Exploiting Rules to Enhance Machine Learning in Extracting Information From Multi-Institutional Prostate Pathology Reports

2020 ◽  
pp. 865-874
Author(s):  
Enrico Santus ◽  
Tal Schuster ◽  
Amir M. Tahmasebi ◽  
Clara Li ◽  
Adam Yala ◽  
...  
Keyword(s):  
Machine Learning ◽  
Hybrid Systems ◽  
High Performance ◽  
Feature Model ◽  
Training Data ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Extreme Gradient Boosting ◽  
Pathology Reports

PURPOSE Literature on clinical note mining has highlighted the superiority of machine learning (ML) over hand-crafted rules. Nevertheless, most studies assume the availability of large training sets, which is rarely the case. For this reason, in the clinical setting, rules are still common. We suggest 2 methods to leverage the knowledge encoded in pre-existing rules to inform ML decisions and obtain high performance, even with scarce annotations. METHODS We collected 501 prostate pathology reports from 6 American hospitals. Reports were split into 2,711 core segments, annotated with 20 attributes describing the histology, grade, extension, and location of tumors. The data set was split by institutions to generate a cross-institutional evaluation setting. We assessed 4 systems, namely a rule-based approach, an ML model, and 2 hybrid systems integrating the previous methods: a Rule as Feature model and a Classifier Confidence model. Several ML algorithms were tested, including logistic regression (LR), support vector machine (SVM), and eXtreme gradient boosting (XGB). RESULTS When training on data from a single institution, LR lags behind the rules by 3.5% (F1 score: 92.2% v 95.7%). Hybrid models, instead, obtain competitive results, with Classifier Confidence outperforming the rules by +0.5% (96.2%). When a larger amount of data from multiple institutions is used, LR improves by +1.5% over the rules (97.2%), whereas hybrid systems obtain +2.2% for Rule as Feature (97.7%) and +2.6% for Classifier Confidence (98.3%). Replacing LR with SVM or XGB yielded similar performance gains. CONCLUSION We developed methods to use pre-existing handcrafted rules to inform ML algorithms. These hybrid systems obtain better performance than either rules or ML models alone, even when training data are limited.

A Critical Literature Review on Rock Petrophysical Properties Estimation from Images Based on Direct Simulation and Machine Learning Techniques

2021 ◽  
Author(s):  
Ahmed Samir Rizk ◽  
Moussa Tembely ◽  
Waleed AlAmeri ◽  
Emad W. Al-Shalabi
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Literature Review ◽  
Training Data ◽  
Rock Properties ◽  
Gradient Boosting ◽  
Petrophysical Properties ◽  
Direct Simulation ◽  
Data Set ◽  
Extreme Gradient Boosting

Abstract Estimation of petrophysical properties is essential for accurate reservoir predictions. In recent years, extensive work has been dedicated into training different machine-learning (ML) models to predict petrophysical properties of digital rock using dry rock images along with data from single-phase direct simulations, such as lattice Boltzmann method (LBM) and finite volume method (FVM). The objective of this paper is to present a comprehensive literature review on petrophysical properties estimation from dry rock images using different ML workflows and direct simulation methods. The review provides detailed comparison between different ML algorithms that have been used in the literature to estimate porosity, permeability, tortuosity, and effective diffusivity. In this paper, various ML workflows from the literature are screened and compared in terms of the training data set, the testing data set, the extracted features, the algorithms employed as well as their accuracy. A thorough description of the most commonly used algorithms is also provided to better understand the functionality of these algorithms to encode the relationship between the rock images and their respective petrophysical properties. The review of various ML workflows for estimating rock petrophysical properties from dry images shows that models trained using features extracted from the image (physics-informed models) outperformed models trained on the dry images directly. In addition, certain tree-based ML algorithms, such as random forest, gradient boosting, and extreme gradient boosting can produce accurate predictions that are comparable to deep learning algorithms such as deep neural networks (DNNs) and convolutional neural networks (CNNs). To the best of our knowledge, this is the first work dedicated to exploring and comparing between different ML frameworks that have recently been used to accurately and efficiently estimate rock petrophysical properties from images. This work will enable other researchers to have a broad understanding about the topic and help in developing new ML workflows or further modifying exiting ones in order to improve the characterization of rock properties. Also, this comparison represents a guide to understand the performance and applicability of different ML algorithms. Moreover, the review helps the researchers in this area to cope with digital innovations in porous media characterization in this fourth industrial age – oil and gas 4.0.

