scholarly journals Predicting miRNA-disease associations using a hybrid feature representation in the heterogeneous network

2020 ◽  
Vol 13 (S10) ◽  
Author(s):  
Minghui Liu ◽  
Jingyi Yang ◽  
Jiacheng Wang ◽  
Lei Deng
Keyword(s):  
Prediction Model ◽  
Heterogeneous Network ◽  
Biological Activities ◽  
Predictive Performance ◽  
Feature Representation ◽  
Global Network ◽  
Gradient Boosting ◽  
Data Sets ◽  
Extreme Gradient Boosting ◽  
Disease Associations

Abstract Background Studies have found that miRNAs play an important role in many biological activities involved in human diseases. Revealing the associations between miRNA and disease by biological experiments is time-consuming and expensive. The computational approaches provide a new alternative. However, because of the limited knowledge of the associations between miRNAs and diseases, it is difficult to support the prediction model effectively. Methods In this work, we propose a model to predict miRNA-disease associations, MDAPCOM, in which protein information associated with miRNAs and diseases is introduced to build a global miRNA-protein-disease network. Subsequently, diffusion features and HeteSim features, extracted from the global network, are combined to train the prediction model by eXtreme Gradient Boosting (XGBoost). Results The MDAPCOM model achieves AUC of 0.991 based on 10-fold cross-validation, which is significantly better than that of other two state-of-the-art methods RWRMDA and PRINCE. Furthermore, the model performs well on three unbalanced data sets. Conclusions The results suggest that the information behind proteins associated with miRNAs and diseases is crucial to the prediction of the associations between miRNAs and diseases, and the hybrid feature representation in the heterogeneous network is very effective for improving predictive performance.

scholarly journals Dementia risks identified by vocal features via telephone conversations: A novel machine learning prediction model

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0253988
Author(s):  
Akihiro Shimoda ◽  
Yue Li ◽  
Hana Hayashi ◽  
Naoki Kondo
Keyword(s):  
Machine Learning ◽  
Prediction Model ◽  
Predictive Performance ◽  
Gradient Boosting ◽  
Validation Data ◽  
Audio File ◽  
Extreme Gradient Boosting ◽  
Audio Data ◽  
Data Files ◽  
Audio Files

Due to difficulty in early diagnosis of Alzheimer’s disease (AD) related to cost and differentiated capability, it is necessary to identify low-cost, accessible, and reliable tools for identifying AD risk in the preclinical stage. We hypothesized that cognitive ability, as expressed in the vocal features in daily conversation, is associated with AD progression. Thus, we have developed a novel machine learning prediction model to identify AD risk by using the rich voice data collected from daily conversations, and evaluated its predictive performance in comparison with a classification method based on the Japanese version of the Telephone Interview for Cognitive Status (TICS-J). We used 1,465 audio data files from 99 Healthy controls (HC) and 151 audio data files recorded from 24 AD patients derived from a dementia prevention program conducted by Hachioji City, Tokyo, between March and May 2020. After extracting vocal features from each audio file, we developed machine-learning models based on extreme gradient boosting (XGBoost), random forest (RF), and logistic regression (LR), using each audio file as one observation. We evaluated the predictive performance of the developed models by describing the receiver operating characteristic (ROC) curve, calculating the areas under the curve (AUCs), sensitivity, and specificity. Further, we conducted classifications by considering each participant as one observation, computing the average of their audio files’ predictive value, and making comparisons with the predictive performance of the TICS-J based questionnaire. Of 1,616 audio files in total, 1,308 (81.0%) were randomly allocated to the training data and 308 (19.1%) to the validation data. For audio file-based prediction, the AUCs for XGboost, RF, and LR were 0.863 (95% confidence interval [CI]: 0.794–0.931), 0.882 (95% CI: 0.840–0.924), and 0.893 (95%CI: 0.832–0.954), respectively. For participant-based prediction, the AUC for XGboost, RF, LR, and TICS-J were 1.000 (95%CI: 1.000–1.000), 1.000 (95%CI: 1.000–1.000), 0.972 (95%CI: 0.918–1.000) and 0.917 (95%CI: 0.918–1.000), respectively. There was difference in predictive accuracy of XGBoost and TICS-J with almost approached significance (p = 0.065). Our novel prediction model using the vocal features of daily conversations demonstrated the potential to be useful for the AD risk assessment.

scholarly journals Development and Validation of an Efficient MRI Radiomics Signature for Improving the Predictive Performance of 1p/19q Co-Deletion in Lower-Grade Gliomas

