A Very Large-Scale Bioactivity Comparison of Deep Learning and Multiple Machine Learning Algorithms for Drug Discovery

2020 ◽  
Author(s):  
Thomas R. Lane ◽  
Daniel H. Foil ◽  
Eni Minerali ◽  
Fabio Urbina ◽  
Kimberley M. Zorn ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Drug Discovery ◽  
Deep Neural Networks ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

<p>Machine learning methods are attracting considerable attention from the pharmaceutical industry for use in drug discovery and applications beyond. In recent studies we have applied multiple machine learning algorithms, modeling metrics and in some cases compared molecular descriptors to build models for individual targets or properties on a relatively small scale. Several research groups have used large numbers of datasets from public databases such as ChEMBL in order to evaluate machine learning methods of interest to them. The largest of these types of studies used on the order of 1400 datasets. We have now extracted well over 5000 datasets from CHEMBL for use with the ECFP6 fingerprint and comparison of our proprietary software Assay Central<sup>TM</sup> with random forest, k-Nearest Neighbors, support vector classification, naïve Bayesian, AdaBoosted decision trees, and deep neural networks (3 levels). Model performance <a>was</a> assessed using an array of five-fold cross-validation metrics including area-under-the-curve, F1 score, Cohen’s kappa and Matthews correlation coefficient. <a>Based on ranked normalized scores for the metrics or datasets all methods appeared comparable while the distance from the top indicated Assay Central<sup>TM</sup> and support vector classification were comparable. </a>Unlike prior studies which have placed considerable emphasis on deep neural networks (deep learning), no advantage was seen in this case where minimal tuning was performed of any of the methods. If anything, Assay Central<sup>TM</sup> may have been at a slight advantage as the activity cutoff for each of the over 5000 datasets representing over 570,000 unique compounds was based on Assay Central<sup>TM</sup>performance, but support vector classification seems to be a strong competitor. We also apply Assay Central<sup>TM</sup> to prospective predictions for PXR and hERG to further validate these models. This work currently appears to be the largest comparison of machine learning algorithms to date. Future studies will likely evaluate additional databases, descriptors and algorithms, as well as further refining methods for evaluating and comparing models. </p><p><b> </b></p>

A Very Large-Scale Bioactivity Comparison of Deep Learning and Multiple Machine Learning Algorithms for Drug Discovery

2020 ◽  
Author(s):  
Thomas R. Lane ◽  
Daniel H. Foil ◽  
Eni Minerali ◽  
Fabio Urbina ◽  
Kimberley M. Zorn ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Drug Discovery ◽  
Deep Neural Networks ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

<p>Machine learning methods are attracting considerable attention from the pharmaceutical industry for use in drug discovery and applications beyond. In recent studies we have applied multiple machine learning algorithms, modeling metrics and in some cases compared molecular descriptors to build models for individual targets or properties on a relatively small scale. Several research groups have used large numbers of datasets from public databases such as ChEMBL in order to evaluate machine learning methods of interest to them. The largest of these types of studies used on the order of 1400 datasets. We have now extracted well over 5000 datasets from CHEMBL for use with the ECFP6 fingerprint and comparison of our proprietary software Assay Central<sup>TM</sup> with random forest, k-Nearest Neighbors, support vector classification, naïve Bayesian, AdaBoosted decision trees, and deep neural networks (3 levels). Model performance <a>was</a> assessed using an array of five-fold cross-validation metrics including area-under-the-curve, F1 score, Cohen’s kappa and Matthews correlation coefficient. <a>Based on ranked normalized scores for the metrics or datasets all methods appeared comparable while the distance from the top indicated Assay Central<sup>TM</sup> and support vector classification were comparable. </a>Unlike prior studies which have placed considerable emphasis on deep neural networks (deep learning), no advantage was seen in this case where minimal tuning was performed of any of the methods. If anything, Assay Central<sup>TM</sup> may have been at a slight advantage as the activity cutoff for each of the over 5000 datasets representing over 570,000 unique compounds was based on Assay Central<sup>TM</sup>performance, but support vector classification seems to be a strong competitor. We also apply Assay Central<sup>TM</sup> to prospective predictions for PXR and hERG to further validate these models. This work currently appears to be the largest comparison of machine learning algorithms to date. Future studies will likely evaluate additional databases, descriptors and algorithms, as well as further refining methods for evaluating and comparing models. </p><p><b> </b></p>

scholarly journals Evaluation of Different Machine Learning Methods and Deep-Learning Convolutional Neural Networks for Landslide Detection

