Daily Papers

The deployment of Multimodal Large Language Models (MLLMs) in agriculture is currently stalled by a critical trade-off: the existing literature lacks the large-scale agricultural datasets required for robust model development and evaluation, while current state-of-the-art models lack the verified domain expertise necessary to reason across diverse taxonomies. To address these challenges, we propose the Vision-to-Verified-Knowledge (V2VK) pipeline, a novel generative AI-driven annotation framework that integrates visual captioning with web-augmented scientific retrieval to autonomously generate the AgriMM benchmark, effectively eliminating biological hallucinations by grounding training data in verified phytopathological literature. The AgriMM benchmark contains over 3,000 agricultural classes and more than 607k VQAs spanning multiple tasks, including fine-grained plant species identification, plant disease symptom recognition, crop counting, and ripeness assessment. Leveraging this verifiable data, we present AgriChat, a specialized MLLM that presents broad knowledge across thousands of agricultural classes and provides detailed agricultural assessments with extensive explanations. Extensive evaluation across diverse tasks, datasets, and evaluation conditions reveals both the capabilities and limitations of current agricultural MLLMs, while demonstrating AgriChat's superior performance over other open-source models, including internal and external benchmarks. The results validate that preserving visual detail combined with web-verified knowledge constitutes a reliable pathway toward robust and trustworthy agricultural AI. The code and dataset are publicly available at https://github.com/boudiafA/AgriChat .

Foundation models and vision-language pre-training have significantly advanced Vision-Language Models (VLMs), enabling multimodal processing of visual and linguistic data. However, their application in domain-specific agricultural tasks, such as plant pathology, remains limited due to the lack of large-scale, comprehensive multimodal image--text datasets and benchmarks. To address this gap, we introduce LeafNet, a comprehensive multimodal dataset, and LeafBench, a visual question-answering benchmark developed to systematically evaluate the capabilities of VLMs in understanding plant diseases. The dataset comprises 186,000 leaf digital images spanning 97 disease classes, paired with metadata, generating 13,950 question-answer pairs spanning six critical agricultural tasks. The questions assess various aspects of plant pathology understanding, including visual symptom recognition, taxonomic relationships, and diagnostic reasoning. Benchmarking 12 state-of-the-art VLMs on our LeafBench dataset, we reveal substantial disparity in their disease understanding capabilities. Our study shows performance varies markedly across tasks: binary healthy--diseased classification exceeds 90% accuracy, while fine-grained pathogen and species identification remains below 65%. Direct comparison between vision-only models and VLMs demonstrates the critical advantage of multimodal architectures: fine-tuned VLMs outperform traditional vision models, confirming that integrating linguistic representations significantly enhances diagnostic precision. These findings highlight critical gaps in current VLMs for plant pathology applications and underscore the need for LeafBench as a rigorous framework for methodological advancement and progress evaluation toward reliable AI-assisted plant disease diagnosis. Code is available at https://github.com/EnalisUs/LeafBench.

India loses 35% of the annual crop yield due to plant diseases. Early detection of plant diseases remains difficult due to the lack of lab infrastructure and expertise. In this paper, we explore the possibility of computer vision approaches for scalable and early plant disease detection. The lack of availability of sufficiently large-scale non-lab data set remains a major challenge for enabling vision based plant disease detection. Against this background, we present PlantDoc: a dataset for visual plant disease detection. Our dataset contains 2,598 data points in total across 13 plant species and up to 17 classes of diseases, involving approximately 300 human hours of effort in annotating internet scraped images. To show the efficacy of our dataset, we learn 3 models for the task of plant disease classification. Our results show that modelling using our dataset can increase the classification accuracy by up to 31%. We believe that our dataset can help reduce the entry barrier of computer vision techniques in plant disease detection.

The agriculture sector is essential for every country because it provides a basic income to a large number of people and food as well, which is a fundamental requirement to survive on this planet. We see as time passes, significant changes come in the present era, which begins with Green Revolution. Due to improper knowledge of plant diseases, farmers use fertilizers in excess, which ultimately degrade the quality of food. Earlier farmers use experts to determine the type of plant disease, which was expensive and time-consuming. In today time, Image processing is used to recognize and catalog plant diseases using the lesion region of plant leaf, and there are different modus-operandi for plant disease scent from leaf using Neural Networks (NN), Support Vector Machine (SVM), and others. In this paper, we improving the architecture of the Neural Networking by working on ten different types of training algorithms and the proper choice of neurons in the concealed layer. Our proposed approach gives 98.30% accuracy on general plant leaf disease and 100% accuracy on specific plant leaf disease based on Bayesian regularization, automation of cluster and without over-fitting on considered plant diseases over various other implemented methods.

