Glucose-Insulin regulator for type 1 diabetes using high order neural networks

In this paper a Glucose-Insulin regulator for Type 1 Diabetes using artificial neural networks (ANN) is proposed. This is done using a discrete recurrent high order neural network in order to identify and control a nonlinear dynamical system which represents the pancreas? beta-cells behavior of a virtual patient. The ANN which reproduces and identifies the dynamical behavior system, is configured as series parallel and trained on line using the extended Kalman filter algorithm to achieve a quickly convergence identification in silico. The control objective is to regulate the glucose-insulin level under different glucose inputs and is based on a nonlinear neural block control law. A safety block is included between the control output signal and the virtual patient with type 1 diabetes mellitus. Simulations include a period of three days. Simulation results are compared during the overnight fasting period in Open-Loop (OL) versus Closed- Loop (CL). Tests in Semi-Closed-Loop (SCL) are made feedforward in order to give information to the control algorithm. We conclude the controller is able to drive the glucose to target in overnight periods and the feedforward is necessary to control the postprandial period.

Overtopping of harbour breakwaters: a comparison of semi-empirical equations, neural networks, and physical model tests

This paper reports extensive tests of empirical equations developed by different authors for harbour breakwater overtopping. First, the existing equations are compiled and evaluated as tools for estimating the overtopping rates on sloping and vertical breakwaters. These equations are then tested using the data obtained in a number of laboratory studies performed in the Centre for Harbours and Coastal Studies of the CEDEX, Spain. It was found that the recommended application ranges of the empirical equations typically deviate from those revealed in the experimental tests. In addition, a neural network model developed within the European CLASH Project is tested. The wind effects on overtopping are also assessed using a reduced scale physical model

Monitorización de estructuras aeronáuticas mediante técnicas de inteligencia artificial

Una de las barreras para la aplicación de las técnicas de monitorización de la integridad estructural (SHM) basadas en ondas elásticas guiadas (GLW) en aeronaves es la influencia perniciosa de las condiciones ambientales y de operación (EOC). En esta tesis se ha estudiado dicha influencia y la compensación de la misma, particularizando en variaciones del estado de carga y temperatura. La compensación de dichos efectos se fundamenta en Redes Neuronales Artificiales (ANN) empleando datos experimentales procesados con la Transformada Chirplet. Los cambios en la geometría y en las propiedades del material respecto al estado inicial de la estructura (lo daños) provocan cambios en la forma de onda de las GLW (lo que denominamos característica sensible al daño o DSF). Mediante técnicas de tratamiento de señal se puede buscar una relación entre dichas variaciones y los daños, esto se conoce como SHM. Sin embargo, las variaciones en las EOC producen también cambios en los datos adquiridos relativos a las GLW (DSF) que provocan errores en los algoritmos de diagnóstico de daño (SHM). Esto sucede porque las firmas de daño y de las EOC en la DSF son del mismo orden. Por lo tanto, es necesario cuantificar y compensar el efecto de las EOC sobre la GLW. Si bien existen diversas metodologías para compensar los efectos de las EOC como por ejemplo “Optimal Baseline Selection” (OBS) o “Baseline Signal Stretching” (BSS), estas, se emplean exclusivamente en la compensación de los efectos térmicos. El método propuesto en esta tesis mezcla análisis de datos experimentales, como en el método OBS, y modelos basados en Redes Neuronales Artificiales (ANN) que reemplazan el modelado físico requerido por el método BSS. El análisis de datos experimentales consiste en aplicar la Transformada Chirplet (CT) para extraer la firma de las EOC sobre la DSF. Con esta información, obtenida bajo diversas EOC, se entrena una ANN. A continuación, la ANN actuará como un interpolador de referencias de la estructura sin daño, generando información de referencia para cualquier EOC. La comparación de las mediciones reales de la DSF con los valores simulados por la ANN, dará como resultado la firma daño en la DSF, lo que permite el diagnóstico de daño. Este esquema se ha aplicado y verificado, en diversas EOC, para una estructura unidimensional con un único camino de daño, y para una estructura representativa de un fuselaje de una aeronave, con curvatura y múltiples elementos rigidizadores, sometida a un estado de cargas complejo, con múltiples caminos de daños. Los efectos de las EOC se han estudiado en detalle en la estructura unidimensional y se han generalizado para el fuselaje, demostrando la independencia del método respecto a la configuración de la estructura y el tipo de sensores utilizados para la adquisición de datos GLW. Por otra parte, esta metodología se puede utilizar para la compensación simultánea de una variedad medible de EOC, que afecten a la adquisición de datos de la onda elástica guiada. El principal resultado entre otros, de esta tesis, es la metodología CT-ANN para la compensación de EOC en técnicas SHM basadas en ondas elásticas guiadas para el diagnóstico de daño. ABSTRACT One of the open problems to implement Structural Health Monitoring techniques based on elastic guided waves in real aircraft structures at operation is the influence of the environmental and operational conditions (EOC) on the damage diagnosis problem. This thesis deals with the compensation of these environmental and operational effects, specifically, the temperature and the external loading, by the use of the Chirplet Transform working with Artificial Neural Networks. It is well known that the guided elastic wave form is affected by the damage appearance (what is known as the damage sensitive feature or DSF). The DSF is modified by the temperature and by the load applied to the structure. The EOC promotes variations in the acquired data (DSF) and cause mistakes in damage diagnosis algorithms. This effect promotes changes on the waveform due to the EOC variations of the same order than the damage occurrence. It is difficult to separate both effects in order to avoid damage diagnosis mistakes. Therefore it is necessary to quantify and compensate the effect of EOC over the GLW forms. There are several approaches to compensate the EOC effects such as Optimal Baseline Selection (OBS) or Baseline Signal Stretching (BSS). Usually, they are used for temperature compensation. The new method proposed here mixes experimental data analysis, as in the OBS method, and Artificial Neural Network (ANN) models to replace the physical modelling which involves the BSS method. The experimental data analysis studied is based on apply the Chirplet Transform (CT) to extract the EOC signature on the DSF. The information obtained varying EOC is employed to train an ANN. Then, the ANN will act as a baselines interpolator of the undamaged structure. The ANN generates reference information at any EOC. By comparing real measurements of the DSF against the ANN simulated values, the damage signature appears clearly in the DSF, enabling an accurate damage diagnosis. This schema has been applied in a range of EOC for a one-dimensional structure containing single damage path and two dimensional real fuselage structure with stiffener elements and multiple damage paths. The EOC effects tested in the one-dimensional structure have been generalized to the fuselage showing its independence from structural arrangement and the type of sensors used for GLW data acquisition. Moreover, it can be used for the simultaneous compensation of a variety of measurable EOC, which affects the guided wave data acquisition. The main result, among others, of this thesis is the CT-ANN methodology for the compensation of EOC in GLW based SHM technique for damage diagnosis.

