Radiomic profiles via machine learning to predict response, overall survival, and KRAS status in metastatic colorectal tumors treated with FOLFOX/bevacizumab/hydroxychloroquine.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15125-e15125
Author(s):  
Saima Rathore ◽  
Mark H. O'Hara ◽  
Thomas Benjamin Karasic ◽  
Maryann Redlinger ◽  
Mark Alan Rosen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Overall Survival ◽  
Clinical Decision Making ◽  
Pearson Correlation ◽  
Ct Imaging ◽  
Support Vector ◽  
Imaging Features ◽  
Data Set ◽  
Mutational Status ◽  
Tp53 Mutational Status

e15125 Background: Autophagy is a resistance mechanism to chemotherapy that is inhibited by hydroxychloroquine (HCQ). We have reported a phase II trial of FOLFOX/bevacizumab/HCQ in 28 evaluable patients with untreated metastatic colorectal cancer (mCRC). Overall response rate was 68%, with 11% complete response (CR) and 57% partial response (PR), while stable disease (SD) was seen in 30%. We hypothesize that analysis of CT imaging features via machine learning (ML) will enhance subtle yet important radiographic characteristics, and reveal imaging signatures determinant of outcome and mutational status. Methods: Baseline CT images were collected and 1265 quantitative imaging (QI) features extracted across all the metastatic sites – liver, lung, and lymph nodes – including descriptors of size, morphology, texture, and intensity. Cross-validated sequential feature selection coupled with support vector machine (SVM) was used to determine the most discriminative QI features for our integrative predictor of response and mutational status, and support vector regression (SVR) was used to derive imaging predictors of overall survival. The model predictions were compared with actual clinical results, including response, survival, and genomic aberrations. Results: Various QI features, primarily descriptive of texture and tumor volume, were determined as most important by the ML predictor. Using this signature, our predictor classified “Responder (PR+CR) vs Non-responder (SD)” with an accuracy of 85% [sensitivity(se) = 0.84, specificity(sp) = 0.71, AUC = 0.85]. The QI features were also able to detect KRAS and TP53 mutational status with an accuracy of 88% [se = 0.92, sp = 0.85, AUC = 0.87] and 86% [se = 0.80, sp = 0.90, AUC = 0.84], respectively. The SVM model predicted overall survival greater than the median (32 mo) with an accuracy of 86% [se = 0.93, sp = 0.79, AUC = 0.87]. The Pearson correlation coefficient between the SVR score and overall survival was estimated to be 0.73 (p < 0.0001). Conclusions: Radiomic analysis of baseline CT imaging features analyzed by ML yielded an imaging signature predictive of response, survival, and KRAS and TP53 mutational status. If validated in a larger clinical data set, machine learning may offer a predictive biomarker to aid clinical decision making for mCRC patients.

scholarly journals Machine Learning Models for Breast Lesions Based on Ultrasound Imaging Features: A Observational Study

2020 ◽  
Author(s):  
Yao Tan ◽  
Ling Huo ◽  
Shu Wang ◽  
Cuizhi Geng ◽  
Yi Li ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Regression Model ◽  
Ultrasound Imaging ◽  
Logistic Model ◽  
Logistic Regression Model ◽  
Support Vector ◽  
Imaging Features ◽  
Data Set ◽  
Class A

Abstract Background: The accuracy of breast cancer (BC) screening based on conventional ultrasound imaging examination largely depends on the experience of clinicians. Further, the effectiveness of BC screening and diagnosis in primary hospitals need to be improved. This study aimed to establish and evaluate the usefulness of a simple, practical, and easy-to-promote machine learning model based on ultrasound imaging features for diagnosing BC.Methods: Logistic regression, random forest, extra trees, support vector, multilayer perceptron, and XG boost models were developed. The modeling data set was divided into a training set and test set in a 75%:25% ratio, and these were used to establish the models and test their performance, respectively. The validation data set of primary hospitals was used for external validation of the model. The area under the receiver operating characteristic curve (AUC) was used as the main evaluation index, and pathological biopsy was used as the gold standard for evaluating each model. Diagnostic capability was also compared with those of clinicians. Results: Among the six models, the logistic model showed superior capability, with an AUC of 0.771 and 0.906 in the test and validation sets, respectively, and Brier scores of 0.18 and 0.165. The AUC of the logistic model in tertiary class A hospitals and primary hospitals was 0.875 and 0.921, respectively. The AUCs of the clinician diagnosis and the logistic model were 0.913 and 0.906. Their AUCs in the tertiary class A hospitals were 0.890 and 0.875, respectively, and were 0.924 and 0.921 in primary hospitals, respectively. Conclusions: The logistic regression model has better overall performance in primary hospitals, and the logistic regression model can be further extended to the basic level. A more balanced clinical prediction model can be further established on the premise of improving accuracy to assist clinicians in decision making and improve diagnosis.Trial Registration: http://www.clinicaltrials.gov. ClinicalTrials.gov ID: NCT03080623.

