Deep Learning Techniques and COVID-19 Drug Discovery: Fundamentals, State-of-the-Art and Future Directions

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.

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Representation Learning for Fine-Grained Change Detection

Sensors ◽

10.3390/s21134486 ◽

2021 ◽

Vol 21 (13) ◽

pp. 4486

Author(s):

Niall O’Mahony ◽

Sean Campbell ◽

Lenka Krpalkova ◽

Anderson Carvalho ◽

Joseph Walsh ◽

...

Keyword(s):

Deep Learning ◽

Change Detection ◽

Model Calibration ◽

State Of The Art ◽

Representation Learning ◽

Machine Intelligence ◽

The State ◽

Sensor Data ◽

Fine Grained ◽

Learning Techniques

Fine-grained change detection in sensor data is very challenging for artificial intelligence though it is critically important in practice. It is the process of identifying differences in the state of an object or phenomenon where the differences are class-specific and are difficult to generalise. As a result, many recent technologies that leverage big data and deep learning struggle with this task. This review focuses on the state-of-the-art methods, applications, and challenges of representation learning for fine-grained change detection. Our research focuses on methods of harnessing the latent metric space of representation learning techniques as an interim output for hybrid human-machine intelligence. We review methods for transforming and projecting embedding space such that significant changes can be communicated more effectively and a more comprehensive interpretation of underlying relationships in sensor data is facilitated. We conduct this research in our work towards developing a method for aligning the axes of latent embedding space with meaningful real-world metrics so that the reasoning behind the detection of change in relation to past observations may be revealed and adjusted. This is an important topic in many fields concerned with producing more meaningful and explainable outputs from deep learning and also for providing means for knowledge injection and model calibration in order to maintain user confidence.

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A Survey on Bias and Fairness in Machine Learning

ACM Computing Surveys ◽

10.1145/3457607 ◽

2021 ◽

Vol 54 (6) ◽

pp. 1-35

Author(s):

Ninareh Mehrabi ◽

Fred Morstatter ◽

Nripsuta Saxena ◽

Kristina Lerman ◽

Aram Galstyan

Keyword(s):

Artificial Intelligence ◽

Machine Learning ◽

Deep Learning ◽

Real World ◽

State Of The Art ◽

Future Directions ◽

Discriminatory Behavior ◽

Real World Applications ◽

Near Future ◽

Different Sources

With the widespread use of artificial intelligence (AI) systems and applications in our everyday lives, accounting for fairness has gained significant importance in designing and engineering of such systems. AI systems can be used in many sensitive environments to make important and life-changing decisions; thus, it is crucial to ensure that these decisions do not reflect discriminatory behavior toward certain groups or populations. More recently some work has been developed in traditional machine learning and deep learning that address such challenges in different subdomains. With the commercialization of these systems, researchers are becoming more aware of the biases that these applications can contain and are attempting to address them. In this survey, we investigated different real-world applications that have shown biases in various ways, and we listed different sources of biases that can affect AI applications. We then created a taxonomy for fairness definitions that machine learning researchers have defined to avoid the existing bias in AI systems. In addition to that, we examined different domains and subdomains in AI showing what researchers have observed with regard to unfair outcomes in the state-of-the-art methods and ways they have tried to address them. There are still many future directions and solutions that can be taken to mitigate the problem of bias in AI systems. We are hoping that this survey will motivate researchers to tackle these issues in the near future by observing existing work in their respective fields.

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An Efficient Method for Detection of DDoS Attacks on the Web Using Deep Learning Algorithms

International Journal of Advanced Trends in Computer Science and Engineering ◽

10.30534/ijatcse/2021/271042021 ◽

2021 ◽

Vol 10 (4) ◽

pp. 2821-2829

Keyword(s):

Neural Network ◽

Deep Learning ◽

Deep Neural Network ◽

State Of The Art ◽

Ddos Attacks ◽

Problem Statement ◽

Neural Network Approach ◽

Learning Techniques ◽

Attack Data ◽

Deep Learning Neural Network

Recently, DDoS attacks is the most significant threat in network security. Both industry and academia are currently debating how to detect and protect against DDoS attacks. Many studies are provided to detect these types of attacks. Deep learning techniques are the most suitable and efficient algorithm for categorizing normal and attack data. Hence, a deep neural network approach is proposed in this study to mitigate DDoS attacks effectively. We used a deep learning neural network to identify and classify traffic as benign or one of four different DDoS attacks. We will concentrate on four different DDoS types: Slowloris, Slowhttptest, DDoS Hulk, and GoldenEye. The rest of the paper is organized as follow: Firstly, we introduce the work, Section 2 defines the related works, Section 3 presents the problem statement, Section 4 describes the proposed methodology, Section 5 illustrate the results of the proposed methodology and shows how the proposed methodology outperforms state-of-the-art work and finally Section VI concludes the paper.

