Reachability Analysis of Communicating Pushdown Systems

The reachability analysis of recursive programs that communicate asynchronously over reliable FIFO channels calls for restrictions to ensure decidability. Our first result characterizes communication topologies with a decidable reachability problem restricted to eager runs (i.e., runs where messages are either received immediately after being sent, or never received). The problem is EXPTIME-complete in the decidable case. The second result is a doubly exponential time algorithm for bounded context analysis in this setting, together with a matching lower bound. Both results extend and improve previous work from La Torre et al

Amorphous slicing of extended finite state machines

Slicing is useful for many Software Engineering applications and has been widely studied for three decades, but there has been comparatively little work on slicing Extended Finite State Machines (EFSMs). This paper introduces a set of dependency based EFSM slicing algorithms and an accompanying tool. We demonstrate that our algorithms are suitable for dependence based slicing. We use our tool to conduct experiments on ten EFSMs, including benchmarks and industrial EFSMs. Ours is the first empirical study of dependence based program slicing for EFSMs. Compared to the only previously published dependence based algorithm, our average slice is smaller 40% of the time and larger only 10% of the time, with an average slice size of 35% for termination insensitive slicing

Automatic document classification of biological literature

Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusions: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept

Logic Programming Applications: What Are the Abstractions and Implementations?

This article presents an overview of applications of logic programming, classifying them based on the abstractions and implementations of logic languages that support the applications. The three key abstractions are join, recursion, and constraint. Their essential implementations are for-loops, fixed points, and backtracking, respectively. The corresponding kinds of applications are database queries, inductive analysis, and combinatorial search, respectively. We also discuss language extensions and programming paradigms, summarize example application problems by application areas, and touch on example systems that support variants of the abstractions with different implementations

On Petri Nets with Hierarchical Special Arcs

We investigate the decidability of termination, reachability, coverability and deadlock-freeness of Petri nets endowed with a hierarchy of places, and with inhibitor arcs, reset arcs and transfer arcs that respect this hierarchy. We also investigate what happens when we have a mix of these special arcs, some of which respect the hierarchy, while others do not. We settle the decidability status of the above four problems for all combinations of hierarchy, inhibitor, reset and transfer arcs, except the termination problem for two combinations. For both these combinations, we show that deciding termination is as hard as deciding the positivity problem on linear recurrence sequences -- a long-standing open problem