Evaluating Deep Learning models for predicting ALK-5 inhibition

Computational methods have been widely used in drug design. The recent developments in machine learning techniques and the ever-growing chemical and biological databases are fertile ground for discoveries in this area. In this study, we evaluated the performance of Deep Learning models in comparison to Random Forest, and Support Vector Regression for predicting the biological activity (pIC50) of ALK-5 inhibitors as candidates to treat cancer. The generalization power of the models was assessed by internal and external validation procedures. A deep neural network model obtained the best performance in this comparative study, achieving a coefficient of determination of 0.658 on the external validation set with mean square error and mean absolute error of 0.373 and 0.450, respectively. Additionally, the relevance of the chemical descriptors for the prediction of biological activity was estimated using Permutation Importance. We can conclude that the forecast model obtained by the deep neural network is suitable for the problem and can be employed to predict the biological activity of new ALK-5 inhibitors.

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Anomaly Detection Using Deep Neural Network for IoT Architecture

Applied Sciences ◽

10.3390/app11157050 ◽

2021 ◽

Vol 11 (15) ◽

pp. 7050

Author(s):

Zeeshan Ahmad ◽

Adnan Shahid Khan ◽

Kashif Nisar ◽

Iram Haider ◽

Rosilah Hassan ◽

...

Keyword(s):

Neural Network ◽

Deep Learning ◽

Anomaly Detection ◽

Deep Neural Network ◽

Detection System ◽

Traffic Monitoring ◽

Detection Accuracy ◽

Learning Models ◽

Prime Concern ◽

Entry Points

The revolutionary idea of the internet of things (IoT) architecture has gained enormous popularity over the last decade, resulting in an exponential growth in the IoT networks, connected devices, and the data processed therein. Since IoT devices generate and exchange sensitive data over the traditional internet, security has become a prime concern due to the generation of zero-day cyberattacks. A network-based intrusion detection system (NIDS) can provide the much-needed efficient security solution to the IoT network by protecting the network entry points through constant network traffic monitoring. Recent NIDS have a high false alarm rate (FAR) in detecting the anomalies, including the novel and zero-day anomalies. This paper proposes an efficient anomaly detection mechanism using mutual information (MI), considering a deep neural network (DNN) for an IoT network. A comparative analysis of different deep-learning models such as DNN, Convolutional Neural Network, Recurrent Neural Network, and its different variants, such as Gated Recurrent Unit and Long Short-term Memory is performed considering the IoT-Botnet 2020 dataset. Experimental results show the improvement of 0.57–2.6% in terms of the model’s accuracy, while at the same time reducing the FAR by 0.23–7.98% to show the effectiveness of the DNN-based NIDS model compared to the well-known deep learning models. It was also observed that using only the 16–35 best numerical features selected using MI instead of 80 features of the dataset result in almost negligible degradation in the model’s performance but helped in decreasing the overall model’s complexity. In addition, the overall accuracy of the DL-based models is further improved by almost 0.99–3.45% in terms of the detection accuracy considering only the top five categorical and numerical features.

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Covid-19 detection via deep neural network and occlusion sensitivity maps

10.36227/techrxiv.14100890 ◽

2021 ◽

Author(s):

Noor Ahmad ◽

Muhammad Aminu ◽

Mohd Halim Mohd Noor

Keyword(s):

Neural Network ◽

Deep Learning ◽

Deep Neural Network ◽

State Of The Art ◽

Color Images ◽

Fine Tuning ◽

Training Dataset ◽

Learning Approaches ◽

Learning Models ◽

Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

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A Similarity-Based Object Classification Using Deep Neural Networks

Handbook of Research on Deep Learning Innovations and Trends - Advances in Computational Intelligence and Robotics ◽

10.4018/978-1-5225-7862-8.ch012 ◽

2019 ◽

pp. 197-219

Author(s):

Parvathi R. ◽

Pattabiraman V.