Peptide design by artificial neural networks and computer-based evolutionary search

A technique for systematic peptide variation by a combination of rational and evolutionary approaches is presented. The design scheme consists of five consecutive steps: (i) identification of a “seed peptide” with a desired activity, (ii) generation of variants selected from a physicochemical space around the seed peptide, (iii) synthesis and testing of this biased library, (iv) modeling of a quantitative sequence-activity relationship by an artificial neural network, and (v) de novo design by a computer-based evolutionary search in sequence space using the trained neural network as the fitness function. This strategy was successfully applied to the identification of novel peptides that fully prevent the positive chronotropic effect of anti-β1-adrenoreceptor autoantibodies from the serum of patients with dilated cardiomyopathy. The seed peptide, comprising 10 residues, was derived by epitope mapping from an extracellular loop of human β1-adrenoreceptor. A set of 90 peptides was synthesized and tested to provide training data for neural network development. De novo design revealed peptides with desired activities that do not match the seed peptide sequence. These results demonstrate that computer-based evolutionary searches can generate novel peptides with substantial biological activity.

Deciphering a neural code for vision

Deciphering the information that eyes, ears, and other sensory organs transmit to the brain is important for understanding the neural basis of behavior. Recordings from single sensory nerve cells have yielded useful insights, but single neurons generally do not mediate behavior; networks of neurons do. Monitoring the activity of all cells in a neural network of a behaving animal, however, is not yet possible. Taking an alternative approach, we used a realistic cell-based model to compute the ensemble of neural activity generated by one sensory organ, the lateral eye of the horseshoe crab, Limulus polyphemus. We studied how the neural network of this eye encodes natural scenes by presenting to the model movies recorded with a video camera mounted above the eye of an animal that was exploring its underwater habitat. Model predictions were confirmed by simultaneously recording responses from single optic nerve fibers of the same animal. We report here that the eye transmits to the brain robust “neural images” of objects having the size, contrast, and motion of potential mates. The neural code for such objects is not found in ambiguous messages of individual optic nerve fibers but rather in patterns of coherent activity that extend over small ensembles of nerve fibers and are bound together by stimulus motion. Integrative properties of neurons in the first synaptic layer of the brain appear well suited to detecting the patterns of coherent activity. Neural coding by this relatively simple eye helps explain how horseshoe crabs find mates and may lead to a better understanding of how more complex sensory organs process information.

