Integrating the whole from the sum of the parts: vignettes in computational biology

2017 ◽  
Vol 1 (3) ◽  
pp. 241-243
Author(s):  
Jeffrey Skolnick
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Synthetic Biology ◽  
Personalized Medicine ◽  
Computational Biology ◽  
Biological Systems ◽  
Deep Understanding ◽  
Biological Processes ◽  
Practical Applications ◽  
Biological Variables

As is typical of contemporary cutting-edge interdisciplinary fields, computational biology touches and impacts many disciplines ranging from fundamental studies in the areas of genomics, proteomics transcriptomics, lipidomics to practical applications such as personalized medicine, drug discovery, and synthetic biology. This editorial examines the multifaceted role computational biology plays. Using the tools of deep learning, it can make powerful predictions of many biological variables, which may not provide a deep understanding of what factors contribute to the phenomena. Alternatively, it can provide the how and the why of biological processes. Most importantly, it can help guide and interpret what experiments and biological systems to study.

Biology Meets Computation

2017 ◽  
Author(s):  
Arlindo Oliveira
Keyword(s):  
Synthetic Biology ◽  
Computational Biology ◽  
Systematic Approach ◽  
Biological Systems ◽  
Deep Understanding ◽  
Decisive Role ◽  
Computer Models ◽  
Living Cells ◽  
Open The Doors ◽  
The Way

This chapter describes how computers played a decisive role in the sequencing and understanding of the genomes of humans and other organisms. The discovery of the structure of DNA, by Watson and Crick, opened the way to a systematic approach to biology, based on the study of the way DNA encodes the proteins in all living cells. The area that became known as computational biology, or bioinformatics, aims at modelling, simulating, and understanding the behaviour of biological systems, using computer models and algorithms. Such a deep understanding will enable us to create computer models of cells and of entire organisms and even, in the future, open the doors to the creation of entirely new lifeforms, a field known as synthetic biology.

Practical Applications of Deep Learning To Impute Heterogeneous Drug Discovery Data

2020 ◽  
Vol 60 (6) ◽  
pp. 2848-2857 ◽  
Author(s):  
Benedict W. J. Irwin ◽  
Julian R. Levell ◽  
Thomas M. Whitehead ◽  
Matthew D. Segall ◽  
Gareth J. Conduit
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Practical Applications

A unified framework for automated person re-indentification

2020 ◽  
Vol 71 (7) ◽  
pp. 868-880
Author(s):  
Nguyen Hong-Quan ◽  
Nguyen Thuy-Binh ◽  
Tran Duc-Long ◽  
Le Thi-Lan
Keyword(s):  
Deep Learning ◽  
Video Analysis ◽  
Camera Network ◽  
Unified Framework ◽  
Person Detection ◽  
Practical Applications ◽  
Detection And Tracking ◽  
Analysis System ◽  
Bounding Boxes

Along with the strong development of camera networks, a video analysis system has been become more and more popular and has been applied in various practical applications. In this paper, we focus on person re-identification (person ReID) task that is a crucial step of video analysis systems. The purpose of person ReID is to associate multiple images of a given person when moving in a non-overlapping camera network. Many efforts have been made to person ReID. However, most of studies on person ReID only deal with well-alignment bounding boxes which are detected manually and considered as the perfect inputs for person ReID. In fact, when building a fully automated person ReID system the quality of the two previous steps that are person detection and tracking may have a strong effect on the person ReID performance. The contribution of this paper are two-folds. First, a unified framework for person ReID based on deep learning models is proposed. In this framework, the coupling of a deep neural network for person detection and a deep-learning-based tracking method is used. Besides, features extracted from an improved ResNet architecture are proposed for person representation to achieve a higher ReID accuracy. Second, our self-built dataset is introduced and employed for evaluation of all three steps in the fully automated person ReID framework.

