Program debugging and validation using semantic approximations and partial specifications

The technique of Abstract Interpretation [11] has allowed the development of sophisticated program analyses which are provably correct and practical. The semantic approximations produced by such analyses have been traditionally applied to optimization during program compilation. However, recently, novel and promising applications of semantic approximations have been proposed in the more general context of program validation and debugging [3,9,7].

Partial order and contextual net semantics for atomic and locally atomic CC programs

We present two concurrent semantics (i.e. semantics where concurrency is explicitely represented) for CC programs with atomic tells. One is based on simple partial orders of computation steps, while the other one is based on contextual nets and it is an extensión of a previous one for eventual CC programs. Both such semantics allow us to derive concurrency, dependency, and nondeterminism information for the considered languages. We prove some properties about the relation between the two semantics, and also about the relation between them and the operational semantics. Moreover, we discuss how to use the contextual net semantics in the context of CLP programs. More precisely, by interpreting concurrency as possible parallelism, our semantics can be useful for a safe parallelization of some CLP computation steps. Dually, the dependency information may also be interpreted as necessary sequentialization, thus possibly exploiting it for the task of scheduling CC programs. Moreover, our semantics is also suitable for CC programs with a new kind of atomic tell (called locally atomic tell), which checks for consistency only the constraints it depends on. Such a tell achieves a reasonable trade-off between efficiency and atomicity, since the checked constraints can be stored in a local memory and are thus easily accessible even in a distributed implementation.

Using global analysis, partial specifications, and an extensible assertion language for program validation and debugging

We discuss a framework for the application of abstract interpretation as an aid during program development, rather than in the more traditional application of program optimization. Program validation and detection of errors is first performed statically by comparing (partial) specifications written in terms of assertions against information obtained from (global) static analysis of the program. The results of this process are expressed in the user assertion language. Assertions (or parts of assertions) which cannot be checked statically are translated into run-time tests. The framework allows the use of assertions to be optional. It also allows using very general properties in assertions, beyond the predefined set understandable by the static analyzer and including properties defined by user programs. We also report briefly on an implementation of the framework. The resulting tool generates and checks assertions for Prolog, CLP(R), and CHIP/CLP(fd) programs, and integrates compile-time and run-time checking in a uniform way. The tool allows using properties such as types, modes, non-failure, determinacy, and computational cost, and can treat modules separately, performing incremental analysis.

An integration of partial evaluation in a generic abstract interpretation framework

Information generated by abstract interpreters has long been used to perform program specialization. Additionally, if the abstract interpreter generates a multivariant analysis, it is also possible to perform múltiple specialization. Information about valúes of variables is propagated by simulating program execution and performing fixpoint computations for recursive calis. In contrast, traditional partial evaluators (mainly) use unfolding for both propagating valúes of variables and transforming the program. It is known that abstract interpretation is a better technique for propagating success valúes than unfolding. However, the program transformations induced by unfolding may lead to important optimizations which are not directly achievable in the existing frameworks for múltiple specialization based on abstract interpretation. The aim of this work is to devise a specialization framework which integrates the better information propagation of abstract interpretation with the powerful program transformations performed by partial evaluation, and which can be implemented via small modifications to existing generic abstract interpreters. With this aim, we will relate top-down abstract interpretation with traditional concepts in partial evaluation and sketch how the sophisticated techniques developed for controlling partial evaluation can be adapted to the proposed specialization framework. We conclude that there can be both practical and conceptual advantages in the proposed integration of partial evaluation and abstract interpretation.

Towards Integrating Partial Evaluation in a Specialization Framework based on Generic Abstract Interpretation

Abstract is not available

Using global analysis, partial specifications, and an extensible assertion language for program validation and debugging

We present a framework for the application of abstract interpretation as an aid during program development, rather than in the more traditional application of program optimization. Program validation and detection of errors is first performed statically by comparing (partial) specifications written in terms of assertions against information obtained from static analysis of the program. The results of this process are expressed in the user assertion language. Assertions (or parts of assertions) which cannot be verified statically are translated into run-time tests. The framework allows the use of assertions to be optional. It also allows using very general properties in assertions, beyond the predefined set understandable by the static analyzer and including properties defined by means of user programs. We also report briefly on an implementation of the framework. The resulting tool generates and checks assertions for Prolog, CLP(R), and CHIP/CLP(fd) programs, and integrates compile-time and run-time checking in a uniform way. The tool allows using properties such as types, modes, non-failure, determinacy, and computational cost, and can treat modules separately, performing incremental analysis. In practice, this modularity allows detecting statically bugs in user programs even if they do not contain any assertions.

