Parallel Flow-Sensitive Pointer Analysis by Graph-Rewriting

Precise pointer analysis is a problem of interest to both the compiler and the program verification community. Flow-sensitivity is an important dimension of pointer analysis that affects the precision of the final result computed. Scaling flow-sensitive pointer analysis to millions of lines of code is a major challenge. Recently, staged flow-sensitive pointer analysis has been proposed, which exploits a sparse representation of program code created by staged analysis. In this paper we formulate the staged flow-sensitive pointer analysis as a graph-rewriting problem. Graph-rewriting has already been used for flow-insensitive analysis. However, formulating flow-sensitive pointer analysis as a graph-rewriting problem adds additional challenges due to the nature of flow-sensitivity. We implement our parallel algorithm using Intel Threading Building Blocks and demonstrate considerable scaling (upto 2.6x) for 8 threads on a set of 10 benchmarks. Compared to the sequential implementation of staged flow-sensitive analysis, a single threaded execution of our implementation performs better in 8 of the benchmarks.

A computational algorithm for the verification of tautologies in propositional calculus

A computational algorithm (based on Smullyan's analytic tableau method) that varifies whether a given well-formed formula in propositional calculus is a tautology or not has been implemented on a DEC system 10. The stepwise refinement approch of program development used for this implementation forms the subject matter of this paper. The top-down design has resulted in a modular and reliable program package. This computational algoritlhm compares favourably with the algorithm based on the well-known resolution principle used in theorem provers.

Null Dereference Verification via Over-approximated Weakest Pre-conditions Analysis

Null dereferences are a bane of programming in languages such as Java. In this paper we propose a sound, demand-driven, inter-procedurally context-sensitive dataflow analysis technique to verify a given dereference as safe or potentially unsafe. Our analysis uses an abstract lattice of formulas to find a pre-condition at the entry of the program such that a null-dereference can occur only if the initial state of the program satisfies this pre-condition. We use a simplified domain of formulas, abstracting out integer arithmetic, as well as unbounded access paths due to recursive data structures. For the sake of precision we model aliasing relationships explicitly in our abstract lattice, enable strong updates, and use a limited notion of path sensitivity. For the sake of scalability we prune formulas continually as they get propagated, reducing to true conjuncts that are less likely to be useful in validating or invalidating the formula. We have implemented our approach, and present an evaluation of it on a set of ten real Java programs. Our results show that the set of design features we have incorporated enable the analysis to (a) explore long, inter-procedural paths to verify each dereference, with (b) reasonable accuracy, and (c) very quick response time per dereference, making it suitable for use in desktop development environments.

Two techniques to improve the precision of a demand-driven null-dereference verification approach

The problem addressed in this paper is sound, scalable, demand-driven null-dereference verification for Java programs. Our approach consists conceptually of a base analysis, plus two major extensions for enhanced precision. The base analysis is a dataflow analysis wherein we propagate formulas in the backward direction from a given dereference, and compute a necessary condition at the entry of the program for the dereference to be potentially unsafe. The extensions are motivated by the presence of certain ``difficult'' constructs in real programs, e.g., virtual calls with too many candidate targets, and library method calls, which happen to need excessive analysis time to be analyzed fully. The base analysis is hence configured to skip such a difficult construct when it is encountered by dropping all information that has been tracked so far that could potentially be affected by the construct. Our extensions are essentially more precise ways to account for the effect of these constructs on information that is being tracked, without requiring full analysis of these constructs. The first extension is a novel scheme to transmit formulas along certain kinds of def-use edges, while the second extension is based on using manually constructed backward-direction summary functions of library methods. We have implemented our approach, and applied it on a set of real-life benchmarks. The base analysis is on average able to declare about 84% of dereferences in each benchmark as safe, while the two extensions push this number up to 91%. (C) 2014 Elsevier B.V. All rights reserved.

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

Background: A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN) from transcript profiling data. Results: The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (l1-constrained fitting) problem and solved finally by formulating a Linear Program (LP). A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the INSILICO1, INSILICO2 and INSILICO3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published Saccharomyces cerevisae cell cycle transcript profiling data sets capture known regulatory associations. In each S. cerevisiae LP-SLGN, the number of nodes with a particular degree follows an approximate power law suggesting that its degree distributions is similar to that observed in real-world networks. Inspection of these LP-SLGNs suggests biological hypotheses amenable to experimental verification. Conclusion: A statistically robust and computationally efficient LP-based method for estimating the topology of a large sparse undirected graph from high-dimensional data yields representations of genetic networks that are biologically plausible and useful abstractions of the structures of real genetic networks. Analysis of the statistical and topological properties of learned LP-SLGNs may have practical value; for example, genes with high random walk betweenness, a measure of the centrality of a node in a graph, are good candidates for intervention studies and hence integrated computational – experimental investigations designed to infer more realistic and sophisticated probabilistic directed graphical model representations of genetic networks. The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcription factor networks from transcript profiling and transcription factor binding motif data.

A Pattern Recognition Model of Voice-Based Personal Verification Systems for Forensic Applications

Abstract-The success of automatic speaker recognition in laboratory environments suggests applications in forensic science for establishing the Identity of individuals on the basis of features extracted from speech. A theoretical model for such a verification scheme for continuous normaliy distributed featureIss developed. The three cases of using a) single feature, b)multipliendependent measurements of a single feature, and c)multpleindependent features are explored.The number iofndependent features needed for areliable personal identification is computed based on the theoretcal model and an expklatory study of some speech featues.

