An Algebraic Framework for Compositional Program Analysis

The purpose of a program analysis is to compute an abstract meaning for a program which approximates its dynamic behaviour. A compositional program analysis accomplishes this task with a divide-and-conquer strategy: the meaning of a program is computed by dividing it into sub-programs, computing their meaning, and then combining the results. Compositional program analyses are desirable because they can yield scalable (and easily parallelizable) program analyses. This paper presents algebraic framework for designing, implementing, and proving the correctness of compositional program analyses. A program analysis in our framework defined by an algebraic structure equipped with sequencing, choice, and iteration operations. From the analysis design perspective, a particularly interesting consequence of this is that the meaning of a loop is computed by applying the iteration operator to the loop body. This style of compositional loop analysis can yield interesting ways of computing loop invariants that cannot be defined iteratively. We identify a class of algorithms, the so-called path-expression algorithms [Tarjan1981,Scholz2007], which can be used to efficiently implement analyses in our framework. Lastly, we develop a theory for proving the correctness of an analysis by establishing an approximation relationship between an algebra defining a concrete semantics and an algebra defining an analysis.Comment: 15 page

Giving Parks Back to People: Increasing the Bikeability and Walkability of New Orleans City Park

The purpose of this study was to gain an understanding of current transportation patterns of City Park users; to identify lessons learned from other large urban parks; to determine how to increase the walkability and bikeability of New Orleans City Park; and to examine the feasibility of temporary or permanent street closures

Approximation and inference methods for stochastic biochemical kinetics-a tutorial review

Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose dynamics are governed by the chemical master equation. Despite its simple structure, no analytic solutions to the chemical master equation are known for most systems. Moreover, stochastic simulations are computationally expensive, making systematic analysis and statistical inference a challenging task. Consequently, significant effort has been spent in recent decades on the development of efficient approximation and inference methods. This article gives an introduction to basic modelling concepts as well as an overview of state of the art methods. First, we motivate and introduce deterministic and stochastic methods for modelling chemical networks, and give an overview of simulation and exact solution methods. Next, we discuss several approximation methods, including the chemical Langevin equation, the system size expansion, moment closure approximations, time-scale separation approximations and hybrid methods. We discuss their various properties and review recent advances and remaining challenges for these methods. We present a comparison of several of these methods by means of a numerical case study and highlight some of their respective advantages and disadvantages. Finally, we discuss the problem of inference from experimental data in the Bayesian framework and review recent methods developed the literature. In summary, this review gives a self-contained introduction to modelling, approximations and inference methods for stochastic chemical kinetics

Loop summarization using state and transition invariants

This paper presents algorithms for program abstraction based on the principle of loop summarization, which, unlike traditional program approximation approaches (e.g., abstract interpretation), does not employ iterative fixpoint computation, but instead computes symbolic abstract transformers with respect to a set of abstract domains. This allows for an effective exploitation of problem-specific abstract domains for summarization and, as a consequence, the precision of an abstract model may be tailored to specific verification needs. Furthermore, we extend the concept of loop summarization to incorporate relational abstract domains to enable the discovery of transition invariants, which are subsequently used to prove termination of programs. Well-foundedness of the discovered transition invariants is ensured either by a separate decision procedure call or by using abstract domains that are well-founded by construction. We experimentally evaluate several abstract domains related to memory operations to detect buffer overflow problems. Also, our light-weight termination analysis is demonstrated to be effective on a wide range of benchmarks, including OS device driver

Verification of Generalized Inconsistency-Aware Knowledge and Action Bases (Extended Version)

Knowledge and Action Bases (KABs) have been put forward as a semantically rich representation of a domain, using a DL KB to account for its static aspects, and actions to evolve its extensional part over time, possibly introducing new objects. Recently, KABs have been extended to manage inconsistency, with ad-hoc verification techniques geared towards specific semantics. This work provides a twofold contribution along this line of research. On the one hand, we enrich KABs with a high-level, compact action language inspired by Golog, obtaining so called Golog-KABs (GKABs). On the other hand, we introduce a parametric execution semantics for GKABs, so as to elegantly accomodate a plethora of inconsistency-aware semantics based on the notion of repair. We then provide several reductions for the verification of sophisticated first-order temporal properties over inconsistency-aware GKABs, and show that it can be addressed using known techniques, developed for standard KABs