Cancers ◽  
2021 ◽  
Vol 13 (21) ◽  
pp. 5398
Author(s):  
Quang-Hien Kha ◽  
Viet-Huan Le ◽  
Truong Nguyen Khanh Hung ◽  
Nguyen Quoc Khanh Le
Keyword(s):  
Gold Standard ◽  
Binary Classification ◽  
Predictive Performance ◽  
Deletion Mutation ◽  
Gradient Boosting ◽  
Low Grade ◽  
Lower Grade ◽  
Chromosome 1P ◽  
Extreme Gradient Boosting ◽  
External Test

The prognosis and treatment plans for patients diagnosed with low-grade gliomas (LGGs) may significantly be improved if there is evidence of chromosome 1p/19q co-deletion mutation. Many studies proved that the codeletion status of 1p/19q enhances the sensitivity of the tumor to different types of therapeutics. However, the current clinical gold standard of detecting this chromosomal mutation remains invasive and poses implicit risks to patients. Radiomics features derived from medical images have been used as a new approach for non-invasive diagnosis and clinical decisions. This study proposed an eXtreme Gradient Boosting (XGBoost)-based model to predict the 1p/19q codeletion status in a binary classification task. We trained our model on the public database extracted from The Cancer Imaging Archive (TCIA), including 159 LGG patients with 1p/19q co-deletion mutation status. The XGBoost was the baseline algorithm, and we combined the SHapley Additive exPlanations (SHAP) analysis to select the seven most optimal radiomics features to build the final predictive model. Our final model achieved an accuracy of 87% and 82.8% on the training set and external test set, respectively. With seven wavelet radiomics features, our XGBoost-based model can identify the 1p/19q codeletion status in LGG-diagnosed patients for better management and address the drawbacks of invasive gold-standard tests in clinical practice.

scholarly journals Mapping of the Canopy Openings in Mixed Beech–Fir Forest at Sentinel-2 Subpixel Level Using UAV and Machine Learning Approach

2020 ◽  
Vol 12 (23) ◽  
pp. 3925
Author(s):  
Ivan Pilaš ◽  
Mateo Gašparović ◽  
Alan Novkinić ◽  
Damir Klobučar
Keyword(s):  
Machine Learning ◽  
Forest Canopy ◽  
Vegetation Index ◽  
Predictive Performance ◽  
Spatial Extent ◽  
Gradient Boosting ◽  
Support Vector ◽  
Stochastic Gradient Boosting ◽  
Extreme Gradient Boosting ◽  
Sentinel 2

The presented study demonstrates a bi-sensor approach suitable for rapid and precise up-to-date mapping of forest canopy gaps for the larger spatial extent. The approach makes use of Unmanned Aerial Vehicle (UAV) red, green and blue (RGB) images on smaller areas for highly precise forest canopy mask creation. Sentinel-2 was used as a scaling platform for transferring information from the UAV to a wider spatial extent. Various approaches to an improvement in the predictive performance were examined: (I) the highest R2 of the single satellite index was 0.57, (II) the highest R2 using multiple features obtained from the single-date, S-2 image was 0.624, and (III) the highest R2 on the multitemporal set of S-2 images was 0.697. Satellite indices such as Atmospherically Resistant Vegetation Index (ARVI), Infrared Percentage Vegetation Index (IPVI), Normalized Difference Index (NDI45), Pigment-Specific Simple Ratio Index (PSSRa), Modified Chlorophyll Absorption Ratio Index (MCARI), Color Index (CI), Redness Index (RI), and Normalized Difference Turbidity Index (NDTI) were the dominant predictors in most of the Machine Learning (ML) algorithms. The more complex ML algorithms such as the Support Vector Machines (SVM), Random Forest (RF), Stochastic Gradient Boosting (GBM), Extreme Gradient Boosting (XGBoost), and Catboost that provided the best performance on the training set exhibited weaker generalization capabilities. Therefore, a simpler and more robust Elastic Net (ENET) algorithm was chosen for the final map creation.

scholarly journals SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting

2019 ◽  
Vol 36 (4) ◽  
pp. 1074-1081 ◽  
Author(s):  
Bin Yu ◽  
Wenying Qiu ◽  
Cheng Chen ◽  
Anjun Ma ◽  
Jing Jiang ◽  
...  
Keyword(s):  
Drug Design ◽  
Protein Function ◽  
Predictive Performance ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Source Codes ◽  
Extreme Gradient Boosting ◽  
Auto Correlation Function ◽  
Abnormal Mitochondria ◽  
Leave One Out