The neural development and organization of letter recognition: Evidence from functional neuroimaging, computational modeling, and behavioral studies

Although much of the brain’s functional organization is genetically predetermined, it appears that some noninnate functions can come to depend on dedicated and segregated neural tissue. In this paper, we describe a series of experiments that have investigated the neural development and organization of one such noninnate function: letter recognition. Functional neuroimaging demonstrates that letter and digit recognition depend on different neural substrates in some literate adults. How could the processing of two stimulus categories that are distinguished solely by cultural conventions become segregated in the brain? One possibility is that correlation-based learning in the brain leads to a spatial organization in cortex that reflects the temporal and spatial clustering of letters with letters in the environment. Simulations confirm that environmental co-occurrence does indeed lead to spatial localization in a neural network that uses correlation-based learning. Furthermore, behavioral studies confirm one critical prediction of this co-occurrence hypothesis, namely, that subjects exposed to a visual environment in which letters and digits occur together rather than separately (postal workers who process letters and digits together in Canadian postal codes) do indeed show less behavioral evidence for segregated letter and digit processing.

Self-organized phase transitions in neural networks as a neural mechanism of information processing.

Transitions between dynamically stable activity patterns imposed on an associative neural network are shown to be induced by self-organized infinitesimal changes in synaptic connection strength and to be a kind of phase transition. A key event for the neural process of information processing in a population coding scheme is transition between the activity patterns encoding usual entities. We propose that the infinitesimal and short-term synaptic changes based on the Hebbian learning rule are the driving force for the transition. The phase transition between the following two dynamical stable states is studied in detail, the state where the firing pattern is changed temporally so as to itinerate among several patterns and the state where the firing pattern is fixed to one of several patterns. The phase transition from the pattern itinerant state to a pattern fixed state may be induced by the Hebbian learning process under a weak input relevant to the fixed pattern. The reverse transition may be induced by the Hebbian unlearning process without input. The former transition is considered as recognition of the input stimulus, while the latter is considered as clearing of the used input data to get ready for new input. To ensure that information processing based on the phase transition can be made by the infinitesimal and short-term synaptic changes, it is absolutely necessary that the network always stays near the critical state corresponding to the phase transition point.

Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

We present a general approach to forming structure-activity relationships (SARs). This approach is based on representing chemical structure by atoms and their bond connectivities in combination with the inductive logic programming (ILP) algorithm PROGOL. Existing SAR methods describe chemical structure by using attributes which are general properties of an object. It is not possible to map chemical structure directly to attribute-based descriptions, as such descriptions have no internal organization. A more natural and general way to describe chemical structure is to use a relational description, where the internal construction of the description maps that of the object described. Our atom and bond connectivities representation is a relational description. ILP algorithms can form SARs with relational descriptions. We have tested the relational approach by investigating the SARs of 230 aromatic and heteroaromatic nitro compounds. These compounds had been split previously into two subsets, 188 compounds that were amenable to regression and 42 that were not. For the 188 compounds, a SAR was found that was as accurate as the best statistical or neural network-generated SARs. The PROGOL SAR has the advantages that it did not need the use of any indicator variables handcrafted by an expert, and the generated rules were easily comprehensible. For the 42 compounds, PROGOL formed a SAR that was significantly (P < 0.025) more accurate than linear regression, quadratic regression, and back-propagation. This SAR is based on an automatically generated structural alert for mutagenicity.

