scholarly journals Influence of calcineurin inhibitors and genetic polymorphism of transporters on enterohepatic circulation and exposure of mycophenolic acid in Chinese adult renal allograft recipients

2022 ◽  
Author(s):  
Sha-Sha Sun ◽  
Kun Shao ◽  
Jia-Qian Lu ◽  
Hui-Min An ◽  
Hao-Qiang Shi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Genetic Polymorphisms ◽  
Mycophenolic Acid ◽  
Renal Allograft ◽  
Enterohepatic Circulation ◽  
Calcineurin Inhibitors ◽  
Prediction Performance ◽  
Chinese Adult ◽  
Extreme Gradient Boosting ◽  
The Impact

Aim: Study the influence of calcineurin inhibitors (CNI) and genetic polymorphisms of transporters on enterohepatic circulation (EHC) of mycophenolic acid (MPA) in Chinese adult renal allograft recipients and estimate the effect of various covariates on prediction performance of MPA AUC0-12h. Method: MPA concentrations of 125 Chinese patients were collected 0-12 hours after administration. Genotypes of transporters were determined in 64 patients. The influence of type of CNI and genetic polymorphisms on MPA exposure was studied. Shapley additive explanations method was used to study the impact of sampling times and covariates related to EHC on AUC0-12h. Extreme gradient boosting (XGboost) machine learning-based model was established to predict AUC0-12h. Results: Dn-AUC6-12h was significantly lower in patients co-administered with CsA (P<0.05). When co-administered with TAC, for SLCO1B1 T521C or ABCC C-24T, patients with wild-type genotype had significantly higher dn-AUC6-12h (P <0.05). Patients with SLCO1B3 334T/699G alleles had significantly lower dn-AUC6-12h than homozygotes (P=0.004). No significant difference was found in CsA subgroup. For estimating AUC0-12h, C0h, C2h, C8h, type of CNI, transporters genotypes and the difference between C0h and C2h were retained in the final model, which had good prediction performance (r2=0.9739). Conclusion: Patients co-administered with CsA had lower MPA EHC than those who received TAC. MPA EHC is affected by ABCC2 C-24T, SLCO1B3 T334G/G699A, and SLCO1B1 T521C genotypes in patients treated with TAC. Type of CNI and genetic polymorphisms of transporters can improve prediction performance of MPA AUC0-12h estimating model, developed using XGboost machine learning method.

scholarly journals Explainable machine learning can outperform Cox regression predictions and provide insights in breast cancer survival

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arturo Moncada-Torres ◽  
Marissa C. van Maaren ◽  
Mathijs P. Hendriks ◽  
Sabine Siesling ◽  
Gijs Geleijnse
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Explicit Knowledge ◽  
Cox Regression ◽  
Metastatic Breast ◽  
Gradient Boosting ◽  
Support Vector ◽  
Netherlands Cancer Registry ◽  
Extreme Gradient Boosting ◽  
The Impact

AbstractCox Proportional Hazards (CPH) analysis is the standard for survival analysis in oncology. Recently, several machine learning (ML) techniques have been adapted for this task. Although they have shown to yield results at least as good as classical methods, they are often disregarded because of their lack of transparency and little to no explainability, which are key for their adoption in clinical settings. In this paper, we used data from the Netherlands Cancer Registry of 36,658 non-metastatic breast cancer patients to compare the performance of CPH with ML techniques (Random Survival Forests, Survival Support Vector Machines, and Extreme Gradient Boosting [XGB]) in predicting survival using the $$c$$ c -index. We demonstrated that in our dataset, ML-based models can perform at least as good as the classical CPH regression ($$c$$ c -index $$\sim \,0.63$$ ∼ 0.63 ), and in the case of XGB even better ($$c$$ c -index $$\sim 0.73$$ ∼ 0.73 ). Furthermore, we used Shapley Additive Explanation (SHAP) values to explain the models’ predictions. We concluded that the difference in performance can be attributed to XGB’s ability to model nonlinearities and complex interactions. We also investigated the impact of specific features on the models’ predictions as well as their corresponding insights. Lastly, we showed that explainable ML can generate explicit knowledge of how models make their predictions, which is crucial in increasing the trust and adoption of innovative ML techniques in oncology and healthcare overall.

