scholarly journals Machine learning methods, databases and tools for drug combination prediction

2021 ◽  
Author(s):  
Lianlian Wu ◽  
Yuqi Wen ◽  
Dongjin Leng ◽  
Qinglong Zhang ◽  
Chong Dai ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Combination ◽  
Predictive Performance ◽  
Search Space ◽  
Drug Combinations ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
High Throughput Screens ◽  
Novel Drug ◽  
Future Work

Abstract Combination therapy has shown an obvious efficacy on complex diseases and can greatly reduce the development of drug resistance. However, even with high-throughput screens, experimental methods are insufficient to explore novel drug combinations. In order to reduce the search space of drug combinations, there is an urgent need to develop more efficient computational methods to predict novel drug combinations. In recent decades, more and more machine learning (ML) algorithms have been applied to improve the predictive performance. The object of this study is to introduce and discuss the recent applications of ML methods and the widely used databases in drug combination prediction. In this study, we first describe the concept and controversy of synergism between drug combinations. Then, we investigate various publicly available data resources and tools for prediction tasks. Next, ML methods including classic ML and deep learning methods applied in drug combination prediction are introduced. Finally, we summarize the challenges to ML methods in prediction tasks and provide a discussion on future work.

scholarly journals Machine-learning based prediction of Cushing’s syndrome in dogs attending UK primary-care veterinary practice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Imogen Schofield ◽  
David C. Brodbelt ◽  
Noel Kennedy ◽  
Stijn J. M. Niessen ◽  
David B. Church ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cushing’S Syndrome ◽  
Clinical Decision Making ◽  
Predictive Performance ◽  
Clinical Decision ◽  
Cushing's Syndrome ◽  
Machine Learning Algorithms ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Clinical Records

AbstractCushing’s syndrome is an endocrine disease in dogs that negatively impacts upon the quality-of-life of affected animals. Cushing’s syndrome can be a challenging diagnosis to confirm, therefore new methods to aid diagnosis are warranted. Four machine-learning algorithms were applied to predict a future diagnosis of Cushing's syndrome, using structured clinical data from the VetCompass programme in the UK. Dogs suspected of having Cushing's syndrome were included in the analysis and classified based on their final reported diagnosis within their clinical records. Demographic and clinical features available at the point of first suspicion by the attending veterinarian were included within the models. The machine-learning methods were able to classify the recorded Cushing’s syndrome diagnoses, with good predictive performance. The LASSO penalised regression model indicated the best overall performance when applied to the test set with an AUROC = 0.85 (95% CI 0.80–0.89), sensitivity = 0.71, specificity = 0.82, PPV = 0.75 and NPV = 0.78. The findings of our study indicate that machine-learning methods could predict the future diagnosis of a practicing veterinarian. New approaches using these methods could support clinical decision-making and contribute to improved diagnosis of Cushing’s syndrome in dogs.

scholarly journals A Predictive Performance Analysis of Vitamin D Deficiency Severity Using Machine Learning Methods

IEEE Access ◽  
2020 ◽  
Vol 8 ◽  
pp. 109492-109507
Author(s):  
G. Sambasivam ◽  
J. Amudhavel ◽  
G. Sathya
Keyword(s):  
Machine Learning ◽  
Vitamin D ◽  
Performance Analysis ◽  
Vitamin D Deficiency ◽  
Predictive Performance ◽  
Learning Methods ◽  
Machine Learning Methods

Advances of Quantum Machine Learning

2021 ◽  
pp. 257-275
Author(s):  
Bhanu Chander
Keyword(s):  
Machine Learning ◽  
Kernel Methods ◽  
High Quality ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Quantum Machine Learning ◽  
Time Quantum ◽  
Computational Resources ◽  
Future Consequences ◽  
Future Work

The basic idea of artificial intelligence and machine learning is that machines have the talent to learn from data, previous experience, and perform the work in future consequences. In the era of the digitalized world which holds big data has long-established machine learning methods consistently with requisite high-quality computational resources in numerous useful and realistic tasks. At the same time, quantum machine learning methods work exponentially faster than their counterparts by making use of quantum mechanics. Through taking advantage of quantum effects such as interference or entanglement, quantum computers can proficiently explain selected issues that are supposed to be tough for traditional machines. Quantum computing is unexpectedly related to that of kernel methods in machine learning. Hence, this chapter provides quantum computation, advance of QML techniques, QML kernel space and optimization, and future work of QML.

