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.

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 A Comparison of Machine Learning and Bayesian Modelling for Molecular Serotyping

2017 ◽  
Author(s):  
Richard Newton ◽  
Lorenz Wernisch
Keyword(s):  
Machine Learning ◽  
Bayesian Model ◽  
Learning Algorithms ◽  
Biological Data ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
Gradient Boosting ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Molecular Serotyping

AbstractBackgroundStreptococcus pneumoniae is a human pathogen that is a major cause of infant mortality. Identifying the pneumococcal serotype is an important step in monitoring the impact of vaccines used to protect against disease. Genomic microarrays provide an effective method for molecular serotyping. Previously we developed an empirical Bayesian model for the classification of serotypes from a molecular serotyping array. With only few samples available, a model driven approach was the only option. In the meanwhile, several thousand samples have been made available to us, providing an opportunity to investigate serotype classification by machine learning methods, which could complement the Bayesian model.ResultsWe compare the performance of the original Bayesian model with two machine learning algorithms: Gradient Boosting Machines and Random Forests. We present our results as an example of a generic strategy whereby a preliminary probabilistic model is complemented or replaced by a machine learning classifier once enough data are available. Despite the availability of thousands of serotyping arrays, a problem encountered when applying machine learning methods is the lack of training data containing mixtures of serotypes; due to the large number of possible combinations. Most of the available training data comprises samples with only a single serotype. To overcome the lack of training data we implemented an iterative analysis, creating artificial training data of serotype mixtures by combining raw data from single serotype arrays.ConclusionsWith the enhanced training set the machine learning algorithms out perform the original Bayesian model. However, for serotypes currently lacking sufficient training data the best performing implementation was a combination of the results of the Bayesian Model and the Gradient Boosting Machine. As well as being an effective method for classifying biological data, machine learning can also be used as an efficient method for revealing subtle biological insights, which we illustrate with an example.

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 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.

scholarly journals Prediction of Hanwoo Cattle Phenotypes from Genotypes Using Machine Learning Methods

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2066
Author(s):  
Swati Srivastava ◽  
Bryan Irvine Lopez ◽  
Himansu Kumar ◽  
Myoungjin Jang ◽  
Han-Ha Chai ◽  
...  
Keyword(s):  
Machine Learning ◽  
Support Vector ◽  
Learning Methods ◽  
Eye Muscle ◽  
Important Species ◽  
Machine Learning Methods ◽  
Extreme Gradient Boosting ◽  
Boosting Method ◽  
Predictive Correlation ◽  
Hanwoo Cattle

Hanwoo was originally raised for draft purposes, but the increase in local demand for red meat turned that purpose into full-scale meat-type cattle rearing; it is now considered one of the most economically important species and a vital food source for Koreans. The application of genomic selection in Hanwoo breeding programs in recent years was expected to lead to higher genetic progress. However, better statistical methods that can improve the genomic prediction accuracy are required. Hence, this study aimed to compare the predictive performance of three machine learning methods, namely, random forest (RF), extreme gradient boosting method (XGB), and support vector machine (SVM), when predicting the carcass weight (CWT), marbling score (MS), backfat thickness (BFT) and eye muscle area (EMA). Phenotypic and genotypic data (53,866 SNPs) from 7324 commercial Hanwoo cattle that were slaughtered at the age of around 30 months were used. The results showed that the boosting method XGB showed the highest predictive correlation for CWT and MS, followed by GBLUP, SVM, and RF. Meanwhile, the best predictive correlation for BFT and EMA was delivered by GBLUP, followed by SVM, RF, and XGB. Although XGB presented the highest predictive correlations for some traits, we did not find an advantage of XGB or any machine learning methods over GBLUP according to the mean squared error of prediction. Thus, we still recommend the use of GBLUP in the prediction of genomic breeding values for carcass traits in Hanwoo cattle.

scholarly journals Possibility of Autonomous Estimation of Shiba Goat’s Estrus and Non-Estrus Behavior by Machine Learning Methods

