scholarly journals Permutation-based identification of important biomarkers for complex diseases via machine learning models

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xinlei Mi ◽  
Baiming Zou ◽  
Fei Zou ◽  
Jianhua Hu
Keyword(s):  
Machine Learning ◽  
Human Disease ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Support Vector ◽  
Individual Feature ◽  
Learning Models ◽  
Efficient Manner ◽  
Feature Importance ◽  
Machine Learning Models

AbstractStudy of human disease remains challenging due to convoluted disease etiologies and complex molecular mechanisms at genetic, genomic, and proteomic levels. Many machine learning-based methods have been developed and widely used to alleviate some analytic challenges in complex human disease studies. While enjoying the modeling flexibility and robustness, these model frameworks suffer from non-transparency and difficulty in interpreting each individual feature due to their sophisticated algorithms. However, identifying important biomarkers is a critical pursuit towards assisting researchers to establish novel hypotheses regarding prevention, diagnosis and treatment of complex human diseases. Herein, we propose a Permutation-based Feature Importance Test (PermFIT) for estimating and testing the feature importance, and for assisting interpretation of individual feature in complex frameworks, including deep neural networks, random forests, and support vector machines. PermFIT (available at https://github.com/SkadiEye/deepTL) is implemented in a computationally efficient manner, without model refitting. We conduct extensive numerical studies under various scenarios, and show that PermFIT not only yields valid statistical inference, but also improves the prediction accuracy of machine learning models. With the application to the Cancer Genome Atlas kidney tumor data and the HITChip atlas data, PermFIT demonstrates its practical usage in identifying important biomarkers and boosting model prediction performance.

scholarly journals Permutation-based Identification of Important Biomarkers for Complex Diseases via Black-box Models

2020 ◽  
Author(s):  
Xinlei Mi ◽  
Baiming Zou ◽  
Fei Zou ◽  
Jianhua Hu
Keyword(s):  
Human Disease ◽  
Molecular Mechanisms ◽  
Black Box ◽  
The Cancer Genome Atlas ◽  
Human Diseases ◽  
Support Vector ◽  
Individual Feature ◽  
Box Models ◽  
Feature Importance ◽  
Black Box Models

AbstractStudy of human disease remains challenging due to convoluted disease etiologies and complex molecular mechanisms at genetic, genomic, and proteomic levels. Many machine learning-based methods, including deep learning and random forest, have been developed and widely used to alleviate some analytic challenges in complex human disease studies. While enjoying the modeling flexibility and robustness, these model frameworks suffer from non-transparency and difficulty in interpreting the role of each individual feature due to their intrinsic black-box natures. However, identifying important biomarkers associated with complex human diseases is a critical pursuit towards assisting researchers to establish novel hypotheses regarding prevention, diagnosis and treatment of complex human diseases. Herein, we propose a Permutation-based Feature Importance Test (PermFIT) for estimating and testing the feature importance, and for assisting interpretation of individual feature in various black-box frameworks, including deep neural networks, random forests, and support vector machines. PermFIT (available at https://github.com/SkadiEye/deepTL) is implemented in a computationally efficient manner, without model refitting for each permuted data. We conduct extensive numerical studies under various scenarios, and show that PermFIT not only yields valid statistical inference, but also helps to improve the prediction accuracy of black-box models with top selected features. With the application to the Cancer Genome Atlas (TCGA) kidney tumor data and the HITChip atlas BMI data, PermFIT clearly demonstrates its practical usage in identifying important biomarkers and boosting performance of black-box predictive models.

scholarly journals Machine Learning Models to Predict Primary Sites of Metastatic Cervical Carcinoma From Unknown Primary

2020 ◽  
Vol 11 ◽  
Author(s):  
Di Lu ◽  
Jianjun Jiang ◽  
Xiguang Liu ◽  
He Wang ◽  
Siyang Feng ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cervical Carcinoma ◽  
Predictive Accuracy ◽  
External Validation ◽  
Primary Site ◽  
The Cancer Genome Atlas ◽  
Unknown Primary ◽  
Support Vector ◽  
Learning Models ◽  
Machine Learning Models

