Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Deep Neural Networks based Meta-Learning for Network Intrusion Detection

The digitization of different components of industry and inter-connectivity among indigenous networks have increased the risk of network attacks. Designing an intrusion detection system to ensure security of the industrial ecosystem is difficult as network traffic encompasses various attack types, including new and evolving ones with minor changes. The data used to construct a predictive model for computer networks has a skewed class distribution and limited representation of attack types, which differ from real network traffic. These limitations result in dataset shift, negatively impacting the machine learning models' predictive abilities and reducing the detection rate against novel attacks. To address the challenges, we propose a novel deep neural network based Meta-Learning framework; INformation FUsion and Stacking Ensemble (INFUSE) for network intrusion detection. First, a hybrid feature space is created by integrating decision and feature spaces. Five different classifiers are utilized to generate a pool of decision spaces. The feature space is then enriched through a deep sparse autoencoder that learns the semantic relationships between attacks. Finally, the deep Meta-Learner acts as an ensemble combiner to analyze the hybrid feature space and make a final decision. Our evaluation on stringent benchmark datasets and comparison to existing techniques showed the effectiveness of INFUSE with an F-Score of 0.91, Accuracy of 91.6%, and Recall of 0.94 on the Test+ dataset, and an F-Score of 0.91, Accuracy of 85.6%, and Recall of 0.87 on the stringent Test-21 dataset. These promising results indicate the strong generalization capability and the potential to detect network attacks.Comment: Pages: 15, Figures: 10 and Tables:

Overlap-based undersampling method for classification of imbalanced medical datasets.

Early diagnosis of some life-threatening diseases such as cancers and heart is crucial for effective treatments. Supervised machine learning has proved to be a very useful tool to serve this purpose. Historical data of patients including clinical and demographic information is used for training learning algorithms. This builds predictive models that provide initial diagnoses. However, in the medical domain, it is common to have the positive class under-represented in a dataset. In such a scenario, a typical learning algorithm tends to be biased towards the negative class, which is the majority class, and misclassify positive cases. This is known as the class imbalance problem. In this paper, a framework for predictive diagnostics of diseases with imbalanced records is presented. To reduce the classification bias, we propose the usage of an overlap-based undersampling method to improve the visibility of minority class samples in the region where the two classes overlap. This is achieved by detecting and removing negative class instances from the overlapping region. This will improve class separability in the data space. Experimental results show achievement of high accuracy in the positive class, which is highly preferable in the medical domain, while good trade-offs between sensitivity and specificity were obtained. Results also show that the method often outperformed other state-of-the-art and well-established techniques

Computer vision and machine learning for medical image analysis: recent advances, challenges, and way forward.

The recent development in the areas of deep learning and deep convolutional neural networks has significantly progressed and advanced the field of computer vision (CV) and image analysis and understanding. Complex tasks such as classifying and segmenting medical images and localising and recognising objects of interest have become much less challenging. This progress has the potential of accelerating research and deployment of multitudes of medical applications that utilise CV. However, in reality, there are limited practical examples being physically deployed into front-line health facilities. In this paper, we examine the current state of the art in CV as applied to the medical domain. We discuss the main challenges in CV and intelligent data-driven medical applications and suggest future directions to accelerate research, development, and deployment of CV applications in health practices. First, we critically review existing literature in the CV domain that addresses complex vision tasks, including: medical image classification; shape and object recognition from images; and medical segmentation. Second, we present an in-depth discussion of the various challenges that are considered barriers to accelerating research, development, and deployment of intelligent CV methods in real-life medical applications and hospitals. Finally, we conclude by discussing future directions

Automatic Brain Tumor Segmentation using Cascaded Anisotropic Convolutional Neural Networks