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

scholarly journals Olympic Games Event Recognition via Transfer Learning with Photobombing Guided Data Augmentation

2021 ◽  
Vol 7 (2) ◽  
pp. 12
Author(s):  
Yousef I. Mohamad ◽  
Samah S. Baraheem ◽  
Tam V. Nguyen
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
Data Augmentation ◽  
Olympic Games ◽  
Event Recognition ◽  
Surveillance Systems ◽  
Video Captioning ◽  
Practical Applications ◽  
Sport Events ◽  
The Olympic Games

Automatic event recognition in sports photos is both an interesting and valuable research topic in the field of computer vision and deep learning. With the rapid increase and the explosive spread of data, which is being captured momentarily, the need for fast and precise access to the right information has become a challenging task with considerable importance for multiple practical applications, i.e., sports image and video search, sport data analysis, healthcare monitoring applications, monitoring and surveillance systems for indoor and outdoor activities, and video captioning. In this paper, we evaluate different deep learning models in recognizing and interpreting the sport events in the Olympic Games. To this end, we collect a dataset dubbed Olympic Games Event Image Dataset (OGED) including 10 different sport events scheduled for the Olympic Games Tokyo 2020. Then, the transfer learning is applied on three popular deep convolutional neural network architectures, namely, AlexNet, VGG-16 and ResNet-50 along with various data augmentation methods. Extensive experiments show that ResNet-50 with the proposed photobombing guided data augmentation achieves 90% in terms of accuracy.

scholarly journals A Survey on Deep Learning Based Methods and Datasets for Monocular 3D Object Detection

Electronics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 517
Author(s):  
Seong-heum Kim ◽  
Youngbae Hwang
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Low Cost ◽  
Detection Methods ◽  
Future Research ◽  
3D Object ◽  
Practical Applications ◽  
Depth Sensors ◽  
Significant Research ◽  
3D Object Detection

Owing to recent advancements in deep learning methods and relevant databases, it is becoming increasingly easier to recognize 3D objects using only RGB images from single viewpoints. This study investigates the major breakthroughs and current progress in deep learning-based monocular 3D object detection. For relatively low-cost data acquisition systems without depth sensors or cameras at multiple viewpoints, we first consider existing databases with 2D RGB photos and their relevant attributes. Based on this simple sensor modality for practical applications, deep learning-based monocular 3D object detection methods that overcome significant research challenges are categorized and summarized. We present the key concepts and detailed descriptions of representative single-stage and multiple-stage detection solutions. In addition, we discuss the effectiveness of the detection models on their baseline benchmarks. Finally, we explore several directions for future research on monocular 3D object detection.

Data augmentation and transfer learning strategies for reaction prediction in low chemical data regimes

2021 ◽  
Author(s):  
Yun Zhang ◽  
Ling Wang ◽  
Xinqiao Wang ◽  
Chengyun Zhang ◽  
Jiamin Ge ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Deep Learning ◽  
Drug Discovery ◽  
Research And Development ◽  
Learning Strategies ◽  
Transfer Learning ◽  
Chemical Reactions ◽  
Data Augmentation ◽  
Learning Method ◽  
Reaction Prediction

An effective and rapid deep learning method to predict chemical reactions contributes to the research and development of organic chemistry and drug discovery.

scholarly journals A Systematic Deep Learning Based Overhead Tracking and Counting System Using RGB-D Remote Cameras

2021 ◽  
Vol 11 (12) ◽  
pp. 5503
Author(s):  
Munkhjargal Gochoo ◽  
Syeda Amna Rizwan ◽  
Yazeed Yasin Ghadi ◽  
Ahmad Jalal ◽  
Kibum Kim
Keyword(s):  
Deep Learning ◽  
Human Head ◽  
Point Clouds ◽  
Head Tracking ◽  
Complex Environments ◽  
People Tracking ◽  
Practical Applications ◽  
Remote Cameras ◽  
Video Frames ◽  
Benchmark Datasets

Automatic head tracking and counting using depth imagery has various practical applications in security, logistics, queue management, space utilization and visitor counting. However, no currently available system can clearly distinguish between a human head and other objects in order to track and count people accurately. For this reason, we propose a novel system that can track people by monitoring their heads and shoulders in complex environments and also count the number of people entering and exiting the scene. Our system is split into six phases; at first, preprocessing is done by converting videos of a scene into frames and removing the background from the video frames. Second, heads are detected using Hough Circular Gradient Transform, and shoulders are detected by HOG based symmetry methods. Third, three robust features, namely, fused joint HOG-LBP, Energy based Point clouds and Fused intra-inter trajectories are extracted. Fourth, the Apriori-Association is implemented to select the best features. Fifth, deep learning is used for accurate people tracking. Finally, heads are counted using Cross-line judgment. The system was tested on three benchmark datasets: the PCDS dataset, the MICC people counting dataset and the GOTPD dataset and counting accuracy of 98.40%, 98%, and 99% respectively was achieved. Our system obtained remarkable results.

Sign in / Sign up

Export Citation Format

Share Document