Talukder Z. Jubery

Muhammad Arbab Arshad, Talukder Zaki Jubery, Tirtho Roy et al.

As Vision Language Models (VLMs) become increasingly accessible to farmers and agricultural experts, there is a growing need to evaluate their potential in specialized tasks. We present AgEval, a comprehensive benchmark for assessing VLMs' capabilities in plant stress phenotyping, offering a solution to the challenge of limited annotated data in agriculture. Our study explores how general-purpose VLMs can be leveraged for domain-specific tasks with only a few annotated examples, providing insights into their behavior and adaptability. AgEval encompasses 12 diverse plant stress phenotyping tasks, evaluating zero-shot and few-shot in-context learning performance of state-of-the-art models including Claude, GPT, Gemini, and LLaVA. Our results demonstrate VLMs' rapid adaptability to specialized tasks, with the best-performing model showing an increase in F1 scores from 46.24% to 73.37% in 8-shot identification. To quantify performance disparities across classes, we introduce metrics such as the coefficient of variation (CV), revealing that VLMs' training impacts classes differently, with CV ranging from 26.02% to 58.03%. We also find that strategic example selection enhances model reliability, with exact category examples improving F1 scores by 15.38% on average. AgEval establishes a framework for assessing VLMs in agricultural applications, offering valuable benchmarks for future evaluations. Our findings suggest that VLMs, with minimal few-shot examples, show promise as a viable alternative to traditional specialized models in plant stress phenotyping, while also highlighting areas for further refinement. Results and benchmark details are available at: https://github.com/arbab-ml/AgEval

Shivani Chiranjeevi, Mojdeh Sadaati, Zi K Deng et al.

Insect-pests significantly impact global agricultural productivity and quality. Effective management involves identifying the full insect community, including beneficial insects and harmful pests, to develop and implement integrated pest management strategies. Automated identification of insects under real-world conditions presents several challenges, including differentiating similar-looking species, intra-species dissimilarity and inter-species similarity, several life cycle stages, camouflage, diverse imaging conditions, and variability in insect orientation. A deep-learning model, InsectNet, is proposed to address these challenges. InsectNet is endowed with five key features: (a) utilization of a large dataset of insect images collected through citizen science; (b) label-free self-supervised learning for large models; (c) improving prediction accuracy for species with a small sample size; (d) enhancing model trustworthiness; and (e) democratizing access through streamlined MLOps. This approach allows accurate identification (>96% accuracy) of over 2500 insect species, including pollinator (e.g., butterflies, bees), parasitoid (e.g., some wasps and flies), predator species (e.g., lady beetles, mantises, dragonflies) and harmful pest species (e.g., armyworms, cutworms, grasshoppers, stink bugs). InsectNet can identify invasive species, provide fine-grained insect species identification, and work effectively in challenging backgrounds. It also can abstain from making predictions when uncertain, facilitating seamless human intervention and making it a practical and trustworthy tool. InsectNet can guide citizen science data collection, especially for invasive species where early detection is crucial. Similar approaches may transform other agricultural challenges like disease detection and underscore the importance of data collection, particularly through citizen science efforts..

Jiabin Lin, Xian Yeow Lee, Talukder Jubery et al.

Many physical systems have underlying safety considerations that require that the strategy deployed ensures the satisfaction of a set of constraints. Further, often we have only partial information on the state of the system. We study the problem of safe real-time decision making under uncertainty. In this paper, we formulate a conservative stochastic contextual bandit formulation for real-time decision making when an adversary chooses a distribution on the set of possible contexts and the learner is subject to certain safety/performance constraints. The learner observes only the context distribution and the exact context is unknown, and the goal is to develop an algorithm that selects a sequence of optimal actions to maximize the cumulative reward without violating the safety constraints at any time step. By leveraging the UCB algorithm for this setting, we propose a conservative linear UCB algorithm for stochastic bandits with context distribution. We prove an upper bound on the regret of the algorithm and show that it can be decomposed into three terms: (i) an upper bound for the regret of the standard linear UCB algorithm, (ii) a constant term (independent of time horizon) that accounts for the loss of being conservative in order to satisfy the safety constraint, and (ii) a constant term (independent of time horizon) that accounts for the loss for the contexts being unknown and only the distribution being known. To validate the performance of our approach we perform extensive simulations on synthetic data and on real-world maize data collected through the Genomes to Fields (G2F) initiative.