scholarly journals Exploring the Mechanism of Crashes with Autonomous Vehicles Using Machine Learning

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Hengrui Chen ◽  
Hong Chen ◽  
Ruiyu Zhou ◽  
Zhizhen Liu ◽  
Xiaoke Sun
Keyword(s):  
Machine Learning ◽  
Autonomous Vehicles ◽  
Classification And Regression Tree ◽  
Gradient Boosting ◽  
Support Vector ◽  
Crash Severity ◽  
Apriori Algorithm ◽  
Driving Mode ◽  
Extreme Gradient Boosting ◽  
The Impact

The safety issue has become a critical obstacle that cannot be ignored in the marketization of autonomous vehicles (AVs). The objective of this study is to explore the mechanism of AV-involved crashes and analyze the impact of each feature on crash severity. We use the Apriori algorithm to explore the causal relationship between multiple factors to explore the mechanism of crashes. We use various machine learning models, including support vector machine (SVM), classification and regression tree (CART), and eXtreme Gradient Boosting (XGBoost), to analyze the crash severity. Besides, we apply the Shapley Additive Explanations (SHAP) to interpret the importance of each factor. The results indicate that XGBoost obtains the best result (recall = 75%; G-mean = 67.82%). Both XGBoost and Apriori algorithm effectively provided meaningful insights about AV-involved crash characteristics and their relationship. Among all these features, vehicle damage, weather conditions, accident location, and driving mode are the most critical features. We found that most rear-end crashes are conventional vehicles bumping into the rear of AVs. Drivers should be extremely cautious when driving in fog, snow, and insufficient light. Besides, drivers should be careful when driving near intersections, especially in the autonomous driving mode.

scholarly journals Learning-Based Stock Market Trending Analysis by Incorporating Social Media Sentiment Analysis

2021 ◽  
Author(s):  
Zhaoxia Wang ◽  
Zhenda HU ◽  
Fang LI ◽  
Seng-Beng HO
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Stock Market ◽  
Sentiment Analysis ◽  
Prediction Performance ◽  
Support Vector ◽  
Stock Market Prediction ◽  
Stock Price Prediction ◽  
Extreme Gradient Boosting ◽  
Media Sentiment

Abstract Stock market trending analysis is one of the key research topics in financial analysis. Various theories once highlighted the non-viability of stock market prediction. With the advent of machine learning and Artificial Intelligence (AI), more and more efforts have been devoted to this research area, and predicting the stock market has been demonstrated to be possible. Learning-based methods have been popularly studied for stock price prediction. However, due to the dynamic nature of the stock market and its non-linearity, stock market prediction is still one of the most dificult tasks. With the rise of social networks, huge amount of data is being generated every day and there is a gaining in popularity of incorporating these data into prediction model in the effort to enhance the prediction performance. Therefore, this paper explores the possibilities of the viability of learning-based stock market trending prediction by incorporating social media sentiment analysis. Six machine learning methods including Multi-Layer Perception, Support Vector Machine, Naïve Bayes, Random Forest, Logistic Regression and Extreme Gradient Boosting are selected as the baseline model. The result indicates the possibilities of successful stock market trending prediction and the performance of different learning-based methods is discussed. It is discovered that the distribution of the value of stocks may affect the prediction performance of the methods involved. This research not only demonstrates the merits and weaknesses of different learning-based methods, but also points out that incorporating social opinion is a right direction for improving the performance of stock market trending prediction.

The Impact of Renal Allograft Function on Exposure and Elimination of Mycophenolic Acid (MPA) and Its Metabolite MPA 7-O-glucuronide

2007 ◽  
Vol 84 (3) ◽  
pp. 362-373 ◽  
Author(s):  
Maarten Naesens ◽  
Henriette de Loor ◽  
Yves Vanrenterghem ◽  
Dirk R. J. Kuypers
Keyword(s):  
Mycophenolic Acid ◽  
Renal Allograft ◽  
Allograft Function ◽  
The Impact

scholarly journals Evaluation of Short-Term Freeway Speed Prediction Based on Periodic Analysis Using Statistical Models and Machine Learning Models

