Algoritmos de aprendizado semi-supervisionado baseados em grafos aplicados na bioinformática

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

Segmentação interativa de imagens utilizando competição e cooperação entre partículas

Pós-graduação em Ciência da Computação - IBILCE

Network-based high level data classification

Traditional supervised data classification considers only physical features (e. g., distance or similarity) of the input data. Here, this type of learning is called low level classification. On the other hand, the human (animal) brain performs both low and high orders of learning and it has facility in identifying patterns according to the semantic meaning of the input data. Data classification that considers not only physical attributes but also the pattern formation is, here, referred to as high level classification. In this paper, we propose a hybrid classification technique that combines both types of learning. The low level term can be implemented by any classification technique, while the high level term is realized by the extraction of features of the underlying network constructed from the input data. Thus, the former classifies the test instances by their physical features or class topologies, while the latter measures the compliance of the test instances to the pattern formation of the data. Our study shows that the proposed technique not only can realize classification according to the pattern formation, but also is able to improve the performance of traditional classification techniques. Furthermore, as the class configuration's complexity increases, such as the mixture among different classes, a larger portion of the high level term is required to get correct classification. This feature confirms that the high level classification has a special importance in complex situations of classification. Finally, we show how the proposed technique can be employed in a real-world application, where it is capable of identifying variations and distortions of handwritten digit images. As a result, it supplies an improvement in the overall pattern recognition rate.

On the use of a low-cost thermal sensor to improve kinect people detection in a mobile robot

[EN]Detecting people is a key capability for robots that operate in populated environments. In this paper, we have adopted a hierarchical approach that combines classifiers created using supervised learning in order to identify whether a person is in the view-scope of the robot or not. Our approach makes use of vision, depth and thermal sensors mounted on top of a mobile platform.

Efficient ultrasonic signal processing techniques for aided medical diagnostics

Ultrasound imaging is widely used in medical diagnostics as it is the fastest, least invasive, and least expensive imaging modality. However, ultrasound images are intrinsically difficult to be interpreted. In this scenario, Computer Aided Detection (CAD) systems can be used to support physicians during diagnosis providing them a second opinion. This thesis discusses efficient ultrasound processing techniques for computer aided medical diagnostics, focusing on two major topics: (i) Ultrasound Tissue Characterization (UTC), aimed at characterizing and differentiating between healthy and diseased tissue; (ii) Ultrasound Image Segmentation (UIS), aimed at detecting the boundaries of anatomical structures to automatically measure organ dimensions and compute clinically relevant functional indices. Research on UTC produced a CAD tool for Prostate Cancer detection to improve the biopsy protocol. In particular, this thesis contributes with: (i) the development of a robust classification system; (ii) the exploitation of parallel computing on GPU for real-time performance; (iii) the introduction of both an innovative Semi-Supervised Learning algorithm and a novel supervised/semi-supervised learning scheme for CAD system training that improve system performance reducing data collection effort and avoiding collected data wasting. The tool provides physicians a risk map highlighting suspect tissue areas, allowing them to perform a lesion-directed biopsy. Clinical validation demonstrated the system validity as a diagnostic support tool and its effectiveness at reducing the number of biopsy cores requested for an accurate diagnosis. For UIS the research developed a heart disease diagnostic tool based on Real-Time 3D Echocardiography. Thesis contributions to this application are: (i) the development of an automated GPU based level-set segmentation framework for 3D images; (ii) the application of this framework to the myocardium segmentation. Experimental results showed the high efficiency and flexibility of the proposed framework. Its effectiveness as a tool for quantitative analysis of 3D cardiac morphology and function was demonstrated through clinical validation.

Classification and selection of biomarkers in genomic data using LASSO

High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. Most of the work has been on assessing univariate associations between gene expression with clinical outcome (variable selection) or on developing classification procedures with gene expression data (supervised learning). We consider a hybrid variable selection/classification approach that is based on linear combinations of the gene expression profiles that maximize an accuracy measure summarized using the receiver operating characteristic curve. Under a specific probability model, this leads to consideration of linear discriminant functions. We incorporate an automated variable selection approach using LASSO. An equivalence between LASSO estimation with support vector machines allows for model fitting using standard software. We apply the proposed method to simulated data as well as data from a recently published prostate cancer study.

Building the View Graph of a Category by Exploiting Image Realism

We propose a weakly supervised method to arrange images of a given category based on the relative pose between the camera and the object in the scene. Relative poses are points on a sphere centered at the object in a given canonical pose, which we call object viewpoints. Our method builds a graph on this sphere by assigning images with similar viewpoint to the same node and by connecting nodes if they are related by a small rotation. The key idea is to exploit a large unlabeled dataset to validate the likelihood of dominant 3D planes of the object geometry. A number of 3D plane hypotheses are evaluated by applying small 3D rotations to each hypothesis and by measuring how well the deformed images match other images in the dataset. Correct hypotheses will result in deformed images that correspond to plausible views of the object, and thus will likely match well other images in the same category. The identified 3D planes are then used to compute affinities between images related by a change of viewpoint. We then use the affinities to build a view graph via a greedy method and the maximum spanning tree.

