Tools for transforming wheat breeding: genomic selection, rapid generation advance and database-based decision support.

Author(s):  
Umesh R. Rosyara ◽  
Kate Dreher ◽  
Bhoja R. Basnet ◽  
Susanne Dreisigacker

Abstract This chapter discusses the increased implications in the current breeding methodology of wheat, such as rapid evolution of new sequencing and genotyping technologies, automation of phenotyping, sequencing and genotyping methods and increased use of prediction and machine learning methods. Some of the strategies that will further transform wheat breeding in the next few years are also presented.

2018 ◽  
Vol 11 (2) ◽  
pp. 170104 ◽  
Author(s):  
Juan Manuel González‐Camacho ◽  
Leonardo Ornella ◽  
Paulino Pérez‐Rodríguez ◽  
Daniel Gianola ◽  
Susanne Dreisigacker ◽  
...  

JAMIA Open ◽  
2020 ◽  
Vol 3 (2) ◽  
pp. 216-224
Author(s):  
Jonathan X Wang ◽  
Delaney K Sullivan ◽  
Alex C Wells ◽  
Jonathan H Chen

Abstract Objective This study assesses whether neural networks trained on electronic health record (EHR) data can anticipate what individual clinical orders and existing institutional order set templates clinicians will use more accurately than existing decision support tools. Materials and Methods We process 57 624 patients worth of clinical event EHR data from 2008 to 2014. We train a feed-forward neural network (ClinicNet) and logistic regression applied to the traditional problem structure of predicting individual clinical items as well as our proposed workflow of predicting existing institutional order set template usage. Results ClinicNet predicts individual clinical orders (precision = 0.32, recall = 0.47) better than existing institutional order sets (precision = 0.15, recall = 0.46). The ClinicNet model predicts clinician usage of existing institutional order sets (avg. precision = 0.31) with higher average precision than a baseline of order set usage frequencies (avg. precision = 0.20) or a logistic regression model (avg. precision = 0.12). Discussion Machine learning methods can predict clinical decision-making patterns with greater accuracy and less manual effort than existing static order set templates. This can streamline existing clinical workflows, but may not fit if historical clinical ordering practices are incorrect. For this reason, manually authored content such as order set templates remain valuable for the purposeful design of care pathways. ClinicNet’s capability of predicting such personalized order set templates illustrates the potential of combining both top-down and bottom-up approaches to delivering clinical decision support content. Conclusion ClinicNet illustrates the capability for machine learning methods applied to the EHR to anticipate both individual clinical orders and existing order set templates, which has the potential to improve upon current standards of practice in clinical order entry.


Author(s):  
Jarosław Koźlak ◽  
Bartlomiej Sniezynski ◽  
Dorota Wilk-Kołodziejczyk ◽  
Albert Leśniak ◽  
Krzysztof Jaśkowiec

2020 ◽  
Vol 10 (9) ◽  
pp. 3307 ◽  
Author(s):  
Khishigsuren Davagdorj ◽  
Jong Seol Lee ◽  
Van Huy Pham ◽  
Keun Ho Ryu

Smoking is one of the major public health issues, which has a significant impact on premature death. In recent years, numerous decision support systems have been developed to deal with smoking cessation based on machine learning methods. However, the inevitable class imbalance is considered a major challenge in deploying such systems. In this paper, we study an empirical comparison of machine learning techniques to deal with the class imbalance problem in the prediction of smoking cessation intervention among the Korean population. For the class imbalance problem, the objective of this paper is to improve the prediction performance based on the utilization of synthetic oversampling techniques, which we called the synthetic minority over-sampling technique (SMOTE) and an adaptive synthetic (ADASYN). This has been achieved by the experimental design, which comprises three components. First, the selection of the best representative features is performed in two phases: the lasso method and multicollinearity analysis. Second, generate the newly balanced data utilizing SMOTE and ADASYN technique. Third, machine learning classifiers are applied to construct the prediction models among all subjects and each gender. In order to justify the effectiveness of the prediction models, the f-score, type I error, type II error, balanced accuracy and geometric mean indices are used. Comprehensive analysis demonstrates that Gradient Boosting Trees (GBT), Random Forest (RF) and multilayer perceptron neural network (MLP) classifiers achieved the best performances in all subjects and each gender when SMOTE and ADASYN were utilized. The SMOTE with GBT and RF models also provide feature importance scores that enhance the interpretability of the decision-support system. In addition, it is proven that the presented synthetic oversampling techniques with machine learning models outperformed baseline models in smoking cessation prediction.


2019 ◽  
Vol 56 (4) ◽  
pp. 512-525 ◽  
Author(s):  
Abdullah Awaysheh ◽  
Jeffrey Wilcke ◽  
François Elvinger ◽  
Loren Rees ◽  
Weiguo Fan ◽  
...  

Machine-learning methods can assist with the medical decision-making processes at the both the clinical and diagnostic levels. In this article, we first review historical milestones and specific applications of computer-based medical decision support tools in both veterinary and human medicine. Next, we take a mechanistic look at 3 archetypal learning algorithms—naive Bayes, decision trees, and neural network—commonly used to power these medical decision support tools. Last, we focus our discussion on the data sets used to train these algorithms and examine methods for validation, data representation, transformation, and feature selection. From this review, the reader should gain some appreciation for how these decision support tools have and can be used in medicine along with insight on their inner workings.


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