Mozhgan Hadadi, Mehdi Saraeian, Jackson Godbersen et al.

This study introduces a robust framework for generating procedural 3D models of maize (Zea mays) plants from LiDAR point cloud data, offering a scalable alternative to traditional field-based phenotyping. Our framework leverages Non-Uniform Rational B-Spline (NURBS) surfaces to model the leaves of maize plants, combining Particle Swarm Optimization (PSO) for an initial approximation of the surface and a differentiable programming framework for precise refinement of the surface to fit the point cloud data. In the first optimization phase, PSO generates an approximate NURBS surface by optimizing its control points, aligning the surface with the LiDAR data, and providing a reliable starting point for refinement. The second phase uses NURBS-Diff, a differentiable programming framework, to enhance the accuracy of the initial fit by refining the surface geometry and capturing intricate leaf details. Our results demonstrate that, while PSO establishes a robust initial fit, the integration of differentiable NURBS significantly improves the overall quality and fidelity of the reconstructed surface. This hierarchical optimization strategy enables accurate 3D reconstruction of maize leaves across diverse genotypes, facilitating the subsequent extraction of complex traits like phyllotaxy. We demonstrate our approach on diverse genotypes of field-grown maize plants. All our codes are open-source to democratize these phenotyping approaches.

Hossein Zaremehrjerdi, Lisa Coffey, Talukder Jubery et al.

Quantifying the variation in yield component traits of maize (Zea mays L.), which together determine the overall productivity of this globally important crop, plays a critical role in plant genetics research, plant breeding, and the development of improved farming practices. Grain yield per acre is calculated by multiplying the number of plants per acre, ears per plant, number of kernels per ear, and the average kernel weight. The number of kernels per ear is determined by the number of kernel rows per ear multiplied by the number of kernels per row. Traditional manual methods for measuring these two traits are time-consuming, limiting large-scale data collection. Recent automation efforts using image processing and deep learning encounter challenges such as high annotation costs and uncertain generalizability. We tackle these issues by exploring Large Vision Models for zero-shot, annotation-free maize kernel segmentation. By using an open-source large vision model, the Segment Anything Model (SAM), we segment individual kernels in RGB images of maize ears and apply a graph-based algorithm to calculate the number of kernels per row. Our approach successfully identifies the number of kernels per row across a wide range of maize ears, showing the potential of zero-shot learning with foundation vision models combined with image processing techniques to improve automation and reduce subjectivity in agronomic data collection. All our code is open-sourced to make these affordable phenotyping methods accessible to everyone.

Muhammad Arbab Arshad, Talukder Jubery, James Afful et al.

We evaluate different Neural Radiance Fields (NeRFs) techniques for the 3D reconstruction of plants in varied environments, from indoor settings to outdoor fields. Traditional methods usually fail to capture the complex geometric details of plants, which is crucial for phenotyping and breeding studies. We evaluate the reconstruction fidelity of NeRFs in three scenarios with increasing complexity and compare the results with the point cloud obtained using LiDAR as ground truth. In the most realistic field scenario, the NeRF models achieve a 74.6% F1 score after 30 minutes of training on the GPU, highlighting the efficacy of NeRFs for 3D reconstruction in challenging environments. Additionally, we propose an early stopping technique for NeRF training that almost halves the training time while achieving only a reduction of 7.4% in the average F1 score. This optimization process significantly enhances the speed and efficiency of 3D reconstruction using NeRFs. Our findings demonstrate the potential of NeRFs in detailed and realistic 3D plant reconstruction and suggest practical approaches for enhancing the speed and efficiency of NeRFs in the 3D reconstruction process.