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.

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 Estimation of Soil Cohesion Using Machine Learning Method: A Random Forest Approach

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Hai-Bang Ly ◽  
Thuy-Anh Nguyen ◽  
Binh Thai Pham
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Soil Properties ◽  
Clay Content ◽  
Absolute Error ◽  
Experimental Methods ◽  
Liquid Limit ◽  
Support Vector ◽  
Data Set ◽  
Soil Cohesion

Soil cohesion (C) is one of the critical soil properties and is closely related to basic soil properties such as particle size distribution, pore size, and shear strength. Hence, it is mainly determined by experimental methods. However, the experimental methods are often time-consuming and costly. Therefore, developing an alternative approach based on machine learning (ML) techniques to solve this problem is highly recommended. In this study, machine learning models, namely, support vector machine (SVM), Gaussian regression process (GPR), and random forest (RF), were built based on a data set of 145 soil samples collected from the Da Nang-Quang Ngai expressway project, Vietnam. The database also includes six input parameters, that is, clay content, moisture content, liquid limit, plastic limit, specific gravity, and void ratio. The performance of the model was assessed by three statistical criteria, namely, the correlation coefficient (R), mean absolute error (MAE), and root mean square error (RMSE). The results demonstrated that the proposed RF model could accurately predict soil cohesion with high accuracy (R = 0.891) and low error (RMSE = 3.323 and MAE = 2.511), and its predictive capability is better than SVM and GPR. Therefore, the RF model can be used as a cost-effective approach in predicting soil cohesion forces used in the design and inspection of constructions.

scholarly journals Big Data for Health Care Analytics using Extreme Machine Learning Based on Map Reduce

2020 ◽  
Vol 9 (3) ◽  
pp. 2758-2762
Keyword(s):  
Machine Learning ◽  
Big Data ◽  
Data Storage ◽  
Clinical Data ◽  
Disease Risk ◽  
Learning Algorithm ◽  
Information Storage ◽  
Support Vector ◽  
Machine Learning Algorithm ◽  
Data Set

A large volume of datasets is available in various fields that are stored to be somewhere which is called big data. Big Data healthcare has clinical data set of every patient records in huge amount and they are maintained by Electronic Health Records (EHR). More than 80 % of clinical data is the unstructured format and reposit in hundreds of forms. The challenges and demand for data storage, analysis is to handling large datasets in terms of efficiency and scalability. Hadoop Map reduces framework uses big data to store and operate any kinds of data speedily. It is not solely meant for storage system however conjointly a platform for information storage moreover as processing. It is scalable and fault-tolerant to the systems. Also, the prediction of the data sets is handled by machine learning algorithm. This work focuses on the Extreme Machine Learning algorithm (ELM) that can utilize the optimized way of finding a solution to find disease risk prediction by combining ELM with Cuckoo Search optimization-based Support Vector Machine (CS-SVM). The proposed work also considers the scalability and accuracy of big data models, thus the proposed algorithm greatly achieves the computing work and got good results in performance of both veracity and efficiency.

scholarly journals Quantitative Methods for Analyzing Intimate Partner Violence in Microblogs: Observational Study

10.2196/15347 ◽  
2020 ◽  
Vol 22 (11) ◽  
pp. e15347
Author(s):  
Christopher Michael Homan ◽  
J Nicolas Schrading ◽  
Raymond W Ptucha ◽  
Catherine Cerulli ◽  
Cecilia Ovesdotter Alm
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Intimate Partner Violence ◽  
Language Processing ◽  
Partner Violence ◽  
Quantitative Methods ◽  
Intimate Partner ◽  
Support Vector ◽  
Data Set ◽  
Part Of Speech

Background Social media is a rich, virtually untapped source of data on the dynamics of intimate partner violence, one that is both global in scale and intimate in detail. Objective The aim of this study is to use machine learning and other computational methods to analyze social media data for the reasons victims give for staying in or leaving abusive relationships. Methods Human annotation, part-of-speech tagging, and machine learning predictive models, including support vector machines, were used on a Twitter data set of 8767 #WhyIStayed and #WhyILeft tweets each. Results Our methods explored whether we can analyze micronarratives that include details about victims, abusers, and other stakeholders, the actions that constitute abuse, and how the stakeholders respond. Conclusions Our findings are consistent across various machine learning methods, which correspond to observations in the clinical literature, and affirm the relevance of natural language processing and machine learning for exploring issues of societal importance in social media.

