Imbalance Learning and Its Application on Medical Datasets

To gain more valuable information from the increasing large amount of data, data mining has been a hot topic that attracts growing attention in this two decades. One of the challenges in data mining is imbalance learning, which refers to leaning from imbalanced datasets. The imbalanced datasets is dominated by some classes (majority) and other under-represented classes (minority). The imbalanced datasets degrade the learning ability of traditional methods, which are designed on the assumption that all classes are balanced and have equal misclassification costs, leading to the poor performance on the minority classes. This phenomenon is usually called the class imbalance problem. However, it is usually the minority classes of more interest and importance, such as sick cases in the medical dataset. Additionally, traditional methods are optimized to achieve maximum accuracy, which is not suitable for evaluating the performance on imbalanced datasets. From the view of data space, class imbalance could be classified as extrinsic imbalance and intrinsic imbalance. Extrinsic imbalance is caused by external factors, such as data transmission or data storage, while intrinsic imbalance means the dataset is inherently imbalanced due to its nature.  As extrinsic imbalance could be fixed by collecting more samples, this thesis mainly focus on on two scenarios of the intrinsic imbalance,  machine learning for imbalanced structured datasets and deep learning for imbalanced image datasets.  Normally, the solutions for the class imbalance problem are named as imbalance learning methods, which could be grouped into data-level methods (re-sampling), algorithm-level (re-weighting) methods and hybrid methods. Data-level methods modify the class distribution of the training dataset to create balanced training sets, and typical examples are over-sampling and under-sampling. Instead of modifying the data distribution, algorithm-level methods adjust the misclassification cost to alleviate the class imbalance problem, and one typical example is cost sensitive methods. Hybrid methods usually combine data-level methods and algorithm-level methods. However, existing imbalance learning methods encounter different kinds of problems. Over-sampling methods increase the minority samples to create balanced training sets, which might lead the trained model overfit to the minority class. Under-sampling methods create balanced training sets by discarding majority samples, which lead to the information loss and poor performance of the trained model. Cost-sensitive methods usually need assistance from domain expert to define the misclassification costs which are task specified. Thus, the generalization ability of cost-sensitive methods is poor. Especially, when it comes to the deep learning methods under class imbalance, re-sampling methods may introduce large computation cost and existing re-weighting methods could lead to poor performance. The object of this dissertation is to understand features difference under class imbalance, to improve the classification performance on structured datasets or image datasets. This thesis proposes two machine learning methods for imbalanced structured datasets and one deep learning method for imbalance image datasets. The proposed methods are evaluated on several medical datasets, which are intrinsically imbalanced.  Firstly, we study the feature difference between the majority class and the minority class of an imbalanced medical dataset, which is collected from a Chinese hospital. After data cleaning and structuring, we get 3292 kidney stone cases treated by Percutaneous Nephrolithonomy from 2012 to 2019. There are 651 (19.78% ) cases who have postoperative complications, which makes the complication prediction an imbalanced classification task. We propose a sampling-based method SMOTE-XGBoost and implement it to build a postoperative complication prediction model. Experimental results show that the proposed method outperforms classic machine learning methods. Furthermore, traditional prediction models of Percutaneous Nephrolithonomy are designed to predict the kidney stone status and overlook complication related features, which could degrade their prediction performance on complication prediction tasks. To this end, we merge more features into the proposed sampling-based method and further improve the classification performance. Overall, SMOTE-XGBoost achieves an AUC of 0.7077 which is 41.54% higher than that of S.T.O.N.E. nephrolithometry, a traditional prediction model of Percutaneous Nephrolithonomy. After reviewing the existing machine learning methods under class imbalance, we propose a novel ensemble learning approach called Multiple bAlance Subset Stacking (MASS). MASS first cuts the majority class into multiple subsets by the size of the minority set, and combines each majority subset with the minority set as one balanced subsets. In this way, MASS could overcome the problem of information loss because it does not discard any majority sample. Each balanced subset is used to train one base classifier. Then, the original dataset is feed to all the trained base classifiers, whose output are used to generate the stacking dataset. One stack model is trained by the staking dataset to get the optimal weights for the base classifiers. As the stacking dataset keeps the same labels as the original dataset, which could avoid the overfitting problem. Finally, we can get an ensembled strong model based on the trained base classifiers and the staking model. Extensive experimental results on three medical datasets show that MASS outperforms baseline methods.  The robustness of MASS is proved over implementing different base classifiers. We design a parallel version MASS to reduce the training time cost. The speedup analysis proves that Parallel MASS could reduce training time cost greatly when applied on large datasets. Specially, Parallel MASS reduces 101.8% training time compared with MASS at most in our experiments.  When it comes to the class imbalance problem of image datasets, existing imbalance learning methods suffer from the problem of large training cost and poor performance.  After introducing the problem of implementing resampling methods on image classification tasks, we demonstrate issues of re-weighting strategy using class frequencies through the experimental result on one medical image dataset.  We propose a novel re-weighting method Hardness Aware Dynamic loss to solve the class imbalance problem of image datasets. After each training epoch of deep neural networks, we compute the classification hardness of each class. We will assign higher class weights to the classes have large classification hardness values and vice versa in the next epoch. In this way, HAD could tune the weight of each sample in the loss function dynamically during the training process. The experimental results prove that HAD significantly outperforms the state-of-the-art methods. Moreover, HAD greatly improves the classification accuracies of minority classes while only making a small compromise of majority class accuracies. Especially, HAD loss improves 10.04% average precision compared with the best baseline, Focal loss, on the HAM10000 dataset. At last, I conclude this dissertation with our contributions to the imbalance learning, and provide an overview of potential directions for future research, which include extensions of the three proposed methods, development of task-specified algorithms, and fixing the challenges of within-class imbalance.2021-06-0