Metastatic cervical carcinoma from unknown primary (MCCUP) accounts for 1–4% of all head and neck tumors, and identifying the primary site in MCCUP is challenging. The most common histopathological type of MCCUP is squamous cell carcinoma (SCC), and it remains difficult to identify the primary site pathologically. Therefore, it seems necessary and urgent to develop novel and effective methods to determine the primary site in MCCUP. In the present study, the RNA sequencing data of four types of SCC and Pan-Cancer from the cancer genome atlas (TCGA) were obtained. And after data pre-processing, their differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these significantly changed genes of four types of SCC share lots of similar molecular functions and histological features. Then three machine learning models, [Random Forest (RF), support vector machine (SVM), and neural network (NN)] which consisted of ten genes to distinguish these four types of SCC were developed. Among the three models with prediction tests, the RF model worked best in the external validation set, with an overall predictive accuracy of 88.2%, sensitivity of 88.71%, and specificity of 95.42%. The NN model is the second in efficacy, with an overall accuracy of 82.02%, sensitivity of 81.23%, and specificity of 93.04%. The SVM model is the last, with an overall accuracy of 76.69%, sensitivity of 74.81%, and specificity of 90.84%. The present analysis of similarities and differences among the four types of SCC, and novel models developments for distinguishing four types of SCC with informatics methods shed lights on precision MCCUP diagnosis in the future.

scholarly journals Monitoring the Foliar Nutrients Status of Mango Using Spectroscopy-Based Spectral Indices and PLSR-Combined Machine Learning Models

2021 ◽  
Vol 13 (4) ◽  
pp. 641
Author(s):  
Gopal Ramdas Mahajan ◽  
Bappa Das ◽  
Dayesh Murgaokar ◽  
Ittai Herrmann ◽  
Katja Berger ◽  
...  
Keyword(s):  
Machine Learning ◽  
Remote Sensing ◽  
Partial Least Square ◽  
Least Square ◽  
Partial Least Square Regression ◽  
Support Vector ◽  
Spectral Indices ◽  
Learning Models ◽  
Leaf Nutrients ◽  
Machine Learning Models

Conventional methods of plant nutrient estimation for nutrient management need a huge number of leaf or tissue samples and extensive chemical analysis, which is time-consuming and expensive. Remote sensing is a viable tool to estimate the plant’s nutritional status to determine the appropriate amounts of fertilizer inputs. The aim of the study was to use remote sensing to characterize the foliar nutrient status of mango through the development of spectral indices, multivariate analysis, chemometrics, and machine learning modeling of the spectral data. A spectral database within the 350–1050 nm wavelength range of the leaf samples and leaf nutrients were analyzed for the development of spectral indices and multivariate model development. The normalized difference and ratio spectral indices and multivariate models–partial least square regression (PLSR), principal component regression, and support vector regression (SVR) were ineffective in predicting any of the leaf nutrients. An approach of using PLSR-combined machine learning models was found to be the best to predict most of the nutrients. Based on the independent validation performance and summed ranks, the best performing models were cubist (R2 ≥ 0.91, the ratio of performance to deviation (RPD) ≥ 3.3, and the ratio of performance to interquartile distance (RPIQ) ≥ 3.71) for nitrogen, phosphorus, potassium, and zinc, SVR (R2 ≥ 0.88, RPD ≥ 2.73, RPIQ ≥ 3.31) for calcium, iron, copper, boron, and elastic net (R2 ≥ 0.95, RPD ≥ 4.47, RPIQ ≥ 6.11) for magnesium and sulfur. The results of the study revealed the potential of using hyperspectral remote sensing data for non-destructive estimation of mango leaf macro- and micro-nutrients. The developed approach is suggested to be employed within operational retrieval workflows for precision management of mango orchard nutrients.

