Automatic blood glucose classification for gestational diabetes with feature selection: decision trees vs neural networks

Automatic blood glucose classification may help specialists to provide a better interpretation of blood glucose data, downloaded directly from patients glucose meter and will contribute in the development of decision support systems for gestational diabetes. This paper presents an automatic blood glucose classifier for gestational diabetes that compares 6 different feature selection methods for two machine learning algorithms: neural networks and decision trees. Three searching algorithms, Greedy, Best First and Genetic, were combined with two different evaluators, CSF and Wrapper, for the feature selection. The study has been made with 6080 blood glucose measurements from 25 patients. Decision trees with a feature set selected with the Wrapper evaluator and the Best first search algorithm obtained the best accuracy: 95.92%.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

On Recurrent and Deep Neural Networks

L'apprentissage profond est un domaine de recherche en forte croissance en apprentissage automatique qui est parvenu à des résultats impressionnants dans différentes tâches allant de la classification d'images à la parole, en passant par la modélisation du langage. Les réseaux de neurones récurrents, une sous-classe d'architecture profonde, s'avèrent particulièrement prometteurs. Les réseaux récurrents peuvent capter la structure temporelle dans les données. Ils ont potentiellement la capacité d'apprendre des corrélations entre des événements éloignés dans le temps et d'emmagasiner indéfiniment des informations dans leur mémoire interne. Dans ce travail, nous tentons d'abord de comprendre pourquoi la profondeur est utile. Similairement à d'autres travaux de la littérature, nos résultats démontrent que les modèles profonds peuvent être plus efficaces pour représenter certaines familles de fonctions comparativement aux modèles peu profonds. Contrairement à ces travaux, nous effectuons notre analyse théorique sur des réseaux profonds acycliques munis de fonctions d'activation linéaires par parties, puisque ce type de modèle est actuellement l'état de l'art dans différentes tâches de classification. La deuxième partie de cette thèse porte sur le processus d'apprentissage. Nous analysons quelques techniques d'optimisation proposées récemment, telles l'optimisation Hessian free, la descente de gradient naturel et la descente des sous-espaces de Krylov. Nous proposons le cadre théorique des méthodes à région de confiance généralisées et nous montrons que plusieurs de ces algorithmes développés récemment peuvent être vus dans cette perspective. Nous argumentons que certains membres de cette famille d'approches peuvent être mieux adaptés que d'autres à l'optimisation non convexe. La dernière partie de ce document se concentre sur les réseaux de neurones récurrents. Nous étudions d'abord le concept de mémoire et tentons de répondre aux questions suivantes: Les réseaux récurrents peuvent-ils démontrer une mémoire sans limite? Ce comportement peut-il être appris? Nous montrons que cela est possible si des indices sont fournis durant l'apprentissage. Ensuite, nous explorons deux problèmes spécifiques à l'entraînement des réseaux récurrents, à savoir la dissipation et l'explosion du gradient. Notre analyse se termine par une solution au problème d'explosion du gradient qui implique de borner la norme du gradient. Nous proposons également un terme de régularisation conçu spécifiquement pour réduire le problème de dissipation du gradient. Sur un ensemble de données synthétique, nous montrons empiriquement que ces mécanismes peuvent permettre aux réseaux récurrents d'apprendre de façon autonome à mémoriser des informations pour une période de temps indéfinie. Finalement, nous explorons la notion de profondeur dans les réseaux de neurones récurrents. Comparativement aux réseaux acycliques, la définition de profondeur dans les réseaux récurrents est souvent ambiguë. Nous proposons différentes façons d'ajouter de la profondeur dans les réseaux récurrents et nous évaluons empiriquement ces propositions.

Directly training spiking neural networks for cyber-physical systems: from supervised to reinforcement learning

Spiking Neural Networks (SNNs) are bio-inspired Artificial Neural Networks (ANNs) utilizing discrete spiking signals, akin to neuron communication in the brain, making them ideal for real-time and energy-efficient Cyber-Physical Systems (CPSs). This thesis explores their potential in Structural Health Monitoring (SHM), leveraging low-cost MEMS accelerometers for early damage detection in motorway bridges. The study focuses on Long Short-Term SNNs (LSNNs), although their complex learning processes pose challenges. Comparing LSNNs with other ANN models and training algorithms for SHM, findings indicate LSNNs' effectiveness in damage identification, comparable to ANNs trained using traditional methods. Additionally, an optimized embedded LSNN implementation demonstrates a 54% reduction in execution time, but with longer pre-processing due to spike-based encoding. Furthermore, SNNs are applied in UAV obstacle avoidance, trained directly using a Reinforcement Learning (RL) algorithm with event-based input from a Dynamic Vision Sensor (DVS). Performance evaluation against Convolutional Neural Networks (CNNs) highlights SNNs' superior energy efficiency, showing a 6x decrease in energy consumption. The study also investigates embedded SNN implementations' latency and throughput in real-world deployments, emphasizing their potential for energy-efficient monitoring systems. This research contributes to advancing SHM and UAV obstacle avoidance through SNNs' efficient information processing and decision-making capabilities within CPS domains.

