Deep Learning Methods for Predicting Disease Status Using Genomic Data

Predicting disease status for a complex human disease using genomic data is an important, yet challenging, step in personalized medicine. Among many challenges, the so-called curse of dimensionality problem results in unsatisfied performances of many state-of-art machine learning algorithms. A major recent advance in machine learning is the rapid development of deep learning algorithms that can efficiently extract meaningful features from high-dimensional and complex datasets through a stacked and hierarchical learning process. Deep learning has shown breakthrough performance in several areas including image recognition, natural language processing, and speech recognition. However, the performance of deep learning in predicting disease status using genomic datasets is still not well studied. In this article, we performed a review on the four relevant articles that we found through our thorough literature review. All four articles used auto-encoders to project high-dimensional genomic data to a low dimensional space and then applied the state-of-the-art machine learning algorithms to predict disease status based on the low-dimensional representations. This deep learning approach outperformed existing prediction approaches, such as prediction based on probe-wise screening and prediction based on principal component analysis. The limitations of the current deep learning approach and possible improvements were also discussed.

In the era of digitalization, electronic gadgets such as Google Translate, Siri, and Alexa have at least one characteristic: They are all the products of natural language processing (NLP). “Natural Language” refers to a human language used for daily communication, such as English, Hindi, Bengali, etc. Natural languages, as opposed to artificial languages such as computer languages and mathematical nomenclature, have evolved as they have been transmitted from generation to generation and are challenging to explain with clear limits in the first instance. In natural language processing, artificial intelligence (Singh et al., 2021), linguistics, information processing, and cognitive science are all related fields (NLP). NLP aims to use intelligent computer techniques to process human language. However, NLP technologies such as voice recognition, language comprehension, and machine translation exist. With such limited obvious exclusions, machine learning algorithms in NLP sometimes lacked sufficient capacity to consume massive amounts of training data. In addition, the algorithms, techniques, and infrastructural facilities lack enough strength. Humans design features in traditional machine learning, and feature engineering is a limitation that requires significant human expertise. Simultaneously, the accompanying superficial algorithms lack depiction capability and, as a result, the ability to generate layers of duplicatable concepts that would naturally separate intricate aspects in forming visible linguistic data. Deep learning overcomes the challenges mentioned earlier by using deep, layered modelling architectures, often using neural networks and the corresponding full-stack learning methods. Deep learning has recently enhanced natural language processing by using artificial neural networks based on biological brain systems and Backpropagation. Deep learning approaches that use several processing layers to develop hierarchy data representations have produced cutting-edge results in various areas. This chapter introduces natural language processing (NLP) as an AI component. The history of NLP is next. Distributed language representations are the core of NLP's profound learning revolution. After the survey, the boundaries of deep learning for NLP are investigated. The paper proposes five NLP scientific fields.

In today's socio-economic scenario, people rely heavily on credit cards.Moreover, credit cards are a requisite financial tool that enables its holders to make assets.It is true that credit cards, as a new method of payment, have become socially amenable to the masses.But nowadays, improvements in technology lead to growth in illegal activities.During credit card transactions many fraudsters can breach security and make fraudulent transactions to withdraw or transfer funds from one's account or e-wallets.The relevant literature presents many machine learning-based approaches for credit card detection, such as Logistic Regression, Decision Tree, CatBoost, Random Forest, Support Vector Machine, KNN, RNN, and CNN.The main focus has been to apply the recent development of deep learning algorithms for this purpose.Comparative analysis of both machine learning and deep learning algorithms was performed to find efficient outcomes.A machine learning algorithm was first applied to the dataset, which improved the accuracy of detection of the fraud to some extent.The proposed approaches can be implemented effectively for the real-world detection of credit card fraud.