Precision agriculture relies heavily on accurate image analysis for crop disease identification and treatment recommendation, yet existing vision-language models (VLMs) often underperform in specialized agricultural domains. This work presents a domain-aware framework for agricultural image processing that combines prompt-based expert evaluation with self-consistency mechanisms to enhance VLM reliability in precision agriculture applications. We introduce two key innovations: (1) a prompt-based evaluation protocol that configures a language model as an expert plant pathologist for scalable assessment of image analysis outputs, and (2) a cosine-consistency self-voting mechanism that generates multiple candidate responses from agricultural images and selects the most semantically coherent diagnosis using domain-adapted embeddings. Applied to maize leaf disease identification from field images using a fine-tuned PaliGemma model, our approach improves diagnostic accuracy from 82.2\% to 87.8\%, symptom analysis from 38.9\% to 52.2\%, and treatment recommendation from 27.8\% to 43.3\% compared to standard greedy decoding. The system remains compact enough for deployment on mobile devices, supporting real-time agricultural decision-making in resource-constrained environments. These results demonstrate significant potential for AI-driven precision agriculture tools that can operate reliably in diverse field conditions.

Leaf disease identification plays a pivotal role in smart agriculture. However, many existing studies still struggle to integrate image and textual modalities to compensate for each other's limitations. Furthermore, many of these approaches rely on pretraining with constrained datasets such as ImageNet, which lack domain-specific information. We propose SCOLD (Soft-target COntrastive learning for Leaf Disease identification), a context-aware vision-language foundation model tailored to address these challenges for agricultural tasks. SCOLD is developed using a diverse corpus of plant leaf images and corresponding symptom descriptions, comprising over 186,000 image-caption pairs aligned with 97 unique concepts. Through task-agnostic pretraining, SCOLD leverages contextual soft targets to mitigate overconfidence in contrastive learning by smoothing labels, thereby improving model generalization and robustness on fine-grained classification tasks. Experimental results demonstrate that SCOLD outperforms existing vision-language models such as OpenAI-CLIP-L, BioCLIP, and SigLIP2 across several benchmarks, including zero-shot and few-shot classification, image-text retrieval, and image classification, while maintaining a competitive parameter footprint. Ablation studies further highlight SCOLD's effectiveness in contrast to its counterparts. The proposed approach significantly advances the agricultural vision-language foundation model, offering strong performance with minimal or no supervised fine-tuning. This work lays a solid groundwork for future research on models trained with long-form and simplified contexts, tasks involving class ambiguity, and multi-modal systems for intelligent plant disease diagnostics. The code for this study is available at https://huggingface.co/enalis/scold

One of the critical biotic stress factors paddy farmers face is diseases caused by bacteria, fungi, and other organisms. These diseases affect plants' health severely and lead to significant crop loss. Most of these diseases can be identified by regularly observing the leaves and stems under expert supervision. In a country with vast agricultural regions and limited crop protection experts, manual identification of paddy diseases is challenging. Thus, to add a solution to this problem, it is necessary to automate the disease identification process and provide easily accessible decision support tools to enable effective crop protection measures. However, the lack of availability of public datasets with detailed disease information limits the practical implementation of accurate disease detection systems. This paper presents Paddy Doctor, a visual image dataset for identifying paddy diseases. Our dataset contains 16,225 annotated paddy leaf images across 13 classes (12 diseases and normal leaf). We benchmarked the Paddy Doctor dataset using a Convolutional Neural Network (CNN) and four transfer learning based models (VGG16, MobileNet, Xception, and ResNet34). The experimental results showed that ResNet34 achieved the highest F1-score of 97.50%. We release our dataset and reproducible code in the open source for community use.