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.

414 Deep Neural Networks: A Survey Tool for Obstructive Sleep Apnea Prediction

SLEEP ◽  
2021 ◽  
Vol 44 (Supplement_2) ◽  
pp. A164-A164
Author(s):  
Pahnwat Taweesedt ◽  
JungYoon Kim ◽  
Jaehyun Park ◽  
Jangwoon Park ◽  
Munish Sharma ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Obstructive Sleep Apnea ◽  
Sleep Apnea ◽  
Deep Neural Networks ◽  
Support Vector ◽  
Learning Models ◽  
Obstructive Sleep ◽  
Screening Questionnaires ◽  
Machine Learning Models

Abstract Introduction Obstructive sleep apnea (OSA) is a common sleep-related breathing disorder with an estimation of one billion people. Full-night polysomnography is considered the gold standard for OSA diagnosis. However, it is time-consuming, expensive and is not readily available in many parts of the world. Many screening questionnaires and scores have been proposed for OSA prediction with high sensitivity and low specificity. The present study is intended to develop models with various machine learning techniques to predict the severity of OSA by incorporating features from multiple questionnaires. Methods Subjects who underwent full-night polysomnography in Torr sleep center, Texas and completed 5 OSA screening questionnaires/scores were included. OSA was diagnosed by using Apnea-Hypopnea Index ≥ 5. We trained five different machine learning models including Deep Neural Networks with the scaled principal component analysis (DNN-PCA), Random Forest (RF), Adaptive Boosting classifier (ABC), and K-Nearest Neighbors classifier (KNC) and Support Vector Machine Classifier (SVMC). Training:Testing subject ratio of 65:35 was used. All features including demographic data, body measurement, snoring and sleepiness history were obtained from 5 OSA screening questionnaires/scores (STOP-BANG questionnaires, Berlin questionnaires, NoSAS score, NAMES score and No-Apnea score). Performance parametrics were used to compare between machine learning models. Results Of 180 subjects, 51.5 % of subjects were male with mean (SD) age of 53.6 (15.1). One hundred and nineteen subjects were diagnosed with OSA. Area Under the Receiver Operating Characteristic Curve (AUROC) of DNN-PCA, RF, ABC, KNC, SVMC, STOP-BANG questionnaire, Berlin questionnaire, NoSAS score, NAMES score, and No-Apnea score were 0.85, 0.68, 0.52, 0.74, 0.75, 0.61, 0.63, 0,61, 0.58 and 0,58 respectively. DNN-PCA showed the highest AUROC with sensitivity of 0.79, specificity of 0.67, positive-predictivity of 0.93, F1 score of 0.86, and accuracy of 0.77. Conclusion Our result showed that DNN-PCA outperforms OSA screening questionnaires, scores and other machine learning models. Support (if any):

scholarly journals AB0652 MACHINE LEARNING TO PREDICT EARLY TNF INHIBITOR USERS IN PATIENTS WITH ANKYLOSING SPONDYLITIS

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1620.1-1621
Author(s):  
J. Lee ◽  
H. Kim ◽  
S. Y. Kang ◽  
S. Lee ◽  
Y. H. Eun ◽  
...  
Keyword(s):  
Machine Learning ◽  
Ankylosing Spondylitis ◽  
Tnf Inhibitors ◽  
Tnf Inhibitor ◽  
Ann Model ◽  
Learning Models ◽  
Feature Importance ◽  
Importance Analysis ◽  
Baseline Characteristics ◽  
Machine Learning Models

