Scalable discovery of hybrid process models in a cloud computing environment

Process descriptions are used to create products and deliver services. To lead better processes and services, the first step is to learn a process model. Process discovery is such a technique which can automatically extract process models from event logs. Although various discovery techniques have been proposed, they focus on either constructing formal models which are very powerful but complex, or creating informal models which are intuitive but lack semantics. In this work, we introduce a novel method that returns hybrid process models to bridge this gap. Moreover, to cope with today’s big event logs, we propose an efficient method, called f-HMD, aims at scalable hybrid model discovery in a cloud computing environment. We present the detailed implementation of our approach over the Spark framework, and our experimental results demonstrate that the proposed method is efficient and scalabl

A review of modelling and verification approaches for computational biology

This paper reviews most frequently used computational modelling approaches and formal verification techniques in computational biology. The paper also compares a number of model checking tools and software suits used in analysing biological systems and biochemical networks and verifiying a wide range of biological properties

StocHy: automated verification and synthesis of stochastic processes

StocHy is a software tool for the quantitative analysis of discrete-time stochastic hybrid systems (SHS). StocHy accepts a high-level description of stochastic models and constructs an equivalent SHS model. The tool allows to (i) simulate the SHS evolution over a given time horizon; and to automatically construct formal abstractions of the SHS. Abstractions are then employed for (ii) formal verification or (iii) control (policy, strategy) synthesis. StocHy allows for modular modelling, and has separate simulation, verification and synthesis engines, which are implemented as independent libraries. This allows for libraries to be easily used and for extensions to be easily built. The tool is implemented in C++ and employs manipulations based on vector calculus, the use of sparse matrices, the symbolic construction of probabilistic kernels, and multi-threading. Experiments show StocHy's markedly improved performance when compared to existing abstraction-based approaches: in particular, StocHy beats state-of-the-art tools in terms of precision (abstraction error) and computational effort, and finally attains scalability to large-sized models (12 continuous dimensions). StocHy is available at www.gitlab.com/natchi92/StocHy

Probabilistic reasoning and inference for systems biology

One of the important challenges in Systems Biology is reasoning and performing hypotheses testing in uncertain conditions, when available knowledge may be incomplete and the experimental data may contain substantial noise. In this thesis we develop methods of probabilistic reasoning and inference that operate consistently within an environment of uncertain knowledge and data. Mechanistic mathematical models are used to describe hypotheses about biological systems. We consider both deductive model based reasoning and model inference from data. The main contributions are a novel modelling approach using continuous time Markov chains that enables deductive derivation of model behaviours and their properties, and the application of Bayesian inferential methods to solve the inverse problem of model inference and comparison, given uncertain knowledge and noisy data. In the first part of the thesis, we consider both individual and population based techniques for modelling biochemical pathways using continuous time Markov chains, and demonstrate why the latter is the most appropriate. We illustrate a new approach, based on symbolic intervals of concentrations, with an example portion of the ERK signalling pathway. We demonstrate that the resulting model approximates the same dynamic system as traditionally defined using ordinary differential equations. The advantage of the new approach is quantitative logical analysis; we formulate a number of biologically significant queries in the temporal logic CSL and use probabilistic symbolic model checking to investigate their veracity. In the second part of the thesis, we consider the inverse problem of model inference and testing of alternative hypotheses, when models are defined by non-linear ordinary differential equations and the experimental data is noisy and sparse. We compare and evaluate a number of statistical techniques, and implement an effective Bayesian inferential framework for systems biology based on Markov chain Monte Carlo methods and estimation of marginal likelihoods by annealing-melting integration. We illustrate the framework with two case studies, one of which involves an open problem concerning the mediation of ERK phosphorylation in the ERK pathway

From Epidemic to Pandemic Modelling

We present a methodology for systematically extending epidemic models to multilevel and multiscale spatio-temporal pandemic ones. Our approach builds on the use of coloured stochastic and continuous Petri nets facilitating the sound component-based extension of basic SIR models to include population stratification and also spatio-geographic information and travel connections, represented as graphs, resulting in robust stratified pandemic metapopulation models. This method is inherently easy to use, producing scalable and reusable models with a high degree of clarity and accessibility which can be read either in a deterministic or stochastic paradigm. Our method is supported by a publicly available platform PetriNuts; it enables the visual construction and editing of models; deterministic, stochastic and hybrid simulation as well as structural and behavioural analysis. All the models are available as supplementary material, ensuring reproducibility.Comment: 79 pages (with Appendix), 23 figures, 7 table