Machine learning algorithms to infer trait-matching and predict species interactions in ecological networks
This work addresses ecologists' need for better predictive models to understand species interactions, though it is incremental as it applies existing ML methods to ecological data.
The study tackled the problem of predicting species interactions in ecological networks by comparing traditional generalized linear models (GLMs) with flexible machine learning models, finding that ML models like Random Forest and Deep Neural Networks outperformed GLMs by a substantial margin in predicting interactions and identifying causal trait-matching combinations.
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, naive 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 find 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, without any prior assumptions. 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.