A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins
Traditional food allergen identification mainly relies on in vivo and in vitro experiments, which often needs a long period and high cost. The artificial intelligence (AI)-driven rapid food allergen identification method has solved the above mentioned some drawbacks and is becoming an efficient auxi...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | Foods |
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| Online Access: | https://www.mdpi.com/2304-8158/10/4/809 |
| _version_ | 1827695542173433856 |
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| author | Liyang Wang Dantong Niu Xinjie Zhao Xiaoya Wang Mengzhen Hao Huilian Che |
| author_facet | Liyang Wang Dantong Niu Xinjie Zhao Xiaoya Wang Mengzhen Hao Huilian Che |
| author_sort | Liyang Wang |
| collection | DOAJ |
| description | Traditional food allergen identification mainly relies on in vivo and in vitro experiments, which often needs a long period and high cost. The artificial intelligence (AI)-driven rapid food allergen identification method has solved the above mentioned some drawbacks and is becoming an efficient auxiliary tool. Aiming to overcome the limitations of lower accuracy of traditional machine learning models in predicting the allergenicity of food proteins, this work proposed to introduce deep learning model—transformer with self-attention mechanism, ensemble learning models (representative as Light Gradient Boosting Machine (LightGBM) eXtreme Gradient Boosting (XGBoost)) to solve the problem. In order to highlight the superiority of the proposed novel method, the study also selected various commonly used machine learning models as the baseline classifiers. The results of 5-fold cross-validation showed that the area under the receiver operating characteristic curve (AUC) of the deep model was the highest (0.9578), which was better than the ensemble learning and baseline algorithms. But the deep model need to be pre-trained, and the training time is the longest. By comparing the characteristics of the transformer model and boosting models, it can be analyzed that, each model has its own advantage, which provides novel clues and inspiration for the rapid prediction of food allergens in the future. |
| first_indexed | 2024-03-10T12:28:42Z |
| format | Article |
| id | doaj.art-1c25e8192efe4dd99e3d2d9223c44bcb |
| institution | Directory Open Access Journal |
| issn | 2304-8158 |
| language | English |
| last_indexed | 2024-03-10T12:28:42Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Foods |
| spelling | doaj.art-1c25e8192efe4dd99e3d2d9223c44bcb2023-11-21T14:47:00ZengMDPI AGFoods2304-81582021-04-0110480910.3390/foods10040809A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food ProteinsLiyang Wang0Dantong Niu1Xinjie Zhao2Xiaoya Wang3Mengzhen Hao4Huilian Che5Key Laboratory of Precision Nutrition and Food Quality, The Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaCollege of Information and Electrical Engineering, China Agricultural University, Beijing 100083, ChinaCollege of Humanities and Development Studies, China Agricultural University, Beijing 100083, ChinaKey Laboratory of Precision Nutrition and Food Quality, The Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaKey Laboratory of Precision Nutrition and Food Quality, The Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaKey Laboratory of Precision Nutrition and Food Quality, The Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaTraditional food allergen identification mainly relies on in vivo and in vitro experiments, which often needs a long period and high cost. The artificial intelligence (AI)-driven rapid food allergen identification method has solved the above mentioned some drawbacks and is becoming an efficient auxiliary tool. Aiming to overcome the limitations of lower accuracy of traditional machine learning models in predicting the allergenicity of food proteins, this work proposed to introduce deep learning model—transformer with self-attention mechanism, ensemble learning models (representative as Light Gradient Boosting Machine (LightGBM) eXtreme Gradient Boosting (XGBoost)) to solve the problem. In order to highlight the superiority of the proposed novel method, the study also selected various commonly used machine learning models as the baseline classifiers. The results of 5-fold cross-validation showed that the area under the receiver operating characteristic curve (AUC) of the deep model was the highest (0.9578), which was better than the ensemble learning and baseline algorithms. But the deep model need to be pre-trained, and the training time is the longest. By comparing the characteristics of the transformer model and boosting models, it can be analyzed that, each model has its own advantage, which provides novel clues and inspiration for the rapid prediction of food allergens in the future.https://www.mdpi.com/2304-8158/10/4/809food allergensallergenicity predictiondeep learningensemble learningcomparative analysis |
| spellingShingle | Liyang Wang Dantong Niu Xinjie Zhao Xiaoya Wang Mengzhen Hao Huilian Che A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins Foods food allergens allergenicity prediction deep learning ensemble learning comparative analysis |
| title | A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins |
| title_full | A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins |
| title_fullStr | A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins |
| title_full_unstemmed | A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins |
| title_short | A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins |
| title_sort | comparative analysis of novel deep learning and ensemble learning models to predict the allergenicity of food proteins |
| topic | food allergens allergenicity prediction deep learning ensemble learning comparative analysis |
| url | https://www.mdpi.com/2304-8158/10/4/809 |
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