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Machine learning algorithms to infer trait‐matching and predict species interactions in ecological networks
Open accessAbstract
Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape. Empirical estimates of the importance of trait‐matching for determining species interactions, however, vary significantly among different types of ecological networks. Here, we show that ambiguity among empirical trait‐matching studies may have arisen at least in parts from using overly simple statistical models. Using simulated and real data, we contrast conventional generalized linear models (GLM) with more flexible Machine Learning (ML) models (Random Forest, Boosted Regression Trees, Deep Neural Networks, Convolutional Neural Networks, Support Vector Machines, naïve Bayes, and k‐Nearest‐Neighbor), testing their ability to predict species interactions based on traits, and infer trait combinations causally responsible for species interactions. We found that the best ML models can successfully predict species interactions in plant–pollinator networks, outperforming GLMs by a substantial margin. Our results also demonstrate that ML models can better identify the causally responsible trait‐matching combinations than GLMs. In two case studies, the best ML models successfully predicted species interactions in a global plant–pollinator database and inferred ecologically plausible trait‐matching rules for a plant–hummingbird network from Costa Rica, without any prior assumptions about the system. We conclude that flexible ML models offer many advantages over traditional regression models for understanding interaction networks. We anticipate that these results extrapolate to other ecological network types. More generally, our results highlight the potential of machine learning and artificial intelligence for inference in ecology, beyond standard tasks such as image or pattern recognition.
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“Significant error reduction of ML and DL with respect to traditional generalized regression models has been reported routinely for species richness and diversity estimation33,34.”
From Perspectives in machine learning for wildlife conservation (2022) · cites this paper as [33]
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“Tree-based techniques have also been used to predict species interactions: for example, regression trees significantly outperformed classical generalized linear models in predicting plant-pollinator interactions33.”
From Perspectives in machine learning for wildlife conservation (2022) · cites this paper as [33]
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Network structure indicators predict ecological robustness in food webs
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Connecting the dots: Managing species interaction networks to mitigate the impacts of global change
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Metadata
- Authors
- Pichler, M., Boreux, V., Klein, A., Schleuning, M., & Hartig, F.
- Affiliations
- University of Regensburg (DE)
- University of Freiburg (DE)
- Senckenberg Biodiversity and Climate Research Centre (DE)
- Corresponding author
- Pichler, Maximilian
- Venue
- Methods in Ecology and Evolution
- Publisher
- Wiley
- Published
- 2019-11-19
- Volume
- 11
- Issue
- 2
- Pages
- 281-293
- ISSN
- 2041-210X (ISSN-L)
- OpenAlex
- W2970584612
- Cited by
- 149
- References
- 78
- Citations by year
- 2026: 20 · 2025: 29 · 2024: 24 · 2023: 21 · 2022: 23 · 2021: 19 · 2020: 13
- FWCI
- 10.77
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Methods in Ecology and Evolution (publishedVersion, cc-by)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant and animal studies
- Physical Sciences › Environmental Science › Nature and Landscape Conservation › Ecology and Vegetation Dynamics Studies
- Life Sciences › Agricultural and Biological Sciences › Insect Science › Insect and Arachnid Ecology and Behavior
- Keywords
- trait matching, species interactions, ecological networks, plant-pollinator networks, machine learning, generalized linear models, random forest, boosted regression trees, deep neural network, convolutional neural networks, support vector machine, naive Bayes, k-nearest neighbors, trait combinations, plant-hummingbird interactions, interaction prediction
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