A method using artificial neural networks to morphologically assess mouse blastocyst quality

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mutual Information-based RBM Neural Networks

(Deep) neural networks are increasingly being used for various computer vision and pattern recognition tasks due to their strong ability to learn highly discriminative features. However, quantitative analysis of their classication ability and design philosophies are still nebulous. In this work, we use information theory to analyze the concatenated restricted Boltzmann machines (RBMs) and propose a mutual information-based RBM neural networks (MI-RBM). We develop a novel pretraining algorithm to maximize the mutual information between RBMs. Extensive experimental results on various classication tasks show the eectiveness of the proposed approach.

Machine Learning algorithm on seat comfort level measurement, mapping pressure values with body regions

The comfort level of the seat has a major effect on the usage of a vehicle; thus, car manufacturers have been working on elevating car seat comfort as much as possible. However, still, the testing and evaluation of comfort are done using exhaustive trial and error testing and evaluation of data. In this thesis, we resort to machine learning and Artificial Neural Networks (ANN) to develop a fully automated approach. Even though this approach has its advantages in minimizing time and using a large set of data, it takes away the degree of freedom of the engineer on making decisions. The focus of this study is on filling the gap in a two-step comfort level evaluation which used pressure mapping with body regions to evaluate the average pressure supported by specific body parts and the Self-Assessment Exam (SAE) questions on evaluation of the person’s interest. This study has created a machine learning algorithm that works on giving a degree of freedom to the engineer in making a decision when mapping pressure values with body regions using ANN. The mapping is done with 92% accuracy and with the help of a Graphical User Interface (GUI) that facilitates the process during the testing time of comfort level evaluation of the car seat, which decreases the duration of the test analysis from days to hours.

Artificial neural networks for automatic modelling of the pectus excavatum corrective prosthesis

Pectus excavatum is the most common deformity of the thorax and usually comprises Computed Tomography (CT) examination for pre-operative diagnosis. Aiming at the elimination of the high amounts of CT radiation exposure, this work presents a new methodology for the replacement of CT by a laser scanner (radiation-free) in the treatment of pectus excavatum using personally modeled prosthesis. The complete elimination of CT involves the determination of ribs external outline, at the maximum sternum depression point for prosthesis placement, based on chest wall skin surface information, acquired by a laser scanner. The developed solution resorts to artificial neural networks trained with data vectors from 165 patients. Scaled Conjugate Gradient, Levenberg-Marquardt, Resilient Back propagation and One Step Secant gradient learning algorithms were used. The training procedure was performed using the soft tissue thicknesses, determined using image processing techniques that automatically segment the skin and rib cage. The developed solution was then used to determine the ribs outline in data from 20 patient scanners. Tests revealed that ribs position can be estimated with an average error of about 6.82±5.7 mm for the left and right side of the patient. Such an error range is well below current prosthesis manual modeling (11.7±4.01 mm) even without CT imagiology, indicating a considerable step forward towards CT replacement by a 3D scanner for prosthesis personalization.

Integrating defeasible argumentation with fuzzy ART neural networks for pattern classification

Many classification systems rely on clustering techniques in which a collection of training examples is provided as an input, and a number of clusters c1,...cm modelling some concept C results as an output, such that every cluster ci is labelled as positive or negative. Given a new, unlabelled instance enew, the above classification is used to determine to which particular cluster ci this new instance belongs. In such a setting clusters can overlap, and a new unlabelled instance can be assigned to more than one cluster with conflicting labels. In the literature, such a case is usually solved non-deterministically by making a random choice. This paper presents a novel, hybrid approach to solve this situation by combining a neural network for classification along with a defeasible argumentation framework which models preference criteria for performing clustering.

