DATA MINING AND IMAGE CLASSIFICATION USING GENETIC PROGRAMMING

Genetic programming (GP), a capable machine learning and search method, motivated by Darwinian-evolution, is an evolutionary learning algorithm which automatically evolves computer programs in the form of trees to solve problems. This thesis studies the application of GP for data mining and image processing. Knowledge discovery and data mining have been widely used in business, healthcare, and scientific fields. In data mining, classification is supervised learning that identifies new patterns and maps the data to predefined targets. A GP based classifier is developed in order to perform these mappings. GP has been investigated in a series of studies to classify data; however, there are certain aspects which have not formerly been studied. We propose an optimized GP classifier based on a combination of pruning subtrees and a new fitness function. An orthogonal least squares algorithm is also applied in the training phase to create a robust GP classifier. The proposed GP classifier is validated by 10-fold cross validation. Three areas were studied in this thesis. The first investigation resulted in an optimized genetic-programming-based classifier that directly solves multi-class classification problems. Instead of defining static thresholds as boundaries to differentiate between multiple labels, our work presents a method of classification where a GP system learns the relationships among experiential data and models them mathematically during the evolutionary process. Our approach has been assessed on six multiclass datasets. The second investigation was to develop a GP classifier to segment and detect brain tumors on magnetic resonance imaging (MRI) images. The findings indicated the high accuracy of brain tumor classification provided by our GP classifier. The results confirm the strong ability of the developed technique for complicated image classification problems. The third was to develop a hybrid system for multiclass imbalanced data classification using GP and SMOTE which was tested on satellite images. The finding showed that the proposed approach improves both training and test results when the SMOTE technique is incorporated. We compared our approach in terms of speed with previous GP algorithms as well. The analyzed results illustrate that the developed classifier produces a productive and rapid method for classification tasks that outperforms the previous methods for more challenging multiclass classification problems. We tested the approaches presented in this thesis on publicly available datasets, and images. The findings were statistically tested to conclude the robustness of the developed approaches

Deep Learning Models for Predicting Phenotypic Traits and Diseases from Omics Data

Computational analysis of high-throughput omics data, such as gene expressions, copy number alterations and DNA methylation (DNAm), has become popular in disease studies in recent decades because such analyses can be very helpful to predict whether a patient has certain disease or its subtypes. However, due to the high-dimensional nature of the data sets with hundreds of thousands of variables and very small number of samples, traditional machine learning approaches, such as support vector machines (SVMs) and random forests, have limitations to analyze these data efficiently. In this chapter, we reviewed the progress in applying deep learning algorithms to solve some biological questions. The focus is on potential software tools and public data sources for the tasks. Particularly, we show some case studies using deep neural network (DNN) models for classifying molecular subtypes of breast cancer and DNN-based regression models to account for interindividual variation in triglyceride concentrations measured at different visits of peripheral blood samples using DNAm profiles. We show that integration of multi-omics profiles into DNN-based learning methods could improve the prediction of the molecular subtypes of breast cancer. We also demonstrate the superiority of our proposed DNN models over the SVM model for predicting triglyceride concentrations

Biomedical Data Classification with Improvised Deep Learning Architectures

With the rise of very powerful hardware and evolution of deep learning architectures, healthcare data analysis and its applications have been drastically transformed. These transformations mainly aim to aid a healthcare personnel with diagnosis and prognosis of a disease or abnormality at any given point of healthcare routine workflow. For instance, many of the cancer metastases detection depends on pathological tissue procedures and pathologist reviews. The reports of severity classification vary amongst different pathologist, which then leads to different treatment options for a patient. This labor-intensive work can lead to errors or mistreatments resulting in high cost of healthcare. With the help of machine learning and deep learning modules, some of these traditional diagnosis techniques can be improved and aid a doctor in decision making with an unbiased view. Some of such modules can help reduce the cost, shortage of an expertise, and time in identifying the disease. However, there are many other datapoints that are available with medical images, such as omics data, biomarker calculations, patient demographics and history. All these datapoints can enhance disease classification or prediction of progression with the help of machine learning/deep learning modules. However, it is very difficult to find a comprehensive dataset with all different modalities and features in healthcare setting due to privacy regulations. Hence in this thesis, we explore both medical imaging data with clinical datapoints as well as genomics datasets separately for classification tasks using combinational deep learning architectures. We use deep neural networks with 3D volumetric structural magnetic resonance images of Alzheimer Disease dataset for classification of disease. A separate study is implemented to understand classification based on clinical datapoints achieved by machine learning algorithms. For bioinformatics applications, sequence classification task is a crucial step for many metagenomics applications, however, requires a lot of preprocessing that requires sequence assembly or sequence alignment before making use of raw whole genome sequencing data, hence time consuming especially in bacterial taxonomy classification. There are only a few approaches for sequence classification tasks that mainly involve some convolutions and deep neural network. A novel method is developed using an intrinsic nature of recurrent neural networks for 16s rRNA sequence classification which can be adapted to utilize read sequences directly. For this classification task, the accuracy is improved using optimization techniques with a hybrid neural network