Sarah E. Jones, Timilehin Ayanlade, Benjamin Fallen et al.

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.

Anirudha Powadi, Talukder Zaki Jubery, Michael C. Tross et al.

This study introduces a compositional autoencoder (CAE) framework designed to disentangle the complex interplay between genotypic and environmental factors in high-dimensional phenotype data to improve trait prediction in plant breeding and genetics programs. Traditional predictive methods, which use compact representations of high-dimensional data through handcrafted features or latent features like PCA or more recently autoencoders, do not separate genotype-specific and environment-specific factors. We hypothesize that disentangling these features into genotype-specific and environment-specific components can enhance predictive models. To test this, we developed a compositional autoencoder (CAE) that decomposes high-dimensional data into distinct genotype-specific and environment-specific latent features. Our CAE framework employs a hierarchical architecture within an autoencoder to effectively separate these entangled latent features. Applied to a maize diversity panel dataset, the CAE demonstrates superior modeling of environmental influences and 5-10 times improved predictive performance for key traits like Days to Pollen and Yield, compared to the traditional methods, including standard autoencoders, PCA with regression, and Partial Least Squares Regression (PLSR). By disentangling latent features, the CAE provides powerful tool for precision breeding and genetic research. This work significantly enhances trait prediction models, advancing agricultural and biological sciences.

Mozhgan Hadadi, Talukder Z. Jubery, Patrick S. Schnable et al.

Accurate 3D plant models are crucial for computational phenotyping and physics-based simulation; however, current approaches face significant limitations. Learning-based reconstruction methods require extensive species-specific training data and lack editability. Procedural modeling offers parametric control but demands specialized expertise in geometric modeling and an in-depth understanding of complex procedural rules, making it inaccessible to domain scientists. We present FloraForge, an LLM-assisted framework that enables domain experts to generate biologically accurate, fully parametric 3D plant models through iterative natural language Plant Refinements (PR), minimizing programming expertise. Our framework leverages LLM-enabled co-design to refine Python scripts that generate parameterized plant geometries as hierarchical B-spline surface representations with botanical constraints with explicit control points and parametric deformation functions. This representation can be easily tessellated into polygonal meshes with arbitrary precision, ensuring compatibility with functional structural plant analysis workflows such as light simulation, computational fluid dynamics, and finite element analysis. We demonstrate the framework on maize, soybean, and mung bean, fitting procedural models to empirical point cloud data through manual refinement of the Plant Descriptor (PD), human-readable files. The pipeline generates dual outputs: triangular meshes for visualization and triangular meshes with additional parametric metadata for quantitative analysis. This approach uniquely combines LLM-assisted template creation, mathematically continuous representations enabling both phenotyping and rendering, and direct parametric control through PD. The framework democratizes sophisticated geometric modeling for plant science while maintaining mathematical rigor.

Shivani Chiranjeevi, Hossein Zaremehrjerdi, Zi K. Deng et al.

The rapid global loss of biodiversity, particularly among insects, represents an urgent ecological crisis. Current methods for insect species discovery are manual, slow, and severely constrained by taxonomic expertise, hindering timely conservation actions. We introduce TerraIncognita, a dynamic benchmark designed to evaluate state-of-the-art multimodal models for the challenging problem of identifying unknown, potentially undescribed insect species from image data. Our benchmark dataset combines a mix of expertly annotated images of insect species likely known to frontier AI models, and images of rare and poorly known species, for which few/no publicly available images exist. These images were collected from underexplored biodiversity hotspots, realistically mimicking open-world discovery scenarios faced by ecologists. The benchmark assesses models' proficiency in hierarchical taxonomic classification, their capability to detect and abstain from out-of-distribution (OOD) samples representing novel species, and their ability to generate explanations aligned with expert taxonomic knowledge. Notably, top-performing models achieve over 90\% F1 at the Order level on known species, but drop below 2\% at the Species level, highlighting the sharp difficulty gradient from coarse to fine taxonomic prediction (Order $\rightarrow$ Family $\rightarrow$ Genus $\rightarrow$ Species). TerraIncognita will be updated regularly, and by committing to quarterly dataset expansions (of both known and novel species), will provide an evolving platform for longitudinal benchmarking of frontier AI methods. All TerraIncognita data, results, and future updates are available \href{https://baskargroup.github.io/TerraIncognita/}{here}.