scholarly journals Prediction of Radiation Pneumonitis With Machine Learning in Stage III Lung Cancer: A Pilot Study

2021 ◽  
Vol 20 ◽  
pp. 153303382110163
Author(s):  
Melek Yakar ◽  
Durmus Etiz ◽  
Muzaffer Metintas ◽  
Guntulu Ak ◽  
Ozer Celik
Keyword(s):  
Machine Learning ◽  
Lung Cancer ◽  
Radiation Pneumonitis ◽  
Stage Iii ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Volume Number ◽  
Light Gradient ◽  
Extreme Gradient Boosting

Background: Radiation pneumonitis (RP) is a dose-limiting toxicity in lung cancer radiotherapy (RT). As risk factors in the development of RP, patient and tumor characteristics, dosimetric parameters, and treatment features are intertwined, and it is not always possible to associate RP with a single parameter. This study aimed to determine the algorithm that most accurately predicted RP development with machine learning. Methods: Of the 197 cases diagnosed with stage III lung cancer and underwent RT and chemotherapy between 2014 and 2020, 193 were evaluated. The CTCAE 5.0 grading system was used for the RP evaluation. Synthetic minority oversampling technique was used to create a balanced data set. Logistic regression, artificial neural networks, eXtreme Gradient Boosting (XGB), Support Vector Machines, Random Forest, Gaussian Naive Bayes and Light Gradient Boosting Machine algorithms were used. After the correlation analysis, a permutation-based method was utilized for as a variable selection. Results: RP was seen in 51 of the 193 cases. Parameters affecting RP were determined as, total(t)V5, ipsilateral lung Dmax, contralateral lung Dmax, total lung Dmax, gross tumor volume, number of chemotherapy cycles before RT, tumor size, lymph node localization and asbestos exposure. LGBM was found to be the algorithm that best predicted RP at 85% accuracy (confidence interval: 0.73-0.96), 97% sensitivity, and 50% specificity. Conclusion: When the clinical and dosimetric parameters were evaluated together, the LGBM algorithm had the highest accuracy in predicting RP. However, in order to use this algorithm in clinical practice, it is necessary to increase data diversity and the number of patients by sharing data between centers.

scholarly journals A Predictive Mimicker of Fracture Behavior in Fiber Reinforced Concrete Using Machine Learning

Materials ◽  
2021 ◽  
Vol 14 (24) ◽  
pp. 7669
Author(s):  
Sikandar Ali Khokhar ◽  
Touqeer Ahmed ◽  
Rao Arsalan Khushnood ◽  
Syed Muhammad Ali ◽  
Shahnawaz
Keyword(s):  
Machine Learning ◽  
Reinforced Concrete ◽  
Fracture Behavior ◽  
Fiber Reinforced Concrete ◽  
Gradient Boosting ◽  
Support Vector ◽  
Fiber Reinforced ◽  
Mixed Design ◽  
Data Set ◽  
Extreme Gradient Boosting

Due to the exceptional qualities of fiber reinforced concrete, its application is expanding day by day. However, its mixed design is mainly based on extensive experimentations. This study aims to construct a machine learning model capable of predicting the fracture behavior of all conceivable fiber reinforced concrete subclasses, especially strain hardening engineered cementitious composites. This study evaluates 15x input parameters that include the ingredients of the mixed design and the fiber properties. As a result, it predicts, for the first time, the post-peak fracture behavior of fiber-reinforced concrete matrices. Five machine learning models are developed, and their outputs are compared. These include artificial neural networks, the support vector machine, the classification and regression tree, the Gaussian process of regression, and the extreme gradient boosting tree. Due to the small size of the available dataset, this article employs a unique technique called the generative adversarial network to build a virtual data set to augment the data and improve accuracy. The results indicate that the extreme gradient boosting tree model has the lowest error and, therefore, the best mimicker in predicting fiber reinforced concrete properties. This article is anticipated to provide a considerable improvement in the recipe design of effective fiber reinforced concrete formulations.

scholarly journals Machine Learning Based Prediction of Insufficient Herbage Allowance with Automated Feeding Behaviour and Activity Data

