Water is essential for agricultural productivity. Assessing water shortages and reduced yield potential is a critical factor in decision-making for ensuring agricultural productivity and food security. Crop simulation models, which align with physical processes, offer intrinsic explainability but often perform poorly. Conversely, machine learning models for crop yield modeling are powerful and scalable, yet they commonly operate as black boxes and lack adherence to the physical principles of crop growth. This study bridges this gap by coupling the advantages of both worlds. We postulate that the crop yield is inherently defined by the water availability. Therefore, we formulate crop yield as a function of temporal water scarcity and predict both the crop drought stress and the sensitivity to water scarcity at fine-scale resolution. Sequentially modeling the crop yield response to water enables accurate yield prediction. To enforce physical consistency, a novel physics-informed loss function is proposed. We leverage multispectral satellite imagery, meteorological data, and fine-scale yield data. Further, to account for the uncertainty within the model, we build upon a deep ensemble approach. Our method surpasses state-of-the-art models like LSTM and Transformers in crop yield prediction with a coefficient of determination ($R^2$-score) of up to 0.82 while offering high explainability. This method offers decision support for industry, policymakers, and farmers in building a more resilient agriculture in times of changing climate conditions.

Controlling environmental conditions and monitoring plant status in greenhouses is critical to promptly making appropriate management decisions aimed at promoting crop production. The primary objective of this research study was to develop and test a smart aeroponic greenhouse on an experimental scale where the status of Geranium plant and environmental conditions are continuously monitored through the integration of the internet of things (IoT) and artificial intelligence (AI). An IoT-based platform was developed to control the environmental conditions of plants more efficiently and provide insights to users to make informed management decisions. In addition, we developed an AI-based disease detection framework using VGG-19, InceptionResNetV2, and InceptionV3 algorithms to analyze the images captured periodically after an intentional inoculation. The performance of the AI framework was compared with an expert's evaluation of disease status. Preliminary results showed that the IoT system implemented in the greenhouse environment is able to publish data such as temperature, humidity, water flow, and volume of charge tanks online continuously to users and adjust the controlled parameters to provide an optimal growth environment for the plants. Furthermore, the results of the AI framework demonstrate that the VGG-19 algorithm was able to identify drought stress and rust leaves from healthy leaves with the highest accuracy, 92% among the other algorithms.

Early detection of drought stress is critical for taking timely measures for reducing crop loss before the drought impact becomes irreversible. The subtle phenotypical and physiological changes in response to drought stress are captured by non-invasive imaging techniques and these imaging data serve as valuable resource for machine learning methods to identify drought stress. While convolutional neural networks (CNNs) are in wide use, vision transformers (ViTs) present a promising alternative in capturing long-range dependencies and intricate spatial relationships, thereby enhancing the detection of subtle indicators of drought stress. We propose an explainable deep learning pipeline that leverages the power of ViTs for drought stress detection in potato crops using aerial imagery. We applied two distinct approaches: a synergistic combination of ViT and support vector machine (SVM), where ViT extracts intricate spatial features from aerial images, and SVM classifies the crops as stressed or healthy and an end-to-end approach using a dedicated classification layer within ViT to directly detect drought stress. Our key findings explain the ViT model's decision-making process by visualizing attention maps. These maps highlight the specific spatial features within the aerial images that the ViT model focuses as the drought stress signature. Our findings demonstrate that the proposed methods not only achieve high accuracy in drought stress identification but also shedding light on the diverse subtle plant features associated with drought stress. This offers a robust and interpretable solution for drought stress monitoring for farmers to undertake informed decisions for improved crop management.

Soybean production is susceptible to biotic and abiotic stresses, exacerbated by extreme weather events. Water limiting stress, i.e. drought, emerges as a significant risk for soybean production, underscoring the need for advancements in stress monitoring for crop breeding and production. This project combines multi-modal information to identify the most effective and efficient automated methods to investigate drought response. We investigated a set of diverse soybean accessions using multiple sensors in a time series high-throughput phenotyping manner to: (1) develop a pipeline for rapid classification of soybean drought stress symptoms, and (2) investigate methods for early detection of drought stress. We utilized high-throughput time-series phenotyping using UAVs and sensors in conjunction with machine learning (ML) analytics, which offered a swift and efficient means of phenotyping. The red-edge and green bands were most effective to classify canopy wilting stress. The Red-Edge Chlorophyll Vegetation Index (RECI) successfully differentiated susceptible and tolerant soybean accessions prior to visual symptom development. We report pre-visual detection of soybean wilting using a combination of different vegetation indices. These results can contribute to early stress detection methodologies and rapid classification of drought responses in screening nurseries for breeding and production applications.

