Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Survey of Machine Learning Techniques for Malware Analysis

Coping with malware is getting more and more challenging, given their relentless growth in complexity and volume. One of the most common approaches in literature is using machine learning techniques, to automatically learn models and patterns behind such complexity, and to develop technologies for keeping pace with the speed of development of novel malware. This survey aims at providing an overview on the way machine learning has been used so far in the context of malware analysis. We systematize surveyed papers according to their objectives (i.e., the expected output, what the analysis aims to), what information about malware they specifically use (i.e., the features), and what machine learning techniques they employ (i.e., what algorithm is used to process the input and produce the output). We also outline a number of problems concerning the datasets used in considered works, and finally introduce the novel concept of malware analysis economics, regarding the study of existing tradeoffs among key metrics, such as analysis accuracy and economical costs

A Quantitative Study of Pure Parallel Processes

In this paper, we study the interleaving -- or pure merge -- operator that most often characterizes parallelism in concurrency theory. This operator is a principal cause of the so-called combinatorial explosion that makes very hard - at least from the point of view of computational complexity - the analysis of process behaviours e.g. by model-checking. The originality of our approach is to study this combinatorial explosion phenomenon on average, relying on advanced analytic combinatorics techniques. We study various measures that contribute to a better understanding of the process behaviours represented as plane rooted trees: the number of runs (corresponding to the width of the trees), the expected total size of the trees as well as their overall shape. Two practical outcomes of our quantitative study are also presented: (1) a linear-time algorithm to compute the probability of a concurrent run prefix, and (2) an efficient algorithm for uniform random sampling of concurrent runs. These provide interesting responses to the combinatorial explosion problem

Algebraic Structure of Combined Traces

Traces and their extension called combined traces (comtraces) are two formal models used in the analysis and verification of concurrent systems. Both models are based on concepts originating in the theory of formal languages, and they are able to capture the notions of causality and simultaneity of atomic actions which take place during the process of a system's operation. The aim of this paper is a transfer to the domain of comtraces and developing of some fundamental notions, which proved to be successful in the theory of traces. In particular, we introduce and then apply the notion of indivisible steps, the lexicographical canonical form of comtraces, as well as the representation of a comtrace utilising its linear projections to binary action subalphabets. We also provide two algorithms related to the new notions. Using them, one can solve, in an efficient way, the problem of step sequence equivalence in the context of comtraces. One may view our results as a first step towards the development of infinite combined traces, as well as recognisable languages of combined traces.Comment: Short variant of this paper, with no proofs, appeared in Proceedings of CONCUR 2012 conferenc