Luca G. Bernardini , Christoph Rosinger , Gernot Bodner , Katharina M. Keiblinger , Emma Izquierdo-Verdiguier , Heide Spiegel , Carl O. Retzlaff , Andreas Holzinger
{"title":"学习与理解:在土壤有机碳预测中,人工智能何时才能胜过基于过程的建模?","authors":"Luca G. Bernardini , Christoph Rosinger , Gernot Bodner , Katharina M. Keiblinger , Emma Izquierdo-Verdiguier , Heide Spiegel , Carl O. Retzlaff , Andreas Holzinger","doi":"10.1016/j.nbt.2024.03.001","DOIUrl":null,"url":null,"abstract":"<div><p>In recent years, machine learning (ML) algorithms have gained substantial recognition for ecological modeling across various temporal and spatial scales. However, little evaluation has been conducted for the prediction of soil organic carbon (SOC) on small data sets commonly inherent to long-term soil ecological research. In this context, the performance of ML algorithms for SOC prediction has never been tested against traditional process-based modeling approaches. Here, we compare ML algorithms, calibrated and uncalibrated process-based models as well as multiple ensembles on their performance in predicting SOC using data from five long-term experimental sites (comprising 256 independent data points) in Austria. Using all available data, the ML-based approaches using Random forest and Support vector machines with a polynomial kernel were superior to all process-based models. However, the ML algorithms performed similar or worse when the number of training samples was reduced or when a leave-one-site-out cross validation was applied. This emphasizes that the performance of ML algorithms is strongly dependent on the data-size related quality of learning information following the well-known curse of dimensionality phenomenon, while the accuracy of process-based models significantly relies on proper calibration and combination of different modeling approaches. Our study thus suggests a superiority of ML-based SOC prediction at scales where larger datasets are available, while process-based models are superior tools when targeting the exploration of underlying biophysical and biochemical mechanisms of SOC dynamics in soils. Therefore, we recommend applying ensembles of ML algorithms with process-based models to combine advantages inherent to both approaches.</p></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"81 ","pages":"Pages 20-31"},"PeriodicalIF":4.5000,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1871678424000086/pdfft?md5=63bda49e4bb9729283361b81ea4e3f0f&pid=1-s2.0-S1871678424000086-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Learning vs. understanding: When does artificial intelligence outperform process-based modeling in soil organic carbon prediction?\",\"authors\":\"Luca G. Bernardini , Christoph Rosinger , Gernot Bodner , Katharina M. Keiblinger , Emma Izquierdo-Verdiguier , Heide Spiegel , Carl O. Retzlaff , Andreas Holzinger\",\"doi\":\"10.1016/j.nbt.2024.03.001\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>In recent years, machine learning (ML) algorithms have gained substantial recognition for ecological modeling across various temporal and spatial scales. However, little evaluation has been conducted for the prediction of soil organic carbon (SOC) on small data sets commonly inherent to long-term soil ecological research. In this context, the performance of ML algorithms for SOC prediction has never been tested against traditional process-based modeling approaches. Here, we compare ML algorithms, calibrated and uncalibrated process-based models as well as multiple ensembles on their performance in predicting SOC using data from five long-term experimental sites (comprising 256 independent data points) in Austria. Using all available data, the ML-based approaches using Random forest and Support vector machines with a polynomial kernel were superior to all process-based models. However, the ML algorithms performed similar or worse when the number of training samples was reduced or when a leave-one-site-out cross validation was applied. This emphasizes that the performance of ML algorithms is strongly dependent on the data-size related quality of learning information following the well-known curse of dimensionality phenomenon, while the accuracy of process-based models significantly relies on proper calibration and combination of different modeling approaches. Our study thus suggests a superiority of ML-based SOC prediction at scales where larger datasets are available, while process-based models are superior tools when targeting the exploration of underlying biophysical and biochemical mechanisms of SOC dynamics in soils. Therefore, we recommend applying ensembles of ML algorithms with process-based models to combine advantages inherent to both approaches.