A review of deep learning applications in human genomics using next-generation sequencing data.

Genomics is advancing towards data-driven science. Through the advent of high-throughput data generating technologies in human genomics, we are overwhelmed with the heap of genomic data. To extract knowledge and pattern out of this genomic data, artificial intelligence especially deep learning methods has been instrumental. In the current review, we address development and application of deep learning methods/models in different subarea of human genomics. We assessed over- and under-charted area of genomics by deep learning techniques. Deep learning algorithms underlying the genomic tools have been discussed briefly in later part of this review. Finally, we discussed briefly about the late application of deep learning tools in genomic. Conclusively, this review is timely for biotechnology or genomic scientists in order to guide them why, when and how to use deep learning methods to analyse human genomic data.

Ball-Catching System Using Image Processing and an Omni-Directional Wheeled Mobile Robot.

The ball-catching system examined in this research, which was composed of an omni-directional wheeled mobile robot and an image processing system that included a dynamic stereo vision camera and a static camera, was used to capture a thrown ball. The thrown ball was tracked by the dynamic stereo vision camera, and the omni-directional wheeled mobile robot was navigated through the static camera. A Kalman filter with deep learning was used to decrease the visual measurement noises and to estimate the ball's position and velocity. The ball's future trajectory and landing point was predicted by estimating its position and velocity. Feedback linearization was used to linearize the omni-directional wheeled mobile robot model and was then combined with a proportional-integral-derivative (PID) controller. The visual tracking algorithm was initially simulated numerically, and then the performance of the designed system was verified experimentally. We verified that the designed system was able to precisely catch a thrown ball.

Deep Learning-Based Violin Bowing Action Recognition.

We propose a violin bowing action recognition system that can accurately recognize distinct bowing actions in classical violin performance. This system can recognize bowing actions by analyzing signals from a depth camera and from inertial sensors that are worn by a violinist. The contribution of this study is threefold: (1) a dataset comprising violin bowing actions was constructed from data captured by a depth camera and multiple inertial sensors; (2) data augmentation was achieved for depth-frame data through rotation in three-dimensional world coordinates and for inertial sensing data through yaw, pitch, and roll angle transformations; and, (3) bowing action classifiers were trained using different modalities, to compensate for the strengths and weaknesses of each modality, based on deep learning methods with a decision-level fusion process. In experiments, large external motions and subtle local motions produced from violin bow manipulations were both accurately recognized by the proposed system (average accuracy > 80%).

Deep Learning applications for COVID-19.

This survey explores how Deep Learning has battled the COVID-19 pandemic and provides directions for future research on COVID-19. We cover Deep Learning applications in Natural Language Processing, Computer Vision, Life Sciences, and Epidemiology. We describe how each of these applications vary with the availability of big data and how learning tasks are constructed. We begin by evaluating the current state of Deep Learning and conclude with key limitations of Deep Learning for COVID-19 applications. These limitations include Interpretability, Generalization Metrics, Learning from Limited Labeled Data, and Data Privacy. Natural Language Processing applications include mining COVID-19 research for Information Retrieval and Question Answering, as well as Misinformation Detection, and Public Sentiment Analysis. Computer Vision applications cover Medical Image Analysis, Ambient Intelligence, and Vision-based Robotics. Within Life Sciences, our survey looks at how Deep Learning can be applied to Precision Diagnostics, Protein Structure Prediction, and Drug Repurposing. Deep Learning has additionally been utilized in Spread Forecasting for Epidemiology. Our literature review has found many examples of Deep Learning systems to fight COVID-19. We hope that this survey will help accelerate the use of Deep Learning for COVID-19 research.

Review of deep learning: concepts, CNN architectures, challenges, applications, future directions.

In the last few years, the deep learning (DL) computing paradigm has been deemed the Gold Standard in the machine learning (ML) community. Moreover, it has gradually become the most widely used computational approach in the field of ML, thus achieving outstanding results on several complex cognitive tasks, matching or even beating those provided by human performance. One of the benefits of DL is the ability to learn massive amounts of data. The DL field has grown fast in the last few years and it has been extensively used to successfully address a wide range of traditional applications. More importantly, DL has outperformed well-known ML techniques in many domains, e.g., cybersecurity, natural language processing, bioinformatics, robotics and control, and medical information processing, among many others. Despite it has been contributed several works reviewing the State-of-the-Art on DL, all of them only tackled one aspect of the DL, which leads to an overall lack of knowledge about it. Therefore, in this contribution, we propose using a more holistic approach in order to provide a more suitable starting point from which to develop a full understanding of DL. Specifically, this review attempts to provide a more comprehensive survey of the most important aspects of DL and including those enhancements recently added to the field. In particular, this paper outlines the importance of DL, presents the types of DL techniques and networks. It then presents convolutional neural networks (CNNs) which the most utilized DL network type and describes the development of CNNs architectures together with their main features, e.g., starting with the AlexNet network and closing with the High-Resolution network (HR.Net). Finally, we further present the challenges and suggested solutions to help researchers understand the existing research gaps. It is followed by a list of the major DL applications. Computational tools including FPGA, GPU, and CPU are summarized along with a description of their influence on DL. The paper ends with the evolution matrix, benchmark datasets, and summary and conclusion.

Memory-assisted reinforcement learning for diverse molecular de novo design.

In de novo molecular design, recurrent neural networks (RNN) have been shown to be effective methods for sampling and generating novel chemical structures. Using a technique called reinforcement learning (RL), an RNN can be tuned to target a particular section of chemical space with optimized desirable properties using a scoring function. However, ligands generated by current RL methods so far tend to have relatively low diversity, and sometimes even result in duplicate structures when optimizing towards desired properties. Here, we propose a new method to address the low diversity issue in RL for molecular design. Memory-assisted RL is an extension of the known RL, with the introduction of a so-called memory unit. As proof of concept, we applied our method to generate structures with a desired AlogP value. In a second case study, we applied our method to design ligands for the dopamine type 2 receptor and the 5-hydroxytryptamine type 1A receptor. For both receptors, a machine learning model was developed to predict whether generated molecules were active or not for the receptor. In both case studies, it was found that memory-assisted RL led to the generation of more compounds predicted to be active having higher chemical diversity, thus achieving better coverage of chemical space of known ligands compared to established RL methods.