2019 ◽  
Vol 11 (2) ◽  
pp. 196 ◽  
Author(s):  
Omid Ghorbanzadeh ◽  
Thomas Blaschke ◽  
Khalil Gholamnia ◽  
Sansar Meena ◽  
Dirk Tiede ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Expert Knowledge ◽  
Accuracy Assessment ◽  
Window Size ◽  
Optical Data ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

There is a growing demand for detailed and accurate landslide maps and inventories around the globe, but particularly in hazard-prone regions such as the Himalayas. Most standard mapping methods require expert knowledge, supervision and fieldwork. In this study, we use optical data from the Rapid Eye satellite and topographic factors to analyze the potential of machine learning methods, i.e., artificial neural network (ANN), support vector machines (SVM) and random forest (RF), and different deep-learning convolution neural networks (CNNs) for landslide detection. We use two training zones and one test zone to independently evaluate the performance of different methods in the highly landslide-prone Rasuwa district in Nepal. Twenty different maps are created using ANN, SVM and RF and different CNN instantiations and are compared against the results of extensive fieldwork through a mean intersection-over-union (mIOU) and other common metrics. This accuracy assessment yields the best result of 78.26% mIOU for a small window size CNN, which uses spectral information only. The additional information from a 5 m digital elevation model helps to discriminate between human settlements and landslides but does not improve the overall classification accuracy. CNNs do not automatically outperform ANN, SVM and RF, although this is sometimes claimed. Rather, the performance of CNNs strongly depends on their design, i.e., layer depth, input window sizes and training strategies. Here, we conclude that the CNN method is still in its infancy as most researchers will either use predefined parameters in solutions like Google TensorFlow or will apply different settings in a trial-and-error manner. Nevertheless, deep-learning can improve landslide mapping in the future if the effects of the different designs are better understood, enough training samples exist, and the effects of augmentation strategies to artificially increase the number of existing samples are better understood.

Using Machine Learning Methods To Identify Coal Pay Zones from Drilling and Logging-While-Drilling (LWD) Data

SPE Journal ◽  
2020 ◽  
Vol 25 (03) ◽  
pp. 1241-1258 ◽  
Author(s):  
Ruizhi Zhong ◽  
Raymond L. Johnson ◽  
Zhongwei Chen
Keyword(s):  
Machine Learning ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
Support Vector ◽  
Learning Methods ◽  
Well Completion ◽  
Machine Learning Methods ◽  
Extreme Gradient Boosting ◽  
Logging While Drilling

Summary Accurate coal identification is critical in coal seam gas (CSG) (also known as coalbed methane or CBM) developments because it determines well completion design and directly affects gas production. Density logging using radioactive source tools is the primary tool for coal identification, adding well trips to condition the hole and additional well costs for logging runs. In this paper, machine learning methods are applied to identify coals from drilling and logging-while-drilling (LWD) data to reduce overall well costs. Machine learning algorithms include logistic regression (LR), support vector machine (SVM), artificial neural network (ANN), random forest (RF), and extreme gradient boosting (XGBoost). The precision, recall, and F1 score are used as evaluation metrics. Because coal identification is an imbalanced data problem, the performance on the minority class (i.e., coals) is limited. To enhance the performance on coal prediction, two data manipulation techniques [naive random oversampling (NROS) technique and synthetic minority oversampling technique (SMOTE)] are separately coupled with machine learning algorithms. Case studies are performed with data from six wells in the Surat Basin, Australia. For the first set of experiments (single-well experiments), both the training data and test data are in the same well. The machine learning methods can identify coal pay zones for sections with poor or missing logs. It is found that rate of penetration (ROP) is the most important feature. The second set of experiments (multiple-well experiments) uses the training data from multiple nearby wells, which can predict coal pay zones in a new well. The most important feature is gamma ray. After placing slotted casings, all wells have coal identification rates greater than 90%, and three wells have coal identification rates greater than 99%. This indicates that machine learning methods (either XGBoost or ANN/RF with NROS/SMOTE) can be an effective way to identify coal pay zones and reduce coring or logging costs in CSG developments.

scholarly journals A Research on Deep Learning Advance for Landslide Classification using Convolutional Neural Networks