Apprentissage d'espaces sémantiques

Dans cette dissertation, nous présentons plusieurs techniques d’apprentissage d’espaces sémantiques pour plusieurs domaines, par exemple des mots et des images, mais aussi à l’intersection de différents domaines. Un espace de représentation est appelé sémantique si des entités jugées similaires par un être humain, ont leur similarité préservée dans cet espace. La première publication présente un enchaînement de méthodes d’apprentissage incluant plusieurs techniques d’apprentissage non supervisé qui nous a permis de remporter la compétition “Unsupervised and Transfer Learning Challenge” en 2011. Le deuxième article présente une manière d’extraire de l’information à partir d’un contexte structuré (177 détecteurs d’objets à différentes positions et échelles). On montrera que l’utilisation de la structure des données combinée à un apprentissage non supervisé permet de réduire la dimensionnalité de 97% tout en améliorant les performances de reconnaissance de scènes de +5% à +11% selon l’ensemble de données. Dans le troisième travail, on s’intéresse à la structure apprise par les réseaux de neurones profonds utilisés dans les deux précédentes publications. Plusieurs hypothèses sont présentées et testées expérimentalement montrant que l’espace appris a de meilleures propriétés de mixage (facilitant l’exploration de différentes classes durant le processus d’échantillonnage). Pour la quatrième publication, on s’intéresse à résoudre un problème d’analyse syntaxique et sémantique avec des réseaux de neurones récurrents appris sur des fenêtres de contexte de mots. Dans notre cinquième travail, nous proposons une façon d’effectuer de la recherche d’image ”augmentée” en apprenant un espace sémantique joint où une recherche d’image contenant un objet retournerait aussi des images des parties de l’objet, par exemple une recherche retournant des images de ”voiture” retournerait aussi des images de ”pare-brises”, ”coffres”, ”roues” en plus des images initiales.

Neural Networks

We present an overview of current research on artificial neural networks, emphasizing a statistical perspective. We view neural networks as parameterized graphs that make probabilistic assumptions about data, and view learning algorithms as methods for finding parameter values that look probable in the light of the data. We discuss basic issues in representation and learning, and treat some of the practical issues that arise in fitting networks to data. We also discuss links between neural networks and the general formalism of graphical models.

Adverse drug reaction classification with deep neural networks

We study the problem of detecting sentences describing adverse drug reactions (ADRs) and frame the problem as binary classification. We investigate different neural network (NN) architectures for ADR classification. In particular, we propose two new neural network models, Convolutional Recurrent Neural Network (CRNN) by concatenating convolutional neural networks with recurrent neural networks, and Convolutional Neural Network with Attention (CNNA) by adding attention weights into convolutional neural networks. We evaluate various NN architectures on a Twitter dataset containing informal language and an Adverse Drug Effects (ADE) dataset constructed by sampling from MEDLINE case reports. Experimental results show that all the NN architectures outperform the traditional maximum entropy classifiers trained from n-grams with different weighting strategies considerably on both datasets. On the Twitter dataset, all the NN architectures perform similarly. But on the ADE dataset, CNN performs better than other more complex CNN variants. Nevertheless, CNNA allows the visualisation of attention weights of words when making classification decisions and hence is more appropriate for the extraction of word subsequences describing ADRs.

‘Data Augmentation’ per reti neurali profonde per la classificazione del segnale EEG

I recenti sviluppi nel campo dell’intelligenza artificiale hanno permesso una più adeguata classificazione del segnale EEG. Negli ultimi anni è stato dimostrato come sia possibile ottenere ottime performance di classificazione impiegando tecniche di Machine Learning (ML) e di Deep Learning (DL), facendo uso, per quest’ultime, di reti neurali convoluzionali (Convolutional Neural Networks, CNN). In particolare, il Deep Learning richiede molti dati di training mentre spesso i dataset per EEG sono limitati ed è difficile quindi raggiungere prestazioni elevate. I metodi di Data Augmentation possono alleviare questo problema. Partendo da dati reali, questa tecnica permette, la creazione di dati artificiali fondamentali per aumentare le dimensioni del dataset di partenza. L’applicazione più comune è quella di utilizzare i Data Augmentation per aumentare le dimensioni del training set, in modo da addestrare il modello/rete neurale su un numero di campioni più esteso, riducendo gli errori di classificazione. Partendo da questa idea, i Data Augmentation sono stati applicati in molteplici campi e in particolare per la classificazione del segnale EEG. In questo elaborato di tesi, inizialmente, vengono descritti metodi di Data Augmentation implementati nel corso degli anni, utilizzabili anche nell’ambito di applicazioni EEG. Successivamente, si presentano alcuni studi specifici che applicano metodi di Data Augmentation per migliorare le presentazioni di classificatori basati su EEG per l’identificazione dello stato sonno/veglia, per il riconoscimento delle emozioni, e per la classificazione di immaginazione motoria.