Kibon Ku, Talukder Z Jubery, Elijah Rodriguez et al.

This paper presents a NeRF-based framework for point cloud (PCD) reconstruction, specifically designed for indoor high-throughput plant phenotyping facilities. Traditional NeRF-based reconstruction methods require cameras to move around stationary objects, but this approach is impractical for high-throughput environments where objects are rapidly imaged while moving on conveyors or rotating pedestals. To address this limitation, we develop a variant of NeRF-based PCD reconstruction that uses a single stationary camera to capture images as the object rotates on a pedestal. Our workflow comprises COLMAP-based pose estimation, a straightforward pose transformation to simulate camera movement, and subsequent standard NeRF training. A defined Region of Interest (ROI) excludes irrelevant scene data, enabling the generation of high-resolution point clouds (10M points). Experimental results demonstrate excellent reconstruction fidelity, with precision-recall analyses yielding an F-score close to 100.00 across all evaluated plant objects. Although pose estimation remains computationally intensive with a stationary camera setup, overall training and reconstruction times are competitive, validating the method's feasibility for practical high-throughput indoor phenotyping applications. Our findings indicate that high-quality NeRF-based 3D reconstructions are achievable using a stationary camera, eliminating the need for complex camera motion or costly imaging equipment. This approach is especially beneficial when employing expensive and delicate instruments, such as hyperspectral cameras, for 3D plant phenotyping. Future work will focus on optimizing pose estimation techniques and further streamlining the methodology to facilitate seamless integration into automated, high-throughput 3D phenotyping pipelines.

Bitgoeul Kim, Samuel W. Blair, Talukder Z. Jubery et al.

Plant breeding programs require assessments of days to maturity for accurate selection and placement of entries in appropriate tests. In the early stages of the breeding pipeline, soybean breeding programs assign relative maturity ratings to experimental varieties that indicate their suitable maturity zones. Traditionally, the estimation of maturity value for breeding varieties has involved breeders manually inspecting fields and assessing maturity value visually. This approach relies heavily on rater judgment, making it subjective and time-consuming. This study aimed to develop a machine-learning model for evaluating soybean maturity using UAV-based time-series imagery. Images were captured at three-day intervals, beginning as the earliest varieties started maturing and continuing until the last varieties fully matured. The data collected for this experiment consisted of 22,043 plots collected across three years (2021 to 2023) and represent relative maturity groups 1.6 - 3.9. We utilized contour plot images extracted from the time-series UAV RGB imagery as input for a neural network model. This contour plot approach encoded the temporal and spatial variation within each plot into a single image. A deep learning model was trained to utilize this contour plot to predict maturity ratings. This model significantly improves accuracy and robustness, achieving up to 85% accuracy. We also evaluate the model's accuracy as we reduce the number of time points, quantifying the trade-off between temporal resolution and maturity prediction. The predictive model offers a scalable, objective, and efficient means of assessing crop maturity, enabling phenomics and ML approaches to reduce the reliance on manual inspection and subjective assessment. This approach enables the automatic prediction of relative maturity ratings in a breeding program, saving time and resources.

Nasla Saleem, Aditya Balu, Talukder Zaki Jubery et al.

