Human Limits in Machine Learning: Prediction of Plant Phenotypes Using Soil Microbiome Data

The preservation of soil health has been identified as one of the main challenges of the XXI century given its vast (and potentially threatening) ramifications in agriculture, human health and biodiversity. Here, we provide the first deep investigation of the predictive potential of machine-learning models to understand the connections between soil and biological phenotypes. Indeed, we investigate an integrative framework performing accurate machine-learning-based prediction of plant phenotypes from biological, chemical and physical properties of the soil via two models: random forest and Bayesian neural network. We show that prediction is improved, as evidenced by higher weighted F1 scores, when incorporating into the models environmental features like soil physicochemical properties and microbial population density in addition to the microbiome information. Furthermore, by exploring multiple data preprocessing strategies such as normalization, zero replacement, and data augmentation, we confirm that human decisions have a huge impact on the predictive performance. In particular, we show that the naive total sum scaling normalization that is commonly used in microbiome research is not the optimal strategy to maximize predictive power. In addition, we find that accurately defined labels are more important than normalization, taxonomic level or model characteristics. That is, if humans are unable to classify the samples and provide accurate labels, the performance of machine-learning models will be limited. Lastly, we present strategies for domain scientists via a full model selection decision tree to identify the human choices that maximize the prediction power of the models. Our work is accompanied by open source reproducible scripts (https://github.com/solislemuslab/soil-microbiome-nn) for maximum outreach among the microbiome research community.