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In a changing climate, sustainable agriculture is essential for food security and environmental health. However, it is challenging to understand the complex interactions among its biophysical, social, and economic components. Predictive machine learning (ML), with its capacity to learn from data, is leveraged in sustainable agriculture for applications like yield prediction and weather forecasting. Nevertheless, it cannot explain causal mechanisms and remains descriptive rather than prescriptive. To address this gap, we propose causal ML, which merges ML's data processing with causality's ability to reason about change. This facilitates quantifying intervention impacts for evidence-based decision-making and enhances predictive model robustness. We showcase causal ML through eight diverse applications that benefit stakeholders across the agri-food chain, including farmers, policymakers, and researchers.

The modelling of Earth observation data is a challenging problem, typically approached by either purely mechanistic or purely data-driven methods. Mechanistic models encode the domain knowledge and physical rules governing the system. Such models, however, need the correct specification of all interactions between variables in the problem and the appropriate parameterization is a challenge in itself. On the other hand, machine learning approaches are flexible data-driven tools, able to approximate arbitrarily complex functions, but lack interpretability and struggle when data is scarce or in extrapolation regimes. In this paper, we argue that hybrid learning schemes that combine both approaches can address all these issues efficiently. We introduce Gaussian process (GP) convolution models for hybrid modelling in Earth observation (EO) problems. We specifically propose the use of a class of GP convolution models called latent force models (LFMs) for EO time series modelling, analysis and understanding. LFMs are hybrid models that incorporate physical knowledge encoded in differential equations into a multioutput GP model. LFMs can transfer information across time-series, cope with missing observations, infer explicit latent functions forcing the system, and learn parameterizations which are very helpful for system analysis and interpretability. We consider time series of soil moisture from active (ASCAT) and passive (SMOS, AMSR2) microwave satellites. We show how assuming a first order differential equation as governing equation, the model automatically estimates the e-folding time or decay rate related to soil moisture persistence and discovers latent forces related to precipitation. The proposed hybrid methodology reconciles the two main approaches in remote sensing parameter estimation by blending statistical learning and mechanistic modeling.

Developing accurate models of crop stress, phenology and productivity is of paramount importance, given the increasing need of food. Earth observation remote sensing data provides a unique source of information to monitor crops in a temporally resolved and spatially explicit way. In this study, we propose the combination of multisensor (optical and microwave) remote sensing data for crop yield estimation and forecasting using two novel approaches. We first propose the lag between Enhanced Vegetation Index derived from MODIS and Vegetation Optical Depth derived from SMAP as a new joint metric combining the information from the two satellite sensors in a unique feature or descriptor. Our second approach avoids summarizing statistics and uses machine learning to combine full time series of EVI and VOD. This study considers two statistical methods, a regularized linear regression and its nonlinear extension called kernel ridge regression to directly estimate the county-level surveyed total production, as well as individual yields of the major crops grown in the region: corn, soybean and wheat. The study area includes the US Corn Belt, and we use agricultural survey data from the National Agricultural Statistics Service (USDA-NASS) for year 2015 for quantitative assessment., Comment: 53 pages, 8 figures, 3 tables

Spatially and temporally explicit canopy water content (CWC) data are important for monitoring vegetation status, and constitute essential information for studying ecosystem-climate interactions. Despite many efforts there is currently no operational CWC product available to users. In the context of the Satellite Application Facility for Land Surface Analysis (LSA-SAF), we have developed an algorithm to produce a global dataset of CWC based on data from the Advanced Very High Resolution Radiometer (AVHRR) sensor on board Meteorological Operational (MetOp) satellites forming the EUMETSAT Polar System (EPS). CWC reflects the water conditions at the leaf level and information related to canopy structure. An accuracy assessment of the EPS/AVHRR CWC indicated a close agreement with multi-temporal ground data from SMAPVEX16 in Canada and Dahra in Senegal. The present study further evaluates the consistency of the LSA-SAF product with respect to the Simplified Level 2 Product Prototype Processor (SL2P) product, and demonstrates its applicability at different spatio-temporal resolutions using optical data from MSI/Sentinel-2 and MODIS/Terra and Aqua. We conclude that the EPS/AVHRR CWC product is a promising tool for monitoring vegetation water status at regional and global scales.

