关键词： consensus model   deep learning   drug-induced ototoxicity   machine learning   structural alert  

摘要： Drug-induced ototoxicity has become a serious global problem, because of leading to deafness in hundreds of thousands of people every year. It always results from exposure to drugs or environmental chemicals that cause the impairment and degeneration of the inner ear. Herein, we focused on the in silico modeling of drug-induced ototoxicity of chemicals. We collected 1,102 ototoxic medications and 1,705 non-ototoxic drugs. Based on the data set, a series of computational models were developed with different traditional machine learning and deep learning algorithms implemented on an online chemical database and modeling environment. Six ML models performed best on 5-fold cross-validation and test set. A consensus model was developed with the best individual models. These models were further validated with an external validation. The consensus model showed best predictive ability, with high accuracy of 0.95 on test set and 0.90 on validation set. The consensus model and the data sets used for model development are available at . Besides, 16 structural alerts responsible for drug-induced ototoxicity were identified. We hope the results could provide meaningful knowledge and useful tools for ototoxicity evaluation in drug discovery and environmental risk assessment.

关键词： Lung cancer   Small cell lung cancer (SCLC)   Non-small cell lung cancer (NSCLC)   Radiomic features   Gray level co-occurrence matrix (GLCM)   Gabor filter   Stochastic diffusion search (SDS)   Neural network (NN)   Naive Bayes and decision tree  

摘要： The symptoms of cancer normally appear only in the advanced stages, so it is very hard to detect resulting in a high mortality rate among the other types of cancers. Thus, there is a need for early prediction of lung cancer for the purpose of diagnosing and this can result in better chances of it being able to be treated successfully. Histopathology images of lung scan can be used for classification of lung cancer using image processing methods. The features from lung images are extracted and employed in the system for prediction. Grey level co-occurrence matrix along with the methods of Gabor filter feature extraction are employed in this investigation. Another important step in enhancing the classification is feature selection that tends to provide significant features that helps differentiating between various classes in an accurate and efficient manner. Thus, optimal feature subsets can significantly improve the performance of the classifiers. In this work, a novel algorithm of feature selection that is wrapper-based is proposed by employing the modified stochastic diffusion search (SDS) algorithm. The SDS, will benefit from the direct communication of agents in order to identify optimal feature subsets. The neural network, Naive Bayes and the decision tree have been used for classification. The results of the experiment prove that the proposed method is capable of achieving better levels of performance compared to existing methods like minimum redundancy maximum relevance, and correlation-based feature selection.

关键词： HIV drug resistance   Prediction   Target protein sequences   Weighted machine learning method  

摘要： Acquired immune deficiency syndrome (AIDS) is a fatal disease caused by human immunodeficiency virus (HIV). Although 23 different drugs have been available, the treatment of AIDS remains challenging because the virus mutates very quickly which can lead to drug resistance. Therefore, predicting drug resistance before treatment is crucial for individual treatments. Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods. To transform target sequences into numeric vectors, seven physicochemical properties were used, which can well represent the interacting characteristics of target proteins. Then, principal component analysis (PCA) method was adopted to reduce the feature dimensionality. Random forest (RF) and support vector machine (SVM) based on three different kernel functions, including linear, polynomial and radial basis function (RBF), were all employed. By comparisons, we found that RBF-based SVM method gives a comparative performance with RF model. Further, we added the weight information to RBF-based SVM method by four different weight evaluation methods of RF, eXtreme Gradient Boosting (XGB), CfsSubsetEval and ReliefFAttributeEval, respectively. Results show that the RF-weighted RBF-based SVM yield the superior performance and 13 out of 21 drug models provide the correlation coefficients (R-2) over 0.8 and 3 of them are higher than 0.9. Finally, position-specific importance analysis indicates that most of the mutation residues with high RF weight scores are proved to be closely related with drug resistance, which has been revealed in previous reports. Overall, we can expect that this method can be a supplementary tool for predicting HIV drug resistance for newly discovered mutations. Graphic abstract Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods by fusing the weigh

关键词： Artificial neural network (ANN)   Deep neural network (DNN)   Machine learning   Path loss prediction   Rural measurements   Time-division long term evolution (TD-LTE)  