A Review of Machine Learning Techniques for Anomaly Detection in Static Graphs

2020 ◽  
pp. 146-162
Author(s):  
Hesham M. Al-Ammal
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Anomaly Detection ◽  
Real Life ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Methods ◽  
Data Set ◽  
Learning Techniques ◽  
Vector Machines

Detection of anomalies in a given data set is a vital step in several applications in cybersecurity; including intrusion detection, fraud, and social network analysis. Many of these techniques detect anomalies by examining graph-based data. Analyzing graphs makes it possible to capture relationships, communities, as well as anomalies. The advantage of using graphs is that many real-life situations can be easily modeled by a graph that captures their structure and inter-dependencies. Although anomaly detection in graphs dates back to the 1990s, recent advances in research utilized machine learning methods for anomaly detection over graphs. This chapter will concentrate on static graphs (both labeled and unlabeled), and the chapter summarizes some of these recent studies in machine learning for anomaly detection in graphs. This includes methods such as support vector machines, neural networks, generative neural networks, and deep learning methods. The chapter will reflect the success and challenges of using these methods in the context of graph-based anomaly detection.

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.

scholarly journals Learning to Identify At-Risk Students in Distance Education Using Interaction Counts

2016 ◽  
Vol 23 (2) ◽  
pp. 124 ◽  
Author(s):  
Douglas Detoni ◽  
Cristian Cechinel ◽  
Ricardo Araujo Matsumura ◽  
Daniela Francisco Brauner
Keyword(s):  
Machine Learning ◽  
At Risk ◽  
At Risk Students ◽  
Drop Out ◽  
Support Vector ◽  
Learning Models ◽  
Data Set ◽  
Student Dropout ◽  
Vector Machines ◽  
Machine Learning Models

Student dropout is one of the main problems faced by distance learning courses. One of the major challenges for researchers is to develop methods to predict the behavior of students so that teachers and tutors are able to identify at-risk students as early as possible and provide assistance before they drop out or fail in their courses. Machine Learning models have been used to predict or classify students in these settings. However, while these models have shown promising results in several settings, they usually attain these results using attributes that are not immediately transferable to other courses or platforms. In this paper, we provide a methodology to classify students using only interaction counts from each student. We evaluate this methodology on a data set from two majors based on the Moodle platform. We run experiments consisting of training and evaluating three machine learning models (Support Vector Machines, Naive Bayes and Adaboost decision trees) under different scenarios. We provide evidences that patterns from interaction counts can provide useful information for classifying at-risk students. This classification allows the customization of the activities presented to at-risk students (automatically or through tutors) as an attempt to avoid students drop out.

scholarly journals The Application of Machine Learning to a General Risk–Need Assessment Instrument in the Prediction of Criminal Recidivism

2020 ◽  
pp. 009385482096975
Author(s):  
Mehdi Ghasemi ◽  
Daniel Anvari ◽  
Mahshid Atapour ◽  
J. Stephen wormith ◽  
Keira C. Stockdale ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Accuracy ◽  
Characteristic Curve ◽  
Assessment Instrument ◽  
Support Vector ◽  
Data Set ◽  
Applied Machine Learning ◽  
Vector Machines ◽  
Individual Scores

The Level of Service/Case Management Inventory (LS/CMI) is one of the most frequently used tools to assess criminogenic risk–need in justice-involved individuals. Meta-analytic research demonstrates strong predictive accuracy for various recidivism outcomes. In this exploratory study, we applied machine learning (ML) algorithms (decision trees, random forests, and support vector machines) to a data set with nearly 100,000 LS/CMI administrations to provincial corrections clientele in Ontario, Canada, and approximately 3 years follow-up. The overall accuracies and areas under the receiver operating characteristic curve (AUCs) were comparable, although ML outperformed LS/CMI in terms of predictive accuracy for the middle scores where it is hardest to predict the recidivism outcome. Moreover, ML improved the AUCs for individual scores to near 0.60, from 0.50 for the LS/CMI, indicating that ML also improves the ability to rank individuals according to their probability of recidivating. Potential considerations, applications, and future directions are discussed.

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