Objectives: Language detection is the process of identifying a language associated with a text. The proposed system aims to detect the Dravidian language that is associated with the given text using different machine learning and deep learning algorithms. The paper presents an empirical analysis of the results obtained using the different models. It also aims to evaluate the performance of a language agnostic model for the purpose of language detection. Method: An empirical analysis of Dravidian language identification in social media text using machine learning and deep learning approaches with k-fold cross validation has been implemented. The identification of Dravidian languages, including Tamil, Malayalam, Tamil Code Mix, and Malayalam Code Mix, is performed using both machine learning (ML) and deep learning algorithms. The machine learning algorithms used for language detection are Naive Bayes (NB), Multinomial Logistic Regression (MLR), Support Vector Machine (SVM), and Random Forest (RF). The supervised Deep Learning (DL) models used include BERT, mBERT and language agnostic models. Findings: The language agnostic model outperform all other models considering the task of language detection in Dravidian languages. The results of both the ML and DL models are analyzed empirically with performance measures like accuracy, precision, recall, and f1-score. The accuracy associated with different machine learning algorithms varies from 85% to 89%. It is evident from the experimental result that the deep learning model outperformed with an accuracy of 98%. Novelty: The proposed system emphasizes on the use of the language agnostic model to implement the process of detecting Dravidian languages associated with the given text which provides a promising result of 98% accuracy which is higher than the existing methodologies. Keywords: Language, Machine learning, Deep learning, Transformer model, Encoder, Decoder

The rapid development and progress in deep machine-learning techniques have become a key factor in solving the future challenges of humanity. Vision-based target detection and object classification have been improved due to the development of deep learning algorithms. Data fusion in autonomous driving is a fact and a prerequisite task of data preprocessing from multi-sensors that provide a precise, well-engineered, and complete detection of objects, scene or events. The target of the current study is to develop an in-vehicle information system to prevent or at least mitigate traffic issues related to parking detection and traffic congestion detection. In this study we examined to solve these problems described by (1) extracting region-of-interest in the images (2) vehicle detection based on instance segmentation, and (3) building deep learning model based on the key features obtained from input parking images. We build a deep machine learning algorithm that enables collecting real video-camera feeds from vision sensors and predicting free parking spaces. Image augmentation techniques were performed using edge detection, cropping, refined by rotating, thresholding, resizing, or color augment to predict the region of bounding boxes. A deep convolutional neural network F-MTCNN model is proposed that simultaneously capable for compiling, training, validating and testing on parking video frames through video-camera. The results of proposed model employing on publicly available PK-Lot parking dataset and the optimized model achieved a relatively higher accuracy 97.6% than previous reported methodologies. Moreover, this article presents mathematical and simulation results using state-of-the-art deep learning technologies for smart parking space detection. The results are verified using Python, TensorFlow, OpenCV computer simulation frameworks.

Deep learning (also known as deep structured learning, hierarchical learning, or deep machine learning) is a branch of machine learning based on a set of algorithms that attempt to model high-level abstractions in data by using a deep graph with multiple processing layers, composed of multiple linear and nonlinear transformations. Deep learning has been characterized as a class of machine learning algorithms with the following characteristics [257]: • They use a cascade of many layers of nonlinear processing units for feature extraction and transformation. Each successive layer uses the output from the previous layer as input. The algorithms may be supervised or unsupervised and applications include pattern analysis (unsupervised) and classification (supervised). • They are based on the (unsupervised) learning of multiple levels of features or representations of the data. Higher-level features are derived from lower-level features to form a hierarchical representation. • They are part of the broader machine learning field of learning representations of data. • They learn multiple levels of representations that correspond to different levels of abstraction; the levels form a hierarchy of concepts. These definitions have in common: multiple layers of nonlinear processing units and the supervised or unsupervised learning of feature representations in each layer, with the layers forming a hierarchy from low-level to high-level features. Various deep learning architectures such as deep neural networks, convolutional deep neural networks, deep belief networks (DBN), and recurrent neural networks have been applied to fields like computer vision, automatic speech recognition, natural language processing, audio recognition, and bioinformatics where they have been shown to produce state-of-the-art results on various tasks. In this chapter we start in Section 7.1 with an introduction, giving a brief history of this field, the relevant literature, and its applications. Then we study some basic concepts of deep learning such as convolutional neural networks, recurrent neural networks, backpropagation algorithm, restricted Boltzmann machines, and deep learning networks in Section 7.2. Then we illustrate three examples for Apache Spark implementation for mobile big data (MBD), user moving pattern extraction, and combination with nonparametric Bayesian learning, respectively, in Sections 7.3 through 7.5. Finally, we have summary in Section 7.6.