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Complex Data Imputation by Auto-Encoders and Convolutional Neural Networks—A Case Study on Genome Gap-Filling

Computers ◽

10.3390/computers9020037 ◽

2020 ◽

Vol 9 (2) ◽

pp. 37 ◽

Cited By ~ 1

Author(s):

Luca Cappelletti ◽

Tommaso Fontana ◽

Guido Walter Di Donato ◽

Lorenzo Di Tucci ◽

Elena Casiraghi ◽

...

Keyword(s):

Deep Learning ◽

Missing Data ◽

State Of The Art ◽

The State ◽

Complex Data ◽

Data Imputation ◽

Genome Sequences ◽

Missing Data Imputation ◽

The Past ◽

Learning Techniques

Missing data imputation has been a hot topic in the past decade, and many state-of-the-art works have been presented to propose novel, interesting solutions that have been applied in a variety of fields. In the past decade, the successful results achieved by deep learning techniques have opened the way to their application for solving difficult problems where human skill is not able to provide a reliable solution. Not surprisingly, some deep learners, mainly exploiting encoder-decoder architectures, have also been designed and applied to the task of missing data imputation. However, most of the proposed imputation techniques have not been designed to tackle “complex data”, that is high dimensional data belonging to datasets with huge cardinality and describing complex problems. Precisely, they often need critical parameters to be manually set or exploit complex architecture and/or training phases that make their computational load impracticable. In this paper, after clustering the state-of-the-art imputation techniques into three broad categories, we briefly review the most representative methods and then describe our data imputation proposals, which exploit deep learning techniques specifically designed to handle complex data. Comparative tests on genome sequences show that our deep learning imputers outperform the state-of-the-art KNN-imputation method when filling gaps in human genome sequences.

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Deep learning for molecular design—a review of the state of the art

Molecular Systems Design & Engineering ◽

10.1039/c9me00039a ◽

2019 ◽

Vol 4 (4) ◽

pp. 828-849 ◽

Cited By ~ 84

Author(s):

Daniel C. Elton ◽

Zois Boukouvalas ◽

Mark D. Fuge ◽

Peter W. Chung

Keyword(s):

Deep Learning ◽

Molecular Design ◽

State Of The Art ◽

The State ◽

Learning Techniques

We review a recent groundswell of work which uses deep learning techniques to generate and optimize molecules.

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Survey of Machine Learning Techniques in Drug Discovery

Current Drug Metabolism ◽

10.2174/1389200219666180820112457 ◽

2019 ◽

Vol 20 (3) ◽

pp. 185-193 ◽

Cited By ~ 47

Author(s):

Natalie Stephenson ◽

Emily Shane ◽

Jessica Chase ◽

Jason Rowland ◽

David Ries ◽

...

Keyword(s):

Machine Learning ◽

Drug Discovery ◽

Large Scale ◽

State Of The Art ◽

New Drugs ◽

Machine Learning Techniques ◽

Current Status ◽

Learning Techniques ◽

Pharmaceutical Industries ◽

Current Stage

Background:Drug discovery, which is the process of discovering new candidate medications, is very important for pharmaceutical industries. At its current stage, discovering new drugs is still a very expensive and time-consuming process, requiring Phases I, II and III for clinical trials. Recently, machine learning techniques in Artificial Intelligence (AI), especially the deep learning techniques which allow a computational model to generate multiple layers, have been widely applied and achieved state-of-the-art performance in different fields, such as speech recognition, image classification, bioinformatics, etc. One very important application of these AI techniques is in the field of drug discovery.Methods:We did a large-scale literature search on existing scientific websites (e.g, ScienceDirect, Arxiv) and startup companies to understand current status of machine learning techniques in drug discovery.Results:Our experiments demonstrated that there are different patterns in machine learning fields and drug discovery fields. For example, keywords like prediction, brain, discovery, and treatment are usually in drug discovery fields. Also, the total number of papers published in drug discovery fields with machine learning techniques is increasing every year.Conclusion:The main focus of this survey is to understand the current status of machine learning techniques in the drug discovery field within both academic and industrial settings, and discuss its potential future applications. Several interesting patterns for machine learning techniques in drug discovery fields are discussed in this survey.

