Towards Cancer Hybrid Automata

This paper introduces Cancer Hybrid Automata (CHAs), a formalism to model the progression of cancers through discrete phenotypes. The classification of cancer progression using discrete states like stages and hallmarks has become common in the biology literature, but primarily as an organizing principle, and not as an executable formalism. The precise computational model developed here aims to exploit this untapped potential, namely, through automatic verification of progression models (e.g., consistency, causal connections, etc.), classification of unreachable or unstable states and computer-generated (individualized or universal) therapy plans. The paper builds on a phenomenological approach, and as such does not need to assume a model for the biochemistry of the underlying natural progression. Rather, it abstractly models transition timings between states as well as the effects of drugs and clinical tests, and thus allows formalization of temporal statements about the progression as well as notions of timed therapies. The model proposed here is ultimately based on hybrid automata, and we show how existing controller synthesis algorithms can be generalized to CHA models, so that therapies can be generated automatically. Throughout this paper we use cancer hallmarks to represent the discrete states through which cancer progresses, but other notions of discretely or continuously varying state formalisms could also be used to derive similar therapies.Comment: In Proceedings HSB 2012, arXiv:1208.315

LTL Parameter Synthesis of Parametric Timed Automata

The parameter synthesis problem for parametric timed automata is undecidable in general even for very simple reachability properties. In this paper we introduce restrictions on parameter valuations under which the parameter synthesis problem is decidable for LTL properties. The investigated bounded integer parameter synthesis problem could be solved using an explicit enumeration of all possible parameter valuations. We propose an alternative symbolic zone-based method for this problem which results in a faster computation. Our technique extends the ideas of the automata-based approach to LTL model checking of timed automata. To justify the usefulness of our approach, we provide experimental evaluation and compare our method with explicit enumeration technique.Comment: 23 pages, extended versio

Extracting Formal Models from Normative Texts

We are concerned with the analysis of normative texts - documents based on the deontic notions of obligation, permission, and prohibition. Our goal is to make queries about these notions and verify that a text satisfies certain properties concerning causality of actions and timing constraints. This requires taking the original text and building a representation (model) of it in a formal language, in our case the C-O Diagram formalism. We present an experimental, semi-automatic aid that helps to bridge the gap between a normative text in natural language and its C-O Diagram representation. Our approach consists of using dependency structures obtained from the state-of-the-art Stanford Parser, and applying our own rules and heuristics in order to extract the relevant components. The result is a tabular data structure where each sentence is split into suitable fields, which can then be converted into a C-O Diagram. The process is not fully automatic however, and some post-editing is generally required of the user. We apply our tool and perform experiments on documents from different domains, and report an initial evaluation of the accuracy and feasibility of our approach.Comment: Extended version of conference paper at the 21st International Conference on Applications of Natural Language to Information Systems (NLDB 2016). arXiv admin note: substantial text overlap with arXiv:1607.0148

Meeting Deadlines Together

This paper studies safety, progress, and non-zeno properties of Communicating Timed Automata (CTAs), which are timed automata (TA) extended with unbounded communication channels, and presents a procedure to build timed global specifications from systems of CTAs. We define safety and progress properties for CTAs by extending the properties studied in communicating finite-state machines to the timed setting. We then study non-zenoness for CTAs; our aim is to prevent scenarios in which the participants have to execute an infinite number of actions in a finite amount of time. We propose sound and decidable conditions for these properties, and demonstrate the practicality of our approach with an implementation and experimental evaluations of our theory

Model Checking Classes of Metric LTL Properties of Object-Oriented Real-Time Maude Specifications

This paper presents a transformational approach for model checking two important classes of metric temporal logic (MTL) properties, namely, bounded response and minimum separation, for nonhierarchical object-oriented Real-Time Maude specifications. We prove the correctness of our model checking algorithms, which terminate under reasonable non-Zeno-ness assumptions when the reachable state space is finite. These new model checking features have been integrated into Real-Time Maude, and are used to analyze a network of medical devices and a 4-way traffic intersection system.Comment: In Proceedings RTRTS 2010, arXiv:1009.398