Soil moisture (SM) is a key state variable of the hydrological cycle, needed to monitor the effects of a changing climate on natural resources. Soil moisture is highly variable in space and time, presenting seasonalities, anomalies and long-term trends, but also, and important nonlinear behaviours. Here, we introduce a novel fast and nonlinear complex PCA method to analyze the spatio-temporal patterns of the Earth's surface SM. We use global SM estimates acquired during the period 2010-2017 by ESA's SMOS mission. Our approach unveils both time and space modes, trends and periodicities unlike standard PCA decompositions. Results show the distribution of the total SM variance among its different components, and indicate the dominant modes of temporal variability in surface soil moisture for different regions. The relationship of the derived SM spatio-temporal patterns with El Ni{\~n}o Southern Oscillation (ENSO) conditions is also explored.

In many remote sensing applications one wants to estimate variables or parameters of interest from observations. When the target variable is available at a resolution that matches the remote sensing observations, standard algorithms such as neural networks, random forests or Gaussian processes are readily available to relate the two. However, we often encounter situations where the target variable is only available at the group level, i.e. collectively associated to a number of remotely sensed observations. This problem setting is known in statistics and machine learning as {\em multiple instance learning} or {\em distribution regression}. This paper introduces a nonlinear (kernel-based) method for distribution regression that solves the previous problems without making any assumption on the statistics of the grouped data. The presented formulation considers distribution embeddings in reproducing kernel Hilbert spaces, and performs standard least squares regression with the empirical means therein. A flexible version to deal with multisource data of different dimensionality and sample sizes is also presented and evaluated. It allows working with the native spatial resolution of each sensor, avoiding the need of match-up procedures. Noting the large computational cost of the approach, we introduce an efficient version via random Fourier features to cope with millions of points and groups.

Soil moisture impacts exchanges of water, energy and carbon fluxes between the land surface and the atmosphere. Passive microwave remote sensing at L-band can capture spatial and temporal patterns of soil moisture in the landscape. Both ESA and NASA have launched L-band radiometers, in the form of the SMOS and SMAP satellites respectively, to monitor soil moisture globally, every 3-day at about 40 km resolution. However, their coarse scale restricts the range of applications. While SMAP included an L-band radar to downscale the radiometer soil moisture to 9 km, the radar failed after 3 months and this initial approach is not applicable to developing a consistent long term soil moisture product across the two missions anymore. Existing optical-, radiometer-, and oversampling-based downscaling methods could be an alternative to the radar-based approach for delivering such data. Nevertheless, retrieval of a consistent high resolution soil moisture product remains a challenge, and there has been no comprehensive inter-comparison of the alternate approaches. This research undertakes an assessment of the different downscaling approaches using the SMAPEx-4 field campaign data

Global warming is leading to unprecedented changes in our planet, with great societal, economical and environmental implications, especially with the growing demand of biofuels and food. Assessing the impact of climate on vegetation is of pressing need. We approached the attribution problem with a novel nonlinear Granger causal (GC) methodology and used a large data archive of remote sensing satellite products, environmental and climatic variables spatio-temporally gridded over more than 30 years. We generalize kernel Granger causality by considering the variables cross-relations explicitly in Hilbert spaces, and use the covariance in Gaussian processes. The method generalizes the linear and kernel GC methods, and comes with tighter bounds of performance based on Rademacher complexity. Spatially-explicit global Granger footprints of precipitation and soil moisture on vegetation greenness are identified more sharply than previous GC methods., Comment: 7 pages, 3 figures, AI for Earth Sciences Workshop at NeurIPS 2020. arXiv admin note: text overlap with arXiv:2011.14444

Over land the vegetation canopy affects the microwave brightness temperature by emission, scattering and attenuation of surface soil emission. The questions addressed in this study are: 1) what is the transparency of the vegetation canopy for different biomes around the Globe at the low-frequency L-band?, 2) what is the seasonal amplitude of vegetation microwave optical depth for different biomes?, 3) what is the effective scattering at this frequency for different vegetation types?, 4) what is the impact of imprecise characterization of vegetation microwave properties on retrieval of soil surface conditions? These questions are addressed based on the recently completed one full annual cycle measurements by the NASA Soil Moisture Active Passive (SMAP) measurements.