Aim: Machine learning (ML) and deep learning (DL) predictive models have been employed widely in clinical settings. Their potential support and aid to the clinician of providing an objective measure that can be shared among different centers enables the possibility of building more robust multicentric studies. This study aimed to propose a user-friendly and low-cost tool for COVID-19 mortality prediction using both an ML and a DL approach. Method: We enrolled 2348 patients from several hospitals in the Province of Reggio Emilia. Overall, 19 clinical features were provided by the Radiology Units of Azienda USL-IRCCS of Reggio Emilia, and 5892 radiomic features were extracted from each COVID-19 patient’s high-resolution computed tomography. We built and trained two classifiers to predict COVID-19 mortality: a machine learning algorithm, or support vector machine (SVM), and a deep learning model, or feedforward neural network (FNN). In order to evaluate the impact of the different feature sets on the final performance of the classifiers, we repeated the training session three times, first using only clinical features, then employing only radiomic features, and finally combining both information. Results: We obtained similar performances for both the machine learning and deep learning algorithms, with the best area under the receiver operating characteristic (ROC) curve, or AUC, obtained exploiting both clinical and radiomic information: 0.803 for the machine learning model and 0.864 for the deep learning model. Conclusions: Our work, performed on large and heterogeneous datasets (i.e., data from different CT scanners), confirms the results obtained in the recent literature. Such algorithms have the potential to be included in a clinical practice framework since they can not only be applied to COVID-19 mortality prediction but also to other classification problems such as diabetic prediction, asthma prediction, and cancer metastases prediction. Our study proves that the lesion’s inhomogeneity depicted by radiomic features combined with clinical information is relevant for COVID-19 mortality prediction.

A Deep Learning Approach for Histology-Based Nucleus Segmentation and Tumor Microenvironment Characterization

Deep Learning (DL) is an area of artificial intelligence (AI), wherein machine learning (ML) using convolutional neural networks to detect patterns in data and forecast its worth. It excels in tough settings like climate change and can handle sophisticated jobs such as image and speech recognition, natural language processing, and others. Deep learning models have found applications in a variety of fields due to their ability to reflect complicated patterns in data. Deep learning applications have the capacity to analyze and automatically classify large volumes of Internet traffic. Deep learning-based solutions that automate the detection of attacks and address complicated cybersecurity issues are gaining popularity. This study extensively describes the promising uses of deep learning, which is based on many layers of artificial neural networks, in a wide range of security challenges. Before critically and comparatively reviewing state-of-the-art solutions from the literature, we will highlight the main properties of typical deep learning architectures used in cybersecurity applications. Deep learning highlights developing concepts and provides an overview of required resources, such as a general framework and appropriate datasets. The limits of the evaluated works are highlighted, as well as a vision of the present challenges in the field, providing useful insights and best practices for researchers and developers working on related problems.