scholarly journals Empirical asset pricing via machine learning: evidence from the European stock market

2021 ◽  
Author(s):  
Wolfgang Drobetz ◽  
Tizian Otto
Keyword(s):  
Machine Learning ◽  
Stock Returns ◽  
Network Architecture ◽  
Risk Measures ◽  
Predictive Performance ◽  
Support Vector ◽  
Learning Models ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Machine Learning Models

AbstractThis paper evaluates the predictive performance of machine learning methods in forecasting European stock returns. Compared to a linear benchmark model, interactions and nonlinear effects help improve the predictive performance. But machine learning models must be adequately trained and tuned to overcome the high dimensionality problem and to avoid overfitting. Across all machine learning methods, the most important predictors are based on price trends and fundamental signals from valuation ratios. However, the models exhibit substantial variation in statistical predictive performance that translate into pronounced differences in economic profitability. The return and risk measures of long-only trading strategies indicate that machine learning models produce sizeable gains relative to our benchmark. Neural networks perform best, also after accounting for transaction costs. A classification-based portfolio formation, utilizing a support vector machine that avoids estimating stock-level expected returns, performs even better than the neural network architecture.

scholarly journals MACHINE LEARNING METHODS FOR SYSTEMIC RISK ANALYSIS IN FINANCIAL SECTORS

2019 ◽  
Vol 25 (5) ◽  
pp. 716-742 ◽  
Author(s):  
Gang Kou ◽  
Xiangrui Chao ◽  
Yi Peng ◽  
Fawaz E. Alsaadi ◽  
Enrique Herrera-Viedma
Keyword(s):  
Machine Learning ◽  
Financial Markets ◽  
Systemic Risk ◽  
Learning Technologies ◽  
Financial Systems ◽  
Research Topics ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Future Challenges ◽  
Future Work

Financial systemic risk is an important issue in economics and financial systems. Trying to detect and respond to systemic risk with growing amounts of data produced in financial markets and systems, a lot of researchers have increasingly employed machine learning methods. Machine learning methods study the mechanisms of outbreak and contagion of systemic risk in the financial network and improve the current regulation of the financial market and industry. In this paper, we survey existing researches and methodologies on assessment and measurement of financial systemic risk combined with machine learning technologies, including big data analysis, network analysis and sentiment analysis, etc. In addition, we identify future challenges, and suggest further research topics. The main purpose of this paper is to introduce current researches on financial systemic risk with machine learning methods and to propose directions for future work.

scholarly journals Prediction of synergistic drug combinations using PCA-initialized deep learning

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jun Ma ◽  
Alison Motsinger-Reif
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Machine Learning ◽  
Deep Learning ◽  
Drug Combination ◽  
Drug Combinations ◽  
Learning Approach ◽  
Drug Synergy ◽  
Machine Learning Methods ◽  
Synergistic Drug Combinations

Abstract Background Cancer is one of the main causes of death worldwide. Combination drug therapy has been a mainstay of cancer treatment for decades and has been shown to reduce host toxicity and prevent the development of acquired drug resistance. However, the immense number of possible drug combinations and large synergistic space makes it infeasible to screen all effective drug pairs experimentally. Therefore, it is crucial to develop computational approaches to predict drug synergy and guide experimental design for the discovery of rational combinations for therapy. Results We present a new deep learning approach to predict synergistic drug combinations by integrating gene expression profiles from cell lines and chemical structure data. Specifically, we use principal component analysis (PCA) to reduce the dimensionality of the chemical descriptor data and gene expression data. We then propagate the low-dimensional data through a neural network to predict drug synergy values. We apply our method to O’Neil’s high-throughput drug combination screening data as well as a dataset from the AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge. We compare the neural network approach with and without dimension reduction. Additionally, we demonstrate the effectiveness of our deep learning approach and compare its performance with three state-of-the-art machine learning methods: Random Forests, XGBoost, and elastic net, with and without PCA-based dimensionality reduction. Conclusions Our developed approach outperforms other machine learning methods, and the use of dimension reduction dramatically decreases the computation time without sacrificing accuracy.

scholarly journals Predictive modeling of depression and anxiety using electronic health records and a novel machine learning approach with artificial intelligence

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Matthew D. Nemesure ◽  
Michael V. Heinz ◽  
Raphael Huang ◽  
Nicholas C. Jacobson
Keyword(s):  
Machine Learning ◽  
Electronic Health Records ◽  
Undergraduate Students ◽  
General Health ◽  
Predictive Performance ◽  
Future Research ◽  
Learning Methods ◽  
Health Records ◽  
Machine Learning Methods ◽  
Electronic Health

