Evaluation of anti-EGFR-iRGD recombinant protein with GOLD nanoparticles: synergistic effect on antitumor efficiency using optimized deep neural networks

NP screening through a deep learning approach against Anti-EGFR and validation through docking with AuNP. Biochemical pathway and simulation of AuNP with Anti-EGFR and further implementation in biological circuits.

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Assessment of bilateral knee pain from MR imaging using deep neural networks

10.1101/463497 ◽

2018 ◽

Author(s):

Gary H. Chang ◽

David T. Felson ◽

Shangran Qiu ◽

Terence D. Capellini ◽

Vijaya B. Kolachalama

Keyword(s):

Machine Learning ◽

Risk Factors ◽

Neural Networks ◽

Deep Learning ◽

Knee Pain ◽

Deep Neural Networks ◽

Learning Approach ◽

Mr Images ◽

Bilateral Knee ◽

Machine Learning Approach

ABSTRACTBackground and objectiveIt remains difficult to characterize pain in knee joints with osteoarthritis solely by radiographic findings. We sought to understand how advanced machine learning methods such as deep neural networks can be used to analyze raw MRI scans and predict bilateral knee pain, independent of other risk factors.MethodsWe developed a deep learning framework to associate information from MRI slices taken from the left and right knees of subjects from the Osteoarthritis Initiative with bilateral knee pain. Model training was performed by first extracting features from two-dimensional (2D) sagittal intermediate-weighted turbo spin echo slices. The extracted features from all the 2D slices were subsequently combined to directly associate using a fused deep neural network with the output of interest as a binary classification problem.ResultsThe deep learning model resulted in predicting bilateral knee pain on test data with 70.1% mean accuracy, 51.3% mean sensitivity, and 81.6% mean specificity. Systematic analysis of the predictions on the test data revealed that the model performance was consistent across subjects of different Kellgren-Lawrence grades.ConclusionThe study demonstrates a proof of principle that a machine learning approach can be applied to associate MR images with bilateral knee pain.SIGNIFICANCE AND INNOVATIONKnee pain is typically considered as an early indicator of osteoarthritis (OA) risk. Emerging evidence suggests that MRI changes are linked to pre-clinical OA, thus underscoring the need for building image-based models to predict knee pain. We leveraged a state-of-the-art machine learning approach to associate raw MR images with bilateral knee pain, independent of other risk factors.

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Combining content and social features in a deep learning approach to Vietnamese email prioritization

REV Journal on Electronics and Communications ◽

10.21553/rev-jec.271 ◽

2021 ◽

Author(s):

Ha Thanh Nguyen ◽

Quan Dinh Dang ◽

Anh Quang Tran

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Deep Neural Networks ◽

New Method ◽

Learning Approach ◽

Field Of Study ◽

Learning Techniques ◽

Email Overload ◽

Social Features

The email overload problem has been discussed in numerous email-related studies. One of the possible solutions to this problem is email prioritization, which is the act of automatically predicting the importance levels of received emails and sorting the user’s inbox accordingly. Several learning-based methods have been proposed to address the email prioritization problem using content features as well as social features. Although these methods have laid the foundation works in this field of study, the reported performance is far from being practical. Recent works on deep neural networks have achieved good results in various tasks. In this paper, the authors propose a novel email prioritization model which incorporates several deep learning techniques and uses a combination of both content features and social features from email data. This method targets Vietnamese emails and is tested against a self-built Vietnamese email corpus. Conducted experiments explored the effects of different model configurations and compared the effectiveness of the new method to that of a previous work.

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Using deep neural networks to detect complex spikes of cerebellar Purkinje cells

Journal of Neurophysiology ◽

10.1152/jn.00754.2019 ◽

2020 ◽

Vol 123 (6) ◽

pp. 2217-2234

Author(s):

Akshay Markanday ◽

Joachim Bellet ◽

Marie E. Bellet ◽

Junya Inoue ◽

Ziad M. Hafed ◽

...

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Purkinje Cell ◽

Purkinje Cells ◽

Deep Neural Networks ◽

Learning Approach ◽

Sorting Algorithms ◽

Accuracy Level ◽

Cerebellar Purkinje Cells ◽

Complex Spikes

Purkinje cell “complex spikes,” fired at perplexingly low rates, play a crucial role in cerebellum-based motor learning. Careful interpretations of these spikes require manually detecting them, since conventional online or offline spike sorting algorithms are optimized for classifying much simpler waveform morphologies. We present a novel deep learning approach for identifying complex spikes, which also measures additional relevant neurophysiological features, with an accuracy level matching that of human experts yet with very little time expenditure.