In the era of artificial intelligence, machine learning methods are successfully used in various fields. Machine learning has attracted extensive attention from investors in the financial market, especially in stock price prediction. However, one argument for the machine learning methods used in stock price prediction is that they are black-box models which are difficult to interpret. In this paper, we focus on the future stock price prediction with the historical stock price by machine learning and deep learning methods, such as support vector machine (SVM), random forest (RF), Bayesian classifier (BC), decision tree (DT), multilayer perceptron (MLP), convolutional neural network (CNN), bi-directional long-short term memory (BiLSTM), the embedded CNN, and the embedded BiLSTM. Firstly, we manually design several financial time series where the future price correlates with the historical stock prices in pre-designed modes, namely the curve-shape-feature (CSF) and the non-curve-shape-feature (NCSF) modes. In the CSF mode, the future prices can be extracted from the curve shapes of the historical stock prices. Conversely, in the NCSF mode, they can’t. Secondly, we apply various algorithms to those pre-designed and real financial time series. We find that the existing machine learning and deep learning algorithms fail in stock price prediction because in the real financial time series, less information of future prices is contained in the CSF mode, and perhaps more information is contained in the NCSF. Various machine learning and deep learning algorithms are good at handling the CSF in historical data, which are successfully applied in image recognition and natural language processing. However, they are inappropriate for stock price prediction on account of the NCSF. Therefore, accurate stock price prediction is the key to successful investment, and new machine learning algorithms handling the NCSF series are needed.

Deep learning is a complex machine learning algorithm that can learn the deep inner rules of a sample. In recent years, deep learning has achieved good results in the field of image processing. The essence of deep learning is to build a multi-layered machine learning architecture that trains on large-scale data. With the development of computer technology, deep learning has achieved good results in image recognition and natural language processing. Deep learning is also becoming more and more widely used in industry. This paper introduces the applications of deep learning in the industrial field, and finally discusses development and challenges of deep learning in industrial applications in the future.

Software has been the essential element to computers in today's digital era. Unfortunately, it has experienced challenges from various types of malware, which are designed for sabotage, criminal money-making, and information theft. To protect the gadgets from malware, numerous malware detection algorithms have been proposed. In the olden days there were shallow learning algorithms, and in recent years there are deep learning algorithms. With the availability of big data for training of model and affordable and high-performance computing services, deep learning has demonstrated its superiority in many smart city applications, in terms of accuracy, error rate, etc. This chapter intends to conduct a systematic review on the latest development of deep learning algorithms for malware detection. Some future research directions are suggested for further exploration.

Investigating the learning approaches of students in nursing education

In recent years, the widespread utilization of biological data processing technology has been driven by its cost-effectiveness. Consequently, next-generation sequencing (NGS) has become an integral component of biological research. NGS technologies enable the sequencing of billions of nucleotides in the entire genome, transcriptome, or specific target regions. This sequencing generates vast data matrices. Consequently, there is a growing demand for deep learning (DL) approaches, which employ multilayer artificial neural networks and systems capable of extracting meaningful information from these extensive data structures. In this study, the aim was to obtain optimized parameters and assess the prediction performance of deep learning and machine learning (ML) algorithms for binary classification in real and simulated whole genome data using a cloud-based system. The ART-simulated data and paired-end NGS (whole genome) data of Ch22, which includes ethnicity information, were evaluated using XGBoost, LightGBM, and DL algorithms. When the learning rate was set to 0.01 and 0.001, and the epoch values were updated to 500, 1000, and 2000 in the deep learning model for the ART simulated dataset, the median accuracy values of the ART models were as follows: 0.6320, 0.6800, and 0.7340 for epoch 0.01; and 0.6920, 0.7220, and 0.8020 for epoch 0.001, respectively. In comparison, the median accuracy values of the XGBoost and LightGBM models were 0.6990 and 0.6250 respectively. When the same process is repeated for Chr 22, the results are as follows: the median accuracy values of the DL models were 0.5290, 0.5420 and 0.5820 for epoch 0.01; and 0.5510, 0.5830 and 0.6040 for epoch 0.001, respectively. Additionally, the median accuracy values of the XGBoost and LightGBM models were 0.5760 and 0.5250, respectively. While the best classification estimates were obtained at 2000 epochs and a learning rate (LR) value of 0.001 for both real and simulated data, the XGBoost algorithm showed higher performance when the epoch value was 500 and the LR was 0.01. When dealing with class imbalance, the DL algorithm yielded similar and high Recall and Precision values. Conclusively, this study serves as a timely resource for genomic scientists, providing guidance on why, when, and how to effectively utilize deep learning/machine learning methods for the analysis of human genomic data.