Plant diseases pose significant threats to agriculture. It necessitates proper diagnosis and effective treatment to safeguard crop yields. To automate the diagnosis process, image segmentation is usually adopted for precisely identifying diseased regions, thereby advancing precision agriculture. Developing robust image segmentation models for plant diseases demands high-quality annotations across numerous images. However, existing plant disease datasets typically lack segmentation labels and are often confined to controlled laboratory settings, which do not adequately reflect the complexity of natural environments. Motivated by this fact, we established PlantSeg, a large-scale segmentation dataset for plant diseases. PlantSeg distinguishes itself from existing datasets in three key aspects. (1) Annotation type: Unlike the majority of existing datasets that only contain class labels or bounding boxes, each image in PlantSeg includes detailed and high-quality segmentation masks, associated with plant types and disease names. (2) Image source: Unlike typical datasets that contain images from laboratory settings, PlantSeg primarily comprises in-the-wild plant disease images. This choice enhances the practical applicability, as the trained models can be applied for integrated disease management. (3) Scale: PlantSeg is extensive, featuring 11,400 images with disease segmentation masks and an additional 8,000 healthy plant images categorized by plant type. Extensive technical experiments validate the high quality of PlantSeg's annotations. This dataset not only allows researchers to evaluate their image classification methods but also provides a critical foundation for developing and benchmarking advanced plant disease segmentation algorithms.

As the global food security landscape continues to evolve, the need for accurate and reliable crop disease diagnosis has never been more pressing. To address global food security concerns, we extend the widely used PlantVillage dataset with additional apple leaf disease classes, enhancing diversity and complexity. Experimental evaluations on both original and extended datasets reveal that existing models struggle with the new additions, highlighting the need for more robust and generalizable computer vision models. Test F1 scores of 99.63% and 97.87% were obtained on the original and extended datasets, respectively. Our study provides a more challenging and diverse benchmark, paving the way for the development of accurate and reliable models for identifying apple leaf diseases under varying imaging conditions. The expanded dataset is available at https://www.kaggle.com/datasets/akinyemijoseph/apple-leaf-disease-dataset-6-classes-v2 enabling future research to build upon our findings.

Automation in agriculture plays a vital role in addressing challenges related to crop monitoring and disease management, particularly through early detection systems. This study investigates the effectiveness of combining multimodal Large Language Models (LLMs), specifically GPT-4o, with Convolutional Neural Networks (CNNs) for automated plant disease classification using leaf imagery. Leveraging the PlantVillage dataset, we systematically evaluate model performance across zero-shot, few-shot, and progressive fine-tuning scenarios. A comparative analysis between GPT-4o and the widely used ResNet-50 model was conducted across three resolutions (100, 150, and 256 pixels) and two plant species (apple and corn). Results indicate that fine-tuned GPT-4o models achieved slightly better performance compared to the performance of ResNet-50, achieving up to 98.12% classification accuracy on apple leaf images, compared to 96.88% achieved by ResNet-50, with improved generalization and near-zero training loss. However, zero-shot performance of GPT-4o was significantly lower, underscoring the need for minimal training. Additional evaluations on cross-resolution and cross-plant generalization revealed the models' adaptability and limitations when applied to new domains. The findings highlight the promise of integrating multimodal LLMs into automated disease detection pipelines, enhancing the scalability and intelligence of precision agriculture systems while reducing the dependence on large, labeled datasets and high-resolution sensor infrastructure. Large Language Models, Vision Language Models, LLMs and CNNs, Disease Detection with Vision Language Models, VLMs

Crop diseases are a major threat to food security, but their rapid identification remains difficult in many parts of the world due to the lack of the necessary infrastructure. The combination of increasing global smartphone penetration and recent advances in computer vision made possible by deep learning has paved the way for smartphone-assisted disease diagnosis. Using a public dataset of 54,306 images of diseased and healthy plant leaves collected under controlled conditions, we train a deep convolutional neural network to identify 14 crop species and 26 diseases (or absence thereof). The trained model achieves an accuracy of 99.35% on a held-out test set, demonstrating the feasibility of this approach. When testing the model on a set of images collected from trusted online sources - i.e. taken under conditions different from the images used for training - the model still achieves an accuracy of 31.4%. While this accuracy is much higher than the one based on random selection (2.6%), a more diverse set of training data is needed to improve the general accuracy. Overall, the approach of training deep learning models on increasingly large and publicly available image datasets presents a clear path towards smartphone-assisted crop disease diagnosis on a massive global scale.