A cascade of fully convolutional neural networks is proposed to segment multi-modal Magnetic Resonance (MR) images with brain tumor into background and three hierarchical regions: whole tumor, tumor core and enhancing tumor core. The cascade is designed to decompose the multi-class segmentation problem into a sequence of three binary segmentation problems according to the subregion hierarchy. The whole tumor is segmented in the first step and the bounding box of the result is used for the tumor core segmentation in the second step. The enhancing tumor core is then segmented based on the bounding box of the tumor core segmentation result. Our networks consist of multiple layers of anisotropic and dilated convolution filters, and they are combined with multi-view fusion to reduce false positives. Residual connections and multi-scale predictions are employed in these networks to boost the segmentation performance. Experiments with BraTS 2017 validation set show that the proposed method achieved average Dice scores of 0.7859, 0.9050, 0.8378 for enhancing tumor core, whole tumor and tumor core, respectively. The corresponding values for BraTS 2017 testing set were 0.7831, 0.8739, and 0.7748, respectively.Comment: 12 pages, 5 figures. MICCAI Brats Challenge 201

A deep learning framework to classify breast density with noisy labels regularization

Background and objective: Breast density assessed from digital mammograms is a biomarker for higher risk of developing breast cancer. Experienced radiologists assess breast density using the Breast Image and Data System (BI-RADS) categories. Supervised learning algorithms have been developed with this objective in mind, however, the performance of these algorithms depends on the quality of the ground-truth information which is usually labeled by expert readers. These labels are noisy approximations of the ground truth, as there is often intra- and inter-reader variability among labels. Thus, it is crucial to provide a reliable method to obtain digital mammograms matching BI-RADS categories. This paper presents RegL (Labels Regularizer), a methodology that includes different image pre-processes to allow both a correct breast segmentation and the enhancement of image quality through an intensity adjustment, thus allowing the use of deep learning to classify the mammograms into BI-RADS categories. The Confusion Matrix (CM) - CNN network used implements an architecture that models each radiologist's noisy label. The final methodology pipeline was determined after comparing the performance of image pre-processes combined with different DL architectures. Methods: A multi-center study composed of 1395 women whose mammograms were classified into the four BI-RADS categories by three experienced radiologists is presented. A total of 892 mammograms were used as the training corpus, 224 formed the validation corpus, and 279 the test corpus. Results: The combination of five networks implementing the RegL methodology achieved the best results among all the models in the test set. The ensemble model obtained an accuracy of (0.85) and a kappa index of 0.71. Conclusions: The proposed methodology has a similar performance to the experienced radiologists in the classification of digital mammograms into BI-RADS categories. This suggests that the pre-processing steps and modelling of each radiologist's label allows for a better estimation of the unknown ground truth labels.This work was partially funded by Generalitat Valenciana through IVACE (Valencian Institute of Business Competitiveness) distributed nominatively to Valencian technological innovation centres under project expedient IMAMCN/2021/1.S

A Modified LeNet CNN for Breast Cancer Diagnosis in Ultrasound Images

Convolutional neural networks (CNNs) have been extensively utilized in medical image processing to automatically extract meaningful features and classify various medical conditions, enabling faster and more accurate diagnoses. In this paper, LeNet, a classic CNN architecture, has been successfully applied to breast cancer data analysis. It demonstrates its ability to extract discriminative features and classify malignant and benign tumors with high accuracy, thereby supporting early detection and diagnosis of breast cancer. LeNet with corrected Rectified Linear Unit (ReLU), a modification of the traditional ReLU activation function, has been found to improve the performance of LeNet in breast cancer data analysis tasks via addressing the “dying ReLU” problem and enhancing the discriminative power of the extracted features. This has led to more accurate, reliable breast cancer detection and diagnosis and improved patient outcomes. Batch normalization improves the performance and training stability of small and shallow CNN architecture like LeNet. It helps to mitigate the effects of internal covariate shift, which refers to the change in the distribution of network activations during training. This classifier will lessen the overfitting problem and reduce the running time. The designed classifier is evaluated against the benchmarking deep learning models, proving that this has produced a higher recognition rate. The accuracy of the breast image recognition rate is 89.91%. This model will achieve better performance in segmentation, feature extraction, classification, and breast cancer tumor detection