Charalampos Kontoes

Vasileios Sitokonstantinou, Alkiviadis Koukos, Ilias Tsoumas et al.

Crop phenology is crucial information for crop yield estimation and agricultural management. Traditionally, phenology has been observed from the ground; however Earth observation, weather and soil data have been used to capture the physiological growth of crops. In this work, we propose a new approach for the within-season phenology estimation for cotton at the field level. For this, we exploit a variety of Earth observation vegetation indices (derived from Sentinel-2) and numerical simulations of atmospheric and soil parameters. Our method is unsupervised to address the ever-present problem of sparse and scarce ground truth data that makes most supervised alternatives impractical in real-world scenarios. We applied fuzzy c-means clustering to identify the principal phenological stages of cotton and then used the cluster membership weights to further predict the transitional phases between adjacent stages. In order to evaluate our models, we collected 1,285 crop growth ground observations in Orchomenos, Greece. We introduced a new collection protocol, assigning up to two phenology labels that represent the primary and secondary growth stage in the field and thus indicate when stages are transitioning. Our model was tested against a baseline model that allowed to isolate the random agreement and evaluate its true competence. The results showed that our model considerably outperforms the baseline one, which is promising considering the unsupervised nature of the approach. The limitations and the relevant future work are thoroughly discussed. The ground observations are formatted in an ready-to-use dataset and will be available at https://github.com/Agri-Hub/cotton-phenology-dataset upon publication.

Ilias Tsoumas, Georgios Giannarakis, Vasileios Sitokonstantinou et al.

In contrast to the rapid digitalization of several industries, agriculture suffers from low adoption of smart farming tools. While AI-driven digital agriculture tools can offer high-performing predictive functionalities, they lack tangible quantitative evidence on their benefits to the farmers. Field experiments can derive such evidence, but are often costly, time consuming and hence limited in scope and scale of application. To this end, we propose an observational causal inference framework for the empirical evaluation of the impact of digital tools on target farm performance indicators (e.g., yield in this case). This way, we can increase farmers' trust via enhancing the transparency of the digital agriculture market and accelerate the adoption of technologies that aim to secure farmer income resilience and global agricultural sustainability. As a case study, we designed and implemented a recommendation system for the optimal sowing time of cotton based on numerical weather predictions, which was used by a farmers' cooperative during the growing season of 2021. We then leverage agricultural knowledge, collected yield data, and environmental information to develop a causal graph of the farm system. Using the back-door criterion, we identify the impact of sowing recommendations on the yield and subsequently estimate it using linear regression, matching, inverse propensity score weighting and meta-learners. The results reveal that a field sown according to our recommendations exhibited a statistically significant yield increase that ranged from 12% to 17%, depending on the method. The effect estimates were robust, as indicated by the agreement among the estimation methods and four successful refutation tests. We argue that this approach can be implemented for decision support systems of other fields, extending their evaluation beyond a performance assessment of internal functionalities.

Georgios Giannarakis, Ilias Tsoumas, Stelios Neophytides et al.

The concept of sustainable intensification in agriculture necessitates the implementation of management practices that prioritize sustainability without compromising productivity. However, the effects of such practices are known to depend on environmental conditions, and are therefore expected to change as a result of a changing climate. We study the impact of crop diversification on productivity in the context of climate change. We leverage heterogeneous Earth Observation data and contribute a data-driven approach based on causal machine learning for understanding how crop diversification impacts may change in the future. We apply this method to the country of Cyprus throughout a 4-year period. We find that, on average, crop diversification significantly benefited the net primary productivity of crops, increasing it by 2.8%. The effect generally synergized well with higher maximum temperatures and lower soil moistures. In a warmer and more drought-prone climate, we conclude that crop diversification exhibits promising adaptation potential and is thus a sensible policy choice with regards to agricultural productivity for present and future.

Georgios Giannarakis, Vasileios Sitokonstantinou, Roxanne Suzette Lorilla et al.

Understanding the suitability of agricultural land for applying specific management practices is of great importance for sustainable and resilient agriculture against climate change. Recent developments in the field of causal machine learning enable the estimation of intervention impacts on an outcome of interest, for samples described by a set of observed characteristics. We introduce an extensible data-driven framework that leverages earth observations and frames agricultural land suitability as a geospatial impact assessment problem, where the estimated effects of agricultural practices on agroecosystems serve as a land suitability score and guide decision making. We formulate this as a causal machine learning task and discuss how this approach can be used for agricultural planning in a changing climate. Specifically, we extract the agricultural management practices of "crop rotation" and "landscape crop diversity" from crop type maps, account for climate and land use data, and use double machine learning to estimate their heterogeneous effect on Net Primary Productivity (NPP), within the Flanders region of Belgium from 2010 to 2020. We find that the effect of crop rotation was insignificant, while landscape crop diversity had a small negative effect on NPP. Finally, we observe considerable effect heterogeneity in space for both practices and analyze it.