Sensors ◽  
2019 ◽  
Vol 19 (20) ◽  
pp. 4479 ◽  
Author(s):  
Abu Zar Shafiullah ◽  
Jessica Werner ◽  
Emer Kennedy ◽  
Lorenzo Leso ◽  
Bernadette O’Brien ◽  
...  
Keyword(s):  
Machine Learning ◽  
Binary Classification ◽  
Characteristic Curve ◽  
Training Data ◽  
Sensor Data ◽  
Gradient Boosting ◽  
Support Vector ◽  
Pasture Management ◽  
Activity Data ◽  
Extreme Gradient Boosting

Sensor technologies that measure grazing and ruminating behaviour as well as physical activities of individual cows are intended to be included in precision pasture management. One of the advantages of sensor data is they can be analysed to support farmers in many decision-making processes. This article thus considers the performance of a set of RumiWatchSystem recorded variables in the prediction of insufficient herbage allowance for spring calving dairy cows. Several commonly used models in machine learning (ML) were applied to the binary classification problem, i.e., sufficient or insufficient herbage allowance, and the predictive performance was compared based on the classification evaluation metrics. Most of the ML models and generalised linear model (GLM) performed similarly in leave-out-one-animal (LOOA) approach to validation studies. However, cross validation (CV) studies, where a portion of features in the test and training data resulted from the same cows, revealed that support vector machine (SVM), random forest (RF) and extreme gradient boosting (XGBoost) performed relatively better than other candidate models. In general, these ML models attained 88% AUC (area under receiver operating characteristic curve) and around 80% sensitivity, specificity, accuracy, precision and F-score. This study further identified that number of rumination chews per day and grazing bites per minute were the most important predictors and examined the marginal effects of the variables on model prediction towards a decision support system.

In silico Prediction of Inhibitory Constant of Thrombin Inhibitors Using Machine Learning

2019 ◽  
Vol 21 (9) ◽  
pp. 662-669 ◽  
Author(s):  
Junnan Zhao ◽  
Lu Zhu ◽  
Weineng Zhou ◽  
Lingfeng Yin ◽  
Yuchen Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Regression Tree ◽  
Large Data ◽  
Thrombin Inhibitors ◽  
Coagulation Cascade ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Descriptor Selection

Background: Thrombin is the central protease of the vertebrate blood coagulation cascade, which is closely related to cardiovascular diseases. The inhibitory constant Ki is the most significant property of thrombin inhibitors. Method: This study was carried out to predict Ki values of thrombin inhibitors based on a large data set by using machine learning methods. Taking advantage of finding non-intuitive regularities on high-dimensional datasets, machine learning can be used to build effective predictive models. A total of 6554 descriptors for each compound were collected and an efficient descriptor selection method was chosen to find the appropriate descriptors. Four different methods including multiple linear regression (MLR), K Nearest Neighbors (KNN), Gradient Boosting Regression Tree (GBRT) and Support Vector Machine (SVM) were implemented to build prediction models with these selected descriptors. Results: The SVM model was the best one among these methods with R2=0.84, MSE=0.55 for the training set and R2=0.83, MSE=0.56 for the test set. Several validation methods such as yrandomization test and applicability domain evaluation, were adopted to assess the robustness and generalization ability of the model. The final model shows excellent stability and predictive ability and can be employed for rapid estimation of the inhibitory constant, which is full of help for designing novel thrombin inhibitors.

scholarly journals Machine learning models to identify low adherence to influenza vaccination among Korean adults with cardiovascular disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Moojung Kim ◽  
Young Jae Kim ◽  
Sung Jin Park ◽  
Kwang Gi Kim ◽  
Pyung Chun Oh ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cardiovascular Disease ◽  
Influenza Vaccination ◽  
Machine Learning Techniques ◽  
Gradient Boosting ◽  
Support Vector ◽  
Age Group ◽  
Learning Models ◽  
Extreme Gradient Boosting ◽  
Machine Learning Models