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Deep learning in Arabic sentiment analysis: An overview

Journal of Information Science ◽

10.1177/0165551519865488 ◽

2019 ◽

pp. 016555151986548

Author(s):

Amal Alharbi ◽

Mounira Taileb ◽

Manal Kalkatawi

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Sentiment Analysis ◽

Deep Neural Networks ◽

The Internet ◽

Learning Approach ◽

Comprehensive Overview ◽

Exponential Increase ◽

Arabic Sentiment Analysis

Sentiment analysis became a very motivating area in both academic and industrial fields due to the exponential increase of the online published reviews and recommendations. To solve the problem of analysing and classifying those reviews and recommendations, several techniques have been proposed. Lately, deep neural networks showed promising outcomes in sentiment analysis. The growing number of Arab users on the Internet along with the increasing amount of published Arabic reviews and comments encouraged researchers to apply deep learning to analyse them. This article is a comprehensive overview of research works that utilised the deep learning approach for Arabic sentiment analysis.

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A Deep Learning Approach for Malware and Software Piracy Threat Detection

Engineering, Technology & Applied Science Research ◽

10.48084/etasr.4412 ◽

2021 ◽

Vol 11 (6) ◽

pp. 7757-7762

Author(s):

K. Aldriwish

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Deep Neural Networks ◽

Software Piracy ◽

Classification Performance ◽

Learning Approach ◽

Threat Detection ◽

Deep Convolutional Neural Networks ◽

Combined Model ◽

Security Of Iot

Internet of Things (IoT) -based systems need to be up to date on cybersecurity threats. The security of IoT networks is challenged by software piracy and malware attacks, and much important information can be stolen and used for cybercrimes. This paper attempts to improve IoT cybersecurity by proposing a combined model based on deep learning to detect malware and software piracy across the IoT network. The malware’s model is based on Deep Convolutional Neural Networks (DCNNs). Apart from this, TensorFlow Deep Neural Networks (TFDNNs) are introduced to detect software piracy threats according to source code plagiarism. The investigation is conducted on the Google Code Jam (GCJ) dataset. The conducted experiments prove that the classification performance achieves high accuracy of about 98%.

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Automatic Detection of Arrhythmia Based on Multi-Resolution Representation of ECG Signal

Sensors ◽

10.3390/s20061579 ◽

2020 ◽

Vol 20 (6) ◽

pp. 1579

Author(s):

Dongqi Wang ◽

Qinghua Meng ◽

Dongming Chen ◽

Hupo Zhang ◽

Lisheng Xu

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Deep Neural Networks ◽

Channel Model ◽

Expert Knowledge ◽

Automatic Detection ◽

Data Representation ◽

Learning Technology ◽

Arrhythmia Detection ◽

Automatic Feature Extraction

Automatic detection of arrhythmia is of great significance for early prevention and diagnosis of cardiovascular disease. Traditional feature engineering methods based on expert knowledge lack multidimensional and multi-view information abstraction and data representation ability, so the traditional research on pattern recognition of arrhythmia detection cannot achieve satisfactory results. Recently, with the increase of deep learning technology, automatic feature extraction of ECG data based on deep neural networks has been widely discussed. In order to utilize the complementary strength between different schemes, in this paper, we propose an arrhythmia detection method based on the multi-resolution representation (MRR) of ECG signals. This method utilizes four different up to date deep neural networks as four channel models for ECG vector representations learning. The deep learning based representations, together with hand-crafted features of ECG, forms the MRR, which is the input of the downstream classification strategy. The experimental results of big ECG dataset multi-label classification confirm that the F1 score of the proposed method is 0.9238, which is 1.31%, 0.62%, 1.18% and 0.6% higher than that of each channel model. From the perspective of architecture, this proposed method is highly scalable and can be employed as an example for arrhythmia recognition.

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Enabling deeper learning on big data for materials informatics applications

Scientific Reports ◽

10.1038/s41598-021-83193-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Dipendra Jha ◽

Vishu Gupta ◽

Logan Ward ◽

Zijiang Yang ◽

Christopher Wolverton ◽

...

Keyword(s):

Neural Networks ◽

Big Data ◽

Deep Learning ◽

Deep Neural Networks ◽

Materials Science ◽

Prediction Models ◽

Model Performance ◽

Materials Informatics ◽

Learning Framework ◽

Significant Attention

AbstractThe application of machine learning (ML) techniques in materials science has attracted significant attention in recent years, due to their impressive ability to efficiently extract data-driven linkages from various input materials representations to their output properties. While the application of traditional ML techniques has become quite ubiquitous, there have been limited applications of more advanced deep learning (DL) techniques, primarily because big materials datasets are relatively rare. Given the demonstrated potential and advantages of DL and the increasing availability of big materials datasets, it is attractive to go for deeper neural networks in a bid to boost model performance, but in reality, it leads to performance degradation due to the vanishing gradient problem. In this paper, we address the question of how to enable deeper learning for cases where big materials data is available. Here, we present a general deep learning framework based on Individual Residual learning (IRNet) composed of very deep neural networks that can work with any vector-based materials representation as input to build accurate property prediction models. We find that the proposed IRNet models can not only successfully alleviate the vanishing gradient problem and enable deeper learning, but also lead to significantly (up to 47%) better model accuracy as compared to plain deep neural networks and traditional ML techniques for a given input materials representation in the presence of big data.