Abstract Motivation Mitochondria are an essential organelle in most eukaryotes. They not only play an important role in energy metabolism but also take part in many critical cytopathological processes. Abnormal mitochondria can trigger a series of human diseases, such as Parkinson's disease, multifactor disorder and Type-II diabetes. Protein submitochondrial localization enables the understanding of protein function in studying disease pathogenesis and drug design. Results We proposed a new method, SubMito-XGBoost, for protein submitochondrial localization prediction. Three steps are included: (i) the g-gap dipeptide composition (g-gap DC), pseudo-amino acid composition (PseAAC), auto-correlation function (ACF) and Bi-gram position-specific scoring matrix (Bi-gram PSSM) are employed to extract protein sequence features, (ii) Synthetic Minority Oversampling Technique (SMOTE) is used to balance samples, and the ReliefF algorithm is applied for feature selection and (iii) the obtained feature vectors are fed into XGBoost to predict protein submitochondrial locations. SubMito-XGBoost has obtained satisfactory prediction results by the leave-one-out-cross-validation (LOOCV) compared with existing methods. The prediction accuracies of the SubMito-XGBoost method on the two training datasets M317 and M983 were 97.7% and 98.9%, which are 2.8–12.5% and 3.8–9.9% higher than other methods, respectively. The prediction accuracy of the independent test set M495 was 94.8%, which is significantly better than the existing studies. The proposed method also achieves satisfactory predictive performance on plant and non-plant protein submitochondrial datasets. SubMito-XGBoost also plays an important role in new drug design for the treatment of related diseases. Availability and implementation The source codes and data are publicly available at https://github.com/QUST-AIBBDRC/SubMito-XGBoost/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Xiuzhi Sang ◽  
Wanyue Xiao ◽  
Huiwen Zheng ◽  
Yang Yang ◽  
Taigang Liu
Keyword(s):  
Feature Selection ◽  
Dna Binding ◽  
Binding Proteins ◽  
Biological Activities ◽  
Dna Binding Proteins ◽  
Gradient Boosting ◽  
Support Vector ◽  
Svm Classifier ◽  
Cross Covariance ◽  
Extreme Gradient Boosting

Prediction of DNA-binding proteins (DBPs) has become a popular research topic in protein science due to its crucial role in all aspects of biological activities. Even though considerable efforts have been devoted to developing powerful computational methods to solve this problem, it is still a challenging task in the field of bioinformatics. A hidden Markov model (HMM) profile has been proved to provide important clues for improving the prediction performance of DBPs. In this paper, we propose a method, called HMMPred, which extracts the features of amino acid composition and auto- and cross-covariance transformation from the HMM profiles, to help train a machine learning model for identification of DBPs. Then, a feature selection technique is performed based on the extreme gradient boosting (XGBoost) algorithm. Finally, the selected optimal features are fed into a support vector machine (SVM) classifier to predict DBPs. The experimental results tested on two benchmark datasets show that the proposed method is superior to most of the existing methods and could serve as an alternative tool to identify DBPs.

scholarly journals Property Rental Price Prediction Using the Extreme Gradient Boosting Algorithm

2020 ◽  
Vol 3 (2) ◽  
pp. 54-59
Author(s):  
Marco Febriadi Kokasih ◽  
Adi Suryaputra Paramita
Keyword(s):  
Prediction Model ◽  
Prediction Models ◽  
Gradient Boosting ◽  
Fair Price ◽  
Price Prediction ◽  
Online Marketplace ◽  
Extreme Gradient Boosting ◽  
Property Owners ◽  
Boosting Algorithm

Online marketplace in the field of property renting like Airbnb is growing. Many property owners have begun renting out their properties to fulfil this demand. Determining a fair price for both property owners and tourists is a challenge. Therefore, this study aims to create a software that can create a prediction model for property rent price. Variable that will be used for this study is listing feature, neighbourhood, review, date and host information. Prediction model is created based on the dataset given by the user and processed with Extreme Gradient Boosting algorithm which then will be stored in the system. The result of this study is expected to create prediction models for property rent price for property owners and tourists consideration when considering to rent a property. In conclusion, Extreme Gradient Boosting algorithm is able to create property rental price prediction with the average of RMSE of 10.86 or 13.30%.

scholarly journals Monitoring forest health using hyperspectral imagery: Does feature selection improve the performance of machine-learning techniques?

2020 ◽  
Author(s):  
Patrick Schratz ◽  
Jannes Muenchow ◽  
Eugenia Iturritxa ◽  
José Cortés ◽  
Bernd Bischl ◽  
...  
Keyword(s):  
Feature Selection ◽  
Predictive Performance ◽  
Environmental Modeling ◽  
Gradient Boosting ◽  
Support Vector ◽  
Substantial Impact ◽  
Feature Sets ◽  
Filter Methods ◽  
Extreme Gradient Boosting ◽  
Feature Importance

