Phase transitions and memory effects in the dynamics of Boolean networks

The generating functional method is employed to investigate the synchronous dynamics of Boolean networks, providing an exact result for the system dynamics via a set of macroscopic order parameters. The topology of the networks studied and its constituent Boolean functions represent the system's quenched disorder and are sampled from a given distribution. The framework accommodates a variety of topologies and Boolean function distributions and can be used to study both the noisy and noiseless regimes; it enables one to calculate correlation functions at different times that are inaccessible via commonly used approximations. It is also used to determine conditions for the annealed approximation to be valid, explore phases of the system under different levels of noise and obtain results for models with strong memory effects, where existing approximations break down. Links between Boolean networks and general Boolean formulas are identified and results common to both system types are highlighted. © 2012 Copyright Taylor and Francis Group, LLC.

Computing with noise: phase transitions in Boolean formulas

Computing circuits composed of noisy logical gates and their ability to represent arbitrary Boolean functions with a given level of error are investigated within a statistical mechanics setting. Existing bounds on their performance are straightforwardly retrieved, generalized, and identified as the corresponding typical-case phase transitions. Results on error rates, function depth, and sensitivity, and their dependence on the gate-type and noise model used are also obtained.

Dynamics of Boolean networks: an exact solution

The dynamics of Boolean networks (BN) with quenched disorder and thermal noise is studied via the generating functional method. A general formulation, suitable for BN with any distribution of Boolean functions, is developed. It provides exact solutions and insight into the evolution of order parameters and properties of the stationary states, which are inaccessible via existing methodology. We identify cases where the commonly used annealed approximation is valid and others where it breaks down. Broader links between BN and general Boolean formulas are highlighted.

On the construction of new bent functions from the max-weight and min-weight functions of old bent functions

Given a bent function f (x) of n variables, its max-weight and min-weight functions are introduced as the Boolean functions f + (x) and f − (x) whose supports are the sets {a ∈ Fn2 | w( f ⊕la) = 2n−1+2 n 2 −1} and {a ∈ Fn2 | w( f ⊕la) = 2n−1−2 n 2 −1} respectively, where w( f ⊕ la) denotes the Hamming weight of the Boolean function f (x) ⊕ la(x) and la(x) is the linear function defined by a ∈ Fn2 . f + (x) and f − (x) are proved to be bent functions. Furthermore, combining the 4 minterms of 2 variables with the max-weight or min-weight functions of a 4-tuple ( f0(x), f1(x), f2(x), f3(x)) of bent functions of n variables such that f0(x) ⊕ f1(x) ⊕ f2(x) ⊕ f3(x) = 1, a bent function of n + 2 variables is obtained. A family of 4-tuples of bent functions satisfying the above condition is introduced, and finally, the number of bent functions we can construct using the method introduced in this paper are obtained. Also, our construction is compared with other constructions of bent functions.

Efficient Hill Climber for Constrained Pseudo-Boolean Optimization Problems

Efficient hill climbers have been recently proposed for single- and multi-objective pseudo-Boolean optimization problems. For $k$-bounded pseudo-Boolean functions where each variable appears in at most a constant number of subfunctions, it has been theoretically proven that the neighborhood of a solution can be explored in constant time. These hill climbers, combined with a high-level exploration strategy, have shown to improve state of the art methods in experimental studies and open the door to the so-called Gray Box Optimization, where part, but not all, of the details of the objective functions are used to better explore the search space. One important limitation of all the previous proposals is that they can only be applied to unconstrained pseudo-Boolean optimization problems. In this work, we address the constrained case for multi-objective $k$-bounded pseudo-Boolean optimization problems. We find that adding constraints to the pseudo-Boolean problem has a linear computational cost in the hill climber.

Cheaper Faster Drug Development Validated By The Repositioning Of Drugs Against Neglected Tropical Diseases.

There is an urgent need to make drug discovery cheaper and faster. This will enable the development of treatments for diseases currently neglected for economic reasons, such as tropical and orphan diseases, and generally increase the supply of new drugs. Here, we report the Robot Scientist 'Eve' designed to make drug discovery more economical. A Robot Scientist is a laboratory automation system that uses artificial intelligence (AI) techniques to discover scientific knowledge through cycles of experimentation. Eve integrates and automates library-screening, hit-confirmation, and lead generation through cycles of quantitative structure activity relationship learning and testing. Using econometric modelling we demonstrate that the use of AI to select compounds economically outperforms standard drug screening. For further efficiency Eve uses a standardized form of assay to compute Boolean functions of compound properties. These assays can be quickly and cheaply engineered using synthetic biology, enabling more targets to be assayed for a given budget. Eve has repositioned several drugs against specific targets in parasites that cause tropical diseases. One validated discovery is that the anti-cancer compound TNP-470 is a potent inhibitor of dihydrofolate reductase from the malaria-causing parasite Plasmodium vivax.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