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 771
Author(s):  
Toshiya Arakawa
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Random Forest ◽  
Markov Models ◽  
Tracking System ◽  
Video Tracking ◽  
Training Data ◽  
Support Vector ◽  
Learning Methods ◽  
Machine Learning Methods

Mammalian behavior is typically monitored by observation. However, direct observation requires a substantial amount of effort and time, if the number of mammals to be observed is sufficiently large or if the observation is conducted for a prolonged period. In this study, machine learning methods as hidden Markov models (HMMs), random forests, support vector machines (SVMs), and neural networks, were applied to detect and estimate whether a goat is in estrus based on the goat’s behavior; thus, the adequacy of the method was verified. Goat’s tracking data was obtained using a video tracking system and used to estimate whether they, which are in “estrus” or “non-estrus”, were in either states: “approaching the male”, or “standing near the male”. Totally, the PC of random forest seems to be the highest. However, The percentage concordance (PC) value besides the goats whose data were used for training data sets is relatively low. It is suggested that random forest tend to over-fit to training data. Besides random forest, the PC of HMMs and SVMs is high. However, considering the calculation time and HMM’s advantage in that it is a time series model, HMM is better method. The PC of neural network is totally low, however, if the more goat’s data were acquired, neural network would be an adequate method for estimation.

scholarly journals MODIS-FIRMS and ground-truthing based wildfire likelihood mapping of Sikkim Himalaya using machine learning algorithms.

2021 ◽  
Author(s):  
Polash Banerjee
Keyword(s):  
Machine Learning ◽  
Machine Learning Algorithms ◽  
Tree Cover ◽  
Anthropogenic Factors ◽  
Gradient Boosting ◽  
Support Vector ◽  
Learning Methods ◽  
Sikkim Himalaya ◽  
Environmental Features ◽  
Machine Learning Methods

Abstract Wildfires in limited extent and intensity can be a boon for the forest ecosystem. However, recent episodes of wildfires of 2019 in Australia and Brazil are sad reminders of their heavy ecological and economical costs. Understanding the role of environmental factors in the likelihood of wildfires in a spatial context would be instrumental in mitigating it. In this study, 14 environmental features encompassing meteorological, topographical, ecological, in situ and anthropogenic factors have been considered for preparing the wildfire likelihood map of Sikkim Himalaya. A comparative study on the efficiency of machine learning methods like Generalized Linear Model (GLM), Support Vector Machine (SVM), Random Forest (RF) and Gradient Boosting Model (GBM) has been performed to identify the best performing algorithm in wildfire prediction. The study indicates that all the machine learning methods are good at predicting wildfires. However, RF has outperformed, followed by GBM in the prediction. Also, environmental features like average temperature, average wind speed, proximity to roadways and tree cover percentage are the most important determinants of wildfires in Sikkim Himalaya. This study can be considered as a decision support tool for preparedness, efficient resource allocation and sensitization of people towards mitigation of wildfires in Sikkim.

scholarly journals Landslide susceptibility mapping using machine learning for Wenchuan County, Sichuan province, China

2020 ◽  
Vol 198 ◽  
pp. 03023
Author(s):  
Xin Yang ◽  
Rui Liu ◽  
Luyao Li ◽  
Mei Yang ◽  
Yuantao Yang
Keyword(s):  
Machine Learning ◽  
Landslide Susceptibility ◽  
Susceptibility Mapping ◽  
Machine Learning Algorithms ◽  
Landslide Susceptibility Mapping ◽  
Support Vector ◽  
Roc Curve Analysis ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Boosted Decision Tree

Landslide susceptibility mapping is a method used to assess the probability and spatial distribution of landslide occurrences. Machine learning methods have been widely used in landslide susceptibility in recent years. In this paper, six popular machine learning algorithms namely logistic regression, multi-layer perceptron, random forests, support vector machine, Adaboost, and gradient boosted decision tree were leveraged to construct landslide susceptibility models with a total of 1365 landslide points and 14 predisposing factors. Subsequently, the landslide susceptibility maps (LSM) were generated by the trained models. LSM shows the main landslide zone is concentrated in the southeastern area of Wenchuan County. The result of ROC curve analysis shows that all models fitted the training datasets and achieved satisfactory results on validation datasets. The results of this paper reveal that machine learning methods are feasible to build robust landslide susceptibility models.