Neural Network Configurations Analysis for Multilevel Speech Pattern Recognition System with Mixture of Experts

This chapter proposes to analyze two configurations of neural networks to compose the expert set in the development of a multilevel speech signal pattern recognition system of 30 commands in the Brazilian Portuguese language. Then, multilayer perceptron (MLP) and learning vector quantization (LVQ) networks have their performances verified during the training, validation and test stages in the speech signal recognition, whose patterns are given by two-dimensional time matrices, result from mel-cepstral coefficients coding by the discrete cosine transform (DCT). In order to avoid the pattern separability problem, the patterns are modified by a nonlinear transformation to a high-dimensional space through a suitable set of Gaussian radial base functions (GRBF). The performance of MLP and LVQ experts is improved and configurations are trained with few examples of each modified pattern. Several combinations were performed for the neural network topologies and algorithms previously established to determine the network structures with the best hit and generalization results

Smartphone-based human activity recognition

Cotutela Universitat Politècnica de Catalunya i Università degli Studi di GenovaHuman Activity Recognition (HAR) is a multidisciplinary research field that aims to gather data regarding people's behavior and their interaction with the environment in order to deliver valuable context-aware information. It has nowadays contributed to develop human-centered areas of study such as Ambient Intelligence and Ambient Assisted Living, which concentrate on the improvement of people's Quality of Life. The first stage to accomplish HAR requires to make observations from ambient or wearable sensor technologies. However, in the second case, the search for pervasive, unobtrusive, low-powered, and low-cost devices for achieving this challenging task still has not been fully addressed. In this thesis, we explore the use of smartphones as an alternative approach for performing the identification of physical activities. These self-contained devices, which are widely available in the market, are provided with embedded sensors, powerful computing capabilities and wireless communication technologies that make them highly suitable for this application. This work presents a series of contributions regarding the development of HAR systems with smartphones. In the first place we propose a fully operational system that recognizes in real-time six physical activities while also takes into account the effects of postural transitions that may occur between them. For achieving this, we cover some research topics from signal processing and feature selection of inertial data, to Machine Learning approaches for classification. We employ two sensors (the accelerometer and the gyroscope) for collecting inertial data. Their raw signals are the input of the system and are conditioned through filtering in order to reduce noise and allow the extraction of informative activity features. We also emphasize on the study of Support Vector Machines (SVMs), which are one of the state-of-the-art Machine Learning techniques for classification, and reformulate various of the standard multiclass linear and non-linear methods to find the best trade off between recognition performance, computational costs and energy requirements, which are essential aspects in battery-operated devices such as smartphones. In particular, we propose two multiclass SVMs for activity classification:one linear algorithm which allows to control over dimensionality reduction and system accuracy; and also a non-linear hardware-friendly algorithm that only uses fixed-point arithmetic in the prediction phase and enables a model complexity reduction while maintaining the system performance. The efficiency of the proposed system is verified through extensive experimentation over a HAR dataset which we have generated and made publicly available. It is composed of inertial data collected from a group of 30 participants which performed a set of common daily activities while carrying a smartphone as a wearable device. The results achieved in this research show that it is possible to perform HAR in real-time with a precision near 97\% with smartphones. In this way, we can employ the proposed methodology in several higher-level applications that require HAR such as