Background:Tumor necrosis factor (TNF) inhibitors are important drugs in treating patients with ankylosing spondylitis (AS). However, they are not used as a first-line treatment for AS. There is an insufficient treatment response to the first-line treatment, non-steroidal anti-inflammatory drugs (NSAIDs), in over 40% of patients. If we can predict who will need TNF inhibitors at an earlier phase, adequate treatment can be provided at an appropriate time and potential damages can be avoided. There is no precise predictive model at present. Recently, various machine learning methods show great performances in predictions using clinical data.Objectives:We aim to generate an artificial neural network (ANN) model to predict early TNF inhibitor users in patients with ankylosing spondylitis.Methods:The baseline demographic and laboratory data of patients who visited Samsung Medical Center rheumatology clinic from Dec. 2003 to Sep. 2018 were analyzed. Patients were divided into two groups: early TNF inhibitor users treated by TNF inhibitors within six months of their follow-up (early-TNF users), and the others (non-early-TNF users). Machine learning models were formulated to predict the early-TNF users using the baseline data. Additionally, feature importance analysis was performed to delineate significant baseline characteristics.Results:The numbers of early-TNF and non-early-TNF users were 90 and 509, respectively. The best performing ANN model utilized 3 hidden layers with 50 hidden nodes each; its performance (area under curve (AUC) = 0.75) was superior to logistic regression model, support vector machine, and random forest model (AUC = 0.72, 0.65, and 0.71, respectively) in predicting early-TNF users. Feature importance analysis revealed erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and height as the top significant baseline characteristics for predicting early-TNF users. Among these characteristics, height was revealed by machine learning models but not by conventional statistical techniques.Conclusion:Our model displayed superior performance in predicting early TNF users compared with logistic regression and other machine learning models. Machine learning can be a vital tool in predicting treatment response in various rheumatologic diseases.Disclosure of Interests:None declared

scholarly journals QUBO formulations for training machine learning models

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Prasanna Date ◽  
Davis Arthur ◽  
Lauren Pusey-Nazzaro
Keyword(s):  
Machine Learning ◽  
Linear Regression ◽  
Large Scale ◽  
Support Vector ◽  
Quantum Computers ◽  
Np Hard ◽  
Learning Models ◽  
Moore’S Law ◽  
Moore's Law ◽  
Machine Learning Models

AbstractTraining machine learning models on classical computers is usually a time and compute intensive process. With Moore’s law nearing its inevitable end and an ever-increasing demand for large-scale data analysis using machine learning, we must leverage non-conventional computing paradigms like quantum computing to train machine learning models efficiently. Adiabatic quantum computers can approximately solve NP-hard problems, such as the quadratic unconstrained binary optimization (QUBO), faster than classical computers. Since many machine learning problems are also NP-hard, we believe adiabatic quantum computers might be instrumental in training machine learning models efficiently in the post Moore’s law era. In order to solve problems on adiabatic quantum computers, they must be formulated as QUBO problems, which is very challenging. In this paper, we formulate the training problems of three machine learning models—linear regression, support vector machine (SVM) and balanced k-means clustering—as QUBO problems, making them conducive to be trained on adiabatic quantum computers. We also analyze the computational complexities of our formulations and compare them to corresponding state-of-the-art classical approaches. We show that the time and space complexities of our formulations are better (in case of SVM and balanced k-means clustering) or equivalent (in case of linear regression) to their classical counterparts.

scholarly journals A Comparative Study of Machine Learning Models with Hyperparameter Optimization Algorithm for Mapping Mineral Prospectivity

Minerals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 159
Author(s):  
Nan Lin ◽  
Yongliang Chen ◽  
Haiqi Liu ◽  
Hanlin Liu
Keyword(s):  
Machine Learning ◽  
Swarm Intelligence ◽  
Optimization Algorithm ◽  
Geochemical Data ◽  
Support Vector ◽  
Learning Models ◽  
Hyperparameter Optimization ◽  
Mineral Prospectivity ◽  
Swarm Intelligence Optimization ◽  
Machine Learning Models

