Encoding Higher Level Extensions of Petri Nets in Answer Set Programming

Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require simulation based reasoning. To answer such questions, we need formalisms to build pathway models, add extensions, simulate, and reason with them. We chose Petri Nets and Answer Set Programming (ASP) as suitable formalisms, since Petri Net models are similar to biological pathway diagrams; and ASP provides easy extension and strong reasoning abilities. We found that certain aspects of biological pathways, such as locations and substance types, cannot be represented succinctly using regular Petri Nets. As a result, we need higher level constructs like colored tokens. In this paper, we show how Petri Nets with colored tokens can be encoded in ASP in an intuitive manner, how additional Petri Net extensions can be added by making small code changes, and how this work furthers our long term research goals. Our approach can be adapted to other domains with similar modeling needs

A Benchmark for ASP Systems: Resource Allocation in Business Processes

The goal of this paper is to benchmark Answer Set Programming (ASP) systems to test their performance when dealing with a complex optimization problem. In particular, the problem tackled is resource allocation in the area of Business Process Management (BPM). Like many other scheduling problems, the allocation of resources and starting times to business process activities is a challenging optimization problem for ASP solvers. Our problem encoding is ASP Core-2 standard compliant and it is realized in a declarative and compact fashion. We develop an instance generator that produces problem instances of different size and hardness with respect to adjustable parameters. By using the baseline encoding and the instance generator, we provide a comparison between the two award-winning ASP solvers clasp and wasp and report the grounding performance of gringo and i-dlv. The benchmark suggests that there is room for improvement concerning both the grounders and the solvers. Fostered by the relevance of the problem addressed, of which several variants have been described in different domains, we believe this is a solid application-oriented benchmark for the ASP community.Series: Working Papers on Information Systems, Information Business and Operation

A Benchmark for ASP Systems: Resource Allocation in Business Processes

The goal of this paper is to benchmark Answer Set Programming (ASP) systems to test their performance when dealing with a complex optimization problem. In particular, the problem tackled is resource allocation in the area of Business Process Management (BPM). Like many other scheduling problems, the allocation of resources and starting times to business process activities is a challenging optimization problem for ASP solvers. Our problem encoding is ASP Core-2 standard compliant and it is realized in a declarative and compact fashion. We develop an instance generator that produces problem instances of different size and hardness with respect to adjustable parameters. By using the baseline encoding and the instance generator, we provide a comparison between the two award-winning ASP solvers CLASP and WASP and report the grounding performance of GRINGO and I-DLV. The benchmark suggests that there is room for improvement concerning both the grounders and the solvers. Fostered by the relevance of the problem addressed, of which several variants have been described in different domains, we believe this is a solid application-oriented benchmark for the ASP community.Austrian Research Promotion Agency (FFG) 845638 (SHAPE

Representing, reasoning and answering questions about biological pathways - various applications

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a primary task in biomedical research and a prerequisite for diagnosing diseases, and drug development. Scientists studying these processes have identified various pathways responsible for drug metabolism, and signal transduction, etc. Newer techniques and speed improvements have resulted in deeper knowledge about these pathways, resulting in refined models that tend to be large and complex, making it difficult for a person to remember all aspects of it. Thus, computer models are needed to analyze them. We want to build such a system that allows modeling of biological systems and pathways in such a way that we can answer questions about them. Many existing models focus on structural and/or factoid questions, using surface-level knowledge that does not require understanding the underlying model. We believe these are not the kind of questions that a biologist may ask someone to test their understanding of the biological processes. We want our system to answer the kind of questions a biologist may ask. Such questions appear in early college level text books. Thus the main goal of our thesis is to develop a system that allows us to encode knowledge about biological pathways and answer such questions about them demonstrating understanding of the pathway. To that end, we develop a language that will allow posing such questions and illustrate the utility of our framework with various applications in the biological domain. We use some existing tools with modifications to accomplish our goal. Finally, we apply our system to real world applications by extracting pathway knowledge from text and answering questions related to drug development.Comment: thesi

Applying Formal Methods to Networking: Theory, Techniques and Applications

Despite its great importance, modern network infrastructure is remarkable for the lack of rigor in its engineering. The Internet which began as a research experiment was never designed to handle the users and applications it hosts today. The lack of formalization of the Internet architecture meant limited abstractions and modularity, especially for the control and management planes, thus requiring for every new need a new protocol built from scratch. This led to an unwieldy ossified Internet architecture resistant to any attempts at formal verification, and an Internet culture where expediency and pragmatism are favored over formal correctness. Fortunately, recent work in the space of clean slate Internet design---especially, the software defined networking (SDN) paradigm---offers the Internet community another chance to develop the right kind of architecture and abstractions. This has also led to a great resurgence in interest of applying formal methods to specification, verification, and synthesis of networking protocols and applications. In this paper, we present a self-contained tutorial of the formidable amount of work that has been done in formal methods, and present a survey of its applications to networking.Comment: 30 pages, submitted to IEEE Communications Surveys and Tutorial

Automating the transformation-based analysis of visual languages

The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-009-0114-yWe present a novel approach for the automatic generation of model-to-model transformations given a description of the operational semantics of the source language in the form of graph transformation rules. The approach is geared to the generation of transformations from Domain-Specific Visual Languages (DSVLs) into semantic domains with an explicit notion of transition, like for example Petri nets. The generated transformation is expressed in the form of operational triple graph grammar rules that transform the static information (initial model) and the dynamics (source rules and their execution control structure). We illustrate these techniques with a DSVL in the domain of production systems, for which we generate a transformation into Petri nets. We also tackle the description of timing aspects in graph transformation rules, and its analysis through their automatic translation into Time Petri netsWork sponsored by the Spanish Ministry of Science and Innovation, project METEORIC (TIN2008-02081/TIN) and by the Canadian Natural Sciences and Engineering Research Council (NSERC)

Model Checking Linear Logic Specifications

The overall goal of this paper is to investigate the theoretical foundations of algorithmic verification techniques for first order linear logic specifications. The fragment of linear logic we consider in this paper is based on the linear logic programming language called LO enriched with universally quantified goal formulas. Although LO was originally introduced as a theoretical foundation for extensions of logic programming languages, it can also be viewed as a very general language to specify a wide range of infinite-state concurrent systems. Our approach is based on the relation between backward reachability and provability highlighted in our previous work on propositional LO programs. Following this line of research, we define here a general framework for the bottom-up evaluation of first order linear logic specifications. The evaluation procedure is based on an effective fixpoint operator working on a symbolic representation of infinite collections of first order linear logic formulas. The theory of well quasi-orderings can be used to provide sufficient conditions for the termination of the evaluation of non trivial fragments of first order linear logic.Comment: 53 pages, 12 figures "Under consideration for publication in Theory and Practice of Logic Programming