Towards robust network based complex systems : from evolutionary cellular automata to biological models

Abstract Sitting between your past and your future doesn't mean you are in the present. Dakota Skye Complex systems science is an interdisciplinary field grouping under the same umbrella dynamical phenomena from social, natural or mathematical sciences. The emergence of a higher order organization or behavior, transcending that expected of the linear addition of the parts, is a key factor shared by all these systems. Most complex systems can be modeled as networks that represent the interactions amongst the system's components. In addition to the actual nature of the part's interactions, the intrinsic topological structure of underlying network is believed to play a crucial role in the remarkable emergent behaviors exhibited by the systems. Moreover, the topology is also a key a factor to explain the extraordinary flexibility and resilience to perturbations when applied to transmission and diffusion phenomena. In this work, we study the effect of different network structures on the performance and on the fault tolerance of systems in two different contexts. In the first part, we study cellular automata, which are a simple paradigm for distributed computation. Cellular automata are made of basic Boolean computational units, the cells; relying on simple rules and information from- the surrounding cells to perform a global task. The limited visibility of the cells can be modeled as a network, where interactions amongst cells are governed by an underlying structure, usually a regular one. In order to increase the performance of cellular automata, we chose to change its topology. We applied computational principles inspired by Darwinian evolution, called evolutionary algorithms, to alter the system's topological structure starting from either a regular or a random one. The outcome is remarkable, as the resulting topologies find themselves sharing properties of both regular and random network, and display similitudes Watts-Strogtz's small-world network found in social systems. Moreover, the performance and tolerance to probabilistic faults of our small-world like cellular automata surpasses that of regular ones. In the second part, we use the context of biological genetic regulatory networks and, in particular, Kauffman's random Boolean networks model. In some ways, this model is close to cellular automata, although is not expected to perform any task. Instead, it simulates the time-evolution of genetic regulation within living organisms under strict conditions. The original model, though very attractive by it's simplicity, suffered from important shortcomings unveiled by the recent advances in genetics and biology. We propose to use these new discoveries to improve the original model. Firstly, we have used artificial topologies believed to be closer to that of gene regulatory networks. We have also studied actual biological organisms, and used parts of their genetic regulatory networks in our models. Secondly, we have addressed the improbable full synchronicity of the event taking place on. Boolean networks and proposed a more biologically plausible cascading scheme. Finally, we tackled the actual Boolean functions of the model, i.e. the specifics of how genes activate according to the activity of upstream genes, and presented a new update function that takes into account the actual promoting and repressing effects of one gene on another. Our improved models demonstrate the expected, biologically sound, behavior of previous GRN model, yet with superior resistance to perturbations. We believe they are one step closer to the biological reality.

Utilisation de splines monotones afin de condenser des tables de mortalité dans un contexte bayésien

Dans ce mémoire, nous cherchons à modéliser des tables à deux entrées monotones en lignes et/ou en colonnes, pour une éventuelle application sur les tables de mortalité. Nous adoptons une approche bayésienne non paramétrique et représentons la forme fonctionnelle des données par splines bidimensionnelles. L’objectif consiste à condenser une table de mortalité, c’est-à-dire de réduire l’espace d’entreposage de la table en minimisant la perte d’information. De même, nous désirons étudier le temps nécessaire pour reconstituer la table. L’approximation doit conserver les mêmes propriétés que la table de référence, en particulier la monotonie des données. Nous travaillons avec une base de fonctions splines monotones afin d’imposer plus facilement la monotonie au modèle. En effet, la structure flexible des splines et leurs dérivées faciles à manipuler favorisent l’imposition de contraintes sur le modèle désiré. Après un rappel sur la modélisation unidimensionnelle de fonctions monotones, nous généralisons l’approche au cas bidimensionnel. Nous décrivons l’intégration des contraintes de monotonie dans le modèle a priori sous l’approche hiérarchique bayésienne. Ensuite, nous indiquons comment obtenir un estimateur a posteriori à l’aide des méthodes de Monte Carlo par chaînes de Markov. Finalement, nous étudions le comportement de notre estimateur en modélisant une table de la loi normale ainsi qu’une table t de distribution de Student. L’estimation de nos données d’intérêt, soit la table de mortalité, s’ensuit afin d’évaluer l’amélioration de leur accessibilité.