The population of the earth is constantly growing and therefore also the demand for food. In consequence, breeding crop plants which most efficiently make use of the available cropland is one of the greatest challenges nowadays. In particular, plants which are resilient and resistant to environmental stresses are desirable. The development of such plants relies on the investigation of the interaction between the plant's genes and the environmental stresses. In order to be able to investigate the interaction a quantitative representation of the environmental stresses is needed. Here, we consider this representation combining state-of-the-art data-driven methods with expert-driven modeling from agriculture. Briefly put, it has been reported that environmental stress such as inappropriate or extreme temperature conditions, lack of sufficient moisture, etc., can significantly impede the life cycle development of corn, thus leading to yield reductions (cf.

Environmental stresses such as drought and heat can cause substantial yield loss in agriculture. As such, hybrid crops which are tolerant to drought and heat stress would produce more consistent yields compared to the hybrids which are not tolerant to these stresses. In the 2019 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the yield performances of 2,452 corn hybrids planted in 1,560 locations between 2008 and 2017 and asked participants to classify the corn hybrids as either tolerant or susceptible to drought stress, heat stress, and combined drought and heat stress. As one of the winning teams, we designed a two-step approach to solve this problem in an unsupervised way since no data was provided that classified any set of hybrids as tolerant or susceptible to any type of stress. First, we designed a deep convolutional neural network (CNN) that took advantage of state-of-the-art modeling and solution techniques to extract stress metrics for each type of stress. Our CNN model was found to successfully distinguish between the low and high stress environments due to considering multiple factors such as planting/harvest dates, daily weather, and soil conditions. Then, we conducted a linear regression of the yield of hybrid against each stress metric, and classified the hybrid based on the slope of the regression line, since the slope of the regression line showed how sensitive a hybrid was to a specific environmental stress. Our results suggested that only 14 % of the corn hybrids were tolerant to at least one type of stress.

Understanding the adaptation process of plants to drought stress is essential in improving management practices, breeding strategies as well as engineering viable crops for a sustainable agriculture in the coming decades. Hyper-spectral imaging provides a particularly promising approach to gain such understanding since it allows to discover non-destructively spectral characteristics of plants governed primarily by scattering and absorption characteristics of the leaf internal structure and biochemical constituents. Several drought stress indices have been derived using hyper-spectral imaging. However, they are typically based on few hyper-spectral images only, rely on interpretations of experts, and consider few wavelengths only. In this study, we present the first data-driven approach to discovering spectral drought stress indices, treating it as an unsupervised labeling problem at massive scale. To make use of short range dependencies of spectral wavelengths, we develop an online variational Bayes algorithm for latent Dirichlet allocation with convolved Dirichlet regularizer. This approach scales to massive datasets and, hence, provides a more objective complement to plant physiological practices. The spectral topics found conform to plant physiological knowledge and can be computed in a fraction of the time compared to existing LDA approaches.

Pre-symptomatic drought stress prediction is of great relevance in precision plant protection, ultimately helping to meet the challenge of "How to feed a hungry world?". Unfortunately, it also presents unique computational problems in scale and interpretability: it is a temporal, large-scale prediction task, e.g., when monitoring plants over time using hyperspectral imaging, and features are `things' with a `biological' meaning and interpretation and not just mathematical abstractions computable for any data. In this paper we propose Dirichlet-aggregation regression (DAR) to meet the challenge. DAR represents all data by means of convex combinations of only few extreme ones computable in linear time and easy to interpret.Then, it puts a Gaussian process prior on the Dirichlet distributions induced on the simplex spanned by the extremes. The prior can be a function of any observed meta feature such as time, location, type of fertilization, and plant species. We evaluated DAR on two hyperspectral image series of plants over time with about 2 (resp. 5.8) Billion matrix entries. The results demonstrate that DAR can be learned efficiently and predicts stress well before it becomes visible to the human eye.