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Representing Deep Neural Networks Latent Space Geometries with Graphs

Algorithms ◽

10.3390/a14020039 ◽

2021 ◽

Vol 14 (2) ◽

pp. 39

Author(s):

Carlos Lassance ◽

Vincent Gripon ◽

Antonio Ortega

Keyword(s):

Machine Learning ◽

Neural Networks ◽

Deep Learning ◽

Objective Function ◽

Learning Process ◽

Deep Neural Networks ◽

State Of The Art ◽

The Core ◽

Learning Tasks ◽

Latent Space

Deep Learning (DL) has attracted a lot of attention for its ability to reach state-of-the-art performance in many machine learning tasks. The core principle of DL methods consists of training composite architectures in an end-to-end fashion, where inputs are associated with outputs trained to optimize an objective function. Because of their compositional nature, DL architectures naturally exhibit several intermediate representations of the inputs, which belong to so-called latent spaces. When treated individually, these intermediate representations are most of the time unconstrained during the learning process, as it is unclear which properties should be favored. However, when processing a batch of inputs concurrently, the corresponding set of intermediate representations exhibit relations (what we call a geometry) on which desired properties can be sought. In this work, we show that it is possible to introduce constraints on these latent geometries to address various problems. In more detail, we propose to represent geometries by constructing similarity graphs from the intermediate representations obtained when processing a batch of inputs. By constraining these Latent Geometry Graphs (LGGs), we address the three following problems: (i) reproducing the behavior of a teacher architecture is achieved by mimicking its geometry, (ii) designing efficient embeddings for classification is achieved by targeting specific geometries, and (iii) robustness to deviations on inputs is achieved via enforcing smooth variation of geometry between consecutive latent spaces. Using standard vision benchmarks, we demonstrate the ability of the proposed geometry-based methods in solving the considered problems.

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Off-the-shelf deep learning is not enough, and requires parsimony, Bayesianity, and causality

npj Computational Materials ◽

10.1038/s41524-020-00487-0 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Rama K. Vasudevan ◽

Maxim Ziatdinov ◽

Lukas Vlcek ◽

Sergei V. Kalinin

Keyword(s):

Neural Networks ◽

Computer Vision ◽

Deep Learning ◽

Bayesian Methods ◽

Deep Neural Networks ◽

Applied Research ◽

Modern Science ◽

Generative Models ◽

Knowledge Development ◽

Physical Constraints

AbstractDeep neural networks (‘deep learning’) have emerged as a technology of choice to tackle problems in speech recognition, computer vision, finance, etc. However, adoption of deep learning in physical domains brings substantial challenges stemming from the correlative nature of deep learning methods compared to the causal, hypothesis driven nature of modern science. We argue that the broad adoption of Bayesian methods incorporating prior knowledge, development of solutions with incorporated physical constraints and parsimonious structural descriptors and generative models, and ultimately adoption of causal models, offers a path forward for fundamental and applied research.

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Diversity oriented Deep Reinforcement Learning for targeted molecule generation

Journal of Cheminformatics ◽

10.1186/s13321-021-00498-z ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Tiago Pereira ◽

Maryam Abbasi ◽

Bernardete Ribeiro ◽

Joel P. Arrais

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Reinforcement Learning ◽

Deep Neural Networks ◽

Chemical Space ◽

Biological Properties ◽

Training Process ◽

Training Strategy ◽

Inhibitory Power ◽

Exploratory Strategy

AbstractIn this work, we explore the potential of deep learning to streamline the process of identifying new potential drugs through the computational generation of molecules with interesting biological properties. Two deep neural networks compose our targeted generation framework: the Generator, which is trained to learn the building rules of valid molecules employing SMILES strings notation, and the Predictor which evaluates the newly generated compounds by predicting their affinity for the desired target. Then, the Generator is optimized through Reinforcement Learning to produce molecules with bespoken properties. The innovation of this approach is the exploratory strategy applied during the reinforcement training process that seeks to add novelty to the generated compounds. This training strategy employs two Generators interchangeably to sample new SMILES: the initially trained model that will remain fixed and a copy of the previous one that will be updated during the training to uncover the most promising molecules. The evolution of the reward assigned by the Predictor determines how often each one is employed to select the next token of the molecule. This strategy establishes a compromise between the need to acquire more information about the chemical space and the need to sample new molecules, with the experience gained so far. To demonstrate the effectiveness of the method, the Generator is trained to design molecules with an optimized coefficient of partition and also high inhibitory power against the Adenosine $$A_{2A}$$ A 2 A and $$\kappa$$ κ opioid receptors. The results reveal that the model can effectively adjust the newly generated molecules towards the wanted direction. More importantly, it was possible to find promising sets of unique and diverse molecules, which was the main purpose of the newly implemented strategy.

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