Amplification de l'amplitude : analyse et applications

Ce mémoire étudie l'algorithme d'amplification de l'amplitude et ses applications dans le domaine de test de propriété. On utilise l'amplification de l'amplitude pour proposer le plus efficace algorithme quantique à ce jour qui teste la linéarité de fonctions booléennes et on généralise notre nouvel algorithme pour tester si une fonction entre deux groupes abéliens finis est un homomorphisme. Le meilleur algorithme quantique connu qui teste la symétrie de fonctions booléennes est aussi amélioré et l'on utilise ce nouvel algorithme pour tester la quasi-symétrie de fonctions booléennes. Par la suite, on approfondit l'étude du nombre de requêtes à la boîte noire que fait l'algorithme d'amplification de l'amplitude pour amplitude initiale inconnue. Une description rigoureuse de la variable aléatoire représentant ce nombre est présentée, suivie du résultat précédemment connue de la borne supérieure sur l'espérance. Suivent de nouveaux résultats sur la variance de cette variable. Il est notamment montré que, dans le cas général, la variance est infinie, mais nous montrons aussi que, pour un choix approprié de paramètres, elle devient bornée supérieurement.

Multilevel Training of Binary Morphological Operators

The design of binary morphological operators that are translation-invariant and locally defined by a finite neighborhood window corresponds to the problem of designing Boolean functions. As in any supervised classification problem, morphological operators designed from a training sample also suffer from overfitting. Large neighborhood tends to lead to performance degradation of the designed operator. This work proposes a multilevel design approach to deal with the issue of designing large neighborhood-based operators. The main idea is inspired by stacked generalization (a multilevel classifier design approach) and consists of, at each training level, combining the outcomes of the previous level operators. The final operator is a multilevel operator that ultimately depends on a larger neighborhood than of the individual operators that have been combined. Experimental results show that two-level operators obtained by combining operators designed on subwindows of a large window consistently outperform the single-level operators designed on the full window. They also show that iterating two-level operators is an effective multilevel approach to obtain better results.

Arquitetura multiprocessada e reconfigurável para a síntese de redes de Petri em hardware

Uma arquitetura reconfigurável e multiprocessada para a implementação física de Redes de Petri foi desenvolvida em VHDL e mapeada sobre um FPGA. Convencionalmente, as Redes de Petri são transformadas em uma linguagem de descrição de hardware no nível de transferências entre registradores e um processo de síntese de alto nível é utilizado para gerar as funções booleanas e tabelas de transição de estado para que se possa, finalmente, mapeá-las num FPGA (Morris et al., 2000) (Soto and Pereira, 2001). A arquitetura proposta possui blocos lógicos reconfiguráveis desenvolvidos exclusivamente para a implementação dos lugares e das transições da rede, não sendo necessária a descrição da rede em níveis de abstração intermediários e nem a utilização de um processo de síntese para realizar o mapeamento da rede na arquitetura. A arquitetura permite o mapeamento de modelos de Redes de Petri com diferenciação entre as marcas e associação de tempo no disparo das transições, sendo composta por um arranjo de processadores reconfiguráveis, cada um dos quais representando o comportamento de uma transição da Rede de Petri a ser mapeada e por um sistema de comunicação, implementado por um conjunto de roteadores que são capazes de enviar pacotes de dados de um processador reconfigurável a outro. A arquitetura proposta foi validada num FPGA de 10.570 elementos lógicos com uma topologia que permitiu a implementação de Redes de Petri de até 9 transições e 36 lugares, atingindo uma latência de 15,4ns e uma vazão de até 17,12GB/s com uma freqüência de operação de 64,58MHz.

Branch and bound algorithm for transmission network expansion planning using DC model

This paper presents an algorithm to solve the network transmission system expansion planning problem using the DC model which is a mixed non-linear integer programming problem. The major feature of this work is the use of a Branch-and-Bound (B&B) algorithm to directly solve mixed non-linear integer problems. An efficient interior point method is used to solve the non-linear programming problem at each node of the B&B tree. Tests with several known systems are presented to illustrate the performance of the proposed method. ©2007 IEEE.

Aperfeiçoamento do método clause-column table para a geração eficiente de implicantes primos

Pós-graduação em Engenharia Elétrica - FEIS

Bit noise from an optical logic gate with laser diodes

Output bits from an optical logic cell present noise due to the type of technique used to obtain the Boolean functions of two input data bits. We have simulated the behavior of an optically programmable logic cell working with Fabry Perot-laser diodes of the same type employed in optical communications (1550nm) but working here as amplifiers. We will report in this paper a study of the bit noise generated from the optical non-linearity process allowing the Boolean function operation of two optical input data signals. Two types of optical logic cells will be analyzed. Firstly, a classical "on-off" behavior, with transmission operation of LD amplifier and, secondly, a more complicated configuration with two LD amplifiers, one working on transmission and the other one in reflection mode. This last configuration has nonlinear behavior emulating SEED-like properties. In both cases, depending on the value of a "1" input data signals to be processed, a different logic function can be obtained. Also a CW signal, known as control signal, may be apply to fix the type of logic function. The signal to noise ratio will be analyzed for different parameters, as wavelength signals and the hysteresis cycles regions associated to the device, in relation with the signals power level applied. With this study we will try to obtain a better understanding of the possible effects present on an optical logic gate with Laser Diodes.