Aplicação de uma rede neural artificial para a avaliação da rugosidade e soprosidade vocal

A avaliação perceptivo-auditiva tem papel fundamental no estudo e na avaliação da voz, no entanto, por ser subjetiva está sujeita a imprecisões e variações. Por outro lado, a análise acústica permite a reprodutibilidade de resultados, porém precisa ser aprimorada, pois não analisa com precisão vozes com disfonias mais intensas e com ondas caóticas. Assim, elaborar medidas que proporcionem conhecimentos confiáveis em relação à função vocal resulta de uma necessidade antiga dentro desta linha de pesquisa e atuação clínica. Neste contexto, o uso da inteligência artificial, como as redes neurais artificiais, indica ser uma abordagem promissora. Objetivo: Validar um sistema automático utilizando redes neurais artificiais para a avaliação de vozes rugosas e soprosas. Materiais e métodos: Foram selecionadas 150 vozes, desde neutras até com presença em grau intenso de rugosidade e/ou soprosidade, do banco de dados da Clínica de Fonoaudiologia da Faculdade de Odontologia de Bauru (FOB/USP). Dessas vozes, 23 foram excluídas por não responderem aos critérios de inclusão na amostra, assim utilizaram-se 123 vozes. Procedimentos: avaliação perceptivo-auditiva pela escala visual analógica de 100 mm e pela escala numérica de quatro pontos; extração de características do sinal de voz por meio da Transformada Wavelet Packet e dos parâmetros acústicos: jitter, shimmer, amplitude da derivada e amplitude do pitch; e validação do classificador por meio da parametrização, treino, teste e avaliação das redes neurais artificiais. Resultados: Na avaliação perceptivo-auditiva encontrou-se, por meio do teste Coeficiente de Correlação Intraclasse (CCI), concordâncias inter e intrajuiz excelentes, com p = 0,85 na concordância interjuízes e p variando de 0,87 a 0,93 nas concordâncias intrajuiz. Em relação ao desempenho da rede neural artificial, na discriminação da soprosidade e da rugosidade e dos seus respectivos graus, encontrou-se o melhor desempenho para a soprosidade no subconjunto composto pelo jitter, amplitude do pitch e frequência fundamental, no qual obteve-se taxa de acerto de 74%, concordância excelente com a avaliação perceptivo-auditiva da escala visual analógica (0,80 no CCI) e erro médio de 9 mm. Para a rugosidade, o melhor subconjunto foi composto pela Transformada Wavelet Packet com 1 nível de decomposição, jitter, shimmer, amplitude do pitch e frequência fundamental, no qual obteve-se 73% de acerto, concordância excelente (0,84 no CCI), e erro médio de 10 mm. Conclusão: O uso da inteligência artificial baseado em redes neurais artificiais na identificação, e graduação da rugosidade e da soprosidade, apresentou confiabilidade excelente (CCI > 0,80), com resultados semelhantes a concordância interjuízes. Dessa forma, a rede neural artificial revela-se como uma metodologia promissora de avaliação vocal, tendo sua maior vantagem a objetividade na avaliação.

Representation of 2D objects with a topology preserving network

Comunicación presentada en el 2nd International Workshop on Pattern Recognition in Information Systems, Alicante, April, 2002.

Real time motion estimation using a neural architecture implemented on GPUs

This work describes a neural network based architecture that represents and estimates object motion in videos. This architecture addresses multiple computer vision tasks such as image segmentation, object representation or characterization, motion analysis and tracking. The use of a neural network architecture allows for the simultaneous estimation of global and local motion and the representation of deformable objects. This architecture also avoids the problem of finding corresponding features while tracking moving objects. Due to the parallel nature of neural networks, the architecture has been implemented on GPUs that allows the system to meet a set of requirements such as: time constraints management, robustness, high processing speed and re-configurability. Experiments are presented that demonstrate the validity of our architecture to solve problems of mobile agents tracking and motion analysis.

3D model reconstruction using neural gas accelerated on GPU

In this work, we propose the use of the neural gas (NG), a neural network that uses an unsupervised Competitive Hebbian Learning (CHL) rule, to develop a reverse engineering process. This is a simple and accurate method to reconstruct objects from point clouds obtained from multiple overlapping views using low-cost sensors. In contrast to other methods that may need several stages that include downsampling, noise filtering and many other tasks, the NG automatically obtains the 3D model of the scanned objects. To demonstrate the validity of our proposal we tested our method with several models and performed a study of the neural network parameterization computing the quality of representation and also comparing results with other neural methods like growing neural gas and Kohonen maps or classical methods like Voxel Grid. We also reconstructed models acquired by low cost sensors that can be used in virtual and augmented reality environments for redesign or manipulation purposes. Since the NG algorithm has a strong computational cost we propose its acceleration. We have redesigned and implemented the NG learning algorithm to fit it onto Graphics Processing Units using CUDA. A speed-up of 180× faster is obtained compared to the sequential CPU version.