Learning from small and imbalanced dataset of images using generative adversarial neural networks.

The performance of deep learning models is unmatched by any other approach in supervised computer vision tasks such as image classification. However, training these models requires a lot of labeled data, which are not always available. Labelling a massive dataset is largely a manual and very demanding process. Thus, this problem has led to the development of techniques that bypass the need for labelling at scale. Despite this, existing techniques such as transfer learning, data augmentation and semi-supervised learning have not lived up to expectations. Some of these techniques do not account for other classification challenges, such as a class-imbalance problem. Thus, these techniques mostly underperform when compared with fully supervised approaches. In this thesis, we propose new methods to train a deep model on image classification with a limited number of labeled examples. This was achieved by extending state-of-the-art generative adversarial networks with multiple fake classes and network switchers. These new features enabled us to train a classifier using large unlabeled data, while generating class specific samples. The proposed model is label agnostic and is suitable for different classification scenarios, ranging from weakly supervised to fully supervised settings. This was used to address classification challenges with limited labeled data and a class-imbalance problem. Extensive experiments were carried out on different benchmark datasets. Firstly, the proposed approach was used to train a classification model and our findings indicated that the proposed approach achieved better classification accuracies, especially when the number of labeled samples is small. Secondly, the proposed approach was able to generate high-quality samples from class-imbalance datasets. The samples' quality is evident in improved classification performances when generated samples were used in neutralising class-imbalance. The results are thoroughly analyzed and, overall, our method showed superior performances over popular resampling technique and the AC-GAN model. Finally, we successfully applied the proposed approach as a new augmentation technique to two challenging real-world problems: face with attributes and legacy engineering drawings. The results obtained demonstrate that the proposed approach is effective even in extreme cases

Seleção de embriões pela análise de imagens: uma abordagem Deep Learning

Infertility affects about 186 million people worldwide and 9-10% of couples in Portugal, causing financial, social and medical problems. Evaluation of embryo quality based morphological features is the standard in vitro fertilization (IVF) clinics around the world. This process is subjective and time-consuming, and results in discrepant classifications among embryologists and clinics, leading to fail in predict accurately embryo implantation and live birth potential. Although assisted reproductive technologies (ART) such as IVF coupled with time lapse elimination of periodic transfer to microscopy assessment and stable embryo culture conditions for embryos development, has alleviated the infertility problem, there are significant limitations even considering morphokinetic analysis. Likewise, many patients require multiple IVF cycles to achieve pregnancy, making the selection of single embryo for transfer a critical challenge. Here, we demonstrate the reliability of machine learning, especially deep learning based on TensorFlow open source and Keras libraries for embryo raw TLI images features extraction and classification in clinical practice. Equally, we present a follow up pipeline for clinicians and researchers, with no expertise in machine learning, to easily, rapid and accurately utilize deep learning as a clinical decision support tool in embryos viability studies, as well in other medical field where the analysis of images is preeminentA infertilidade afeta cerca de 186 milhões de pessoas em todo o mundo e 9-10% dos casais em Portugal, causando problemas financeiros, sociais e de saúde. Constitui procedimento padrão a avaliação da qualidade dos embriões baseadas em características morfológicas. No entanto, tais avaliações são subjetivas e demoradas e resultam em classificações discrepantes entre embriologistas e clínicas causando problemas na avaliação do potencial do embrião. Embora as tecnologias de reprodução medicamente assistida, como a fertilização in vitro, acoplada à tecnologia time-lapse, tenham diminuído o problema da infertilidade, existem limitações significativas, mesmo considerando a análise morfocinética. Outrossim, muitas pacientes necessitam de múltiplos ciclos de fertilização para alcançar a gravidez, tornando a seleção do embrião com maior potencial de implantação e geração de nados vivos um desafio crítico. No presente projeto demonstramos a prova do conceito da confiabilidade de Machine Learning (aprendizagem automática), especialmente Deep Learning baseado em TensorFlow e Keras, para extrair e discriminar caraterísticas associadas ao potencial embrionário, em imagens time-lapse. Igualmente, apresentamos um pipeline para que clínicos e investigadores, sem experiência em Machine Learning, possam utilizar com facilidade, rapidez e precisão Deep Learning como ferramenta de apoio à decisão clínica em estudos de viabilidade de embriões, bem como noutras áreas médicas onde a análise de imagens seja proeminenteMestrado em Biologia Molecular e Celula