Deep (machine) learning in recent years has significantly increased the predictive modeling strengths for applications in the areas of computer vision, speech recognition, and natural language processing. Being heavily data-driven, conventional general-purpose deep learning methods mainly rely on training data to learn task-specific data representations. In this thesis, we focus on leveraging novel learning algorithms in deep learning to tackle visual recognition challenges at the three key levels -- namely pixel, object, and image levels. Throughout the thesis, we demonstrate how each and every of our proposed methods can address a specific visual recognition problem. Firstly, we apply deep learning to improve the saliency detection performance of deep networks. A coarse saliency map of the input image's salient object is initially predicted by a convolutional-deconvolutional network (or equivalently a fully convolutional network). Following that, the coarse saliency map is sequentially refined by a separate network called Recurrent Attentional Convolutional-Deconvolutional Network (RACDNN) that shares its network weights across its sequential steps. At every sequential (temporal) step, the same RACDNN is applied to a newly selected/attended image sub-region and it performs saliency map refinement for that particular sub-region. Despite having many learnable network parameters and no access to additional training data, RADCNN can be trained well and it outperforms the "single-step" (coarse saliency detection) baseline and state-of-the-art saliency detection methods by large margins, on several saliency detection benchmark datasets. Secondly, we introduce auto-encoder weight transfer networks (AE-WTN+), a deep model for scaling up object detection. Conventional WTN transfers object class knowledge from the classification weights of a pretrained large-scale image classification network, to the classification weights of an object detection network. However, they suffer from under-fitting and are not able to preserve the rich object class information of novel classes. In this work, we propose a new WTN method -- AE-WTN+ which makes use of normalization techniques to ease network optimization. Inputs and intermediate features are normalized to improve trainability for reduced under-fitting. More importantly, a novel auto-encoding (reconstruction) loss is proposed to encourage information preservation of all classes in the weight predictions of AE-WTN+. This enables the predicted weights of AE-WTN+ to maintain the class discriminability and neighbourhood relationships contained in the pre-trained large-scale classification weights. Experiments on large-scale detection datasets validate the effectiveness of AE-WTN+ on both seen and novel classes. Thirdly, we improve the efficiency of cross-layer network connections for very deep convolutional network in the context of image classification. This gives rise to a new convolutional network architecture called Deluge Networks (DelugeNets) which pass the output (feature activations) of any preceding composite network layer as direct inputs to all succeeding composite layers. For the incoming feature activations of preceding composite layers, the succeeding composite layers first apply rather lightweight cross-layer depthwise convolutional weights on them for feature aggregation. The heavy lifting is carried out by the last convolutional weight layer in each preceding composite layer that performs cross-channel convolutions. The proposed technique enables unimpeded information flow among many layers in very deep DelugeNets with great efficiency. Experiments on small-scale and large-scale datasets show that DelugeNets perform competitively to state-of-the-art deep convolutional networks at lower computational and parameter costs. Fourthly, we propose Stochastic Downsampling (SDPoint), a method to overcome a major limitation suffered by conventional deep convolutional networks -- their computational costs during inference are fixed and cannot be changed. SDPoint downsamples the feature maps at a randomly selected point (layer index) in the network hierarchy during training. The many downsampling configurations known as SDPoint instances each entail a unique downsampling point and downsampling ratio. The same convolutional network weights are shared across the different SDPoint instances that downsample feature maps differently. During inference, the computational cost of a network trained with SDPoint can be instantaneously adjusted to fit a given computational budget, by manually selecting an appropriate SDPoint instance. Additionally, sharing weights between different feature map scales provides significant regularization benefits, making the networks trained with SDPoint less sensitive to scales and more competent. In image classification experiments, SDPoint demonstrates significant cost-accuracy and computational advantages, over independently-trained (non-weight-shared) baselines with various inference costs.