Verification of the applicability of lattice model to concrete fracture by AE study

Notched three-point bend specimens (TPB) were tested under crack mouth opening displacement (CMOD) control at a rate of 0.0004 mm/s and the entire fracture process was simulated using a regular triangular two-dimensional lattice network only over the expected fracture proces zone width. The rest of the beam specimen was discretised by a coarse triangular finite element mesh. The discrete grain structure of the concrete was generated assuming the grains to be spherical. The load versus CMOD plots thus simulated agreed reasonably well with the experimental results. Moreover, acoustic emission (AE) hits were recorded during the test and compared with the number of fractured lattice elements. It was found that the cumulative AE hits correlated well with the cumulative fractured lattice elements at all load levels thus providing a useful means for predicting when the micro-cracks form during the fracturing process, both in the pre-peak and in the post-peak regimes.

Formal Verification of Full-Wave Rectifier: A Case Study

We present a case study of formal verification of full-wave rectifier for analog and mixed signal designs. We have used the Checkmate tool from CMU [1], which is a public domain formal verification tool for hybrid systems. Due to the restriction imposed by Checkmate it necessitates to make the changes in the Checkmate implementation to implement the complex and non-linear system. Full-wave rectifier has been implemented by using the Checkmate custom blocks and the Simulink blocks from MATLAB from Math works. After establishing the required changes in the Checkmate implementation we are able to efficiently verify, the safety properties of the full-wave rectifier.

A generalized mathematical theory and experimental verification of proportional notches

A theory and generalized synthesis procedure is advocated for the design of weir notches and orifice-notches having a base in any given shape, to a depth a, such that the discharge through it is proportional to any singular monotonically-increasing function of the depth of flow measured above a certain datum. The problem is reduced to finding an exact solution of a Volterra integral equation in Abel form. The maximization of the depth of the datum below the crest of the notch is investigated. Proof is given that for a weir notch made out of one continuous curve, and for a flow proportional to the mth power of the head, it is impossible to bring the datum lower than (2m − 1)a below the crest of the notch. A new concept of an orifice-notch, having discontinuity in the curve and a division of flow into two distinct portions, is presented. The division of flow is shown to have a beneficial effect in reducing the datum below (2m − 1)a from the crest of the weir and still maintaining the proportionality of the flow. Experimental proof with one such orifice-notch is found to have a constant coefficient of discharge of 0.625. The importance of this analysis in the design of grit chambers is emphasized.

Wavelength/Time Multiple-Pulses-per-Row codes: Construction and verification

Two dimensional Optical Orthogonal Codes (OOCs) named Wavelength/Time Multiple-Pulses-per-Row (W/T MPR) codes suitable for use in incoherent fiber-optic code division multiple access (FO-CDMA) networks are reported in [6]. In this paper, we report the construction of W/T MPR codes, using Greedy Algorithm (GA), with distinct 1-D OOCs [1] as the row vectors. We present the W/T MPR codes obtained using the GA. Further, we verify the correlation properties of the generated W/T MPR codes using Matlab.

Experimental Verification of the Lateral Periodicity of Axially Periodic Incoherent Fields Using the Lau Effect

General' objects, which are specially prepared to possess restricted spatial frequency spectra, have been used in the conventional Lau experiment to obtain experimental proof for the existence of lateral periodicity arising from axial periodicity, for a subclass of axially periodic wavefields in an incoherent situation.

A microcomputer program to analyze the CD spectrum of proteins and nucleic acids—Use of LOTUS 1-2-3 spread sheet

A user friendly interactive computer program, CIRDIC, is developed which calculates the molar ellipticity and molar circular dichroic absorption coefficients from the CD spectrum. This, in combination with LOTUS 1-2-3 spread sheet, will give the spectra of above parameters vs wavelength. The code is implemented in MicroSoft FORTRAN 77 which runs on any IBM compatible PC under MSDOS environment.

Development of a structured program for conversion to prenex normal form

The method of structured programming or program development using a top-down, stepwise refinement technique provides a systematic approach for the development of programs of considerable complexity. The aim of this paper is to present the philosophy of structured programming through a case study of a nonnumeric programming task. The problem of converting a well-formed formula in first-order logic into prenex normal form is considered. The program has been coded in the programming language PASCAL and implemented on a DEC-10 system. The program has about 500 lines of code and comprises 11 procedures.

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Indian Nanoelectronics Users Program An Outreach Vehicle to Expedite Nanoelectronics Research in India

The worldwide research in nanoelectronics is motivated by the fact that scaling of MOSFETs by conventional top down approach will not continue for ever due to fundamental limits imposed by physics even if it is delayed for some more years. The research community in this domain has largely become multidisciplinary trying to discover novel transistor structures built with novel materials so that semiconductor industry can continue to follow its projected roadmap. However, setting up and running a nanoelectronics facility for research is hugely expensive. Therefore it is a common model to setup a central networked facility that can be shared with large number of users across the research community. The Centres for Excellence in Nanoelectronics (CEN) at Indian Institute of Science, Bangalore (IISc) and Indian Institute of Technology, Bombay (IITB) are such central networked facilities setup with funding of about USD 20 million from the Department of Information Technology (DIT), Ministry of Communications and Information Technology (MCIT), Government of India, in 2005. Indian Nanoelectronics Users Program (INUP) is a missionary program not only to spread awareness and provide training in nanoelectronics but also to provide easy access to the latest facilities at CEN in IISc and at IITB for the wider nanoelectronics research community in India. This program, also funded by MCIT, aims to train researchers by conducting workshops, hands-on training programs, and providing access to CEN facilities. This is a unique program aiming to expedite nanoelectronics research in the country, as the funding for projects required for projects proposed by researchers from around India has prior financial approval from the government and requires only technical approval by the IISc/ IITB team. This paper discusses the objectives of INUP, gives brief descriptions of CEN facilities, the training programs conducted by INUP and list various research activities currently under way in the program.