</p></div>\",\"PeriodicalId\":19190,\"journal\":{\"name\":\"New biotechnology\",\"volume\":\"81 \",\"pages\":\"Pages 20-31\"},\"PeriodicalIF\":4.5000,\"publicationDate\":\"2024-03-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S1871678424000086/pdfft?md5=63bda49e4bb9729283361b81ea4e3f0f&pid=1-s2.0-S1871678424000086-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"New biotechnology\",\"FirstCategoryId\":\"5\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1871678424000086\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"New biotechnology","FirstCategoryId":"5","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1871678424000086","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
摘要
近年来,机器学习(ML)算法在各种时空尺度的生态建模中获得了广泛认可。然而,对于长期土壤生态研究中常见的小型数据集上的土壤有机碳(SOC)预测,却很少进行评估。在这种情况下,用于 SOC 预测的 ML 算法的性能从未与传统的基于过程的建模方法进行过对比测试。在此,我们利用奥地利五个长期实验点的数据(包括 256 个独立数据点),比较了 ML 算法、校准和未校准的基于过程的模型以及多个集合在预测 SOC 方面的性能。在使用所有可用数据的情况下,使用随机森林和多项式内核支持向量机的基于 ML 的方法优于所有基于过程的模型。然而,当训练样本数量减少或采用 "一地不进 "交叉验证时,ML 算法的性能相近或更差。这突出表明,根据众所周知的 "维度诅咒 "现象,ML 算法的性能在很大程度上取决于与数据大小相关的学习信息质量,而基于过程的模型的准确性则在很大程度上依赖于适当的校准和不同建模方法的组合。因此,我们的研究表明,在有较大数据集的情况下,基于 ML 的 SOC 预测更有优势,而在探索土壤中 SOC 动态的生物物理和生物化学机制时,基于过程的模型则是更好的工具。因此,我们建议将 ML 算法集合与基于过程的模型相结合,以综合两种方法的固有优势。
Learning vs. understanding: When does artificial intelligence outperform process-based modeling in soil organic carbon prediction?
In recent years, machine learning (ML) algorithms have gained substantial recognition for ecological modeling across various temporal and spatial scales. However, little evaluation has been conducted for the prediction of soil organic carbon (SOC) on small data sets commonly inherent to long-term soil ecological research. In this context, the performance of ML algorithms for SOC prediction has never been tested against traditional process-based modeling approaches. Here, we compare ML algorithms, calibrated and uncalibrated process-based models as well as multiple ensembles on their performance in predicting SOC using data from five long-term experimental sites (comprising 256 independent data points) in Austria. Using all available data, the ML-based approaches using Random forest and Support vector machines with a polynomial kernel were superior to all process-based models. However, the ML algorithms performed similar or worse when the number of training samples was reduced or when a leave-one-site-out cross validation was applied. This emphasizes that the performance of ML algorithms is strongly dependent on the data-size related quality of learning information following the well-known curse of dimensionality phenomenon, while the accuracy of process-based models significantly relies on proper calibration and combination of different modeling approaches. Our study thus suggests a superiority of ML-based SOC prediction at scales where larger datasets are available, while process-based models are superior tools when targeting the exploration of underlying biophysical and biochemical mechanisms of SOC dynamics in soils. Therefore, we recommend applying ensembles of ML algorithms with process-based models to combine advantages inherent to both approaches.
期刊介绍:
New Biotechnology is the official journal of the European Federation of Biotechnology (EFB) and is published bimonthly. It covers both the science of biotechnology and its surrounding political, business and financial milieu. The journal publishes peer-reviewed basic research papers, authoritative reviews, feature articles and opinions in all areas of biotechnology. It reflects the full diversity of current biotechnology science, particularly those advances in research and practice that open opportunities for exploitation of knowledge, commercially or otherwise, together with news, discussion and comment on broader issues of general interest and concern. The outlook is fully international.
The scope of the journal includes the research, industrial and commercial aspects of biotechnology, in areas such as: Healthcare and Pharmaceuticals; Food and Agriculture; Biofuels; Genetic Engineering and Molecular Biology; Genomics and Synthetic Biology; Nanotechnology; Environment and Biodiversity; Biocatalysis; Bioremediation; Process engineering.