2019 ◽  
Vol 8 (6S4) ◽  
pp. 903-906
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Feature Extraction ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Data Set ◽  
Proposed Model

Landslides can easily be tragic to human life and property. Increase in the rate of human settlement in the mountains has resulted in safety concerns. Landslides have caused economic loss between 1-2% of the GDP in many developing countries. In this study, we discuss a deep learning approach to detect landslides. Convolutional Neural Networks are used for feature extraction for our proposed model. As there was no source of an exact and precise data set for feature extraction, therefore, a new data set was built for testing the model. We have tested and compared this work with our proposed model and with other machine-learning algorithms such as Logistic Regression, Random Forest, AdaBoost, K-Nearest Neighbors and Support Vector Machine. Our proposed deep learning model produces a classification accuracy of 96.90% outperforming the classical machine-learning algorithms.

scholarly journals An Empirical Comparison of Machine-Learning Methods on Bank Client Credit Assessments

2019 ◽  
Vol 11 (3) ◽  
pp. 699 ◽  
Author(s):  
Lkhagvadorj Munkhdalai ◽  
Tsendsuren Munkhdalai ◽  
Oyun-Erdene Namsrai ◽  
Jong Lee ◽  
Keun Ryu
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Random Forest ◽  
Deep Neural Networks ◽  
Credit Scoring ◽  
Support Vector ◽  
Learning Approaches ◽  
Learning Methods ◽  
Human Expert ◽  
Machine Learning Methods

Machine learning and artificial intelligence have achieved a human-level performance in many application domains, including image classification, speech recognition and machine translation. However, in the financial domain expert-based credit risk models have still been dominating. Establishing meaningful benchmark and comparisons on machine-learning approaches and human expert-based models is a prerequisite in further introducing novel methods. Therefore, our main goal in this study is to establish a new benchmark using real consumer data and to provide machine-learning approaches that can serve as a baseline on this benchmark. We performed an extensive comparison between the machine-learning approaches and a human expert-based model—FICO credit scoring system—by using a Survey of Consumer Finances (SCF) data. As the SCF data is non-synthetic and consists of a large number of real variables, we applied two variable-selection methods: the first method used hypothesis tests, correlation and random forest-based feature importance measures and the second method was only a random forest-based new approach (NAP), to select the best representative features for effective modelling and to compare them. We then built regression models based on various machine-learning algorithms ranging from logistic regression and support vector machines to an ensemble of gradient boosted trees and deep neural networks. Our results demonstrated that if lending institutions in the 2001s had used their own credit scoring model constructed by machine-learning methods explored in this study, their expected credit losses would have been lower, and they would be more sustainable. In addition, the deep neural networks and XGBoost algorithms trained on the subset selected by NAP achieve the highest area under the curve (AUC) and accuracy, respectively.

scholarly journals Comparative analysis of machine learning methods by the example of the problem of determining muon decay

2020 ◽  
Vol 28 (2) ◽  
pp. 105-119
Author(s):  
Migran N. Gevorkyan ◽  
Anastasia V. Demidova ◽  
Dmitry S. Kulyabov
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Large Hadron Collider ◽  
Open Source ◽  
Hadron Collider ◽  
Learning Algorithms ◽  
Muon Decay ◽  
Machine Learning Algorithms ◽  
Learning Methods ◽  
Machine Learning Methods

The history of using machine learning algorithms to analyze statistical models is quite long. The development of computer technology has given these algorithms a new breath. Nowadays deep learning is mainstream and most popular area in machine learning. However, the authors believe that many researchers are trying to use deep learning methods beyond their applicability. This happens because of the widespread availability of software systems that implement deep learning algorithms, and the apparent simplicity of research. All this motivate the authors to compare deep learning algorithms and classical machine learning algorithms. The Large Hadron Collider experiment is chosen for this task, because the authors are familiar with this scientific field, and also because the experiment data is open source. The article compares various machine learning algorithms in relation to the problem of recognizing the decay reaction + + + at the Large Hadron Collider. The authors use open source implementations of machine learning algorithms. We compare algorithms with each other based on calculated metrics. As a result of the research, we can conclude that all the considered machine learning methods are quite comparable with each other (taking into account the selected metrics), while different methods have different areas of applicability.

scholarly journals APPLICATION OF MACHINE LEARNING METHODS TO APPROXIMATE THE EXPERIMENTAL CHARACTERISTICS OF A MEMRISTOR

