Protein-protein interactions(PPIs)are of great importance to understand genetic mechanisms,delineate disease pathogenesis,and guide drug design.With the increase of PPI data and development of machine learning technol...Protein-protein interactions(PPIs)are of great importance to understand genetic mechanisms,delineate disease pathogenesis,and guide drug design.With the increase of PPI data and development of machine learning technologies,prediction and identification of PPIs have become a research hotspot in proteomics.In this study,we propose a new prediction pipeline for PPIs based on gradient tree boosting(GTB).First,the initial feature vector is extracted by fusing pseudo amino acid composition(Pse AAC),pseudo position-specific scoring matrix(Pse PSSM),reduced sequence and index-vectors(RSIV),and autocorrelation descriptor(AD).Second,to remove redundancy and noise,we employ L1-regularized logistic regression(L1-RLR)to select an optimal feature subset.Finally,GTB-PPI model is constructed.Five-fold cross-validation showed that GTB-PPI achieved the accuracies of 95.15% and 90.47% on Saccharomyces cerevisiae and Helicobacter pylori datasets,respectively.In addition,GTB-PPI could be applied to predict the independent test datasets for Caenorhabditis elegans,Escherichia coli,Homo sapiens,and Mus musculus,the one-core PPI network for CD9,and the crossover PPI network for the Wnt-related signaling pathways.The results show that GTB-PPI can significantly improve accuracy of PPI prediction.The code and datasets of GTB-PPI can be downloaded from https://github.com/QUST-AIBBDRC/GTB-PPI/.展开更多
BACKGROUND Liver disease indicates any pathology that can harm or destroy the liver or prevent it from normal functioning.The global community has recently witnessed an increase in the mortality rate due to liver dise...BACKGROUND Liver disease indicates any pathology that can harm or destroy the liver or prevent it from normal functioning.The global community has recently witnessed an increase in the mortality rate due to liver disease.This could be attributed to many factors,among which are human habits,awareness issues,poor healthcare,and late detection.To curb the growing threats from liver disease,early detection is critical to help reduce the risks and improve treatment outcome.Emerging technologies such as machine learning,as shown in this study,could be deployed to assist in enhancing its prediction and treatment.AIM To present a more efficient system for timely prediction of liver disease using a hybrid eXtreme Gradient Boosting model with hyperparameter tuning with a view to assist in early detection,diagnosis,and reduction of risks and mortality associated with the disease.METHODS The dataset used in this study consisted of 416 people with liver problems and 167 with no such history.The data were collected from the state of Andhra Pradesh,India,through https://www.kaggle.com/datasets/uciml/indian-liver-patientrecords.The population was divided into two sets depending on the disease state of the patient.This binary information was recorded in the attribute"is_patient".RESULTS The results indicated that the chi-square automated interaction detection and classification and regression trees models achieved an accuracy level of 71.36%and 73.24%,respectively,which was much better than the conventional method.The proposed solution would assist patients and physicians in tackling the problem of liver disease and ensuring that cases are detected early to prevent it from developing into cirrhosis(scarring)and to enhance the survival of patients.The study showed the potential of machine learning in health care,especially as it concerns disease prediction and monitoring.CONCLUSION This study contributed to the knowledge of machine learning application to health and to the efforts toward combating the problem of liver disease.However,relevant authorities have to invest more into machine learning research and other health technologies to maximize their potential.展开更多
Human Activity Recognition(HAR)plays an important role in life care and health monitoring since it involves examining various activities of patients at homes,hospitals,or offices.Hence,the proposed system integrates H...Human Activity Recognition(HAR)plays an important role in life care and health monitoring since it involves examining various activities of patients at homes,hospitals,or offices.Hence,the proposed system integrates Human-Human Interaction(HHI)and Human-Object Interaction(HOI)recognition to provide in-depth monitoring of the daily routine of patients.We propose a robust system comprising both RGB(red,green,blue)and depth information.In particular,humans in HHI datasets are segmented via connected components analysis and skin detection while the human and object in HOI datasets are segmented via saliency map.To track the movement of humans,we proposed orientation and thermal features.A codebook is generated using Linde-Buzo-Gray(LBG)algorithm for vector quantization.Then,the quantized vectors generated from image sequences of HOI are given to Artificial Neural Network(ANN)while the quantized vectors generated from image sequences of HHI are given to K-ary tree hashing for classification.There are two publicly available datasets used for experimentation on HHI recognition:Stony Brook University(SBU)Kinect interaction and the University of Lincoln’s(UoL)3D social activity dataset.Furthermore,two publicly available datasets are used for experimentation on HOI recognition:Nanyang Technological University(NTU)RGB-D and Sun Yat-Sen University(SYSU)3D HOI datasets.The results proved the validity of the proposed system.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.61863010)the Key Research and Development Program of Shandong Province of China(Grant No.2019GGX101001)the Natural Science Foundation of Shandong Province of China(Grant No.ZR2018MC007)。