The Role of Synthetic Data in Improving Supervised Learning Methods: The Case of Land Use/Land Cover Classification

A thesis submitted in partial fulfillment of the requirements for the degree of Doctor in Information ManagementIn remote sensing, Land Use/Land Cover (LULC) maps constitute important assets for various applications, promoting environmental sustainability and good resource management. Although, their production continues to be a challenging task. There are various factors that contribute towards the difficulty of generating accurate, timely updated LULC maps, both via automatic or photo-interpreted LULC mapping. Data preprocessing, being a crucial step for any Machine Learning task, is particularly important in the remote sensing domain due to the overwhelming amount of raw, unlabeled data continuously gathered from multiple remote sensing missions. However a significant part of the state-of-the-art focuses on scenarios with full access to labeled training data with relatively balanced class distributions. This thesis focuses on the challenges found in automatic LULC classification tasks, specifically in data preprocessing tasks. We focus on the development of novel Active Learning (AL) and imbalanced learning techniques, to improve ML performance in situations with limited training data and/or the existence of rare classes. We also show that much of the contributions presented are not only successful in remote sensing problems, but also in various other multidisciplinary classification problems. The work presented in this thesis used open access datasets to test the contributions made in imbalanced learning and AL. All the data pulling, preprocessing and experiments are made available at https://github.com/joaopfonseca/publications. The algorithmic implementations are made available in the Python package ml-research at https://github.com/joaopfonseca/ml-research

BagStack Classification for Data Imbalance Problems with Application to Defect Detection and Labeling in Semiconductor Units

abstract: Despite the fact that machine learning supports the development of computer vision applications by shortening the development cycle, finding a general learning algorithm that solves a wide range of applications is still bounded by the ”no free lunch theorem”. The search for the right algorithm to solve a specific problem is driven by the problem itself, the data availability and many other requirements. Automated visual inspection (AVI) systems represent a major part of these challenging computer vision applications. They are gaining growing interest in the manufacturing industry to detect defective products and keep these from reaching customers. The process of defect detection and classification in semiconductor units is challenging due to different acceptable variations that the manufacturing process introduces. Other variations are also typically introduced when using optical inspection systems due to changes in lighting conditions and misalignment of the imaged units, which makes the defect detection process more challenging. In this thesis, a BagStack classification framework is proposed, which makes use of stacking and bagging concepts to handle both variance and bias errors. The classifier is designed to handle the data imbalance and overfitting problems by adaptively transforming the multi-class classification problem into multiple binary classification problems, applying a bagging approach to train a set of base learners for each specific problem, adaptively specifying the number of base learners assigned to each problem, adaptively specifying the number of samples to use from each class, applying a novel data-imbalance aware cross-validation technique to generate the meta-data while taking into account the data imbalance problem at the meta-data level and, finally, using a multi-response random forest regression classifier as a meta-classifier. The BagStack classifier makes use of multiple features to solve the defect classification problem. In order to detect defects, a locally adaptive statistical background modeling is proposed. The proposed BagStack classifier outperforms state-of-the-art image classification techniques on our dataset in terms of overall classification accuracy and average per-class classification accuracy. The proposed detection method achieves high performance on the considered dataset in terms of recall and precision.Dissertation/ThesisDoctoral Dissertation Computer Engineering 201

An Empirical Study on the Joint Impact of Feature Selection and Data Re-sampling on Imbalance Classification

In predictive tasks, real-world datasets often present di erent degrees of imbalanced (i.e., long-tailed or skewed) distributions. While the majority (the head or the most frequent) classes have su cient samples, the minority (the tail or the less frequent or rare) classes can be under-represented by a rather limited number of samples. Data pre-processing has been shown to be very e ective in dealing with such problems. On one hand, data re-sampling is a common approach to tackling class imbalance. On the other hand, dimension reduction, which reduces the feature space, is a conventional technique for reducing noise and inconsistencies in a dataset. However, the possible synergy between feature selection and data re-sampling for high-performance imbalance classification has rarely been investigated before. To address this issue, we carry out a comprehensive empirical study on the joint influence of feature selection and re-sampling on two-class imbalance classification. Specifically, we study the performance of two opposite pipelines for imbalance classification by applying feature selection before or after data re-sampling. We conduct a large number of experiments, with a total of 9225 tests, on 52 publicly available datasets, using 9 feature selection methods, 6 resampling approaches for class imbalance learning, and 3 well-known classification algorithms. Experimental results show that there is no constant winner between the two pipelines; thus both of them should be considered to derive the best performing model for imbalance classification. We find that the performance of an imbalance classification model not only depends on the classifier adopted and the ratio between the number of majority and minority samples, but also depends on the ratio between the number of samples and features. Overall, this study should provide new reference value for researchers and practitioners in imbalance learning.TIN2017-89517-