AbstractGeneralized anxiety disorder (GAD) and major depressive disorder (MDD) are highly prevalent and impairing problems, but frequently go undetected, leading to substantial treatment delays. Electronic health records (EHRs) collect a great deal of biometric markers and patient characteristics that could foster the detection of GAD and MDD in primary care settings. We approached the problem of predicting MDD and GAD using a novel machine learning pipeline to re-analyze data from an observational study. The pipeline constitutes an ensemble of algorithmically distinct machine learning methods, including deep learning. A sample of 4,184 undergraduate students completed the study, undergoing a general health screening and completing a psychiatric assessment for MDD and GAD. After explicitly excluding all psychiatric information, 59 biomedical and demographic features from the general health survey in addition to a set of engineered features were used for model training. We assessed the model's performance on a held-out test set and found an AUC of 0.73 (sensitivity: 0.66, specificity: 0.7) and 0.67 (sensitivity: 0.55, specificity: 0.7) for GAD, and MDD, respectively. Additionally, we used advanced techniques (SHAP values) to illuminate which features had the greatest impact on prediction for each disease. The top predictive features for MDD were being satisfied with living conditions and having public health insurance. The top predictive features for GAD were vaccinations being up to date and marijuana use. Our results indicate moderate predictive performance for the application of machine learning methods in detection of GAD and MDD based on EHR data. By identifying important predictors of GAD and MDD, these results may be used in future research to aid in the early detection of MDD and GAD.

scholarly journals Completing the Market

2019 ◽  
Vol 19 (292) ◽  
Author(s):  
Nan Hu ◽  
Jian Li ◽  
Alexis Meyer-Cirkel
Keyword(s):  
Machine Learning ◽  
Credit Risk ◽  
Prediction Accuracy ◽  
Ensemble Methods ◽  
Predictive Performance ◽  
Gradient Boosting ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Ensemble Machine Learning ◽  
Out Of Sample Prediction

We compared the predictive performance of a series of machine learning and traditional methods for monthly CDS spreads, using firms’ accounting-based, market-based and macroeconomics variables for a time period of 2006 to 2016. We find that ensemble machine learning methods (Bagging, Gradient Boosting and Random Forest) strongly outperform other estimators, and Bagging particularly stands out in terms of accuracy. Traditional credit risk models using OLS techniques have the lowest out-of-sample prediction accuracy. The results suggest that the non-linear machine learning methods, especially the ensemble methods, add considerable value to existent credit risk prediction accuracy and enable CDS shadow pricing for companies missing those securities.

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides

2021 ◽  
Author(s):  
Jing Xu ◽  
Fuyi Li ◽  
André Leier ◽  
Dongxu Xiang ◽  
Hsin-Hui Shen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Antimicrobial Peptides ◽  
Computational Methods ◽  
Cross Validation ◽  
Predictive Performance ◽  
Support Vector ◽  
Data Sets ◽  
Learning Methods ◽  
Data Set ◽  
Machine Learning Methods

Abstract Antimicrobial peptides (AMPs) are a unique and diverse group of molecules that play a crucial role in a myriad of biological processes and cellular functions. AMP-related studies have become increasingly popular in recent years due to antimicrobial resistance, which is becoming an emerging global concern. Systematic experimental identification of AMPs faces many difficulties due to the limitations of current methods. Given its significance, more than 30 computational methods have been developed for accurate prediction of AMPs. These approaches show high diversity in their data set size, data quality, core algorithms, feature extraction, feature selection techniques and evaluation strategies. Here, we provide a comprehensive survey on a variety of current approaches for AMP identification and point at the differences between these methods. In addition, we evaluate the predictive performance of the surveyed tools based on an independent test data set containing 1536 AMPs and 1536 non-AMPs. Furthermore, we construct six validation data sets based on six different common AMP databases and compare different computational methods based on these data sets. The results indicate that amPEPpy achieves the best predictive performance and outperforms the other compared methods. As the predictive performances are affected by the different data sets used by different methods, we additionally perform the 5-fold cross-validation test to benchmark different traditional machine learning methods on the same data set. These cross-validation results indicate that random forest, support vector machine and eXtreme Gradient Boosting achieve comparatively better performances than other machine learning methods and are often the algorithms of choice of multiple AMP prediction tools.

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