This study analyzed highly-correlated, feature-rich datasets from hyperspectral remote sensing data using multiple machine and statistical-learning methods.<br> The effect of filter-based feature-selection methods on predictive performance was compared.<br> Also, the effect of multiple expert-based and data-driven feature sets, derived from the reflectance data, was investigated.<br> Defoliation of trees (%) was modeled as a function of reflectance, and variable importance was assessed using permutation-based feature importance.<br> Overall support vector machine (SVM) outperformed others such as random forest (RF), extreme gradient boosting (XGBoost), lasso (L1) and ridge (L2) regression by at least three percentage points.<br> The combination of certain feature sets showed small increases in predictive performance while no substantial differences between individual feature sets were observed.<br> For some combinations of learners and feature sets, filter methods achieved better predictive performances than the unfiltered feature sets, while ensemble filters did not have a substantial impact on performance.<br><br> Permutation-based feature importance estimated features around the red edge to be most important for the models.<br> However, the presence of features in the near-infrared region (800 nm - 1000 nm) was essential to achieve the best performances.<br><br> More training data and replication in similar benchmarking studies is needed for more generalizable conclusions.<br> Filter methods have the potential to be helpful in high-dimensional situations and are able to improve the interpretation of feature effects in fitted models, which is an essential constraint in environmental modeling studies.

scholarly journals Improvement of Prediction Performance With Conjoint Molecular Fingerprint in Deep Learning

2020 ◽  
Vol 11 ◽  
Author(s):  
Liangxu Xie ◽  
Lei Xu ◽  
Ren Kong ◽  
Shan Chang ◽  
Xiaojun Xu
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Molecular Descriptor ◽  
Predictive Performance ◽  
Gradient Boosting ◽  
Support Vector ◽  
Quantitative Structure ◽  
Structure Activity ◽  
Extreme Gradient Boosting ◽  
The Impact

The accurate predicting of physical properties and bioactivity of drug molecules in deep learning depends on how molecules are represented. Many types of molecular descriptors have been developed for quantitative structure-activity/property relationships quantitative structure-activity relationships (QSPR). However, each molecular descriptor is optimized for a specific application with encoding preference. Considering that standalone featurization methods may only cover parts of information of the chemical molecules, we proposed to build the conjoint fingerprint by combining two supplementary fingerprints. The impact of conjoint fingerprint and each standalone fingerprint on predicting performance was systematically evaluated in predicting the logarithm of the partition coefficient (logP) and binding affinity of protein-ligand by using machine learning/deep learning (ML/DL) methods, including random forest (RF), support vector regression (SVR), extreme gradient boosting (XGBoost), long short-term memory network (LSTM), and deep neural network (DNN). The results demonstrated that the conjoint fingerprint yielded improved predictive performance, even outperforming the consensus model using two standalone fingerprints among four out of five examined methods. Given that the conjoint fingerprint scheme shows easy extensibility and high applicability, we expect that the proposed conjoint scheme would create new opportunities for continuously improving predictive performance of deep learning by harnessing the complementarity of various types of fingerprints.

scholarly journals Stock Portfolio Prediction by Multi-Target Decision Support

2019 ◽  
Vol 12 (1) ◽  
pp. 05-27
Author(s):  
Everton Jose Santana ◽  
João Augusto Provin Ribeiro Da silva ◽  
Saulo Martiello Mastelini ◽  
Sylvio Barbon Jr
Keyword(s):  
Decision Support ◽  
Random Forest ◽  
Stock Market ◽  
Prediction Models ◽  
Deep Structure ◽  
Predictive Performance ◽  
Gradient Boosting ◽  
Support Vector ◽  
Learning Approaches ◽  
Extreme Gradient Boosting

Investing in the stock market is a complex process due to its high volatility caused by factors as exchange rates, political events, inflation and the market history. To support investor's decisions, the prediction of future stock price and economic metrics is valuable. With the hypothesis that there is a relation among investment performance indicators,  the goal of this paper was exploring multi-target regression (MTR) methods to estimate 6 different indicators and finding out the method that would best suit in an automated prediction tool for decision support regarding predictive performance. The experiments were based on 4 datasets, corresponding to 4 different time periods, composed of 63 combinations of weights of stock-picking concepts each, simulated in the US stock market. We compared traditional machine learning approaches with seven state-of-the-art MTR solutions: Stacked Single Target, Ensemble of Regressor Chains, Deep Structure  for Tracking Asynchronous Regressor Stacking,   Deep  Regressor Stacking, Multi-output Tree Chaining,  Multi-target Augment Stacking  and Multi-output Random Forest (MORF). With the exception of MORF, traditional approaches and the MTR methods were evaluated with Extreme Gradient Boosting, Random Forest and Support Vector Machine regressors. By means of extensive experimental evaluation, our results showed that the most recent MTR solutions can achieve suitable predictive performance, improving all the scenarios (14.70% in the best one, considering all target variables and periods). In this sense, MTR is a proper strategy for building stock market decision support system based on prediction models.

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