Pest and disease control plays a key role in agriculture since the damage caused by these agents are responsible for a huge economic loss every year. Based on this assumption, we create an algorithm capable of detecting rust (Hemileia vastatrix) and leaf miner (Leucoptera coffeella) in coffee leaves (Coffea arabica) and quantify disease severity using a mobile application as a high-level interface for the model inferences. We used different convolutional neural network architectures to create the object detector, besides the OpenCV library, k-means, and three treatments: the RGB and value to quantification, and the AFSoft software, in addition to the analysis of variance, where we compare the three methods. The results show an average precision of 81,5% in the detection and that there was no significant statistical difference between treatments to quantify the severity of coffee leaves, proposing a computationally less costly method. The application, together with the trained model, can detect the pest and disease over different image conditions and infection stages and also estimate the disease infection stage.

Accurate and timely detection of plant stress is essential for yield protection, allowing better-targeted intervention strategies. Recent advances in remote sensing and deep learning have shown great potential for rapid non-invasive detection of plant stress in a fully automated and reproducible manner. However, the existing models always face several challenges: 1) computational inefficiency and the misclassifications between the different stresses with similar symptoms; and 2) the poor interpretability of the host-stress interaction. In this work, we propose a novel fast Fourier Convolutional Neural Network (FFDNN) for accurate and explainable detection of two plant stresses with similar symptoms (i.e. Wheat Yellow Rust And Nitrogen Deficiency). Specifically, unlike the existing CNN models, the main components of the proposed model include: 1) a fast Fourier convolutional block, a newly fast Fourier transformation kernel as the basic perception unit, to substitute the traditional convolutional kernel to capture both local and global responses to plant stress in various time-scale and improve computing efficiency with reduced learning parameters in Fourier domain; 2) Capsule Feature Encoder to encapsulate the extracted features into a series of vector features to represent part-to-whole relationship with the hierarchical structure of the host-stress interactions of the specific stress. In addition, in order to alleviate over-fitting, a photochemical vegetation indices-based filter is placed as pre-processing operator to remove the non-photochemical noises from the input Sentinel-2 time series.

Generally, the identification and classification of plant diseases and/or pests are performed by an expert . One of the problems facing coffee farmers in Brazil is crop infestation, particularly by leaf rust Hemileia vastatrix and leaf miner Leucoptera coffeella. The progression of the diseases and or pests occurs spatially and temporarily. So, it is very important to automatically identify the degree of severity. The main goal of this article consists on the development of a method and its i implementation as an App that allow the detection of the foliar damages from images of coffee leaf that are captured using a smartphone, and identify whether it is rust or leaf miner, and in turn the calculation of its severity degree. The method consists of identifying a leaf from the image and separates it from the background with the use of a segmentation algorithm. In the segmentation process, various types of backgrounds for the image using the HSV and YCbCr color spaces are tested. In the segmentation of foliar damages, the Otsu algorithm and the iterative threshold algorithm, in the YCgCr color space, have been used and compared to k-means. Next, features of the segmented foliar damages are calculated. For the classification, artificial neural network trained with extreme learning machine have been used. The results obtained shows the feasibility and effectiveness of the approach to identify and classify foliar damages, and the automatic calculation of the severity. The results obtained are very promising according to experts.

Deep learning plays an important role in modern agriculture, especially in plant pathology using leaf images where convolutional neural networks (CNN) are attracting a lot of attention. While numerous reviews have explored the applications of deep learning within this research domain, there remains a notable absence of an empirical study to offer insightful comparisons due to the employment of varied datasets in the evaluation. Furthermore, a majority of these approaches tend to address the problem as a singular prediction task, overlooking the multifaceted nature of predicting various aspects of plant species and disease types. Lastly, there is an evident need for a more profound consideration of the semantic relationships that underlie plant species and disease types. In this paper, we start our study by surveying current deep learning approaches for plant identification and disease classification. We categorise the approaches into multi-model, multi-label, multi-output, and multi-task, in which different backbone CNNs can be employed. Furthermore, based on the survey of existing approaches in plant pathology and the study of available approaches in machine learning, we propose a new model named Generalised Stacking Multi-output CNN (GSMo-CNN). To investigate the effectiveness of different backbone CNNs and learning approaches, we conduct an intensive experiment on three benchmark datasets Plant Village, Plant Leaves, and PlantDoc. The experimental results demonstrate that InceptionV3 can be a good choice for a backbone CNN as its performance is better than AlexNet, VGG16, ResNet101, EfficientNet, MobileNet, and a custom CNN developed by us. Interestingly, empirical results support the hypothesis that using a single model can be comparable or better than using two models. Finally, we show that the proposed GSMo-CNN achieves state-of-the-art performance on three benchmark datasets.

