Predicting Yield Performance of Parents in Plant Breeding: A Neural Collaborative Filtering Approach
This addresses the challenge of efficiently identifying optimal cross combinations for corn hybrids in plant breeding, which is incremental as it applies an existing collaborative filtering method to a new agricultural dataset.
The paper tackled the problem of predicting yield performance of untested parent combinations in plant breeding using a neural collaborative filtering approach, achieving significant outperformance over models like LASSO, random forest, and neural networks in computational results.
Experimental corn hybrids are created in plant breeding programs by crossing two parents, so-called inbred and tester, together. Identification of best parent combinations for crossing is challenging since the total number of possible cross combinations of parents is large and it is impractical to test all possible cross combinations due to limited resources of time and budget. In the 2020 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the historical yield performances of around 4% of total cross combinations of 593 inbreds with 496 testers which were planted in 280 locations between 2016 and 2018 and asked participants to predict the yield performance of cross combinations of inbreds and testers that have not been planted based on the historical yield data collected from crossing other inbreds and testers. In this paper, we present a collaborative filtering method which is an ensemble of matrix factorization method and neural networks to solve this problem. Our computational results suggested that the proposed model significantly outperformed other models such as LASSO, random forest (RF), and neural networks. Presented method and results were produced within the 2020 Syngenta Crop Challenge.