Fuzzy min-max neural networks for categorical data: application to missing data imputation

The fuzzy min–max neural network classifier is a supervised learning method. This classifier takes the hybrid neural networks and fuzzy systems approach. All input variables in the network are required to correspond to continuously valued variables, and this can be a significant constraint in many real-world situations where there are not only quantitative but also categorical data. The usual way of dealing with this type of variables is to replace the categorical by numerical values and treat them as if they were continuously valued. But this method, implicitly defines a possibly unsuitable metric for the categories. A number of different procedures have been proposed to tackle the problem. In this article, we present a new method. The procedure extends the fuzzy min–max neural network input to categorical variables by introducing new fuzzy sets, a new operation, and a new architecture. This provides for greater flexibility and wider application. The proposed method is then applied to missing data imputation in voting intention polls. The micro data—the set of the respondents’ individual answers to the questions—of this type of poll are especially suited for evaluating the method since they include a large number of numerical and categorical attributes.

Gear dynamics monitoring using discrete wavelet transformation and multi-layer perceptron neural networks

This paper presents a multi-stage algorithm for the dynamic condition monitoring of a gear. The algorithm provides information referred to the gear status (fault or normal condition) and estimates the mesh stiffness per shaft revolution in case that any abnormality is detected. In the first stage, the analysis of coefficients generated through discrete wavelet transformation (DWT) is proposed as a fault detection and localization tool. The second stage consists in establishing the mesh stiffness reduction associated with local failures by applying a supervised learning mode and coupled with analytical models. To do this, a multi-layer perceptron neural network has been configured using as input features statistical parameters sensitive to torsional stiffness decrease and derived from wavelet transforms of the response signal. The proposed method is applied to the gear condition monitoring and results show that it can update the mesh dynamic properties of the gear on line.

Region-dependent vehicle classification using PCA features

Video-based vehicle detection is the focus of increasing interest due to its potential towards collision avoidance. In particular, vehicle verification is especially challenging due to the enormous variability of vehicles in size, color, pose, etc. In this paper, a new approach based on supervised learning using Principal Component Analysis (PCA) is proposed that addresses the main limitations of existing methods. Namely, in contrast to classical approaches which train a single classifier regardless of the relative position of the candidate (thus ignoring valuable pose information), a region-dependent analysis is performed by considering four different areas. In addition, a study on the evolution of the classification performance according to the dimensionality of the principal subspace is carried out using PCA features within a SVM-based classification scheme. Indeed, the experiments performed on a publicly available database prove that PCA dimensionality requirements are region-dependent. Hence, in this work, the optimal configuration is adapted to each of them, rendering very good vehicle verification results.

Efficient Monte Carlo optimization for multi-label classifier chains

Multi-label classification (MLC) is the supervised learning problem where an instance may be associated with multiple labels. Modeling dependencies between labels allows MLC methods to improve their performance at the expense of an increased computational cost. In this paper we focus on the classifier chains (CC) approach for modeling dependencies. On the one hand, the original CC algorithm makes a greedy approximation, and is fast but tends to propagate errors down the chain. On the other hand, a recent Bayes-optimal method improves the performance, but is computationally intractable in practice. Here we present a novel double-Monte Carlo scheme (M2CC), both for finding a good chain sequence and performing efficient inference. The M2CC algorithm remains tractable for high-dimensional data sets and obtains the best overall accuracy, as shown on several real data sets with input dimension as high as 1449 and up to 103 labels.

Knowledge-based analysis of microarray gene expression data by using support vector machines

We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). SVMs are considered a supervised computer learning method because they exploit prior knowledge of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and self-organizing maps. SVMs have many mathematical features that make them attractive for gene expression analysis, including their flexibility in choosing a similarity function, sparseness of solution when dealing with large data sets, the ability to handle large feature spaces, and the ability to identify outliers. We test several SVMs that use different similarity metrics, as well as some other supervised learning methods, and find that the SVMs best identify sets of genes with a common function using expression data. Finally, we use SVMs to predict functional roles for uncharacterized yeast ORFs based on their expression data.

Aplicaciones de procesamiento de lenguaje natural

El campo de procesamiento de lenguaje natural (PLN), ha tenido un gran crecimiento en los últimos años; sus áreas de investigación incluyen: recuperación y extracción de información, minería de datos, traducción automática, sistemas de búsquedas de respuestas, generación de resúmenes automáticos, análisis de sentimientos, entre otras. En este artículo se presentan conceptos y algunas herramientas con el fin de contribuir al entendimiento del procesamiento de texto con técnicas de PLN, con el propósito de extraer información relevante que pueda ser usada en un gran rango de aplicaciones. Se pueden desarrollar clasificadores automáticos que permitan categorizar documentos y recomendar etiquetas; estos clasificadores deben ser independientes de la plataforma, fácilmente personalizables para poder ser integrados en diferentes proyectos y que sean capaces de aprender a partir de ejemplos. En el presente artículo se introducen estos algoritmos de clasificación, se analizan algunas herramientas de código abierto disponibles actualmente para llevar a cabo estas tareas y se comparan diversas implementaciones utilizando la métrica F en la evaluación de los clasificadores.

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.