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Uncertainty-Based Human-in-the-Loop Deep Learning for Land Cover Segmentation

Remote Sensing ◽

10.3390/rs12223836 ◽

2020 ◽

Vol 12 (22) ◽

pp. 3836

Author(s):

Carlos García Rodríguez ◽

Jordi Vitrià ◽

Oscar Mora

Keyword(s):

Neural Network ◽

Neural Networks ◽

Deep Learning ◽

Land Cover ◽

Satellite Images ◽

State Of The Art ◽

Low Cost ◽

Human Intervention ◽

Human In The Loop ◽

Learning Techniques

In recent years, different deep learning techniques were applied to segment aerial and satellite images. Nevertheless, state of the art techniques for land cover segmentation does not provide accurate results to be used in real applications. This is a problem faced by institutions and companies that want to replace time-consuming and exhausting human work with AI technology. In this work, we propose a method that combines deep learning with a human-in-the-loop strategy to achieve expert-level results at a low cost. We use a neural network to segment the images. In parallel, another network is used to measure uncertainty for predicted pixels. Finally, we combine these neural networks with a human-in-the-loop approach to produce correct predictions as if developed by human photointerpreters. Applying this methodology shows that we can increase the accuracy of land cover segmentation tasks while decreasing human intervention.

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Deep Learning Application to Surface Properties Retrieval Using TIR Measurements: A Fast Forward/Reverse Scheme to Deal with Big Data Analysis from New Satellite Generations

Remote Sensing ◽

10.3390/rs13245003 ◽

2021 ◽

Vol 13 (24) ◽

pp. 5003

Author(s):

Elisa Castelli ◽

Enzo Papandrea ◽

Alessio Di Roma ◽

Ilaria Bloise ◽

Mattia Varile ◽

...

Keyword(s):

Deep Learning ◽

Data Analysis ◽

Surface Temperature ◽

Land Surface Temperature ◽

Satellite Data ◽

Land Surface ◽

State Of The Art ◽

Spectral Response ◽

High Spectral Resolution ◽

Learning Techniques

In recent years, technology advancement has led to an enormous increase in the amount of satellite data. The availability of huge datasets of remote sensing measurements to be processed, and the increasing need for near-real-time data analysis for operational uses, has fostered the development of fast, efficient-retrieval algorithms. Deep learning techniques were recently applied to satellite data for retrievals of target quantities. Forward models (FM) are a fundamental part of retrieval code development and mission design, as well. Despite this, the application of deep learning techniques to radiative transfer simulations is still underexplored. The DeepLIM project, described in this work, aimed at testing the feasibility of the application of deep learning techniques at the design of the retrieval chain of an upcoming satellite mission. The Land Surface Temperature Mission (LSTM) is a candidate for Sentinel 9 and has, as the main target, the need, for the agricultural community, to improve sustainable productivity. To do this, the mission will carry a thermal infrared sensor to retrieve land-surface temperature and evapotranspiration rate. The LSTM land-surface temperature retrieval chain is used as a benchmark to test the deep learning performances when applied to Earth observation studies. Starting from aircraft campaign data and state-of-the-art FM simulations with the DART model, deep learning techniques are used to generate new spectral features. Their statistical behavior is compared to the original technique to test the generation performances. Then, the high spectral resolution simulations are convolved with LSTM spectral response functions to obtain the radiance in the LSTM spectral channels. Simulated observations are analyzed using two state-of-the-art retrieval codes and deep learning-based algorithms. The performances of deep learning algorithms show promising results for both the production of simulated spectra and target parameters retrievals, one of the main advances being the reduction in computational costs.

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Quantifying Urban Surroundings Using Deep Learning Techniques: A New Proposal

Urban Science ◽

10.3390/urbansci2030078 ◽

2018 ◽

Vol 2 (3) ◽

pp. 78 ◽

Cited By ~ 1

Author(s):

Deepank Verma ◽

Arnab Jana ◽

Krithi Ramamritham

Keyword(s):

Image Analysis ◽

Deep Learning ◽

State Of The Art ◽

Human Perception ◽

Urban Spaces ◽

Analysis Techniques ◽

Learning Techniques ◽

Environment Variables ◽

Physical Features ◽

Image Analysis Techniques

The assessments on human perception of urban spaces are essential for the management and upkeep of surroundings. A large part of the previous studies is dedicated towards the visual appreciation and judgement of various physical features present in the surroundings. Visual qualities of the environment stimulate feelings of safety, pleasure, and belongingness. Scaling such assessments to cover city boundaries necessitates the assistance of state-of-the-art computer vision techniques. We developed a mobile-based application to collect visual datasets in the form of street-level imagery with the help of volunteers. We further utilised the potential of deep learning-based image analysis techniques in gaining insights into such datasets. In addition, we explained our findings with the help of environment variables which are related to individual satisfaction and wellbeing.

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