Complex Networks from Simple Rewrite Systems

Complex networks are all around us, and they can be generated by simple mechanisms. Understanding what kinds of networks can be produced by following simple rules is therefore of great importance. We investigate this issue by studying the dynamics of extremely simple systems where are `writer' moves around a network, and modifies it in a way that depends upon the writer's surroundings. Each vertex in the network has three edges incident upon it, which are colored red, blue and green. This edge coloring is done to provide a way for the writer to orient its movement. We explore the dynamics of a space of 3888 of these `colored trinet automata' systems. We find a large variety of behaviour, ranging from the very simple to the very complex. We also discover simple rules that generate forms which are remarkably similar to a wide range of natural objects. We study our systems using simulations (with appropriate visualization techniques) and analyze selected rules mathematically. We arrive at an empirical classification scheme which reveals a lot about the kinds of dynamics and networks that can be generated by these systems

Ten virtues of structured graphs

This paper extends the invited talk by the first author about the virtues of structured graphs. The motivation behind the talk and this paper relies on our experience on the development of ADR, a formal approach for the design of styleconformant, reconfigurable software systems. ADR is based on hierarchical graphs with interfaces and it has been conceived in the attempt of reconciling software architectures and process calculi by means of graphical methods. We have tried to write an ADR agnostic paper where we raise some drawbacks of flat, unstructured graphs for the design and analysis of software systems and we argue that hierarchical, structured graphs can alleviate such drawbacks

Compressing Recurrent Neural Network with Tensor Train

Recurrent Neural Network (RNN) are a popular choice for modeling temporal and sequential tasks and achieve many state-of-the-art performance on various complex problems. However, most of the state-of-the-art RNNs have millions of parameters and require many computational resources for training and predicting new data. This paper proposes an alternative RNN model to reduce the number of parameters significantly by representing the weight parameters based on Tensor Train (TT) format. In this paper, we implement the TT-format representation for several RNN architectures such as simple RNN and Gated Recurrent Unit (GRU). We compare and evaluate our proposed RNN model with uncompressed RNN model on sequence classification and sequence prediction tasks. Our proposed RNNs with TT-format are able to preserve the performance while reducing the number of RNN parameters significantly up to 40 times smaller.Comment: Accepted at IJCNN 201

Cell division and migration in a 'genotype' for neural networks

Much research has been dedicated recently to applying genetic algorithms to populations of neural networks. However, while in real organisms the inherited genotype maps in complex ways into the resulting phenotype, in most of this research the development process that creates the individual phenotype is ignored. In this paper we present a model of neural development which includes cell division and cell migration in addition to axonal growth and branching. This reflects, in a very simplified way, what happens in the ontogeny of real organisms. The development process of our artificial organisms shows successive phases of functional differentiation and specialization. In addition, we find that mutations that affect different phases of development have very different evolutionary consequences. A single change in the early stages of cell division/migration can have huge effects on the phenotype while changes in later stages have usually a less drammatic impact. Sometimes changes that affect the first developental stages may be retained producing sudden changes in evolutionary history

Runtime verification for biochemical programs

The biochemical paradigm is well-suited for modelling autonomous systems and new programming languages are emerging from this approach. However, in order to validate such programs, we need to define precisely their semantics and to provide verification techniques. In this paper, we consider a higher-order biochemical calculus that models the structure of system states and its dynamics thanks to rewriting abstractions, namely rules and strategies. We extend this calculus with a runtime verification technique in order to perform automatic discovery of property satisfaction failure. The property specification language is a subclass of LTL safety and liveness properties

Ecological Modelling with the Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.Comment: A preliminary version of this paper has been presented in CMC13 (LNCS 7762, pp 358-377, 2013