Abstract Background Annual influenza vaccination is an important public health measure to prevent influenza infections and is strongly recommended for cardiovascular disease (CVD) patients, especially in the current coronavirus disease 2019 (COVID-19) pandemic. The aim of this study is to develop a machine learning model to identify Korean adult CVD patients with low adherence to influenza vaccination Methods Adults with CVD (n = 815) from a nationally representative dataset of the Fifth Korea National Health and Nutrition Examination Survey (KNHANES V) were analyzed. Among these adults, 500 (61.4%) had answered "yes" to whether they had received seasonal influenza vaccinations in the past 12 months. The classification process was performed using the logistic regression (LR), random forest (RF), support vector machine (SVM), and extreme gradient boosting (XGB) machine learning techniques. Because the Ministry of Health and Welfare in Korea offers free influenza immunization for the elderly, separate models were developed for the < 65 and ≥ 65 age groups. Results The accuracy of machine learning models using 16 variables as predictors of low influenza vaccination adherence was compared; for the ≥ 65 age group, XGB (84.7%) and RF (84.7%) have the best accuracies, followed by LR (82.7%) and SVM (77.6%). For the < 65 age group, SVM has the best accuracy (68.4%), followed by RF (64.9%), LR (63.2%), and XGB (61.4%). Conclusions The machine leaning models show comparable performance in classifying adult CVD patients with low adherence to influenza vaccination.

scholarly journals Explainable machine learning can outperform Cox regression predictions and provide insights in breast cancer survival

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arturo Moncada-Torres ◽  
Marissa C. van Maaren ◽  
Mathijs P. Hendriks ◽  
Sabine Siesling ◽  
Gijs Geleijnse
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Explicit Knowledge ◽  
Cox Regression ◽  
Metastatic Breast ◽  
Gradient Boosting ◽  
Support Vector ◽  
Netherlands Cancer Registry ◽  
Extreme Gradient Boosting ◽  
The Impact

AbstractCox Proportional Hazards (CPH) analysis is the standard for survival analysis in oncology. Recently, several machine learning (ML) techniques have been adapted for this task. Although they have shown to yield results at least as good as classical methods, they are often disregarded because of their lack of transparency and little to no explainability, which are key for their adoption in clinical settings. In this paper, we used data from the Netherlands Cancer Registry of 36,658 non-metastatic breast cancer patients to compare the performance of CPH with ML techniques (Random Survival Forests, Survival Support Vector Machines, and Extreme Gradient Boosting [XGB]) in predicting survival using the $$c$$ c -index. We demonstrated that in our dataset, ML-based models can perform at least as good as the classical CPH regression ($$c$$ c -index $$\sim \,0.63$$ ∼ 0.63 ), and in the case of XGB even better ($$c$$ c -index $$\sim 0.73$$ ∼ 0.73 ). Furthermore, we used Shapley Additive Explanation (SHAP) values to explain the models’ predictions. We concluded that the difference in performance can be attributed to XGB’s ability to model nonlinearities and complex interactions. We also investigated the impact of specific features on the models’ predictions as well as their corresponding insights. Lastly, we showed that explainable ML can generate explicit knowledge of how models make their predictions, which is crucial in increasing the trust and adoption of innovative ML techniques in oncology and healthcare overall.

Abstract 1122‐000047: Machine Learning to Predict Stroke Outcomes after Mechanical Thrombectomy

2021 ◽  
Vol 1 (S1) ◽  
Author(s):  
Mehdi Bouslama ◽  
Leonardo Pisani ◽  
Diogo Haussen ◽  
Raul Nogueira
Keyword(s):  
Machine Learning ◽  
Decision Making ◽  
Cerebral Artery ◽  
Training Data ◽  
Gradient Boosting ◽  
Support Vector ◽  
Anterior Circulation ◽  
Discriminative Performance ◽  
Post Procedure ◽  
Procedural Models

