Deep learning 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 search. All four articles first 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. These deep learning approaches outperformed existing prediction methods, such as prediction based on transcript-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.

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.

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.

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.

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.

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

Investigating the learning approaches of students in nursing education

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

Randomized controlled trials (RCTs) provide the strongest evidence for therapeutic interventions and their effects on groups of subjects. However, the large amount of unstructured information in these trials makes it challenging and time-consuming to make decisions and identify important concepts and valid evidence. This study aims to explore methods for automating or semi-automating information extraction from reports of RCT studies. We conducted a systematic search of PubMed, ACM Digital Library, and Web of Science to identify relevant articles published between January 1, 2010, and 2022. We focused on published Natural Language Processing (NLP), machine learning, and deep learning methods that automate or semi-automate key elements of information extraction in the context of RCTs. A total of 26 publications were included, which discussed the automatic extraction of key characteristics of RCTs using various PICO frameworks (PIBOSO and PECODR). Among these publications, 14 (53.8%) extracted key characteristics based on PICO, PIBOSO, and PECODR, while 12 (46.1%) discussed information extraction methods in RCT studies. Common approaches mentioned included word/phrase matching, machine learning algorithms such as binary classification using the Naïve Bayes algorithm and powerful BERT network for feature extraction, support vector machine for data classification, conditional random field, non-machine-dependent automation, and machine learning or deep learning approaches. The lack of publicly available software and limited access to existing software makes it difficult to determine the most powerful information extraction system. However, deep learning models like Transformers and BERT language models have shown better performance in natural language processing.

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.

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.

In recent years, gesture recognition and speech recognition, as important input methods in Human–Computer Interaction (HCI), have been widely used in the field of virtual reality. In particular, with the rapid development of deep learning, artificial intelligence, and other computer technologies, gesture recognition and speech recognition have achieved breakthrough research progress. The search platform used in this work is mainly the Google Academic and literature database Web of Science. According to the keywords related to HCI and deep learning, such as “intelligent HCI”, “speech recognition”, “gesture recognition”, and “natural language processing”, nearly 1000 studies were selected. Then, nearly 500 studies of research methods were selected and 100 studies were finally selected as the research content of this work after five years (2019–2022) of year screening. First, the current situation of the HCI intelligent system is analyzed, the realization of gesture interaction and voice interaction in HCI is summarized, and the advantages brought by deep learning are selected for research. Then, the core concepts of gesture interaction are introduced and the progress of gesture recognition and speech recognition interaction is analyzed. Furthermore, the representative applications of gesture recognition and speech recognition interaction are described. Finally, the current HCI in the direction of natural language processing is investigated. The results show that the combination of intelligent HCI and deep learning is deeply applied in gesture recognition, speech recognition, emotion recognition, and intelligent robot direction. A wide variety of recognition methods were proposed in related research fields and verified by experiments. Compared with interactive methods without deep learning, high recognition accuracy was achieved. In Human–Machine Interfaces (HMIs) with voice support, context plays an important role in improving user interfaces. Whether it is voice search, mobile communication, or children’s speech recognition, HCI combined with deep learning can maintain better robustness. The combination of convolutional neural networks and long short-term memory networks can greatly improve the accuracy and precision of action recognition. Therefore, in the future, the application field of HCI will involve more industries and greater prospects are expected.

Progressive application of multidisciplinary research and development pushes the evolution of automation in many subsectors of agriculture to increase productivity, economic growth and environmental preservation with the help of robotics and artificial intelligence. Fruit harvesting robots have been developed mainly to provide support in the field for limited labour resources, to enable selective harvesting, to improve the efficiency and to preserve the quality of fruits. Even a small delay in harvesting can cause a maximum impact to the quality of the fruit. Selective fruit harvesting is an integration of different subcomponents. This paper provides a brief analysis of the techniques in selective fruit harvesting for the past 6 years starting from 2017 to 2022, associated principles, limitations and directions for future challenges. The first subcomponent is the vision system, it captures the information about the fruit in a tree canopy to perform efficient 2D and 3D localization. Hence getting accurate information from the vision system is more essential even in a complex agricultural environment. The detection of fruit from the vision system is normally done with two major methods such as traditional image processing and deep learning approaches. The result shows that the traditional methods provide high efficiency but the colour similarity, complex backgrounds and lightning conditions often makes failure in detection. Shortage of standard dataset and high-powered processing devices hinders the development of deep learning algorithms. Also, the usage of large data sets reduces the training speed even in pre-trained networks. For fruit grasping and detachment, the detection of plucking point is more essential to preserve the quality and for further storage. The elaborate description about the framework, limitations in current sensing, fruit and picking point detection algorithms provides guidelines to the researchers in building a fully automated robotic system to increase the processing speed and production rate.

This study examines the interdisciplinary connections that result from deep learning applications in artificial intelligence (AI) across several fields. A division of machine learning recognized as "deep learning" has proven to be remarkably effective at drawing out intricate patterns and representations from enormous datasets. Deep learning algorithms have made important improvements in fields as well as computer vision, natural language processing, robotics, finance, healthcare, advertising, and more by utilizing deep neural networks. This study’s goal is to evaluate the impact of deep learning in AI across disciplines and to draw attention to its revolutionary potential. The study examines the specific uses of deep learning in several fields and talk about the potential and problems that come with its deployment. The study provides a look at how precise object recognition, scene comprehension, and image production made deep learning transform the computer vision. Deep learning approaches have improved machine translation, sentiment analysis, and dialogue systems in natural language processing. This research study offers insights into the possibility of interdisciplinary cooperation by looking at the uses, difficulties, and future prospects of deep learning in AI. It demonstrates the transformative impact of deep learning in fostering creativity and advancement across a variety of sectors, opening the door for the creation of more intelligent and advanced AI systems.