2020 ◽  
Vol 2020 ◽  
pp. 1-16 ◽  
Author(s):  
Xiaoxue Yang ◽  
Yajie Zou ◽  
Jinjun Tang ◽  
Jian Liang ◽  
Muhammad Ijaz
Keyword(s):  
Machine Learning ◽  
Statistical Models ◽  
Prediction Performance ◽  
Periodic Component ◽  
Learning Approaches ◽  
Learning Models ◽  
Short Term ◽  
Speed Prediction ◽  
The Impact ◽  
Machine Learning Models

Accurate prediction of traffic information (i.e., traffic flow, travel time, traffic speed, etc.) is a key component of Intelligent Transportation System (ITS). Traffic speed is an important indicator to evaluate traffic efficiency. Up to date, although a few studies have considered the periodic feature in traffic prediction, very few studies comprehensively evaluate the impact of periodic component on statistical and machine learning prediction models. This paper selects several representative statistical models and machine learning models to analyze the influence of periodic component on short-term speed prediction under different scenarios: (1) multi-horizon ahead prediction (5, 15, 30, 60 minutes ahead predictions), (2) with and without periodic component, (3) two data aggregation levels (5-minute and 15-minute), (4) peak hours and off-peak hours. Specifically, three statistical models (i.e., space time (ST) model, vector autoregressive (VAR) model, autoregressive integrated moving average (ARIMA) model) and three machine learning approaches (i.e., support vector machines (SVM) model, multi-layer perceptron (MLP) model, recurrent neural network (RNN) model) are developed and examined. Furthermore, the periodic features of the speed data are considered via a hybrid prediction method, which assumes that the data consist of two components: a periodic component and a residual component. The periodic component is described by a trigonometric regression function, and the residual component is modeled by the statistical models or the machine learning approaches. The important conclusions can be summarized as follows: (1) the multi-step ahead prediction accuracy improves when considering the periodic component of speed data for both three statistical models and three machine learning models, especially in the peak hours; (2) considering the impact of periodic component for all models, the prediction performance improvement gradually becomes larger as the time step increases; (3) under the same prediction horizon, the prediction performance of all models for 15-minute speed data is generally better than that for 5-minute speed data. Overall, the findings in this paper suggest that the proposed hybrid prediction approach is effective for both statistical and machine learning models in short-term speed prediction.

Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data

2019 ◽  
Vol 35 (20) ◽  
pp. 3989-3995 ◽  
Author(s):  
Hongjian Li ◽  
Jiangjun Peng ◽  
Pavel Sidorov ◽  
Yee Leung ◽  
Kwong-Sak Leung ◽  
...  
Keyword(s):  
Machine Learning ◽  
Protein Structures ◽  
Superior Performance ◽  
Supplementary Information ◽  
Scoring Functions ◽  
Training Set ◽  
Test Set ◽  
Set Size ◽  
Extreme Gradient Boosting ◽  
The Impact

Abstract Motivation Studies have shown that the accuracy of random forest (RF)-based scoring functions (SFs), such as RF-Score-v3, increases with more training samples, whereas that of classical SFs, such as X-Score, does not. Nevertheless, the impact of the similarity between training and test samples on this matter has not been studied in a systematic manner. It is therefore unclear how these SFs would perform when only trained on protein-ligand complexes that are highly dissimilar or highly similar to the test set. It is also unclear whether SFs based on machine learning algorithms other than RF can also improve accuracy with increasing training set size and to what extent they learn from dissimilar or similar training complexes. Results We present a systematic study to investigate how the accuracy of classical and machine-learning SFs varies with protein-ligand complex similarities between training and test sets. We considered three types of similarity metrics, based on the comparison of either protein structures, protein sequences or ligand structures. Regardless of the similarity metric, we found that incorporating a larger proportion of similar complexes to the training set did not make classical SFs more accurate. In contrast, RF-Score-v3 was able to outperform X-Score even when trained on just 32% of the most dissimilar complexes, showing that its superior performance owes considerably to learning from dissimilar training complexes to those in the test set. In addition, we generated the first SF employing Extreme Gradient Boosting (XGBoost), XGB-Score, and observed that it also improves with training set size while outperforming the rest of SFs. Given the continuous growth of training datasets, the development of machine-learning SFs has become very appealing. Availability and implementation https://github.com/HongjianLi/MLSF Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19

