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基于Stacking集成學(xué)習(xí)的水稻表型組學(xué)實體分類研究
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國家自然科學(xué)基金項目(61502236)、中央高校基本科研業(yè)務(wù)費專項資金項目(KJQN201651)和大學(xué)生創(chuàng)新創(chuàng)業(yè)訓(xùn)練專項計劃項目(S20190025)


Classification of Rice Phenomics Entities Based on Stacking Ensemble Learning
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    摘要:

    為研究整合水稻表型組學(xué)相關(guān)知識,系統(tǒng)地建立水稻表型組學(xué)知識圖譜,通過分布式爬蟲框架從國家水稻數(shù)據(jù)中心網(wǎng)站獲取水稻表型組學(xué)數(shù)據(jù)集,,并以互動百科為輔助數(shù)據(jù)源獲取水稻表型組學(xué)數(shù)據(jù)。對水稻表型組學(xué)數(shù)據(jù)采用TF-IDF技術(shù)結(jié)合潛在語義模型進(jìn)行預(yù)處理,并對水稻表型組學(xué)實體進(jìn)行人工分類和標(biāo)注,。為實現(xiàn)水稻表型組學(xué)實體分類,研究了基于堆疊式兩階段集成學(xué)習(xí)的分類器組合模型,,結(jié)合K-近鄰算法,、支持向量機、隨機森林,、梯度提升決策樹機器學(xué)習(xí)方法,,提升水稻表型組學(xué)實體數(shù)據(jù)分類的性能。研究表明,,基于堆疊式兩階段集成學(xué)習(xí)的分類器組合模型對不同類別的水稻表型組學(xué)數(shù)據(jù)都具有較好的多分類能力,,對于不平衡的水稻表型組學(xué)數(shù)據(jù)集,本文方法的分類器組合模型對水稻表型組學(xué)數(shù)據(jù)分類效果最佳,,Gene類別的F1為90.47%,,總體準(zhǔn)確率達(dá)80.55%,比支持向量機、K-近鄰,、隨機森林和梯度提升決策樹4種基分類器的分類準(zhǔn)確率平均高6.78個百分點,。

    Abstract:

    With the development of rice phenomics research, it is of great significance for comprehensively analyzing, mining and applying the rice phenomics data. In order to integrate the knowledge related to rice phenomics and explore the factors affecting rice phenotypic traits,the rice phenomics knowledge graph system was implemented. Rice phenomics knowledge graph system consisted of functional modules such as entity recognition, entity query, relational query and knowledge visualization. The rice phenomics data were downloaded by a distributed data website crawler from the National Rice Data Center website, and the interactive encyclopedia website was taken as auxiliary data sources to obtain rice phenomics dataset. The dataset was preprocessed with TF-IDF and latent semantic indexing method and classified and labeling manually firstly, and then machine learning approaches were applied for training and testing. The rice phenomics entity classification was studied based on stacking ensemble learning integrated with basic learning classifier, such as K-nearest neighbor, support vector machine, random forests and gradient boosting decision tree. Based on stacking ensemble learning classifier, different types of rice phenomics data showed fine ability for entity classification. For the unbalanced rice phenomics entities, comparing with the support vector machine algorithm, the K-nearest neighbor algorithm, the random forest algorithm and the gradient boosting decision tree algorithm, the proposed method showed the best performance, i.e. the F1-Measure of Gene entities can reach 90.47%. The overall accuracy was 80.55%, and it was 6.78 percentage points higher than those of the other four basic classifiers.

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袁培森,楊承林,宋玉紅,翟肇裕,徐煥良.基于Stacking集成學(xué)習(xí)的水稻表型組學(xué)實體分類研究[J].農(nóng)業(yè)機械學(xué)報,2019,50(11):144-152. YUAN Peisen, YANG Chenglin, SONG Yuhong, ZHAI Zhaoyu, XU Huanliang. Classification of Rice Phenomics Entities Based on Stacking Ensemble Learning[J]. Transactions of the Chinese Society for Agricultural Machinery,2019,50(11):144-152.

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  • 收稿日期:2019-07-11
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  • 在線發(fā)布日期: 2019-11-10
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