Evolving artificial cell signaling networks using molecular classifier systems

Nature is a source of inspiration for computational techniques which have been successfully applied to a wide variety of complex application domains. In keeping with this we examine Cell Signaling Networks (CSN) which are chemical networks responsible for coordinating cell activities within their environment. Through evolution they have become highly efficient for governing critical control processes such as immunological responses, cell cycle control or homeostasis. Realising (and evolving) Artificial Cell Signaling Networks (ACSNs) may provide new computational paradigms for a variety of application areas. Our abstraction of Cell Signaling Networks focuses on four characteristic properties distinguished as follows: Computation, Evolution, Crosstalk and Robustness. These properties are also desirable for potential applications in the control systems, computation and signal processing field. These characteristics are used as a guide for the development of an ACSN evolutionary simulation platform. In this paper we present a novel evolutionary approach named Molecular Classifier System (MCS) to simulate such ACSNs. The MCS that we have designed is derived from Holland's Learning Classifier System. The research we are currently involved in is part of the multi disciplinary European funded project, ESIGNET, with the central question of the study of the computational properties of CSNs by evolving them using methods from evolutionary computation, and to re-apply this understanding in developing new ways to model and predict real CSNs

Knowledge acquisition including tags in a classifier system

Congress on Evolutionary Computation. Washington, DC, 6-9 July 1999.One of the major problems related to classifier systems is the loss of rules. This loss is caused by the genetic algorithm being applied on the entire population of rules jointly. Obviously, the genetic operators discriminate rules by the strength value, such that evolution favours the generation of the stronger rules. When the learning system works in an environment in which it is possible to generate a complete training set, the strength of the rules of the CS will reflect the relative relationship between rules satisfactorily and, therefore, the application of the genetic algorithm will produce the desired effects. However, when the learning process presents individual cases and allows the system to learn gradually from these cases, each learning interval with a set of individual cases can lead the strength to be distributed in favour of a given type of rules that would in turn be favoured by the genetic algorithm. Basically, the idea is to divide rules into groups such that they are forced to remain in the system. This contribution is a method of learning that allows similar knowledge to be grouped. A field in which knowledge-based systems researchers have done a lot of work is concept classification and the relationships that are established between these concepts in the stage of knowledge conceptualization for later formalization. This job of classifying and searching relationships is performed in the proposed classifier systems by means of a mechanism. Tags, that allows the classification and the relationships to be discovered without the need for expert knowledge

Fake Malware Classification with CNN via Image Conversion: A Game Theory Approach

Improvements in malware detection techniques have grown significantly over the past decade. These improvements have resulted in better security for systems from various forms of malware attacks. However, it is also the reason for continuous evolution of malware which makes it harder for current security mechanisms to detect them. Hence, there is a need to understand different malwares and study classification techniques using the ever-evolving field of machine learning. The goal of this research project is to identify similarities between malware families and to improve on classification of malwares within different malware families by implementing Convolutional Neural Networks (CNNs) on their executable files. Moreover, there are different algorithms through which we can resize images. Classifying these malware images will help us understand effectiveness of the techniques. As malwares evolve continuously, we will generate fake malware image samples using Auxiliary Classifier Generative Adversarial Network (AC-GANs) and jumble the original dataset to try and break the CNN classifier

Ensemble Learning for Free with Evolutionary Algorithms ?

Evolutionary Learning proceeds by evolving a population of classifiers, from which it generally returns (with some notable exceptions) the single best-of-run classifier as final result. In the meanwhile, Ensemble Learning, one of the most efficient approaches in supervised Machine Learning for the last decade, proceeds by building a population of diverse classifiers. Ensemble Learning with Evolutionary Computation thus receives increasing attention. The Evolutionary Ensemble Learning (EEL) approach presented in this paper features two contributions. First, a new fitness function, inspired by co-evolution and enforcing the classifier diversity, is presented. Further, a new selection criterion based on the classification margin is proposed. This criterion is used to extract the classifier ensemble from the final population only (Off-line) or incrementally along evolution (On-line). Experiments on a set of benchmark problems show that Off-line outperforms single-hypothesis evolutionary learning and state-of-art Boosting and generates smaller classifier ensembles

Learning sequences of rules using classifier systems with tags

IEEE International Conference on Systems, Man, and Cybernetics. Tokyo, 12-15 October 1999.The objective of this paper was to obtain an encoding structure that would allow the genetic evolution of rules in such a manner that the number of rules and relationship in a classifier system (CS) would be learnt in the evolution process. For this purpose, an area that allows the definition of rule groups has been entered into the condition and message part of the encoded rules. This area is called internal tag. This term was coined because the system has some similarities with natural processes that take place in certain animal species, where the existence of tags allows them to communicate and recognize each other. Such CS is called a tag classifier system (TCS). The TCS has been tested in the game of draughts and compared with the classical CS. The results show an improving of the CS performance

Distributed classifier based on genetically engineered bacterial cell cultures

We describe a conceptual design of a distributed classifier formed by a population of genetically engineered microbial cells. The central idea is to create a complex classifier from a population of weak or simple classifiers. We create a master population of cells with randomized synthetic biosensor circuits that have a broad range of sensitivities towards chemical signals of interest that form the input vectors subject to classification. The randomized sensitivities are achieved by constructing a library of synthetic gene circuits with randomized control sequences (e.g. ribosome-binding sites) in the front element. The training procedure consists in re-shaping of the master population in such a way that it collectively responds to the "positive" patterns of input signals by producing above-threshold output (e.g. fluorescent signal), and below-threshold output in case of the "negative" patterns. The population re-shaping is achieved by presenting sequential examples and pruning the population using either graded selection/counterselection or by fluorescence-activated cell sorting (FACS). We demonstrate the feasibility of experimental implementation of such system computationally using a realistic model of the synthetic sensing gene circuits.Comment: 31 pages, 9 figure

Discrete and fuzzy dynamical genetic programming in the XCSF learning classifier system

A number of representation schemes have been presented for use within learning classifier systems, ranging from binary encodings to neural networks. This paper presents results from an investigation into using discrete and fuzzy dynamical system representations within the XCSF learning classifier system. In particular, asynchronous random Boolean networks are used to represent the traditional condition-action production system rules in the discrete case and asynchronous fuzzy logic networks in the continuous-valued case. It is shown possible to use self-adaptive, open-ended evolution to design an ensemble of such dynamical systems within XCSF to solve a number of well-known test problems

An incremental approach to genetic algorithms based classification

Incremental learning has been widely addressed in the machine learning literature to cope with learning tasks where the learning environment is ever changing or training samples become available over time. However, most research work explores incremental learning with statistical algorithms or neural networks, rather than evolutionary algorithms. The work in this paper employs genetic algorithms (GAs) as basic learning algorithms for incremental learning within one or more classifier agents in a multi-agent environment. Four new approaches with different initialization schemes are proposed. They keep the old solutions and use an “integration” operation to integrate them with new elements to accommodate new attributes, while biased mutation and crossover operations are adopted to further evolve a reinforced solution. The simulation results on benchmark classification data sets show that the proposed approaches can deal with the arrival of new input attributes and integrate them with the original input space. It is also shown that the proposed approaches can be successfully used for incremental learning and improve classification rates as compared to the retraining GA. Possible applications for continuous incremental training and feature selection are also discussed