Keyword(s):

Neural Network ◽

Deep Learning ◽

Deep Neural Network ◽

Search Algorithm ◽

Random Projection ◽

Learning Networks ◽

Learning Models ◽

External Conditions ◽

And Training

This chapter proposes a hybrid method for classification of the objects based on deep neural network and a similarity-based search algorithm. The objects are pre-processed with external conditions. After pre-processing and training different deep learning networks with the object dataset, the authors compare the results to find the best model to improve the accuracy of the results based on the features of object images extracted from the feature vector layer of a neural network. RPFOREST (random projection forest) model is used to predict the approximate nearest images. ResNet50, InceptionV3, InceptionV4, and DenseNet169 models are trained with this dataset. A proposal for adaptive finetuning of the deep learning models by determining the number of layers required for finetuning with the help of the RPForest model is given, and this experiment is conducted using the Xception model.

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A Study on Brain Tumor Detection and Segmentation Using Deep Learning Techniques

Journal of Computational and Theoretical Nanoscience ◽

10.1166/jctn.2020.8468 ◽

2020 ◽

Vol 17 (4) ◽

pp. 1925-1930

Author(s):

Ambeshwar Kumar ◽

R. Manikandan ◽

Robbi Rahim

Keyword(s):

Neural Network ◽

Machine Learning ◽

Deep Learning ◽

Brain Tumor ◽

Tumor Detection ◽

Machine Learning Techniques ◽

Support Vector ◽

Learning Techniques ◽

Convolution Algorithm ◽

The Brain

It’s a new era technology in the field of medical engineering giving awareness about the various healthcare features. Deep learning is a part of machine learning, it is capable of handling high dimensional data and is efficient in concentrating on the right features. Tumor is an unbelievably complex disease: a multifaceted cell has more than hundred billion cells; each cell acquires mutation exclusively. Detection of tumor particles in experiment is easily done by MRI or CT. Brain tumors can also be detected by MRI, however, deep learning techniques give a better approach to segment the brain tumor images. Deep Learning models are imprecisely encouraged by information handling and communication designs in biological nervous system. Classification plays an significant role in brain tumor detection. Neural network is creating a well-organized rule for classification. To accomplish medical image data, neural network is trained to use the Convolution algorithm. Multilayer perceptron is intended for identification of a image. In this study article, the brain images are categorized into two types: normal and abnormal. This article emphasize the importance of classification and feature selection approach for predicting the brain tumor. This classification is done by machine learning techniques like Artificial Neural Networks, Support Vector Machine and Deep Neural Network. It could be noted that more than one technique can be applied for the segmentation of tumor. The several samples of brain tumor images are classified using deep learning algorithms, convolution neural network and multi-layer perceptron.

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Human Activity Recognition Based on Deep Learning Techniques

Proceedings ◽

10.3390/ecsa-6-06539 ◽

2019 ◽

Vol 42 (1) ◽

pp. 15

Author(s):

Manuel Gil-Martín ◽

Marcos Sánchez-Hernández ◽

Rubén San-Segundo

Keyword(s):

Neural Network ◽

Deep Learning ◽

Activity Recognition ◽

Human Activity ◽

Deep Neural Network ◽

Human Activity Recognition ◽

Support Vector ◽

Daily Life Activities ◽

Learning Techniques ◽

The Fourier Transform

Deep learning techniques are being widely applied to Human Activity Recognition (HAR). This paper describes the implementation and evaluation of a HAR system for daily life activities using the accelerometer of an iPhone 6S. This system is based on a deep neural network including convolutional layers for feature extraction from accelerations and fully-connected layers for classification. Different transformations have been applied to the acceleration signals in order to find the appropriate input data to the deep neural network. This study has used acceleration recordings from the MotionSense dataset, where 24 subjects performed 6 activities: walking downstairs, walking upstairs, sitting, standing, walking and jogging. The evaluation has been performed using a subject-wise cross-validation: recordings from the same subject do not appear in training and testing sets at the same time. The proposed system has obtained a 9% improvement in accuracy compared to the baseline system based on Support Vector Machines. The best results have been obtained using raw data as input to a deep neural network composed of two convolutional and two max-pooling layers with decreasing kernel sizes. Results suggest that using the module of the Fourier transform as inputs provides better results when classifying only between dynamic activities.