PlantVillageVQA is a large-scale visual question answering (VQA) dataset derived from the widely used PlantVillage image corpus. It was designed to advance the development and evaluation of vision-language models for agricultural decision-making and analysis. The PlantVillageVQA dataset comprises 193,609 high-quality question-answer (QA) pairs grounded over 55,448 images spanning 14 crop species and 38 disease conditions. Questions are organised into 3 levels of cognitive complexity and 9 distinct categories. Each question category was phrased manually following expert guidance and generated via an automated two-stage pipeline: (1) template-based QA synthesis from image metadata and (2) multi-stage linguistic re-engineering. The dataset was iteratively reviewed by domain experts for scientific accuracy and relevancy. The final dataset was evaluated using three state-of-the-art models for quality assessment. Our objective remains to provide a publicly available, standardised and expert-verified database to enhance diagnostic accuracy for plant disease identifications and advance scientific research in the agricultural domain. Our dataset will be open-sourced at https://huggingface.co/datasets/SyedNazmusSakib/PlantVillageVQA.

Given the severe challenges confronting the global growth security of economic crops, precise identification and prevention of plant diseases has emerged as a critical issue in artificial intelligence-enabled agricultural technology. To address the technical challenges in plant disease recognition, including small-sample learning, leaf occlusion, illumination variations, and high inter-class similarity, this study innovatively proposes a Dynamic Dual-Stream Fusion Network (DS_FusionNet). The network integrates a dual-backbone architecture, deformable dynamic fusion modules, and bidirectional knowledge distillation strategy, significantly enhancing recognition accuracy. Experimental results demonstrate that DS_FusionNet achieves classification accuracies exceeding 90% using only 10% of the PlantDisease and CIFAR-10 datasets, while maintaining 85% accuracy on the complex PlantWild dataset, exhibiting exceptional generalization capabilities. This research not only provides novel technical insights for fine-grained image classification but also establishes a robust foundation for precise identification and management of agricultural diseases.

While conversational generative AI has shown considerable potential in enhancing decision-making for agricultural professionals, its exploration has predominantly been anchored in text-based interactions. The evolution of multimodal conversational AI, leveraging vast amounts of image-text data from diverse sources, marks a significant stride forward. However, the application of such advanced vision-language models in the agricultural domain, particularly for crop disease diagnosis, remains underexplored. In this work, we present the crop disease domain multimodal (CDDM) dataset, a pioneering resource designed to advance the field of agricultural research through the application of multimodal learning techniques. The dataset comprises 137,000 images of various crop diseases, accompanied by 1 million question-answer pairs that span a broad spectrum of agricultural knowledge, from disease identification to management practices. By integrating visual and textual data, CDDM facilitates the development of sophisticated question-answering systems capable of providing precise, useful advice to farmers and agricultural professionals. We demonstrate the utility of the dataset by finetuning state-of-the-art multimodal models, showcasing significant improvements in crop disease diagnosis. Specifically, we employed a novel finetuning strategy that utilizes low-rank adaptation (LoRA) to finetune the visual encoder, adapter and language model simultaneously. Our contributions include not only the dataset but also a finetuning strategy and a benchmark to stimulate further research in agricultural technology, aiming to bridge the gap between advanced AI techniques and practical agricultural applications. The dataset is available at https: //github.com/UnicomAI/UnicomBenchmark/tree/main/CDDMBench.