scholarly journals Techniques for Detecting Malware Traffic: A Comprehensive Approach to Feature Selection and Classification

2021 ◽  
Vol 9 (12) ◽  
pp. 1-10
Author(s):  
Harsha A K
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Random Forest ◽  
Learning Algorithms ◽  
Malware Detection ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Support Vector ◽  
Steady Increase ◽  
Extreme Gradient Boosting

Abstract: Since the advent of encryption, there has been a steady increase in malware being transmitted over encrypted networks. Traditional approaches to detect malware like packet content analysis are inefficient in dealing with encrypted data. In the absence of actual packet contents, we can make use of other features like packet size, arrival time, source and destination addresses and other such metadata to detect malware. Such information can be used to train machine learning classifiers in order to classify malicious and benign packets. In this paper, we offer an efficient malware detection approach using classification algorithms in machine learning such as support vector machine, random forest and extreme gradient boosting. We employ an extensive feature selection process to reduce the dimensionality of the chosen dataset. The dataset is then split into training and testing sets. Machine learning algorithms are trained using the training set. These models are then evaluated against the testing set in order to assess their respective performances. We further attempt to tune the hyper parameters of the algorithms, in order to achieve better results. Random forest and extreme gradient boosting algorithms performed exceptionally well in our experiments, resulting in area under the curve values of 0.9928 and 0.9998 respectively. Our work demonstrates that malware traffic can be effectively classified using conventional machine learning algorithms and also shows the importance of dimensionality reduction in such classification problems. Keywords: Malware Detection, Extreme Gradient Boosting, Random Forest, Feature Selection.

Abstract 15895: Machine Learning Algorithms to Predict Major Adverse Cardiovascular Events in Patients Undergoing Orthotopic Liver Transplantation: A Retrospective Cohort Study

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
vardhmaan jain ◽  
Vikram Sharma ◽  
Agam Bansal ◽  
Cerise Kleb ◽  
Chirag Sheth ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Cardiovascular Events ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Major Adverse Cardiovascular Events ◽  
Support Vector ◽  
Post Transplant ◽  
Extreme Gradient Boosting ◽  
All Cause Mortality

Background: Post-transplant major adverse cardiovascular events (MACE) are amongst the leading cause of death amongst orthotopic liver transplant(OLT) recipients. Despite years of guideline directed therapy, there are limited data on predictors of post-OLT MACE. We assessed if machine learning algorithms (MLA) can predict MACE and all-cause mortality in patients undergoing OLT. Methods: We tested three MLA: support vector machine, extreme gradient boosting(XG-Boost) and random forest with traditional logistic regression for prediction of MACE and all-cause mortality on a cohort of consecutive patients undergoing OLT at our center between 2008-2019. The cohort was randomly split into a training (80%) and testing (20%) cohort. Model performance was assessed using c-statistic or AUC. Results: We included 1,459 consecutive patients with mean ± SD age 54.2 ± 13.8 years, 32% female who underwent OLT. There were 199 (13.6%) MACE and 289 (20%) deaths at a mean follow up of 4.56 ± 3.3 years. The random forest MLA was the best performing model for predicting MACE [AUC:0.78, 95% CI: 0.70-0.85] as well as mortality [AUC:0.69, 95% CI: 0.61-0.76], with all models performing better when predicting MACE vs mortality. See Table and Figure. Conclusion: Random forest machine learning algorithms were more predictive and discriminative than traditional regression models for predicting major adverse cardiovascular events and all-cause mortality in patients undergoing OLT. Validation and subsequent incorporation of MLA in clinical decision making for OLT candidacy could help risk stratify patients for post-transplant adverse cardiovascular events.

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