MixINN: Accelerating Plant Breeding by Combining Mixed Models and Deep Learning for Interaction Prediction

Global food security depends on predicting crop responses to climate variability, yet process based crop models remain too computationally expensive for large scale exploration of genotype and environment interactions. Here we develop a probabilistic neural emulator of APSIM that reproduces key maize growth processes across 13 outputs with high fidelity (with R^2 of 0.93) while reducing simulation time by several orders of magnitude. Trained on two million simulations spanning diverse genetic, soil, and management conditions, and augmented with a convolutional synthetic weather generator that produces physically consistent climate sequences, the framework enables scalable exploration of crop responses under realistic and diverse environmental inputs while providing calibrated predictive uncertainty without costly Bayesian inference. Applying this framework across 100,000 trait configurations, six soil environments in Iowa and Illinois, and climate projections through the year 2100 under two emissions scenarios, we identify 181 maize trait combinations that consistently maintain high yield across all tested conditionsan analysis infeasible with the mechanistic model alone. We further show that radiation use efficiency and temperature driven root dynamics are dominant drivers of yield resilience. Notably, projected yield distributions vary substantially across locations, with some lower productivity sites exhibiting yield increases under future climate scenarios, indicating that climate change may reshape regional yield potential in nonintuitive ways. These results demonstrate how uncertainty aware emulation transforms mechanistic crop simulation from a computational bottleneck into an on demand discovery engine, one capable of interrogating the full genotype, environment and management space at a scale no process-based model can match.

Crop yield prediction is one of the most important challenge, which is crucial to world food security and policy-making decisions. The conventional forecasting techniques are limited in their accuracy with reference to the fact that they utilize static data sources that do not reflect the dynamic and intricate relationships that exist between the variables of the environment over time [5,13]. This paper presents Attention-Based Multi-Modal Deep Learning Framework (ABMMDLF), which is suggested to be used in high-accuracy spatio-temporal crop yield prediction. The model we use combines multi-year satellite imagery, high-resolution time-series of meteorological data and initial soil properties as opposed to the traditional models which use only one of the aforementioned factors [12, 21]. The main architecture involves the use of Convolutional Neural Networks (CNN) to extract spatial features and a Temporal Attention Mechanism to adaptively weight important phenological periods targeted by the algorithm to change over time and condition on spatial features of images and video sequences. As can be experimentally seen, the proposed research work provides an R^2 score of 0.89, which is far better than the baseline models do.

Accurate crop yield prediction is crucial for sustainable agriculture and global food security. While existing methods are predominantly developed for single-crop prediction, they often struggle to generalize across diverse crop types, without addressing the unique crop phenological responses that are dynamically modulated by complex weather patterns. In this paper, we propose PhenoYieldNet, a multi-crop yield prediction framework that learns crop-specific phenology by explicitly modeling their responses with temporal drivers. Specifically, we develop a crop-aware temporal decoder consisting of a Crop Phenology Bank (CPB) and a Crop Phenology Attention (CPA) module. The CPB integrates a set of learnable embeddings, which leverage a query to guide the CPA module to learn the most relevant phenology patterns for the specific crop. And the CPA module explicitly captures multi-scale trend and variation components to construct temporal contexts, enabling the model to dynamically adjust the attention across different phenological stages. To learn robust and generalizable features for multi-crop prediction, the encoder is initialized with a pre-trained foundation model, and further adapted via a self-supervised Temporal Contrastive Adaptation strategy to align with agricultural temporal dynamics. Extensive experiments conducted on multi-crop datasets indicate that our proposed method significantly outperforms state-of-the-art methods, exhibiting strong generalization capabilities across different regions and crops.