Data augmentation is a powerful tool for improving deep learning-based image classifiers for plant stress identification and classification. However, selecting an effective set of augmentations from a large pool of candidates remains a key challenge, particularly in imbalanced and confounding datasets. We propose an approach for automated class-specific data augmentation using a genetic algorithm. We demonstrate the utility of our approach on soybean [Glycine max (L.) Merr] stress classification where symptoms are observed on leaves; a particularly challenging problem due to confounding classes in the dataset. Our approach yields substantial performance, achieving a mean-per-class accuracy of 97.61% and an overall accuracy of 98% on the soybean leaf stress dataset. Our method significantly improves the accuracy of the most challenging classes, with notable enhancements from 83.01% to 88.89% and from 85.71% to 94.05%, respectively. A key observation we make in this study is that high-performing augmentation strategies can be identified in a computationally efficient manner. We fine-tune only the linear layer of the baseline model with different augmentations, thereby reducing the computational burden associated with training classifiers from scratch for each augmentation policy while achieving exceptional performance. This research represents an advancement in automated data augmentation strategies for plant stress classification, particularly in the context of confounding datasets. Our findings contribute to the growing body of research in tailored augmentation techniques and their potential impact on disease management strategies, crop yields, and global food security. The proposed approach holds the potential to enhance the accuracy and efficiency of deep learning-based tools for managing plant stresses in agriculture.

Mojdeh Saadati, Aditya Balu, Shivani Chiranjeevi et al.

Deep learning-based approaches have produced models with good insect classification accuracy; Most of these models are conducive for application in controlled environmental conditions. One of the primary emphasis of researchers is to implement identification and classification models in the real agriculture fields, which is challenging because input images that are wildly out of the distribution (e.g., images like vehicles, animals, humans, or a blurred image of an insect or insect class that is not yet trained on) can produce an incorrect insect classification. Out-of-distribution (OOD) detection algorithms provide an exciting avenue to overcome these challenge as it ensures that a model abstains from making incorrect classification prediction of non-insect and/or untrained insect class images. We generate and evaluate the performance of state-of-the-art OOD algorithms on insect detection classifiers. These algorithms represent a diversity of methods for addressing an OOD problem. Specifically, we focus on extrusive algorithms, i.e., algorithms that wrap around a well-trained classifier without the need for additional co-training. We compared three OOD detection algorithms: (i) Maximum Softmax Probability, which uses the softmax value as a confidence score, (ii) Mahalanobis distance-based algorithm, which uses a generative classification approach; and (iii) Energy-Based algorithm that maps the input data to a scalar value, called energy. We performed an extensive series of evaluations of these OOD algorithms across three performance axes: (a) \textit{Base model accuracy}: How does the accuracy of the classifier impact OOD performance? (b) How does the \textit{level of dissimilarity to the domain} impact OOD performance? and (c) \textit{Data imbalance}: How sensitive is OOD performance to the imbalance in per-class sample size?

Koushik Nagasubramanian, Talukder Z. Jubery, Fateme Fotouhi Ardakani et al.

Deep learning models have been successfully deployed for a diverse array of image-based plant phenotyping applications including disease detection and classification. However, successful deployment of supervised deep learning models requires large amount of labeled data, which is a significant challenge in plant science (and most biological) domains due to the inherent complexity. Specifically, data annotation is costly, laborious, time consuming and needs domain expertise for phenotyping tasks, especially for diseases. To overcome this challenge, active learning algorithms have been proposed that reduce the amount of labeling needed by deep learning models to achieve good predictive performance. Active learning methods adaptively select samples to annotate using an acquisition function to achieve maximum (classification) performance under a fixed labeling budget. We report the performance of four different active learning methods, (1) Deep Bayesian Active Learning (DBAL), (2) Entropy, (3) Least Confidence, and (4) Coreset, with conventional random sampling-based annotation for two different image-based classification datasets. The first image dataset consists of soybean [Glycine max L. (Merr.)] leaves belonging to eight different soybean stresses and a healthy class, and the second consists of nine different weed species from the field. For a fixed labeling budget, we observed that the classification performance of deep learning models with active learning-based acquisition strategies is better than random sampling-based acquisition for both datasets. The integration of active learning strategies for data annotation can help mitigate labelling challenges in the plant sciences applications particularly where deep domain knowledge is required.