Ilias Tsoumas, Georgios Giannarakis, Vasileios Sitokonstantinou et al.

In contrast to the rapid digitalization of several industries, agriculture suffers from low adoption of climate-smart farming tools. Even though AI-driven digital agriculture can offer high-performing predictive functionalities, it lacks tangible quantitative evidence on its benefits to the farmers. Field experiments can derive such evidence, but are often costly and time consuming. To this end, we propose an observational causal inference framework for the empirical evaluation of the impact of digital tools on target farm performance indicators. This way, we can increase farmers' trust by enhancing the transparency of the digital agriculture market, and in turn accelerate the adoption of technologies that aim to increase productivity and secure a sustainable and resilient agriculture against a changing climate. As a case study, we perform an empirical evaluation of a recommendation system for optimal cotton sowing, which was used by a farmers' cooperative during the growing season of 2021. We leverage agricultural knowledge to develop a causal graph of the farm system, we use the back-door criterion to identify the impact of recommendations on the yield and subsequently estimate it using several methods on observational data. The results show that a field sown according to our recommendations enjoyed a significant increase in yield (12% to 17%).

Georgios Giannarakis, Vasileios Sitokonstantinou, Roxanne Suzette Lorilla et al.

To fight climate change and accommodate the increasing population, global crop production has to be strengthened. To achieve the "sustainable intensification" of agriculture, transforming it from carbon emitter to carbon sink is a priority, and understanding the environmental impact of agricultural management practices is a fundamental prerequisite to that. At the same time, the global agricultural landscape is deeply heterogeneous, with differences in climate, soil, and land use inducing variations in how agricultural systems respond to farmer actions. The "personalization" of sustainable agriculture with the provision of locally adapted management advice is thus a necessary condition for the efficient uplift of green metrics, and an integral development in imminent policies. Here, we formulate personalized sustainable agriculture as a Conditional Average Treatment Effect estimation task and use Causal Machine Learning for tackling it. Leveraging climate data, land use information and employing Double Machine Learning, we estimate the heterogeneous effect of sustainable practices on the field-level Soil Organic Carbon content in Lithuania. We thus provide a data-driven perspective for targeting sustainable practices and effectively expanding the global carbon sink.

Ornela Nanushi, Vasileios Sitokonstantinou, Ilias Tsoumas et al.

Helicoverpa Armigera, or cotton bollworm, is a serious insect pest of cotton crops that threatens the yield and the quality of lint. The timely knowledge of the presence of the insects in the field is crucial for effective farm interventions. Meteo-climatic and vegetation conditions have been identified as key drivers of crop pest abundance. In this work, we applied an interpretable classifier, i.e., Explainable Boosting Machine, which uses earth observation vegetation indices, numerical weather predictions and insect trap catches to predict the onset of bollworm harmfulness in cotton fields in Greece. The glass-box nature of our approach provides significant insight on the main drivers of the model and the interactions among them. Model interpretability adds to the trustworthiness of our approach and therefore its potential for rapid uptake and context-based implementation in operational farm management scenarios. Our results are satisfactory and the importance of drivers, through our analysis on global and local explainability, is in accordance with the literature.

Thanassis Drivas, Vasileios Sitokonstantinou, Iason Tsardanidis et al.

The modernization of the Common Agricultural Policy (CAP) requires the large scale and frequent monitoring of agricultural land. Towards this direction, the free and open satellite data (i.e., Sentinel missions) have been extensively used as the sources for the required high spatial and temporal resolution Earth observations. Nevertheless, monitoring the CAP at large scales constitutes a big data problem and puts a strain on CAP paying agencies that need to adapt fast in terms of infrastructure and know-how. Hence, there is a need for efficient and easy-to-use tools for the acquisition, storage, processing and exploitation of big satellite data. In this work, we present the Agriculture monitoring Data Cube (ADC), which is an automated, modular, end-to-end framework for discovering, pre-processing and indexing optical and Synthetic Aperture Radar (SAR) images into a multidimensional cube. We also offer a set of powerful tools on top of the ADC, including i) the generation of analysis-ready feature spaces of big satellite data to feed downstream machine learning tasks and ii) the support of Satellite Image Time-Series (SITS) analysis via services pertinent to the monitoring of the CAP (e.g., detecting trends and events, monitoring the growth status etc.). The knowledge extracted from the SITS analyses and the machine learning tasks returns to the data cube, building scalable country-specific knowledge bases that can efficiently answer complex and multi-faceted geospatial queries.

George Choumos, Alkiviadis Koukos, Vasileios Sitokonstantinou et al.