摘要： This paper presents and assesses various machine learning methods that aim at predicting path loss in rural environment. For this purpose, models such as artificial neural network (ANN), support vector regression (SVR), random forest (RF), and bagging with k-nearest neighbor (B-kNN) learners, are exploited and evaluated. They are trained and tested with path loss data collected from an extensive measurement campaign that have been carried out in diverse rural areas in Greece. The results demonstrate that all the proposed machine learning models outperform the empirical ones, exhibiting, in any case, root-mean-square-error (RMSE) values between 4.0 and 6.5 dB. The poorest prediction of the measured data is encountered for SVR with Polynomial kernel. Furthermore, B-kNN and RF algorithms preserve comparable path loss approximations with remarkably low RMSE on the order of 4.2-4.3 dB. The error metrics also reveal that increasing the number of hidden layers in ANNs, their performance is gradually enhanced. However, deeper layouts with more than three hidden layers do not markedly improve any further the prediction accuracy. Finally, the best prediction is achieved when employing a three-hidden layered ANN with 51 neurons evenly distributed among the layers. The specific layout exhibits the lowest RMSE value (4.0 dB), thus being highly recommended for accurate path loss predictions in rural locations.

关键词： Magnetoplasma  

摘要： A rotating tokamak plasma can interact resonantly with the external helical magnetic perturbations, also known as error fields. This can lead to locking and then to disruptions. We leverage machine learning (ML) methods to predict the locking events. We use a coupled third-order nonlinear ordinary differential equation model to represent the interaction of the magnetic perturbation and the plasma rotation with the error field. This model is sufficient to describe qualitatively the locking and unlocking bifurcations. We explore using ML algorithms with the simulation data and experimental data, focusing on the methods that can be used with sparse datasets. These methods lead to the possibility of the avoidance of locking in real-time operations. We describe the operational space in terms of two control parameters: the magnitude of the error field and the rotation frequency associated with the momentum source that maintains the plasma rotation. The outcomes are quantified by order parameters that completely characterize the state, whether locked or unlocked. We use unsupervised ML methods to classify locked/unlocked states and note the usefulness of a certain normalization of the order parameters. Three supervised ML classifiers are used in suite to estimate the probability of locking in the region of control parameter space with hysteresis, i.e., the set of control parameters for which both locked and unlocked states can exist. The results show that a neural network gives the best estimate of the locking probability. An analogy of the present locking model with the van der Waals equation of state is also provided. Published under an exclusive license by AIP Publishing.

关键词： Unmanned Aerial Vehicle (UAV)   precision agriculture   nitrogen management   machine learning   Random Forests   canopy nitrogen weight   maize  

摘要： Management of nitrogen (N) fertilizers is an important agricultural practice and field of research to minimize environmental impacts and the cost of production. To apply N fertilizer at the right rate, time, and place depends on the crop type, desired yield, and field conditions. The objective of this study is to use Unmanned Aerial Vehicle (UAV) multispectral imagery, vegetation indices (VI), crop height, field topographic metrics, and soil properties to predict canopy nitrogen weight (g/m(2)) of a corn field in southwestern Ontario, Canada. Random Forests (RF) and support vector regression (SVR) models were evaluated for canopy nitrogen weight prediction from 29 variables. RF consistently had better performance than SVR, and the top-performing validation model was RF using 15 selected height, spectral, and topographic variables with an R-2 of 0.73 and Root Mean Square Error (RMSE) of 2.21 g/m(2). Of the model's 15 variables, crop height was the most important predictor, followed by 10 VIs, three MicaSense band reflectance mosaics (blue, red, and green), and topographic profile curvature. The model information can be used to improve field nitrogen prediction, leading to more effective and efficient N fertilizer management.