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs

<p>Abstract</p> <p>Background</p> <p>Feed-forward motifs are important functional modules in biological and other complex networks. The functionality of feed-forward motifs and other network motifs is largely dictated by the connectivity of the individual network components. While studies on the dynamics of motifs and networks are usually devoted to the temporal or spatial description of processes, this study focuses on the relationship between the specific architecture and the overall rate of the processes of the feed-forward family of motifs, including double and triple feed-forward loops. The search for the most efficient network architecture could be of particular interest for regulatory or signaling pathways in biology, as well as in computational and communication systems.</p> <p>Results</p> <p>Feed-forward motif dynamics were studied using cellular automata and compared with differential equation modeling. The number of cellular automata iterations needed for a 100% conversion of a substrate into a target product was used as an inverse measure of the transformation rate. Several basic topological patterns were identified that order the specific feed-forward constructions according to the rate of dynamics they enable. At the same number of network nodes and constant other parameters, the bi-parallel and tri-parallel motifs provide higher network efficacy than single feed-forward motifs. Additionally, a topological property of isodynamicity was identified for feed-forward motifs where different network architectures resulted in the same overall rate of the target production.</p> <p>Conclusion</p> <p>It was shown for classes of structural motifs with feed-forward architecture that network topology affects the overall rate of a process in a quantitatively predictable manner. These fundamental results can be used as a basis for simulating larger networks as combinations of smaller network modules with implications on studying synthetic gene circuits, small regulatory systems, and eventually dynamic whole-cell models.</p

Approximation and inference methods for stochastic biochemical kinetics - a tutorial review

Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose dynamics are governed by the Chemical Master Equation. Despite its simple structure, no analytic solutions to the Chemical Master Equation are known for most systems. Moreover, stochastic simulations are computationally expensive, making systematic analysis and statistical inference a challenging task. Consequently, significant effort has been spent in recent decades on the development of efficient approximation and inference methods. This article gives an introduction to basic modelling concepts as well as an overview of state of the art methods. First, we motivate and introduce deterministic and stochastic methods for modelling chemical networks, and give an overview of simulation and exact solution methods. Next, we discuss several approximation methods, including the chemical Langevin equation, the system size expansion, moment closure approximations, time-scale separation approximations and hybrid methods. We discuss their various properties and review recent advances and remaining challenges for these methods. We present a comparison of several of these methods by means of a numerical case study and highlight some of their respective advantages and disadvantages. Finally, we discuss the problem of inference from experimental data in the Bayesian framework and review recent methods developed the literature. In summary, this review gives a self-contained introduction to modelling, approximations and inference methods for stochastic chemical kinetics.Comment: 73 pages, 12 figures in J. Phys. A: Math. Theor. (2016

Self-propelled Bouncing Spherical Robot

25th Annual Denman Undergraduate Research Forum Finalist Second PlaceMost robots that can travel on the ground are either traditional wheeled robots or legged robots. Exploring non-traditional novel robots may provide new solutions for locomotion not previously examined. Currently, self-rolling spherical robots have been designed and manufactured for hobbies, entertainment, or military uses. Similarly, various researchers have built legged robots that walk and run. Our objective in this research project was to design, build, and control a self-propelled bouncing and rolling spherical robot. While some self-bouncing wheeled robots have been built as toys, the self-bouncing spherical robot (one that looks like a ball) remains largely not explored. No one has produced a robot that can bounce continuously and can be steered without any external device to assist its movement. To achieve this goal, we plan to prototype up to three different mechanisms for bouncing. Each prototype would go through brainstorming, computer-aided design and simulation (of the bouncing), initial build, redesign, second build, and final analysis. We follow the classic design cycle: observe, ideation, prototype, and testing. We will also perform dynamic analyses of the robot to improve the design. This thesis reports on current progress towards these goals: we have designed and fabricated (and iterated) on a simple prototype bouncing ball, based on a spinning internal mass; we have performed some 2D and 3D simulations of the spinning mechanism that shows promise for the mechanism to produce persistent bouncing. Future work will consist of improving the current prototype, matching the computer simulations quantitatively to the prototype, performing design optimization and trajectory optimizations for optimal control, exploring other designs closer to hopping robots, and finally, building the ability to control and steer the robot.The Ohio State University Second-year Transformational Experience ProgramThe Ohio State University College of EngineeringNo embargoAcademic Major: Mechanical Engineerin

Lost in optimisation of water distribution systems? A literature review of system design

This is the final version of the article. Available from MDPI via the DOI in this record.Optimisation of water distribution system design is a well-established research field, which has been extremely productive since the end of the 1980s. Its primary focus is to minimise the cost of a proposed pipe network infrastructure. This paper reviews in a systematic manner articles published over the past three decades, which are relevant to the design of new water distribution systems, and the strengthening, expansion and rehabilitation of existing water distribution systems, inclusive of design timing, parameter uncertainty, water quality, and operational considerations. It identifies trends and limits in the field, and provides future research directions. Exclusively, this review paper also contains comprehensive information from over one hundred and twenty publications in a tabular form, including optimisation model formulations, solution methodologies used, and other important details