Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Ethical Challenges in Data-Driven Dialogue Systems

The use of dialogue systems as a medium for human-machine interaction is an increasingly prevalent paradigm. A growing number of dialogue systems use conversation strategies that are learned from large datasets. There are well documented instances where interactions with these system have resulted in biased or even offensive conversations due to the data-driven training process. Here, we highlight potential ethical issues that arise in dialogue systems research, including: implicit biases in data-driven systems, the rise of adversarial examples, potential sources of privacy violations, safety concerns, special considerations for reinforcement learning systems, and reproducibility concerns. We also suggest areas stemming from these issues that deserve further investigation. Through this initial survey, we hope to spur research leading to robust, safe, and ethically sound dialogue systems.Comment: In Submission to the AAAI/ACM conference on Artificial Intelligence, Ethics, and Societ

Expression-based aliasing for OO-languages

Alias analysis has been an interesting research topic in verification and optimization of programs. The undecidability of determining whether two expressions in a program may reference to the same object is the main source of the challenges raised in alias analysis. In this paper we propose an extension of a previously introduced alias calculus based on program expressions, to the setting of unbounded program executions s.a. infinite loops and recursive calls. Moreover, we devise a corresponding executable specification in the K-framework. An important property of our extension is that, in a non-concurrent setting, the corresponding alias expressions can be over-approximated in terms of a notion of regular expressions. This further enables us to show that the associated K-machinery implements an algorithm that always stops and provides a sound over-approximation of the "may aliasing" information, where soundness stands for the lack of false negatives. As a case study, we analyze the integration and further applications of the alias calculus in SCOOP. The latter is an object-oriented programming model for concurrency, recently formalized in Maude; K-definitions can be compiled into Maude for execution

Web and Semantic Web Query Languages

A number of techniques have been developed to facilitate powerful data retrieval on the Web and Semantic Web. Three categories of Web query languages can be distinguished, according to the format of the data they can retrieve: XML, RDF and Topic Maps. This article introduces the spectrum of languages falling into these categories and summarises their salient aspects. The languages are introduced using common sample data and query types. Key aspects of the query languages considered are stressed in a conclusion