2020 ◽  
Author(s):  
V. Lopatenko
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Scientific Community ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Learning Methods ◽  
Passive Element ◽  
Machine Learning Methods ◽  
Boosting Algorithm

Memristor is a passive element in microelectronics, similar in its properties to a biological synapse. The possibility of using a memristor as an analog element in neural networks increases the interest of the scientific community in the study of its properties. In this paper, we study the possibility of modeling some characteristics of a memristor using machine learning algorithms, in particular, the gradient boosting algorithm.

scholarly journals Systematic literature review of machine learning methods used in the analysis of real-world data for patient-provider decision making

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alan Brnabic ◽  
Lisa M. Hess
Keyword(s):  
Machine Learning ◽  
Decision Making ◽  
Literature Review ◽  
Systematic Literature Review ◽  
Real World ◽  
Learning Algorithms ◽  
External Validation ◽  
Machine Learning Algorithms ◽  
Learning Methods ◽  
Machine Learning Methods

Abstract Background Machine learning is a broad term encompassing a number of methods that allow the investigator to learn from the data. These methods may permit large real-world databases to be more rapidly translated to applications to inform patient-provider decision making. Methods This systematic literature review was conducted to identify published observational research of employed machine learning to inform decision making at the patient-provider level. The search strategy was implemented and studies meeting eligibility criteria were evaluated by two independent reviewers. Relevant data related to study design, statistical methods and strengths and limitations were identified; study quality was assessed using a modified version of the Luo checklist. Results A total of 34 publications from January 2014 to September 2020 were identified and evaluated for this review. There were diverse methods, statistical packages and approaches used across identified studies. The most common methods included decision tree and random forest approaches. Most studies applied internal validation but only two conducted external validation. Most studies utilized one algorithm, and only eight studies applied multiple machine learning algorithms to the data. Seven items on the Luo checklist failed to be met by more than 50% of published studies. Conclusions A wide variety of approaches, algorithms, statistical software, and validation strategies were employed in the application of machine learning methods to inform patient-provider decision making. There is a need to ensure that multiple machine learning approaches are used, the model selection strategy is clearly defined, and both internal and external validation are necessary to be sure that decisions for patient care are being made with the highest quality evidence. Future work should routinely employ ensemble methods incorporating multiple machine learning algorithms.

EMOTIONS RECOGNITION IN HUMAN SPEECH USING DEEP NEURAL NETWORKS

2021 ◽  
pp. 44-51
Author(s):  
E. Yu. Shchetinin
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Convolutional Neural Network ◽  
Recurrent Neural Network ◽  
Deep Neural Networks ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Audio Recordings ◽  
Computer Studies

The recognition of human emotions is one of the most relevant and dynamically developing areas of modern speech technologies, and the recognition of emotions in speech (RER) is the most demanded part of them. In this paper, we propose a computer model of emotion recognition based on an ensemble of bidirectional recurrent neural network with LSTM memory cell and deep convolutional neural network ResNet18. In this paper, computer studies of the RAVDESS database containing emotional speech of a person are carried out. RAVDESS-a data set containing 7356 files. Entries contain the following emotions: 0 – neutral, 1 – calm, 2 – happiness, 3 – sadness, 4 – anger, 5 – fear, 6 – disgust, 7 – surprise. In total, the database contains 16 classes (8 emotions divided into male and female) for a total of 1440 samples (speech only). To train machine learning algorithms and deep neural networks to recognize emotions, existing audio recordings must be pre-processed in such a way as to extract the main characteristic features of certain emotions. This was done using Mel-frequency cepstral coefficients, chroma coefficients, as well as the characteristics of the frequency spectrum of audio recordings. In this paper, computer studies of various models of neural networks for emotion recognition are carried out on the example of the data described above. In addition, machine learning algorithms were used for comparative analysis. Thus, the following models were trained during the experiments: logistic regression (LR), classifier based on the support vector machine (SVM), decision tree (DT), random forest (RF), gradient boosting over trees – XGBoost, convolutional neural network CNN, recurrent neural network RNN (ResNet18), as well as an ensemble of convolutional and recurrent networks Stacked CNN-RNN. The results show that neural networks showed much higher accuracy in recognizing and classifying emotions than the machine learning algorithms used. Of the three neural network models presented, the CNN + BLSTM ensemble showed higher accuracy.

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