The recent advances in machine learning and the availability of free and open big Earth data (e.g., Sentinel missions), which cover large areas with high spatial and temporal resolution, have enabled many agriculture monitoring applications. One example is the control of subsidy allocations of the Common Agricultural Policy (CAP). Advanced remote sensing systems have been developed towards the large-scale evidence-based monitoring of the CAP. Nevertheless, the spatial resolution of satellite images is not always adequate to make accurate decisions for all fields. In this work, we introduce the notion of space-to-ground data availability, i.e., from the satellite to the field, in an attempt to make the best out of the complementary characteristics of the different sources. We present a space-to-ground dataset that contains Sentinel-1 radar and Sentinel-2 optical image time-series, as well as street-level images from the crowdsourcing platform Mapillary, for grassland fields in the area of Utrecht for 2017. The multifaceted utility of our dataset is showcased through the downstream task of grassland classification. We train machine and deep learning algorithms on these different data domains and highlight the potential of fusion techniques towards increasing the reliability of decisions.

Hyun-Woo Jo, Alkiviadis Koukos, Vasileios Sitokonstantinou et al.

The continuous increase in global population and the impact of climate change on crop production are expected to affect the food sector significantly. In this context, there is need for timely, large-scale and precise mapping of crops for evidence-based decision making. A key enabler towards this direction are new satellite missions that freely offer big remote sensing data of high spatio-temporal resolution and global coverage. During the previous decade and because of this surge of big Earth observations, deep learning methods have dominated the remote sensing and crop mapping literature. Nevertheless, deep learning models require large amounts of annotated data that are scarce and hard-to-acquire. To address this problem, transfer learning methods can be used to exploit available annotations and enable crop mapping for other regions, crop types and years of inspection. In this work, we have developed and trained a deep learning model for paddy rice detection in South Korea using Sentinel-1 VH time-series. We then fine-tune the model for i) paddy rice detection in France and Spain and ii) barley detection in the Netherlands. Additionally, we propose a modification in the pre-trained weights in order to incorporate extra input features (Sentinel-1 VV). Our approach shows excellent performance when transferring in different areas for the same crop type and rather promising results when transferring in a different area and crop type.

Ilias Tsoumas, Vasileios Sitokonstantinou, Georgios Giannarakis et al.

Pesticides serve as a common tool in agricultural pest control but significantly contribute to the climate crisis. To combat this, Integrated Pest Management (IPM) stands as a climate-smart alternative. Despite its potential, IPM faces low adoption rates due to farmers' skepticism about its effectiveness. To address this challenge, we introduce an advanced data analysis framework tailored to enhance IPM adoption. Our framework provides i) robust pest population predictions across diverse environments with invariant and causal learning, ii) interpretable pest presence predictions using transparent models, iii) actionable advice through counterfactual explanations for in-season IPM interventions, iv) field-specific treatment effect estimations, and v) assessments of the effectiveness of our advice using causal inference. By incorporating these features, our framework aims to alleviate skepticism and encourage wider adoption of IPM practices among farmers.

Konstantinos Alexis, Stella Girtsou, Alexis Apostolakis et al.

In this paper we present a deep learning pipeline for next day fire prediction. The next day fire prediction task consists in learning models that receive as input the available information for an area up until a certain day, in order to predict the occurrence of fire for the next day. Starting from our previous problem formulation as a binary classification task on instances (daily snapshots of each area) represented by tabular feature vectors, we reformulate the problem as a semantic segmentation task on images; there, each pixel corresponds to a daily snapshot of an area, while its channels represent the formerly tabular training features. We demonstrate that this problem formulation, built within a thorough pipeline achieves state of the art results.

Andreas Kalogeras, Dimitrios Bormpoudakis, Iason Tsardanidis et al.

The widespread use of Exogenous Organic Matter in agriculture necessitates monitoring to assess its effects on soil and crop health. This study evaluates optical Sentinel-2 satellite imagery for detecting digestate application, a practice that enhances soil fertility but poses environmental risks like microplastic contamination and nitrogen losses. In the first instance, Sentinel-2 satellite image time series (SITS) analysis of specific indices (EOMI, NDVI, EVI) was used to characterize EOM's spectral behavior after application on the soils of four different crop types in Thessaly, Greece. Furthermore, Machine Learning (ML) models (namely Random Forest, k-NN, Gradient Boosting and a Feed-Forward Neural Network), were used to investigate digestate presence detection, achieving F1-scores up to 0.85. The findings highlight the potential of combining remote sensing and ML for scalable and cost-effective monitoring of EOM applications, supporting precision agriculture and sustainability.

Ioannis Kontogiorgakis, Athanasios Askitopoulos, Iason Tsardanidis et al.