Signal analysis and feature generation for pattern identification of partial discharges in high-voltage equipment

This paper proposes a method for the identification of different partial discharges (PDs) sources through the analysis of a collection of PD signals acquired with a PD measurement system. This method, robust and sensitive enough to cope with noisy data and external interferences, combines the characterization of each signal from the collection, with a clustering procedure, the CLARA algorithm. Several features are proposed for the characterization of the signals, being the wavelet variances, the frequency estimated with the Prony method, and the energy, the most relevant for the performance of the clustering procedure. The result of the unsupervised classification is a set of clusters each containing those signals which are more similar to each other than to those in other clusters. The analysis of the classification results permits both the identification of different PD sources and the discrimination between original PD signals, reflections, noise and external interferences. The methods and graphical tools detailed in this paper have been coded and published as a contributed package of the R environment under a GNU/GPL license.

A partial study of vertical distribution of conventional no-till seeders and spatial variability of seed depth placement of maize in the Alentejo region, Portugal

The requirements for a good stand in a no-till field are the same as those for conventional planting as well as added field and machinery management. Among the various factors that contribute towards producing a successful maize crop, seed depth placement is a key determinant. Although most no-till planters on the market work well under good soil and residue conditions, adjustments and even modifications are frequently needed when working with compacted or wet soils or with heavy residues. The main objective of this study, carried out in 2010, 2011 and 2012, was to evaluate the vertical distribution and spatial variability of seed depth placement in a maize crop under no-till conditions, using precision farming technologies and conventional no-till seeders. The results obtained indicate that the seed depth placement was affected by soil moisture content and forward speed. The seed depth placement was negatively correlated with soil resistance and seeding depth had a significant impact on mean emergence time and the percentage of emerged plants. Shallow average depth values and high coefficients of variation suggest a need for improvements in controlling the seeders’ sowing depth mechanism or more accurate calibration by operators in the field.

A clustering technique for partial discharge and noise sources identification in power cables by means of waveform parameters

On-line partial discharge (PD) measurements have become a common technique for assessing the insulation condition of installed high voltage (HV) insulated cables. When on-line tests are performed in noisy environments, or when more than one source of pulse-shaped signals are present in a cable system, it is difficult to perform accurate diagnoses. In these cases, an adequate selection of the non-conventional measuring technique and the implementation of effective signal processing tools are essential for a correct evaluation of the insulation degradation. Once a specific noise rejection filter is applied, many signals can be identified as potential PD pulses, therefore, a classification tool to discriminate the PD sources involved is required. This paper proposes an efficient method for the classification of PD signals and pulse-type noise interferences measured in power cables with HFCT sensors. By using a signal feature generation algorithm, representative parameters associated to the waveform of each pulse acquired are calculated so that they can be separated in different clusters. The efficiency of the clustering technique proposed is demonstrated through an example with three different PD sources and several pulse-shaped interferences measured simultaneously in a cable system with a high frequency current transformer (HFCT).

Kinematic geometry of mass-triangles and reduction of Schrödinger’s equation of three-body systems to partial differential equations solely defined on triangular parameters

Schrödinger’s equation of a three-body system is a linear partial differential equation (PDE) defined on the 9-dimensional configuration space, ℝ9, naturally equipped with Jacobi’s kinematic metric and with translational and rotational symmetries. The natural invariance of Schrödinger’s equation with respect to the translational symmetry enables us to reduce the configuration space to that of a 6-dimensional one, while that of the rotational symmetry provides the quantum mechanical version of angular momentum conservation. However, the problem of maximizing the use of rotational invariance so as to enable us to reduce Schrödinger’s equation to corresponding PDEs solely defined on triangular parameters—i.e., at the level of ℝ6/SO(3)—has never been adequately treated. This article describes the results on the orbital geometry and the harmonic analysis of (SO(3),ℝ6) which enable us to obtain such a reduction of Schrödinger’s equation of three-body systems to PDEs solely defined on triangular parameters.

Abnormal skeletal patterning in embryos lacking a single Cbp allele: A partial similarity with Rubinstein–Taybi syndrome

CBP is a transcriptional coactivator required by many transcription factors for transactivation. Rubinstein–Taybi syndrome, which is an autosomal dominant syndrome characterized by abnormal pattern formation, has been shown to be associated with mutations in the Cbp gene. Furthermore, Drosophila CBP is required in hedgehog signaling for the expression of decapentapleigic, the Drosophila homologue of bone morphogenetic protein. However, no direct evidence exists to indicate that loss of one copy of the mammalian Cbp gene affects pattern formation. Here, we show that various abnormalities occur at high frequency in the skeletal system of heterozygous Cbp-deficient mice resulting from a C57BL/6-CBA × BALB/c cross. In support of a conserved signaling pathway for pattern formation in insects and mammals, the expression of Bmp7 was found to be reduced in the heterozygous mutants. The frequency of the different abnormalities was significantly lower in a C57BL/6-CBA background, suggesting that the genetic background is an important determinant of the variability and severity of the anomalies seen in Rubinstein–Taybi syndrome patients.

