Studying the capacity of cellular encoding to generate feedforward neural network topologies

Proceeding of: IEEE International Joint Conference on Neural Networks, IJCNN 2004, Budapest, 25-29 July 2004Many methods to codify artificial neural networks have been developed to avoid the disadvantages of direct encoding schema, improving the search into the solution's space. A method to analyse how the search space is covered and how are the movements along search process applying genetic operators is needed in order to evaluate the different encoding strategies for multilayer perceptrons (MLP). In this paper, the generative capacity, this is how the search space is covered for a indirect scheme based on cellular systems, is studied. The capacity of the methods to cover the search space (topologies of MLP space) is compared with the direct encoding scheme.Publicad

Grammars and cellular automata for evolving neural networks architectures

IEEE International Conference on Systems, Man, and Cybernetics. Nashville, TN, 8-11 October 2000The class of feedforward neural networks trained with back-propagation admits a large variety of specific architectures applicable to approximation pattern tasks. Unfortunately, the architecture design is still a human expert job. In recent years, the interest to develop automatic methods to determine the architecture of the feedforward neural network has increased, most of them based on the evolutionary computation paradigm. From this approach, some perspectives can be considered: at one extreme, every connection and node of architecture can be specified in the chromosome representation using binary bits. This kind of representation scheme is called the direct encoding scheme. In order to reduce the length of the genotype and the search space, and to make the problem more scalable, indirect encoding schemes have been introduced. An indirect scheme under a constructive algorithm, on the other hand, starts with a minimal architecture and new levels, neurons and connections are added, step by step, via some sets of rules. The rules and/or some initial conditions are codified into a chromosome of a genetic algorithm. In this work, two indirect constructive encoding schemes based on grammars and cellular automata, respectively, are proposed to find the optimal architecture of a feedforward neural network

Neural Network architectures design by Cellular Automata evolution

4th Conference of Systemics Cybernetics and Informatics. Orlando, 23-26 July 2000The design of the architecture is a crucial step in the successful application of a neural network. However, the architecture design is basically, in most cases, a human experts job. The design depends heavily on both, the expert experience and on a tedious trial-and-error process. Therefore, the development of automatic methods to determine the architecture of feedforward neural networks is a field of interest in the neural network community. These methods are generally based on search techniques, as genetic algorithms, simulated annealing or evolutionary strategies. Most of the designed methods are based on direct representation of the parameters of the network. This representation does not allow scalability, so to represent large architectures very large structures are required. In this work, an indirect constructive encoding scheme is proposed to find optimal architectures of feed-forward neural networks. This scheme is based on cellular automata representations in order to increase the scalability of the method.Publicad

Generative capacities of cellular automata codification for evolution of NN codification

Proceeding of: International Conference on Artificial Neural Networks. ICANN 2002, Madrid, Spain, August 28-30, 2002Automatic methods for designing artificial neural nets are desired to avoid the laborious and erratically human expert’s job. Evolutionary computation has been used as a search technique to find appropriate NN architectures. Direct and indirect encoding methods are used to codify the net architecture into the chromosome. A reformulation of an indirect encoding method, based on two bi-dimensional cellular automata, and its generative capacity are presented.Publicad

Non-Direct Encoding Method Based on Cellular Automata to Design Neural Network Architectures

Architecture design is a fundamental step in the successful application of Feed forward Neural Networks. In most cases a large number of neural networks architectures suitable to solve a problem exist and the architecture design is, unfortunately, still a human expert’s job. It depends heavily on the expert and on a tedious trial-and-error process. In the last years, many works have been focused on automatic resolution of the design of neural network architectures. Most of the methods are based on evolutionary computation paradigms. Some of the designed methods are based on direct representations of the parameters of the network. These representations do not allow scalability; thus, for representing large architectures very large structures are required. More interesting alternatives are represented by indirect schemes. They codify a compact representation of the neural network. In this work, an indirect constructive encoding scheme is proposed. This scheme is based on cellular automata representations and is inspired by the idea that only a few seeds for the initial configuration of a cellular automaton can produce a wide variety of feed forward neural networks architectures. The cellular approach is experimentally validated in different domains and compared with a direct codification scheme.Publicad

Evolutionary cellular configurations for designing feed-forward neural networks architectures