Accurate soil moisture (SM) estimation is critical for precision agriculture, water resources management and climate monitoring. Yet, existing satellite SM products are too coarse (>1km) for farm-level applications. We present a high-resolution (10m) SM estimation framework for vegetated areas across Europe, combining Sentinel-1 SAR, Sentinel-2 optical imagery and ERA-5 reanalysis data through machine learning. Using 113 International Soil Moisture Network (ISMN) stations spanning diverse vegetated areas, we compare modality combinations with temporal parameterizations, using spatial cross-validation, to ensure geographic generalization. We also evaluate whether foundation model embeddings from IBM-NASA's Prithvi model improve upon traditional hand-crafted spectral features. Results demonstrate that hybrid temporal matching - Sentinel-2 current-day acquisitions with Sentinel-1 descending orbit - achieves R^2=0.514, with 10-day ERA5 lookback window improving performance to R^2=0.518. Foundation model (Prithvi) embeddings provide negligible improvement over hand-crafted features (R^2=0.515 vs. 0.514), indicating traditional feature engineering remains highly competitive for sparse-data regression tasks. Our findings suggest that domain-specific spectral indices combined with tree-based ensemble methods offer a practical and computationally efficient solution for operational pan-European field-scale soil moisture monitoring.

Ilias Tsoumas, Dimitrios Bormpoudakis, Vasileios Sitokonstantinou et al.

In causal inference, whether through randomized controlled trials or observational studies, access to both treated and control units is essential for estimating the effect of a treatment on an outcome of interest. When treatment assignment is random, the average treatment effect (ATE) can be estimated directly by comparing outcomes between groups. In non-randomized settings, various techniques are employed to adjust for confounding and approximate the counterfactual scenario to recover an unbiased ATE. A common challenge, especially in observational studies, is the absence of units clearly labeled as controls-that is, units known not to have received the treatment. To address this, we propose positive-unlabeled (PU) learning as a framework for identifying, with high confidence, control units from a pool of unlabeled ones, using only the available treated (positive) units. We evaluate this approach using both simulated and real-world data. We construct a causal graph with diverse relationships and use it to generate synthetic data under various scenarios, assessing how reliably the method recovers control groups that allow estimates of true ATE. We also apply our approach to real-world data on optimal sowing and fertilizer treatments in sustainable agriculture. Our findings show that PU learning can successfully identify control (negative) units from unlabeled data based only on treated units and, through the resulting control group, estimate an ATE that closely approximates the true value. This work has important implications for observational causal inference, especially in fields where randomized experiments are difficult or costly. In domains such as earth, environmental, and agricultural sciences, it enables a plethora of quasi-experiments by leveraging available earth observation and climate data, particularly when treated units are available but control units are lacking.

Ioannis Kontogiorgakis, Iason Tsardanidis, Dimitrios Bormpoudakis et al.

Effective weed management is crucial for improving agricultural productivity, as weeds compete with crops for vital resources like nutrients and water. Accurate maps of weed management methods are essential for policymakers to assess farmer practices, evaluate impacts on vegetation health, biodiversity, and climate, as well as ensure compliance with policies and subsidies. However, monitoring weed management methods is challenging as they commonly rely on ground-based field surveys, which are often costly, time-consuming and subject to delays. In order to tackle this problem, we leverage earth observation data and Machine Learning (ML). Specifically, we developed separate ML models using Sentinel-2 and PlanetScope satellite time series data, respectively, to classify four distinct weed management methods (Mowing, Tillage, Chemical-spraying, and No practice) in orchards. The findings demonstrate the potential of ML-driven remote sensing to enhance the efficiency and accuracy of weed management mapping in orchards.

Iason Tsardanidis, Alkiviadis Koukos, Vasileios Sitokonstantinou et al.

Uninterrupted optical image time series are crucial for the timely monitoring of agricultural land changes, particularly in grasslands. However, the continuity of such time series is often disrupted by clouds. In response to this challenge, we propose an innovative deep learning method that integrates cloud-free optical (Sentinel-2) observations and weather-independent (Sentinel-1) Synthetic Aperture Radar (SAR) data. Our approach employs a hybrid architecture combining Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) to generate continuous Normalized Difference Vegetation Index (NDVI) time series, highlighting the role of NDVI in the synergy between SAR and optical data. We demonstrate the significance of observation continuity by assessing the impact of the generated NDVI time series on the downstream task of grassland mowing event detection. We conducted our study in Lithuania, a country characterized by extensive cloud coverage, and compared our approach with alternative interpolation techniques (i.e., linear, Akima, quadratic). Our method outperformed these techniques, achieving an average Mean Absolute Error (MAE) of 0.024 and a coefficient of determination R^2 of 0.92. Additionally, our analysis revealed improvement in the performance of the mowing event detection, with F1-score up to 84% using two widely applied mowing detection methodologies. Our method also effectively mitigated sudden shifts and noise originating from cloudy observations, which are often missed by conventional cloud masks and adversely affect mowing detection precision.