Incomplete penetrance of familial retinoblastoma linked to germ-line mutations that result in partial loss of RB function

To study the molecular basis for the clinical phenotype of incomplete penetrance of familial retinoblastoma, we have examined the functional properties of three RB mutations identified in the germ line of five different families with low penetrance. RB mutants isolated from common adult cancers and from classic familial retinoblastoma (designated as classic RB mutations) are unstable and generally do not localize to the nucleus, do not undergo cyclin-dependent kinase (cdk)-mediated hyperphosphorylation, show absent protein “pocket” binding activity, and do not suppress colony growth of RB(−) cells. In contrast, two low-penetrant alleles (661W and “deletion of codon 480”) retained the ability to localize to the nucleus, showed normal cdk-mediated hyperphosphorylation in vivo, exhibited a binding pattern to simian virus 40 large T antigen using a quantitative yeast two-hybrid assay that was intermediate between classic mutants (null) and wild-type RB, and had absent E2F1 binding in vitro. A third, low-penetrant allele, “deletion of RB exon 4,” showed minimal hyperphosphorylation in vivo but demonstrated detectable E2F1 binding in vitro. In addition, each low-penetrant RB mutant retained the ability to suppress colony growth of RB(−) tumor cells. These findings suggest two categories of mutant, low-penetrant RB alleles. Class 1 alleles correspond to promoter mutations, which are believed to result in reduced or deregulated levels of wild-type RB protein, whereas class 2 alleles result in mutant proteins that retain partial activity. Characterization of the different subtypes of class 2 low-penetrant genes may help to define more precisely functional domains within the RB product required for tumor suppression.

Altered peptide ligands act as partial agonists by inhibiting phospholipase C activity induced by myasthenogenic T cell epitopes

Myasthenia gravis (MG) is a T cell-regulated, antibody-mediated autoimmune disease. Two peptides representing sequences of the human acetylcholine receptor α-subunit, p195–212 and p259–271, previously were shown to stimulate the proliferation of peripheral blood lymphocytes of patients with MG and were found to be immunodominant T cell epitopes in SJL and BALB/c mice, respectively. Single amino acid-substituted analogs of p195–212 and p259–271, as well as a dual analog composed of the tandemly arranged two single analogs, were shown to inhibit, in vitro and in vivo, MG-associated autoimmune responses. Stimulation of T cells through the antigen-specific T cell receptor activates tyrosine kinases and phospholipase C (PLC). Therefore, in attempts to understand the mechanism of action of the analogs, we first examined whether the myasthenogenic peptides trigger tyrosine phosphorylation and activation of phospholipase C. For that purpose, we measured generation of inositol phosphates and tyrosine phosphorylation of PLC after stimulation of the p195–212- and p259–271-specific T cell lines with these myasthenogenic peptides. Both myasthenogenic peptides stimulated generation of inositol phosphates as well as tyrosine phosphorylation of PLC. However, the single and dual analogs, although inducing tyrosine phosphorylation of PLC, could not induce PLC activity. Furthermore, the single and dual analogs inhibited the induced PLC activity whereas they could not inhibit tyrosine phosphorylation of PLC that was caused by the myasthenogenic peptides. Thus, the altered peptides and the dual analog act as partial agonists. The down-regulation of PLC activity by the analogs may account for their capacity to inhibit in vitro MG-associated T cell responses.

Lune/eye gone, a Pax-like protein, uses a partial paired domain and a homeodomain for DNA recognition

Pax proteins, characterized by the presence of a paired domain, play key regulatory roles during development. The paired domain is a bipartite DNA-binding domain that contains two helix–turn–helix domains joined by a linker region. Each of the subdomains, the PAI and RED domains, has been shown to be a distinct DNA-binding domain. The PAI domain is the most critical, but in specific circumstances, the RED domain is involved in DNA recognition. We describe a Pax protein, originally called Lune, that is the product of the Drosophila eye gone gene (eyg). It is unique among Pax proteins, because it contains only the RED domain. eyg seems to play a role both in the organogenesis of the salivary gland during embryogenesis and in the development of the eye. A high-affinity binding site for the Eyg RED domain was identified by using systematic evolution of ligands by exponential enrichment techniques. This binding site is related to a binding site previously identified for the RED domain of the Pax-6 5a isoform. Eyg also contains another DNA-binding domain, a Prd-class homeodomain (HD), whose palindromic binding site is similar to other Prd-class HDs. The ability of Pax proteins to use the PAI, RED, and HD, or combinations thereof, may be one mechanism that allows them to be used at different stages of development to regulate various developmental processes through the activation of specific target genes.