Computation ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 4
Author(s):  
Wenhuan Zeng ◽  
Anupam Gautam ◽  
Daniel H. Huson
Keyword(s):  
Machine Learning ◽  
Language Processing ◽  
Climatic Factors ◽  
Sequence Data ◽  
Learning Algorithms ◽  
Weather Conditions ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Extreme Gradient Boosting ◽  
The Impact

The current COVID-19 pandemic, caused by the rapid worldwide spread of the SARS-CoV-2 virus, is having severe consequences for human health and the world economy. The virus affects different individuals differently, with many infected patients showing only mild symptoms, and others showing critical illness. To lessen the impact of the epidemic, one problem is to determine which factors play an important role in a patient’s progression of the disease. Here, we construct an enhanced COVID-19 structured dataset from more than one source, using natural language processing to add local weather conditions and country-specific research sentiment. The enhanced structured dataset contains 301,363 samples and 43 features, and we applied both machine learning algorithms and deep learning algorithms on it so as to forecast patient’s survival probability. In addition, we import alignment sequence data to improve the performance of the model. Application of Extreme Gradient Boosting (XGBoost) on the enhanced structured dataset achieves 97% accuracy in predicting patient’s survival; with climatic factors, and then age, showing the most importance. Similarly, the application of a Multi-Layer Perceptron (MLP) achieves 98% accuracy. This work suggests that enhancing the available data, mostly basic information on patients, so as to include additional, potentially important features, such as weather conditions, is useful. The explored models suggest that textual weather descriptions can improve outcome forecast.

scholarly journals Comparative Analysis of Two Machine Learning Algorithms in Predicting Site-Level Net Ecosystem Exchange in Major Biomes

2021 ◽  
Vol 13 (12) ◽  
pp. 2242
Author(s):  
Jianzhao Liu ◽  
Yunjiang Zuo ◽  
Nannan Wang ◽  
Fenghui Yuan ◽  
Xinhao Zhu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Learning Algorithms ◽  
Substantial Reduction ◽  
Model Performance ◽  
Extreme Heat ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
Ecological Data ◽  
Extreme Gradient Boosting ◽  
The Impact

The net ecosystem CO2 exchange (NEE) is a critical parameter for quantifying terrestrial ecosystems and their contributions to the ongoing climate change. The accumulation of ecological data is calling for more advanced quantitative approaches for assisting NEE prediction. In this study, we applied two widely used machine learning algorithms, Random Forest (RF) and Extreme Gradient Boosting (XGBoost), to build models for simulating NEE in major biomes based on the FLUXNET dataset. Both models accurately predicted NEE in all biomes, while XGBoost had higher computational efficiency (6~62 times faster than RF). Among environmental variables, net solar radiation, soil water content, and soil temperature are the most important variables, while precipitation and wind speed are less important variables in simulating temporal variations of site-level NEE as shown by both models. Both models perform consistently well for extreme climate conditions. Extreme heat and dryness led to much worse model performance in grassland (extreme heat: R2 = 0.66~0.71, normal: R2 = 0.78~0.81; extreme dryness: R2 = 0.14~0.30, normal: R2 = 0.54~0.55), but the impact on forest is less (extreme heat: R2 = 0.50~0.78, normal: R2 = 0.59~0.87; extreme dryness: R2 = 0.86~0.90, normal: R2 = 0.81~0.85). Extreme wet condition did not change model performance in forest ecosystems (with R2 changing −0.03~0.03 compared with normal) but led to substantial reduction in model performance in cropland (with R2 decreasing 0.20~0.27 compared with normal). Extreme cold condition did not lead to much changes in model performance in forest and woody savannas (with R2 decreasing 0.01~0.08 and 0.09 compared with normal, respectively). Our study showed that both models need training samples at daily timesteps of >2.5 years to reach a good model performance and >5.4 years of daily samples to reach an optimal model performance. In summary, both RF and XGBoost are applicable machine learning algorithms for predicting ecosystem NEE, and XGBoost algorithm is more feasible than RF in terms of accuracy and efficiency.

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