Designing Regularizers and Architectures for Recurrent Neural Networks

Cette thèse contribue a la recherche vers l'intelligence artificielle en utilisant des méthodes connexionnistes. Les réseaux de neurones récurrents sont un ensemble de modèles séquentiels de plus en plus populaires capable en principe d'apprendre des algorithmes arbitraires. Ces modèles effectuent un apprentissage en profondeur, un type d'apprentissage machine. Sa généralité et son succès empirique en font un sujet intéressant pour la recherche et un outil prometteur pour la création de l'intelligence artificielle plus générale. Le premier chapitre de cette thèse donne un bref aperçu des sujets de fonds: l'intelligence artificielle, l'apprentissage machine, l'apprentissage en profondeur et les réseaux de neurones récurrents. Les trois chapitres suivants couvrent ces sujets de manière de plus en plus spécifiques. Enfin, nous présentons quelques contributions apportées aux réseaux de neurones récurrents. Le chapitre \ref{arxiv1} présente nos travaux de régularisation des réseaux de neurones récurrents. La régularisation vise à améliorer la capacité de généralisation du modèle, et joue un role clé dans la performance de plusieurs applications des réseaux de neurones récurrents, en particulier en reconnaissance vocale. Notre approche donne l'état de l'art sur TIMIT, un benchmark standard pour cette tâche. Le chapitre \ref{cpgp} présente une seconde ligne de travail, toujours en cours, qui explore une nouvelle architecture pour les réseaux de neurones récurrents. Les réseaux de neurones récurrents maintiennent un état caché qui représente leurs observations antérieures. L'idée de ce travail est de coder certaines dynamiques abstraites dans l'état caché, donnant au réseau une manière naturelle d'encoder des tendances cohérentes de l'état de son environnement. Notre travail est fondé sur un modèle existant; nous décrivons ce travail et nos contributions avec notamment une expérience préliminaire.

Designing Regularizers and Architectures for Recurrent Neural Networks

Cette thèse contribue a la recherche vers l'intelligence artificielle en utilisant des méthodes connexionnistes. Les réseaux de neurones récurrents sont un ensemble de modèles séquentiels de plus en plus populaires capable en principe d'apprendre des algorithmes arbitraires. Ces modèles effectuent un apprentissage en profondeur, un type d'apprentissage machine. Sa généralité et son succès empirique en font un sujet intéressant pour la recherche et un outil prometteur pour la création de l'intelligence artificielle plus générale. Le premier chapitre de cette thèse donne un bref aperçu des sujets de fonds: l'intelligence artificielle, l'apprentissage machine, l'apprentissage en profondeur et les réseaux de neurones récurrents. Les trois chapitres suivants couvrent ces sujets de manière de plus en plus spécifiques. Enfin, nous présentons quelques contributions apportées aux réseaux de neurones récurrents. Le chapitre \ref{arxiv1} présente nos travaux de régularisation des réseaux de neurones récurrents. La régularisation vise à améliorer la capacité de généralisation du modèle, et joue un role clé dans la performance de plusieurs applications des réseaux de neurones récurrents, en particulier en reconnaissance vocale. Notre approche donne l'état de l'art sur TIMIT, un benchmark standard pour cette tâche. Le chapitre \ref{cpgp} présente une seconde ligne de travail, toujours en cours, qui explore une nouvelle architecture pour les réseaux de neurones récurrents. Les réseaux de neurones récurrents maintiennent un état caché qui représente leurs observations antérieures. L'idée de ce travail est de coder certaines dynamiques abstraites dans l'état caché, donnant au réseau une manière naturelle d'encoder des tendances cohérentes de l'état de son environnement. Notre travail est fondé sur un modèle existant; nous décrivons ce travail et nos contributions avec notamment une expérience préliminaire.

The applicability of recurrent neural networks for biological sequence analysis

Selection of machine learning techniques requires a certain sensitivity to the requirements of the problem. In particular, the problem can be made more tractable by deliberately using algorithms that are biased toward solutions of the requisite kind. In this paper, we argue that recurrent neural networks have a natural bias toward a problem domain of which biological sequence analysis tasks are a subset. We use experiments with synthetic data to illustrate this bias. We then demonstrate that this bias can be exploitable using a data set of protein sequences containing several classes of subcellular localization targeting peptides. The results show that, compared with feed forward, recurrent neural networks will generally perform better on sequence analysis tasks. Furthermore, as the patterns within the sequence become more ambiguous, the choice of specific recurrent architecture becomes more critical.