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Covid-19 detection via deep neural network and occlusion sensitivity maps

10.36227/techrxiv.14100890.v1 ◽

2021 ◽

Author(s):

Noor Ahmad ◽

Muhammad Aminu ◽

Mohd Halim Mohd Noor

Keyword(s):

Neural Network ◽

Deep Learning ◽

Deep Neural Network ◽

State Of The Art ◽

Color Images ◽

Fine Tuning ◽

Training Dataset ◽

Learning Approaches ◽

Learning Models ◽

Sensitivity Maps

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Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model

BMC Bioinformatics ◽

10.1186/s12859-020-03850-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jiarui Feng ◽

Heming Zhang ◽

Fuhai Li

Keyword(s):

Neural Network ◽

Survival Analysis ◽

Deep Learning ◽

Survival Time ◽

Signaling Pathways ◽

Cancer Patients ◽

Deep Neural Network ◽

Survival Prediction ◽

Omics Data ◽

Learning Models

Abstract Background Survival analysis is an important part of cancer studies. In addition to the existing Cox proportional hazards model, deep learning models have recently been proposed in survival prediction, which directly integrates multi-omics data of a large number of genes using the fully connected dense deep neural network layers, which are hard to interpret. On the other hand, cancer signaling pathways are important and interpretable concepts that define the signaling cascades regulating cancer development and drug resistance. Thus, it is important to investigate potential associations between patient survival and individual signaling pathways, which can help domain experts to understand deep learning models making specific predictions. Results In this exploratory study, we proposed to investigate the relevance and influence of a set of core cancer signaling pathways in the survival analysis of cancer patients. Specifically, we built a simplified and partially biologically meaningful deep neural network, DeepSigSurvNet, for survival prediction. In the model, the gene expression and copy number data of 1967 genes from 46 major signaling pathways were integrated in the model. We applied the model to four types of cancer and investigated the influence of the 46 signaling pathways in the cancers. Interestingly, the interpretable analysis identified the distinct patterns of these signaling pathways, which are helpful in understanding the relevance of signaling pathways in terms of their application to the prediction of cancer patients’ survival time. These highly relevant signaling pathways, when combined with other essential signaling pathways inhibitors, can be novel targets for drug and drug combination prediction to improve cancer patients’ survival time. Conclusion The proposed DeepSigSurvNet model can facilitate the understanding of the implications of signaling pathways on cancer patients’ survival by integrating multi-omics data and clinical factors.

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A Deep Learning Model for Fault Diagnosis with a Deep Neural Network and Feature Fusion on Multi-Channel Sensory Signals

Sensors ◽

10.3390/s20154300 ◽

2020 ◽

Vol 20 (15) ◽

pp. 4300 ◽

Cited By ~ 2

Author(s):

Qing Ye ◽

Shaohu Liu ◽

Changhua Liu

Keyword(s):

Neural Network ◽

Deep Learning ◽

Deep Neural Network ◽

Feature Fusion ◽

Support Vector ◽

Diagnostic Model ◽

Sensory Signals ◽

Sensory Signal ◽

Deep Architecture ◽

Final Drive

Collecting multi-channel sensory signals is a feasible way to enhance performance in the diagnosis of mechanical equipment. In this article, a deep learning method combined with feature fusion on multi-channel sensory signals is proposed. First, a deep neural network (DNN) made up of auto-encoders is adopted to adaptively learn representative features from sensory signal and approximate non-linear relation between symptoms and fault modes. Then, Locality Preserving Projection (LPP) is utilized in the fusion of features extracted from multi-channel sensory signals. Finally, a novel diagnostic model based on multiple DNNs (MDNNs) and softmax is constructed with the input of fused deep features. The proposed method is verified in intelligent failure recognition for automobile final drive to evaluate its performance. A set of contrastive analyses of several intelligent models based on the Back-Propagation Neural Network (BPNN), Support Vector Machine (SVM) and the proposed deep architecture with single sensory signal and multi-channel sensory signals is implemented. The proposed deep architecture of feature extraction and feature fusion on multi-channel sensory signals can effectively recognize the fault patterns of final drive with the best diagnostic accuracy of 95.84%. The results confirm that the proposed method is more robust and effective than other comparative methods in the contrastive experiments.