文摘Protein-protein interactions(PPIs)are of great importance to understand genetic mechanisms,delineate disease pathogenesis,and guide drug design.With the increase of PPI data and development of machine learning technologies,prediction and identification of PPIs have become a research hotspot in proteomics.In this study,we propose a new prediction pipeline for PPIs based on gradient tree boosting(GTB).First,the initial feature vector is extracted by fusing pseudo amino acid composition(Pse AAC),pseudo position-specific scoring matrix(Pse PSSM),reduced sequence and index-vectors(RSIV),and autocorrelation descriptor(AD).Second,to remove redundancy and noise,we employ L1-regularized logistic regression(L1-RLR)to select an optimal feature subset.Finally,GTB-PPI model is constructed.Five-fold cross-validation showed that GTB-PPI achieved the accuracies of 95.15% and 90.47% on Saccharomyces cerevisiae and Helicobacter pylori datasets,respectively.In addition,GTB-PPI could be applied to predict the independent test datasets for Caenorhabditis elegans,Escherichia coli,Homo sapiens,and Mus musculus,the one-core PPI network for CD9,and the crossover PPI network for the Wnt-related signaling pathways.The results show that GTB-PPI can significantly improve accuracy of PPI prediction.The code and datasets of GTB-PPI can be downloaded from https://github.com/QUST-AIBBDRC/GTB-PPI/.
文摘BACKGROUND Liver disease indicates any pathology that can harm or destroy the liver or prevent it from normal functioning.The global community has recently witnessed an increase in the mortality rate due to liver disease.This could be attributed to many factors,among which are human habits,awareness issues,poor healthcare,and late detection.To curb the growing threats from liver disease,early detection is critical to help reduce the risks and improve treatment outcome.Emerging technologies such as machine learning,as shown in this study,could be deployed to assist in enhancing its prediction and treatment.AIM To present a more efficient system for timely prediction of liver disease using a hybrid eXtreme Gradient Boosting model with hyperparameter tuning with a view to assist in early detection,diagnosis,and reduction of risks and mortality associated with the disease.METHODS The dataset used in this study consisted of 416 people with liver problems and 167 with no such history.The data were collected from the state of Andhra Pradesh,India,through https://www.kaggle.com/datasets/uciml/indian-liver-patientrecords.The population was divided into two sets depending on the disease state of the patient.This binary information was recorded in the attribute"is_patient".RESULTS The results indicated that the chi-square automated interaction detection and classification and regression trees models achieved an accuracy level of 71.36%and 73.24%,respectively,which was much better than the conventional method.The proposed solution would assist patients and physicians in tackling the problem of liver disease and ensuring that cases are detected early to prevent it from developing into cirrhosis(scarring)and to enhance the survival of patients.The study showed the potential of machine learning in health care,especially as it concerns disease prediction and monitoring.CONCLUSION This study contributed to the knowledge of machine learning application to health and to the efforts toward combating the problem of liver disease.However,relevant authorities have to invest more into machine learning research and other health technologies to maximize their potential.
基金This research was supported by a grant(2021R1F1A1063634)of the Basic Science Research Program through the National Research Foundation(NRF)funded by the Ministry of Education,Republic of Korea.
文摘Human Activity Recognition(HAR)plays an important role in life care and health monitoring since it involves examining various activities of patients at homes,hospitals,or offices.Hence,the proposed system integrates Human-Human Interaction(HHI)and Human-Object Interaction(HOI)recognition to provide in-depth monitoring of the daily routine of patients.We propose a robust system comprising both RGB(red,green,blue)and depth information.In particular,humans in HHI datasets are segmented via connected components analysis and skin detection while the human and object in HOI datasets are segmented via saliency map.To track the movement of humans,we proposed orientation and thermal features.A codebook is generated using Linde-Buzo-Gray(LBG)algorithm for vector quantization.Then,the quantized vectors generated from image sequences of HOI are given to Artificial Neural Network(ANN)while the quantized vectors generated from image sequences of HHI are given to K-ary tree hashing for classification.There are two publicly available datasets used for experimentation on HHI recognition:Stony Brook University(SBU)Kinect interaction and the University of Lincoln’s(UoL)3D social activity dataset.Furthermore,two publicly available datasets are used for experimentation on HOI recognition:Nanyang Technological University(NTU)RGB-D and Sun Yat-Sen University(SYSU)3D HOI datasets.The results proved the validity of the proposed system.