A survey on generative adversarial networks for imbalance problems in computer vision tasks

Any computer vision application development starts off by acquiring images and data, then preprocessing and pattern recognition steps to perform a task. When the acquired images are highly imbalanced and not adequate, the desired task may not be achievable. Unfortunately, the occurrence of imbalance problems in acquired image datasets in certain complex real-world problems such as anomaly detection, emotion recognition, medical image analysis, fraud detection, metallic surface defect detection, disaster prediction, etc., are inevitable. The performance of computer vision algorithms can significantly deteriorate when the training dataset is imbalanced. In recent years, Generative Adversarial Neural Networks (GANs) have gained immense attention by researchers across a variety of application domains due to their capability to model complex real-world image data. It is particularly important that GANs can not only be used to generate synthetic images, but also its fascinating adversarial learning idea showed good potential in restoring balance in imbalanced datasets. In this paper, we examine the most recent developments of GANs based techniques for addressing imbalance problems in image data. The real-world challenges and implementations of synthetic image generation based on GANs are extensively covered in this survey. Our survey first introduces various imbalance problems in computer vision tasks and its existing solutions, and then examines key concepts such as deep generative image models and GANs. After that, we propose a taxonomy to summarize GANs based techniques for addressing imbalance problems in computer vision tasks into three major categories: 1. Image level imbalances in classification, 2. object level imbalances in object detection and 3. pixel level imbalances in segmentation tasks. We elaborate the imbalance problems of each group, and provide GANs based solutions in each group. Readers will understand how GANs based techniques can handle the problem of imbalances and boost performance of the computer vision algorithms

Intelligent Data Analytics using Deep Learning for Data Science

Nowadays, data science stimulates the interest of academics and practitioners because it can assist in the extraction of significant insights from massive amounts of data. From the years 2018 through 2025, the Global Datasphere is expected to rise from 33 Zettabytes to 175 Zettabytes, according to the International Data Corporation. This dissertation proposes an intelligent data analytics framework that uses deep learning to tackle several difficulties when implementing a data science application. These difficulties include dealing with high inter-class similarity, the availability and quality of hand-labeled data, and designing a feasible approach for modeling significant correlations in features gathered from various data sources. The proposed intelligent data analytics framework employs a novel strategy for improving data representation learning by incorporating supplemental data from various sources and structures. First, the research presents a multi-source fusion approach that utilizes confident learning techniques to improve the data quality from many noisy sources. Meta-learning methods based on advanced techniques such as the mixture of experts and differential evolution combine the predictive capacity of individual learners with a gating mechanism, ensuring that only the most trustworthy features or predictions are integrated to train the model. Then, a Multi-Level Convolutional Fusion is presented to train a model on the correspondence between local-global deep feature interactions to identify easily confused samples of different classes. The convolutional fusion is further enhanced with the power of Graph Transformers, aggregating the relevant neighboring features in graph-based input data structures and achieving state-of-the-art performance on a large-scale building damage dataset. Finally, weakly-supervised strategies, noise regularization, and label propagation are proposed to train a model on sparse input labeled data, ensuring the model\u27s robustness to errors and supporting the automatic expansion of the training set. The suggested approaches outperformed competing strategies in effectively training a model on a large-scale dataset of 500k photos, with just about 7% of the images annotated by a human. The proposed framework\u27s capabilities have benefited various data science applications, including fluid dynamics, geometric morphometrics, building damage classification from satellite pictures, disaster scene description, and storm-surge visualization

Machine learning algorithms for monitoring pavement performance

ABSTRACT: This work introduces the need to develop competitive, low-cost and applicable technologies to real roads to detect the asphalt condition by means of Machine Learning (ML) algorithms. Specifically, the most recent studies are described according to the data collection methods: images, ground penetrating radar (GPR), laser and optic fiber. The main models that are presented for such state-of-the-art studies are Support Vector Machine, Random Forest, Naïve Bayes, Artificial neural networks or Convolutional Neural Networks. For these analyses, the methodology, type of problem, data source, computational resources, discussion and future research are highlighted. Open data sources, programming frameworks, model comparisons and data collection technologies are illustrated to allow the research community to initiate future investigation. There is indeed research on ML-based pavement evaluation but there is not a widely used applicability by pavement management entities yet, so it is mandatory to work on the refinement of models and data collection methods