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Quantifying Seagrass Distribution in Coastal Water with Deep Learning Models

Remote Sensing ◽

10.3390/rs12101581 ◽

2020 ◽

Vol 12 (10) ◽

pp. 1581 ◽

Cited By ~ 2

Author(s):

Daniel Perez ◽

Kazi Islam ◽

Victoria Hill ◽

Richard Zimmerman ◽

Blake Schaeffer ◽

...

Keyword(s):

Neural Network ◽

Deep Learning ◽

Transfer Learning ◽

Satellite Images ◽

Support Vector ◽

Learning Approach ◽

Learning Models ◽

Learning Techniques ◽

The World ◽

New Locations

Coastal ecosystems are critically affected by seagrass, both economically and ecologically. However, reliable seagrass distribution information is lacking in nearly all parts of the world because of the excessive costs associated with its assessment. In this paper, we develop two deep learning models for automatic seagrass distribution quantification based on 8-band satellite imagery. Specifically, we implemented a deep capsule network (DCN) and a deep convolutional neural network (CNN) to assess seagrass distribution through regression. The DCN model first determines whether seagrass is presented in the image through classification. Second, if seagrass is presented in the image, it quantifies the seagrass through regression. During training, the regression and classification modules are jointly optimized to achieve end-to-end learning. The CNN model is strictly trained for regression in seagrass and non-seagrass patches. In addition, we propose a transfer learning approach to transfer knowledge in the trained deep models at one location to perform seagrass quantification at a different location. We evaluate the proposed methods in three WorldView-2 satellite images taken from the coastal area in Florida. Experimental results show that the proposed deep DCN and CNN models performed similarly and achieved much better results than a linear regression model and a support vector machine. We also demonstrate that using transfer learning techniques for the quantification of seagrass significantly improved the results as compared to directly applying the deep models to new locations.

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Assessment of Landslide Susceptibility Combining Deep Learning with Semi-Supervised Learning in Jiaohe County, Jilin Province, China

Applied Sciences ◽

10.3390/app10165640 ◽

2020 ◽

Vol 10 (16) ◽

pp. 5640

Author(s):

Jingyu Yao ◽

Shengwu Qin ◽

Shuangshuang Qiao ◽

Wenchao Che ◽

Yang Chen ◽

...

Keyword(s):

Neural Network ◽

Deep Learning ◽

Supervised Learning ◽

Landslide Susceptibility ◽

Deep Neural Network ◽

Spatial Information ◽

Information Gain ◽

Jilin Province ◽

Landslide Susceptibility Mapping ◽

Support Vector

Accurate and timely landslide susceptibility mapping (LSM) is essential to effectively reduce the risk of landslide. In recent years, deep learning has been successfully applied to landslide susceptibility assessment due to the strong ability of fitting. However, in actual applications, the number of labeled samples is usually not sufficient for the training component. In this paper, a deep neural network model based on semi-supervised learning (SSL-DNN) for landslide susceptibility is proposed, which makes full use of a large number of spatial information (unlabeled data) with limited labeled data in the region to train the mode. Taking Jiaohe County in Jilin Province, China as an example, the landslide inventory from 2000 to 2017 was collected and 12 metrological, geographical, and human explanatory factors were compiled. Meanwhile, supervised models such as deep neural network (DNN), support vector machine (SVM), and logistic regression (LR) were implemented for comparison. Then, the landslide susceptibility was plotted and a series of evaluation tools such as class accuracy, predictive rate curves (AUC), and information gain ratio (IGR) were calculated to compare the prediction of models and factors. Experimental results indicate that the proposed SSL-DNN model (AUC = 0.898) outperformed all the comparison models. Therefore, semi-supervised deep learning could be considered as a potential approach for LSM.

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