A Measurement-Driven Digital Twin Architecture for Plant-Level Biomass Estimation and Growth Forecasting in Hydroponic Systems

Accurate yield forecasting at the individual-plant level is critical for precision agriculture and supply-chain planning, yet public datasets capturing both visual growth dynamics and per-plant measurement labels are scarce. In this paper, we introduce a novel, annotated image time-series dataset of 691 sweet pepper plants monitored over two growing seasons, comprising 4837 images with per-plant fruit counts categorized by maturity. We propose a multimodal deep learning framework that fuses high-dimensional image features, extracted using the DinoV3 encoder, with numerical count measurements. Our architecture utilizes a Long Short-Term Memory (LSTM) network to model temporal dependencies and handles irregular sampling intervals common in greenhouse monitoring. Through quantitative experiments, we demonstrate that this multimodal approach reduces RMSE over a persistence baseline by 33% and 38% in the 2022 and 2023 seasons, respectively, with a further 1.2% average gain over a measurement-only model. Furthermore, we employ Deep Ensembles and Gaussian Negative Log-Likelihood (NLL) to provide calibrated uncertainty estimates, with an Uncertainty Calibration Error (UCE) ranging from 0.39 to 0.89 depending on the cross-season evaluation direction, offering a principled confidence signal for real-world agricultural decision-making. We release the dataset and code to support reproducible research and to accelerate development of data-driven yield forecasting methods for horticultural crops.

Vision-based reinforcement learning holds strong potential for decision-making in controlled environment agriculture (CEA). However, its development is hindered by the scarcity of labelled crop images. To address this gap, LettuceVisSim, a lettuce growth simulator that generates labelled time series of crop images, was developed and validated. The simulator contains a process-based model (PBM) for shoot dry weight dynamics, a canopy layout algorithm for deriving canopy layout representations from shoot dry weight, and a Unity rendering engine for image generation. Five findings support the simulator. First, the PBM reproduced shoot dry weight under dynamic plant-density management with $\mathrm{R}^{2}=0.84$. Second, a piecewise cubic regression mapped shoot dry weight to potential projected area with $\mathrm{R}^{2}=0.94$. Third, the canopy layout representation was validated using 12 experimental datasets each having different dynamic environmental and spacing conditions. It reproduced the ground coverage ratio dynamics observed in measured images, achieving $\mathrm{R}^{2}=0.84$ when driven by measured shoot dry weight and $\mathrm{R}^{2}=0.40$ (0.76 excluding one outlier) when driven by PBM-simulated values. Fourth, the Unity rendering engine converted canopy layout representations into RGB and segmentation images at less than 10~ms. Fifth, a demonstration showed that a lighting-control policy can be learned and applied by observing only crop images that were generated with LettuceVisSim, providing a proof of concept of vision-based reinforcement learning in CEA using LettuceVisSim.

Digital twins of natural systems must remain aligned with physical systems that evolve over time, are only partially observed, and are typically modeled by mechanistic simulators whose parameters cannot be measured directly. In such settings, model adaptation is naturally posed as a simulation-based inference problem. However, sparse and indirect observations often fail to identify a unique and optimal calibration, leaving several simulator parameterizations compatible with the available evidence. This article presents a GFlowNet-based approach to model adaptation for digital twins of natural systems. We formulate adaptation as a generative modeling problem over complete simulator configurations, so that plausible parameterizations can be sampled with probability proportional to a reward derived from agreement between simulated and observed behavior. Using a controlled environment agriculture case study based on a mechanistic tomato model, we show that the learned policy recovers dominant regions of the adaptation landscape, retrieves strong calibration hypotheses, and preserves multiple plausible configurations under uncertainty.