ambulatory monitoring of the disabled and the elderly during periods above five days without the need of a battery recharge. Moreover, the proposed algorithms can be adapted to other commercial wearable devices recently introduced in the market (e.g. smartwatches, phablets, and glasses). This will open up new opportunities for developing practical and innovative HAR applications.El Reconocimiento de Actividades Humanas (RAH) es un campo de investigación multidisciplinario que busca recopilar información sobre el comportamiento de las personas y su interacción con el entorno con el propósito de ofrecer información contextual de alta significancia sobre las acciones que ellas realizan. Recientemente, el RAH ha contribuido en el desarrollo de áreas de estudio enfocadas a la mejora de la calidad de vida del hombre tales como: la inteligència ambiental (Ambient Intelligence) y la vida cotidiana asistida por el entorno para personas dependientes (Ambient Assisted Living). El primer paso para conseguir el RAH consiste en realizar observaciones mediante el uso de sensores fijos localizados en el ambiente, o bien portátiles incorporados de forma vestible en el cuerpo humano. Sin embargo, para el segundo caso, aún se dificulta encontrar dispositivos poco invasivos, de bajo consumo energético, que permitan ser llevados a cualquier lugar, y de bajo costo. En esta tesis, nosotros exploramos el uso de teléfonos móviles inteligentes (Smartphones) como una alternativa para el RAH. Estos dispositivos, de uso cotidiano y fácilmente asequibles en el mercado, están dotados de sensores embebidos, potentes capacidades de cómputo y diversas tecnologías de comunicación inalámbrica que los hacen apropiados para esta aplicación. Nuestro trabajo presenta una serie de contribuciones en relación al desarrollo de sistemas para el RAH con Smartphones. En primera instancia proponemos un sistema que permite la detección de seis actividades físicas en tiempo real y que, además, tiene en cuenta las transiciones posturales que puedan ocurrir entre ellas. Con este fin, hemos contribuido en distintos ámbitos que van desde el procesamiento de señales y la selección de características, hasta algoritmos de Aprendizaje Automático (AA). Nosotros utilizamos dos sensores inerciales (el acelerómetro y el giroscopio) para la captura de las señales de movimiento de los usuarios. Estas han de ser procesadas a través de técnicas de filtrado para la reducción de ruido, segmentación y obtención de características relevantes en la detección de actividad. También hacemos énfasis en el estudio de Máquinas de soporte vectorial (MSV) que son uno de los algoritmos de AA más usados en la actualidad. Para ello reformulamos varios de sus métodos estándar (lineales y no lineales) con el propósito de encontrar la mejor combinación de variables que garanticen un buen desempeño del sistema en cuanto a precisión, coste computacional y requerimientos de energía, los cuales son aspectos esenciales en dispositivos portátiles con suministro de energía mediante baterías. En concreto, proponemos dos MSV multiclase para la clasificación de actividad: un algoritmo lineal que permite el balance entre la reducción de la dimensionalidad y la precisión del sistema; y asimismo presentamos un algoritmo no lineal conveniente para dispositivos con limitaciones de hardware que solo utiliza aritmética de punto fijo en la fase de predicción y que permite reducir la complejidad del modelo de aprendizaje mientras mantiene el rendimiento del sistema. La eficacia del sistema propuesto es verificada a través de una experimentación extensiva sobre la base de datos RAH que hemos generado y hecho pública en la red. Esta contiene la información inercial obtenida de un grupo de 30 participantes que realizaron una serie de actividades de la vida cotidiana en un ambiente controlado mientras tenían sujeto a su cintura un smartphone que capturaba su movimiento. Los resultados obtenidos en esta investigación demuestran que es posible realizar el RAH en tiempo real con una precisión cercana al 97%. De esta manera, podemos emplear la metodología propuesta en aplicaciones de alto nivel que requieran el RAH tales como monitorizaciones ambulatorias para personas dependientes (ej. ancianos o discapacitados) durante periodos mayores a cinco días sin la necesidad de recarga de baterías.Postprint (published version

Genetic Programming for Object Detection : a Two-Phase Approach with an Improved Fitness Function

