed in sublingual group and one case (3.3%) of vomiting was observed in vaginal group. Conclusion: Both routes appear to be equally efficacious for mid trimester pregnancy termination, without significant side effects.
Local Termination: theory and practice  [PDF]
Joerg Endrullis,Roel de Vrijer,Johannes Waldmann
Computer Science , 2010, DOI: 10.2168/LMCS-6(3:20)2010
Abstract: The characterisation of termination using well-founded monotone algebras has been a milestone on the way to automated termination techniques, of which we have seen an extensive development over the past years. Both the semantic characterisation and most known termination methods are concerned with global termination, uniformly of all the terms of a term rewriting system (TRS). In this paper we consider local termination, of specific sets of terms within a given TRS. The principal goal of this paper is generalising the semantic characterisation of global termination to local termination. This is made possible by admitting the well-founded monotone algebras to be partial. We also extend our approach to local relative termination. The interest in local termination naturally arises in program verification, where one is probably interested only in sensible inputs, or just wants to characterise the set of inputs for which a program terminates. Local termination will be also be of interest when dealing with a specific class of terms within a TRS that is known to be non-terminating, such as combinatory logic (CL) or a TRS encoding recursive program schemes or Turing machines. We show how some of the well-known techniques for proving global termination, such as stepwise removal of rewrite rules and semantic labelling, can be adapted to the local case. We also describe transformations reducing local to global termination problems. The resulting techniques for proving local termination have in some cases already been automated. One of our applications concerns the characterisation of the terminating S-terms in CL as regular language. Previously this language had already been found via a tedious analysis of the reduction behaviour of S-terms. These findings have now been vindicated by a fully automated and verified proof.
On termination of meta-programs  [PDF]
Alexander Serebrenik,Danny De Schreye
Computer Science , 2001,
Abstract: The term {\em meta-programming} refers to the ability of writing programs that have other programs as data and exploit their semantics. The aim of this paper is presenting a methodology allowing us to perform a correct termination analysis for a broad class of practical meta-interpreters, including negation and performing different tasks during the execution. It is based on combining the power of general orderings, used in proving termination of term-rewrite systems and programs, and on the well-known acceptability condition, used in proving termination of logic programs. The methodology establishes a relationship between the ordering needed to prove termination of the interpreted program and the ordering needed to prove termination of the meta-interpreter together with this interpreted program. If such a relationship is established, termination of one of those implies termination of the other one, i.e., the meta-interpreter preserves termination. Among the meta-interpreters that are analysed correctly are a proof trees constructing meta-interpreter, different kinds of tracers and reasoners. To appear without appendix in Theory and Practice of Logic Programming.
Better Termination for Prolog with Constraints  [PDF]
Markus Triska,Ulrich Neumerkel,Jan Wielemaker
Computer Science , 2009,
Abstract: Termination properties of actual Prolog systems with constraints are fragile and difficult to analyse. The lack of the occurs-check, moded and overloaded arithmetical evaluation via is/2 and the occasional nontermination of finite domain constraints are all sources for invalidating termination results obtained by current termination analysers that rely on idealized assumptions. In this paper, we present solutions to address these problems on the level of the underlying Prolog system. Improved unification modes meet the requirements of norm based analysers by offering dynamic occurs-check detection. A generalized finite domain solver overcomes the shortcomings of conventional arithmetic without significant runtime overhead. The solver offers unbounded domains, yet propagation always terminates. Our work improves Prolog's termination and makes Prolog a more reliable target for termination and type analysis. It is part of SWI-Prolog since version 5.6.50.
Termination Detection of Local Computations  [PDF]
Emmanuel Godard,Yves Métivier,Gerard Tel
Computer Science , 2010,
Abstract: Contrary to the sequential world, the processes involved in a distributed system do not necessarily know when a computation is globally finished. This paper investigates the problem of the detection of the termination of local computations. We define four types of termination detection: no detection, detection of the local termination, detection by a distributed observer, detection of the global termination. We give a complete characterisation (except in the local termination detection case where a partial one is given) for each of this termination detection and show that they define a strict hierarchy. These results emphasise the difference between computability of a distributed task and termination detection. Furthermore, these characterisations encompass all standard criteria that are usually formulated : topological restriction (tree, rings, or triangu- lated networks ...), topological knowledge (size, diameter ...), and local knowledge to distinguish nodes (identities, sense of direction). These results are now presented as corollaries of generalising theorems. As a very special and important case, the techniques are also applied to the election problem. Though given in the model of local computations, these results can give qualitative insight for similar results in other standard models. The necessary conditions involve graphs covering and quasi-covering; the sufficient conditions (constructive local computations) are based upon an enumeration algorithm of Mazurkiewicz and a stable properties detection algorithm of Szymanski, Shi and Prywes.
Balanced Branching in Transcription Termination  [PDF]
K. J. Harrington,R. B. Laughlin,S. Liang
Physics , 2000, DOI: 10.1073/pnas.240431598
Abstract: The theory of stochastic transcription termination based on free-energy competition requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle but many troubling inconsistencies, most notably anomalous memory effects. These suggest that termination has a deterministic component and may conceivably be not stochastic at all. We find that a key experiment by Wilson and von Hippel allegedly refuting deterministic termination was an incorrectly analyzed regulatory effect of Mg2+ binding.
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