Selecting internal hyperparameters, which can be set by the automatic search algorithm, is important to improve the generalization performance of machine learning models. In this study, the geological, remote sensing and geochemical data of the Lalingzaohuo area in Qinghai province were researched. A multi-source metallogenic information spatial data set was constructed by calculating the Youden index for selecting potential evidence layers. The model for mapping mineral prospectivity of the study area was established by combining two swarm intelligence optimization algorithms, namely the bat algorithm (BA) and the firefly algorithm (FA), with different machine learning models. The receiver operating characteristic (ROC) and prediction-area (P-A) curves were used for performance evaluation and showed that the two algorithms had an obvious optimization effect. The BA and FA differentiated in improving multilayer perceptron (MLP), AdaBoost and one-class support vector machine (OCSVM) models; thus, there was no optimization algorithm that was consistently superior to the other. However, the accuracy of the machine learning models was significantly enhanced after optimizing the hyperparameters. The area under curve (AUC) values of the ROC curve of the optimized machine learning models were all higher than 0.8, indicating that the hyperparameter optimization calculation was effective. In terms of individual model improvement, the accuracy of the FA-AdaBoost model was improved the most significantly, with the AUC value increasing from 0.8173 to 0.9597 and the prediction/area (P/A) value increasing from 3.156 to 10.765, where the mineral targets predicted by the model occupied 8.63% of the study area and contained 92.86% of the known mineral deposits. The targets predicted by the improved machine learning models are consistent with the metallogenic geological characteristics, indicating that the swarm intelligence optimization algorithm combined with the machine learning model is an efficient method for mineral prospectivity mapping.

Machine Learning Models for Finger Bend Evaluation using Implemented Low cost Flex Sensor

2021 ◽  
Vol 9 (VI) ◽  
pp. 3605-3611
Author(s):  
Pratyush Kaware
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Low Cost ◽  
Learning Algorithms ◽  
Cost Effective ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Models ◽  
Machine Learning Models

In this paper a cost-effective sensor has been implemented to read finger bend signals, by attaching the sensor to a finger, so as to classify them based on the degree of bent as well as the joint about which the finger was being bent. This was done by testing with various machine learning algorithms to get the most accurate and consistent classifier. Finally, we found that Support Vector Machine was the best algorithm suited to classify our data, using we were able predict live state of a finger, i.e., the degree of bent and the joints involved. The live voltage values from the sensor were transmitted using a NodeMCU micro-controller which were converted to digital and uploaded on a database for analysis.

scholarly journals Machine Learning Models for Sarcopenia Identification Based on Radiomic Features of Muscles in Computed Tomography

2021 ◽  
Vol 18 (16) ◽  
pp. 8710
Author(s):  
Young Jae Kim
Keyword(s):  
Machine Learning ◽  
Computed Tomography ◽  
Ct Images ◽  
Erector Spinae ◽  
Support Vector ◽  
Gray Level ◽  
Learning Models ◽  
Extreme Gradient Boosting ◽  
Nsclc Patients ◽  
Machine Learning Models

The diagnosis of sarcopenia requires accurate muscle quantification. As an alternative to manual muscle mass measurement through computed tomography (CT), artificial intelligence can be leveraged for the automation of these measurements. Although generally difficult to identify with the naked eye, the radiomic features in CT images are informative. In this study, the radiomic features were extracted from L3 CT images of the entire muscle area and partial areas of the erector spinae collected from non-small cell lung carcinoma (NSCLC) patients. The first-order statistics and gray-level co-occurrence, gray-level size zone, gray-level run length, neighboring gray-tone difference, and gray-level dependence matrices were the radiomic features analyzed. The identification performances of the following machine learning models were evaluated: logistic regression, support vector machine (SVM), random forest, and extreme gradient boosting (XGB). Sex, coarseness, skewness, and cluster prominence were selected as the relevant features effectively identifying sarcopenia. The XGB model demonstrated the best performance for the entire muscle, whereas the SVM was the worst-performing model. Overall, the models demonstrated improved performance for the entire muscle compared to the erector spinae. Although further validation is required, the radiomic features presented here could become reliable indicators for quantifying the phenomena observed in the muscles of NSCLC patients, thus facilitating the diagnosis of sarcopenia.

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