This paper describes two innovations that improve the efficiency and effectiveness of a genetic programming approach to object detection problems. The approach uses genetic programming to construct object detection programs that are applied, in a moving window fashion, to the large images to locate the objects of interest. The first innovation is to break the GP search into two phases with the first phase applied to a selected subset of the training data, and a simplified fitness function. The second phase is initialised with the programs from the first phase, and uses the full set of training data with a complete fitness function to construct the final detection programs. The second innovation is to add a program size component to the fitness function. This approach is examined and compared with a neural network approach on three object detection problems of increasing difficulty. The results suggest that the innovations increase both the effectiveness and the efficiency of the genetic programming search, and also that the genetic programming approach outperforms a neural network approach for the most difficult data set in terms of the object detection accuracy

Visual Transfer Learning in the Absence of the Source Data

Image recognition has become one of the most popular topics in machine learning. With the development of Deep Convolutional Neural Networks (CNN) and the help of the large scale labeled image database such as ImageNet, modern image recognition models can achieve competitive performance compared to human annotation in some general image recognition tasks. Many IT companies have adopted it to improve their visual related tasks. However, training these large scale deep neural networks requires thousands or even millions of labeled images, which is an obstacle when applying it to a specific visual task with limited training data. Visual transfer learning is proposed to solve this problem. Visual transfer learning aims at transferring the knowledge from a source visual task to a target visual task. Typically, the target task is related to the source task, and the training data in the target task is relatively small. In visual transfer learning, the majority of existing methods assume that the source data is freely available and use the source data to measure the discrepancy between the source and target task to help the transfer process. However, in many real applications, source data are often a subject of legal, technical and contractual constraints between data owners and data customers. Beyond privacy and disclosure obligations, customers are often reluctant to share their data. When operating customer care, collected data may include information on recent technical problems which is a highly sensitive topic that companies are not willing to share. This scenario is often called Hypothesis Transfer Learning (HTL) where the source data is absent. Therefore, these previous methods cannot be applied to many real visual transfer learning problems. In this thesis, we investigate the visual transfer learning problem under HTL setting. Instead of using the source data to measure the discrepancy, we use the source model as the proxy to transfer the knowledge from the source task to the target task. Compared to the source data, the well-trained source model is usually freely accessible in many tasks and contains equivalent source knowledge as well. Specifically, in this thesis, we investigate the visual transfer learning in two scenarios: domain adaptation and learning new categories. In contrast to the previous methods in HTL, our methods can both leverage knowledge from more types of source models and achieve better transfer performance. In chapter 3, we investigate the visual domain adaptation problem under the setting of Hypothesis Transfer Learning. We propose Effective Multiclass Transfer Learning (EMTLe) that can effectively transfer the knowledge when the size of the target set is small. Specifically, EMTLe can effectively transfer the knowledge using the outputs of the source models as the auxiliary bias to adjust the prediction in the target task. Experiment results show that EMTLe can outperform other baselines under the setting of HTL. In chapter 4, we investigate the semi-supervised domain adaptation scenario under the setting of HTL and propose our framework Generalized Distillation Semi-supervised Domain Adaptation (GDSDA). Specifically, we show that GDSDA can effectively transfer the knowledge using the unlabeled data. We also demonstrate that the imitation parameter, the hyperparameter in GDSDA that balances the knowledge from source and target task, is important to the transfer performance. Then we propose GDSDA-SVM which uses SVMs as the base classifier in GDSDA. We show that GDSDA-SVM can determine the imitation parameter in GDSDA autonomously. Compared to previous methods, whose imitation parameter can only be determined by either brutal force search or background knowledge, GDSDA-SVM is more effective in real applications. In chapter 5, we investigate the problem of fine-tuning the deep CNN to learn new food categories using the large ImageNet database as our source. Without accessing to the source data, i.e. the ImageNet dataset, we show that by fine-tuning the parameters of the source model with our target food dataset, we can achieve better performance compared to those previous methods. To conclude, the main contribution of is that we investigate the visual transfer learning problem under the HTL setting. We propose several methods to transfer the knowledge from the source task in supervised and semi-supervised learning scenarios. Extensive experiments results show that without accessing to any source data, our methods can outperform previous work