Introduction : Prognostication is an integral part of clinical decision‐making in stroke care. Machine learning (ML) methods have gained increasing popularity in the medical field due to their flexibility and high performance. Using a large comprehensive stroke center registry, we sought to apply various ML techniques for 90‐day stroke outcome predictions after thrombectomy. Methods : We used individual patient data from our prospectively collected thrombectomy database between 09/2010 and 03/2020. Patients with anterior circulation strokes (Internal Carotid Artery, Middle Cerebral Artery M1, M2, or M3 segments and Anterior Cerebral Artery) and complete records were included. Our primary outcome was 90‐day functional independence (defined as modified Rankin Scale score 0–2). Pre‐ and post‐procedure models were developed. Four known ML algorithms (support vector machine, random forest, gradient boosting, and artificial neural network) were implemented using a 70/30 training‐test data split and 10‐fold cross‐validation on the training data for model calibration. Discriminative performance was evaluated using the area under the receiver operator characteristics curve (AUC) metric. Results : Among 1248 patients with anterior circulation large vessel occlusion stroke undergoing thrombectomy during the study period, 1020 had complete records and were included in the analysis. In the training data (n = 714), 49.3% of the patients achieved independence at 90‐days. Fifteen baseline clinical, laboratory and neuroimaging features were used to develop the pre‐procedural models, with four additional parameters included in the post‐procedure models. For the preprocedural models, the highest AUC was 0.797 (95%CI [0.75‐ 0.85]) for the gradient boosting model. Similarly, the same ML technique performed best on post‐procedural data and had an improved discriminative performance compared to the pre‐procedure model with an AUC of 0.82 (95%CI [0.77‐ 0.87]). Conclusions : Our pre‐and post‐procedural models reliably estimated outcomes in stroke patients undergoing thrombectomy. They represent a step forward in creating simple and efficient prognostication tools to aid treatment decision‐making. A web‐based platform and related mobile app are underway.

A sentiment analysis system for social media using machine learning techniques: Social enablement

2018 ◽  
Vol 34 (3) ◽  
pp. 569-581 ◽  
Author(s):  
Sujata Rani ◽  
Parteek Kumar
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Sentiment Analysis ◽  
Media Analysis ◽  
Training Data ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Analysis Tool ◽  
Data Set ◽  
Learning Techniques

Abstract In this article, an innovative approach to perform the sentiment analysis (SA) has been presented. The proposed system handles the issues of Romanized or abbreviated text and spelling variations in the text to perform the sentiment analysis. The training data set of 3,000 movie reviews and tweets has been manually labeled by native speakers of Hindi in three classes, i.e. positive, negative, and neutral. The system uses WEKA (Waikato Environment for Knowledge Analysis) tool to convert these string data into numerical matrices and applies three machine learning techniques, i.e. Naive Bayes (NB), J48, and support vector machine (SVM). The proposed system has been tested on 100 movie reviews and tweets, and it has been observed that SVM has performed best in comparison to other classifiers, and it has an accuracy of 68% for movie reviews and 82% in case of tweets. The results of the proposed system are very promising and can be used in emerging applications like SA of product reviews and social media analysis. Additionally, the proposed system can be used in other cultural/social benefits like predicting/fighting human riots.

scholarly journals Exploring the Mechanism of Crashes with Autonomous Vehicles Using Machine Learning

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Hengrui Chen ◽  
Hong Chen ◽  
Ruiyu Zhou ◽  
Zhizhen Liu ◽  
Xiaoke Sun
Keyword(s):  
Machine Learning ◽  
Autonomous Vehicles ◽  
Classification And Regression Tree ◽  
Gradient Boosting ◽  
Support Vector ◽  
Crash Severity ◽  
Apriori Algorithm ◽  
Driving Mode ◽  
Extreme Gradient Boosting ◽  
The Impact

The safety issue has become a critical obstacle that cannot be ignored in the marketization of autonomous vehicles (AVs). The objective of this study is to explore the mechanism of AV-involved crashes and analyze the impact of each feature on crash severity. We use the Apriori algorithm to explore the causal relationship between multiple factors to explore the mechanism of crashes. We use various machine learning models, including support vector machine (SVM), classification and regression tree (CART), and eXtreme Gradient Boosting (XGBoost), to analyze the crash severity. Besides, we apply the Shapley Additive Explanations (SHAP) to interpret the importance of each factor. The results indicate that XGBoost obtains the best result (recall = 75%; G-mean = 67.82%). Both XGBoost and Apriori algorithm effectively provided meaningful insights about AV-involved crash characteristics and their relationship. Among all these features, vehicle damage, weather conditions, accident location, and driving mode are the most critical features. We found that most rear-end crashes are conventional vehicles bumping into the rear of AVs. Drivers should be extremely cautious when driving in fog, snow, and insufficient light. Besides, drivers should be careful when driving near intersections, especially in the autonomous driving mode.

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