Proceeding of: 6th International Work-Conference on Artificial and Natural Neural Networks, IWANN 2001 Granada, Spain, June 13–15, 2001In the recent years, the interest to develop automatic methods to determine appropriate architectures of feed-forward neural networks has increased. Most of the methods are based on evolutionary computation paradigms. Some of the designed methods are based on direct representations of the parameters of the network. These representations do not allow scalability, so to represent large architectures, very large structures are required. An alternative more interesting are the indirect schemes. They codify a compact representation of the neural network. In this work, an indirect constructive encoding scheme is presented. This scheme is based on cellular automata representations in order to increase the scalability of the method

Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity

This paper shows that the protein-primed DNA polymerases encoded by bacteriophages Nf and GA-1, unlike other DNA polymerases, do not require unwinding or processivity factors for efficient synthesis of full-length terminal protein (TP)-DNA. Analysis of their polymerization activity shows that both DNA polymerases base their replication efficiency on a high processivity and on the capacity to couple polymerization to strand displacement. Both enzymes are endowed with a proofreading activity that acts coordinately with the polymerization one to edit polymerization errors. Additionally, Nf double-stranded DNA binding protein (DBP) greatly stimulated the in vitro formation of the TP-dAMP initiation complex by decreasing the K(m) value for dATP of the Nf DNA polymerase by >20-fold. Whereas Nf DNA polymerase, as the φ29 enzyme, is able to use its homologous TP as well as DNA as primer, GA-1 DNA polymerase appears to have evolved to use its corresponding TP as the only primer of DNA synthesis. Such exceptional behaviour is discussed in the light of the recently solved structure of the DNA polymerase/TP complex of the related bacteriophage φ29

Implementação de um modelo de gestão de cuidados nos Serviços de Saúde Mental Portugueses: base conceptual

ABSTRACT - Case management implementation processes are one of the best examples on how an evidence-based practice can influence health services organisation. This practice helped shaping mental health teams, increasing their multidisciplinarity and interdisciplinary work in the last decades. Examples from several countries show how effectiveness research blends into health policy development to meet different needs in each health system, thus influencing case management inception and improvement of care. Portugal followed its own path in case management implementation, determined mostly by mental health services organisation and closely linked with the capacity to implement a national mental health policy in the last years.RESUMO - Os processos de implementação de um Modelo de Gestão de Cuidados são um dos melhores exemplos de como uma prática baseada na evidência pode influenciar a organização dos serviços de saúde. Esta prática ajudou a moldar as equipas de saúde mental nas últimas décadas, aumentando a sua multidisciplinaridade e o trabalho interdisciplinar. Os exemplos de vários países mostram como a investigação sobre a efectividade se harmoniza com o desenvolvimento de políticas de saúde para fazer face às diferentes necessidades de cada sistema de saúde, influenciando a implementação da gestão de cuidados e a melhoria de cuidados. Portugal seguiu o seu próprio caminho na implementação da gestão de cuidados, determinado maioritariamente pela organização de serviços associada à capacidade de implementar uma política nacional de saúde mental, nos últimos anos.info:eu-repo/semantics/publishedVersio

Involvement of φ29 DNA polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication

φ29 DNA polymerase achieves a functional coupling between its 3′–5′ exonuclease and polymerization activities by means of important contacts with the DNA at both active sites. The placement and orientation of residues Lys538, Lys555, Lys557, Gln560, Thr571, Thr573 and Lys575 in a modelled φ29 DNA polymerase–DNA complex suggest a DNA-binding role. In addition, crystal structure of φ29 DNA polymerase–oligo (dT)(5) complex showed Leu567, placed at the tip of the thumb subdomain, lying between the two 3′-terminal bases at the exonuclease site. Single replacement of these φ29 DNA polymerase residues by alanine was made, and mutant derivatives were overproduced and purified to homogeneity. The results obtained in the assay of their synthetic and degradative activities, as well as their coordination, allow us to propose: (1) a primer-terminus stabilization role at the polymerase active site for residues Lys538, Thr573 and Lys575, (2) a primer-terminus stabilization role at the exonuclease active site for residues Leu567 and Lys555 and (3) a primer-terminus binding role in both editing and polymerization modes for residue Gln560. The results presented here lead us to propose φ29 DNA polymerase thumb as the main subdomain responsible for the coordination of polymerization and exonuclease activities