关键词： Ancestry analysis   Continental populations   Deletion   Insertion polymorphisms   Machine learning  

摘要： A lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populations to pinpoint candidate ancestry informative DIPs. Besides, the effectiveness of machine learning methods for ancestry analysis was explored. Pairwise informativeness (In) values of 30 DIPs revealed that six loci displayed relatively high In values (>0.1) among different continental populations. Besides, more loci showed high population-specific divergence (PSD) values in African population. Based on the pairwise In and PSD values of 30 DIPs, 17 DIPs in the Investigator DIPplex kit were selected to ancestry analyses of African, European, and East Asian populations. Even though 30 DIPs provided better ancestry resolution of these continental populations based on the results of PCA and population genetic structure, we found that 17 DIPs could also distinguish these continental populations. More importantly, these 17 DIPs possessed more balanced cumulative PSD distributions in these populations. Six machine learning methods were used to perform ancestry analyses of these continental populations based on 17 DIPs. Obtained results revealed that naive Bayes manifested the greatest performance;whereas, k nearest neighbor showed relatively low performance. To sum up, these machine learning methods, especially for naive Bayes, could be used as the valuable tool for ancestry analysis.

关键词： forest density   forest degradation   deforestation   land cover change   Sentinel-2   landsat   very high spatial resolution imagery   machine learning  

摘要： Dilijan National Park is one of the most important national parks of Armenia, established in 2002 to protect its rich biodiversity of flora and fauna and to prevent illegal logging. The aim of this study is to provide first, a mapping of forest degradation and deforestation, and second, of land cover/land use changes every 5 years over a 28-year monitoring cycle from 1991 to 2019, using Sentinel-2 and Landsat time series and Machine Learning methods. Very High Spatial Resolution imagery was used for calibration and validation purposes of forest density modelling and related changes. Correlation coefficient R-2 between forest density map and reference values ranges from 0.70 for the earliest epoch to 0.90 for the latest one. Land cover/land use classification yield good results with most classes showing high users' and producers' accuracies above 80%. Although forest degradation and deforestation which initiated about 30 years ago was restrained thanks to protection measures, anthropogenic pressure remains a threat with the increase in settlements, tourism, or agriculture. This case study can be used as a decision-support tool for the Armenian Government for sustainable forest management and policies and serve as a model for a future nationwide forest monitoring system.

关键词： DGAT1   Machine learning method   Pharmacophore model   3D-QSAR   Virtual screening  

摘要： DGAT1 plays a crucial controlling role in triglyceride biosynthetic pathways, which makes it an attractive therapeutic target for obesity. Thus, development of DGAT1 inhibitors with novel chemical scaffolds is desired and important in the drug discovery. In this investigation, the multistep virtual screening methods, including machine learning methods and common feature pharmacophore model, were developed and used to identify novel DGAT1 inhibitors from BioDiversity database with 30,000 compounds. 531 compounds were predicted as DGAT1 inhibitors by combination of machine learning methods comprising of SVM, NB and RP models. Then, 12 agents were filtered from 531 compounds by using the common feature pharmacophore model. The 3D chemical structures of the 12 hits coordinated with surface charges and isosurface have been carefully analyzed by the established 3D-QSAR model. Finally, 8 compounds with desired properties were retained from the final hits and have been assigned to another research group to complete the follow-up compound synthesis and biologic evaluation.

关键词： Chemical-induced hematotoxicity   Machine learning   Deep learning   Consensus model   Structural alert  

摘要： Chemical-induced hematotoxicity is an important concern in the drug discovery, since it can often be fatal when it happens. It is quite useful for us to give special attention to chemicals which can cause hematotoxicity. In the present study, we focused on in silico prediction of chemical-induced hematotoxicity with machine learning (ML) and deep learning (DL) methods. We collected a large data set contained 632 hematotoxic chemicals and 1525 approved drugs without hematotoxicity. Computational models were built using several different machine learning and deep learning algorithms integrated on the Online Chemical Modeling Environment (OCHEM). Based on the three best individual models, a consensus model was developed. It yielded the prediction accuracy of 0.83 and balanced accuracy of 0.77 on external validation. The consensus model and the best individual model developed with random forest regression and classification algorithm (RFR) and QNPR descriptors were made available at https://***/article/135149, respectively. The relevance of 8 commonly used molecular properties and chemical-induced hematotoxicity was also investigated. Several molecular properties have an obvious differentiating effect on chemical-induced hematotoxicity. Besides, 12 structural alerts responsible for chemical hematotoxicity were identified using frequency analysis of substructures from Klekota-Roth fingerprint. These results should provide meaningful knowledge and useful tools for hematotoxicity evaluation in drug discovery and environmental risk assessment.