DeepG2P: Fusing Multi-Modal Data to Improve Crop Production

Agriculture is at the heart of the solution to achieve sustainability in feeding the world population, but advancing our understanding on how agricultural output responds to climatic variability is still needed. Precision Agriculture (PA), which is a management strategy that uses technology such as remote sensing, Geographical Information System (GIS), and machine learning for decision making in the field, has emerged as a promising approach to enhance crop production, increase yield, and reduce water and nutrient losses and environmental impacts. In this context, multiple models to predict agricultural phenotypes, such as crop yield, from genomics (G), environment (E), weather and soil, and field management practices (M) have been developed. These models have traditionally been based on mechanistic or statistical approaches. However, AI approaches are intrinsically well-suited to model complex interactions and have more recently been developed, outperforming classical methods. Here, we present a Natural Language Processing (NLP)-based neural network architecture to process the G, E and M inputs and their interactions. We show that by modeling DNA as natural language, our approach performs better than previous approaches when tested for new environments and similarly to other approaches for unseen seed varieties.

Machine learning can guide experimental approaches for protein digestibility estimations

Food protein digestibility and bioavailability are critical aspects in addressing human nutritional demands, particularly when seeking sustainable alternatives to animal-based proteins. In this study, we propose a machine learning approach to predict the true ileal digestibility coefficient of food items. The model makes use of a unique curated dataset that combines nutritional information from different foods with FASTA sequences of some of their protein families. We extracted the biochemical properties of the proteins and combined these properties with embeddings from a Transformer-based protein Language Model (pLM). In addition, we used SHAP to identify features that contribute most to the model prediction and provide interpretability. This first AI-based model for predicting food protein digestibility has an accuracy of 90% compared to existing experimental techniques. With this accuracy, our model can eliminate the need for lengthy in-vivo or in-vitro experiments, making the process of creating new foods faster, cheaper, and more ethical.