Granger causality (GC) is undoubtedly the most widely used method to infer cause-effect relations from observational time series. Several nonlinear alternatives to GC have been proposed based on kernel methods. We generalize kernel Granger causality by considering the variables cross-relations explicitly in Hilbert spaces. The framework is shown to generalize the linear and kernel GC methods, and comes with tighter bounds of performance based on Rademacher complexity. We successfully evaluate its performance in standard dynamical systems, as well as to identify the arrow of time in coupled R\"ossler systems, and is exploited to disclose the El Ni\~no-Southern Oscillation (ENSO) phenomenon footprints on soil moisture globally., Comment: 8 pages and 7 captioned figures

In the current context of climate change, extreme heatwaves, droughts, and floods are not only impacting the biosphere and atmosphere but the anthroposphere too. Human populations are forcibly displaced, which are now referred to as climate-induced migrants. In this work, we investigate which climate and structural factors forced major human displacements in the presence of floods and storms during the years 2017-2019. We built, curated, and harmonized a database of meteorological and remote sensing indicators along with structural factors of 27 developing countries worldwide. We show how we can use Gaussian Processes to learn what variables can explain the impact of floods and storms in the context of forced displacements and to develop models that reproduce migration flows. Our results at regional, global, and disaster-specific scales show the importance of structural factors in the determination of the magnitude of displacements. The study may have both societal, political, and economical implications., Comment: Presented at NeurIPS 2020 Workshop on Machine Learning for the Developing World

Most problems in Earth sciences aim to do inferences about the system, where accurate predictions are just a tiny part of the whole problem. Inferences mean understanding variables relations, deriving models that are physically interpretable, that are simple parsimonious, and mathematically tractable. Machine learning models alone are excellent approximators, but very often do not respect the most elementary laws of physics, like mass or energy conservation, so consistency and confidence are compromised. In this paper, we describe the main challenges ahead in the field, and introduce several ways to live in the Physics and machine learning interplay: to encode differential equations from data, constrain data-driven models with physics-priors and dependence constraints, improve parameterizations, emulate physical models, and blend data-driven and process-based models. This is a collective long-term AI agenda towards developing and applying algorithms capable of discovering knowledge in the Earth system., Comment: 24 pages, 10 figures, 3 tables, expanded AAAI PGAI 2020 Symposium

Information theory is an excellent framework for analyzing Earth system data because it allows us to characterize uncertainty and redundancy, and is universally interpretable. However, accurately estimating information content is challenging because spatio-temporal data is high-dimensional, heterogeneous and has non-linear characteristics. In this paper, we apply multivariate Gaussianization for probability density estimation which is robust to dimensionality, comes with statistical guarantees, and is easy to apply. In addition, this methodology allows us to estimate information-theoretic measures to characterize multivariate densities: information, entropy, total correlation, and mutual information. We demonstrate how information theory measures can be applied in various Earth system data analysis problems. First we show how the method can be used to jointly Gaussianize radar backscattering intensities, synthesize hyperspectral data, and quantify of information content in aerial optical images. We also quantify the information content of several variables describing the soil-vegetation status in agro-ecosystems, and investigate the temporal scales that maximize their shared information under extreme events such as droughts. Finally, we measure the relative information content of space and time dimensions in remote sensing products and model simulations involving long records of key variables such as precipitation, sensible heat and evaporation. Results confirm the validity of the method, for which we anticipate a wide use and adoption. Code and demos of the implemented algorithms and information-theory measures are provided., Comment: This work has been submitted to the IEEE for possible publication

Remote sensing observations, products and simulations are fundamental sources of information to monitor our planet and its climate variability. Uncovering the main modes of spatial and temporal variability in Earth data is essential to analyze and understand the underlying physical dynamics and processes driving the Earth System. Dimensionality reduction methods can work with spatio-temporal datasets and decompose the information efficiently. Principal Component Analysis (PCA), also known as Empirical Orthogonal Functions (EOF) in geophysics, has been traditionally used to analyze climatic data. However, when nonlinear feature relations are present, PCA/EOF fails. In this work, we propose a nonlinear PCA method to deal with spatio-temporal Earth System data. The proposed method, called Rotated Complex Kernel PCA (ROCK-PCA for short), works in reproducing kernel Hilbert spaces to account for nonlinear processes, operates in the complex kernel domain to account for both space and time features, and adds an extra rotation for improved flexibility. The result is an explicitly resolved spatio-temporal decomposition of the Earth data cube. The method is unsupervised and computationally very efficient.We illustrate its ability to uncover spatio-temporal patterns using synthetic experiments and real data. Results of the decomposition of three essential climate variables are shown: satellite-based global Gross Primary Productivity (GPP) and Soil Moisture (SM), and reanalysis Sea Surface Temperature (SST) data. The ROCK-PCA method allows identifying their annual and seasonal oscillations, as well as their non-seasonal trends and spatial variability patterns.