Precise automated understanding of agricultural tasks such as disease identification is essential for sustainable crop production. Recent advances in vision-language models (VLMs) are expected to further expand the range of agricultural tasks by facilitating human-model interaction through easy, text-based communication. Here, we introduce AgroBench (Agronomist AI Benchmark), a benchmark for evaluating VLM models across seven agricultural topics, covering key areas in agricultural engineering and relevant to real-world farming. Unlike recent agricultural VLM benchmarks, AgroBench is annotated by expert agronomists. Our AgroBench covers a state-of-the-art range of categories, including 203 crop categories and 682 disease categories, to thoroughly evaluate VLM capabilities. In our evaluation on AgroBench, we reveal that VLMs have room for improvement in fine-grained identification tasks. Notably, in weed identification, most open-source VLMs perform close to random. With our wide range of topics and expert-annotated categories, we analyze the types of errors made by VLMs and suggest potential pathways for future VLM development. Our dataset and code are available at https://dahlian00.github.io/AgroBenchPage/ .

Aphid infestations are one of the primary causes of extensive damage to wheat and sorghum fields and are one of the most common vectors for plant viruses, resulting in significant agricultural yield losses. To address this problem, farmers often employ the inefficient use of harmful chemical pesticides that have negative health and environmental impacts. As a result, a large amount of pesticide is wasted on areas without significant pest infestation. This brings to attention the urgent need for an intelligent autonomous system that can locate and spray sufficiently large infestations selectively within the complex crop canopies. We have developed a large multi-scale dataset for aphid cluster detection and segmentation, collected from actual sorghum fields and meticulously annotated to include clusters of aphids. Our dataset comprises a total of 54,742 image patches, showcasing a variety of viewpoints, diverse lighting conditions, and multiple scales, highlighting its effectiveness for real-world applications. In this study, we trained and evaluated four real-time semantic segmentation models and three object detection models specifically for aphid cluster segmentation and detection. Considering the balance between accuracy and efficiency, Fast-SCNN delivered the most effective segmentation results, achieving 80.46% mean precision, 81.21% mean recall, and 91.66 frames per second (FPS). For object detection, RT-DETR exhibited the best overall performance with a 61.63% mean average precision (mAP), 92.6% mean recall, and 72.55 on an NVIDIA V100 GPU. Our experiments further indicate that aphid cluster segmentation is more suitable for assessing aphid infestations than using detection models.

Despite progress in AI-based plant diagnostics, sugarcane farmers in low-resource regions remain vulnerable to leaf diseases due to the lack of scalable, efficient, and interpretable tools. Many deep learning models fail to generalize under real-world conditions and require substantial computational resources, limiting their use in resource-constrained regions. In this paper, we present SugarcaneLD-BD, a curated dataset for sugarcane leaf-disease classification; SugarcaneShuffleNet, an optimized lightweight model for rapid on-device diagnosis; and SugarcaneAI, a Progressive Web Application for field deployment. SugarcaneLD-BD contains 638 curated images across five classes, including four major sugarcane diseases, collected in Bangladesh under diverse field conditions and verified by expert pathologists. To enhance diversity, we combined SugarcaneLD-BD with two additional datasets, yielding a larger and more representative corpus. Our optimized model, SugarcaneShuffleNet, offers the best trade-off between speed and accuracy for real-time, on-device diagnosis. This 9.26 MB model achieved 98.02% accuracy, an F1-score of 0.98, and an average inference time of 4.14 ms per image. For comparison, we fine-tuned five other lightweight convolutional neural networks: MnasNet, EdgeNeXt, EfficientNet-Lite, MobileNet, and SqueezeNet via transfer learning and Bayesian optimization. MnasNet and EdgeNeXt achieved comparable accuracy to SugarcaneShuffleNet, but required significantly more parameters, memory, and computation, limiting their suitability for low-resource deployment. We integrate SugarcaneShuffleNet into SugarcaneAI, delivering Grad-CAM-based explanations in the field. Together, these contributions offer a diverse benchmark, efficient models for low-resource environments, and a practical tool for sugarcane disease classification. It spans varied lighting, backgrounds and devices used on-farm

Farmers face several challenges when growing crops like uncertain irrigation, poor soil quality, etc. Especially in India, a major fraction of farmers do not have the knowledge to select appropriate crops and fertilizers. Moreover, crop failure due to disease causes a significant loss to the farmers, as well as the consumers. While there have been recent developments in the automated detection of these diseases using Machine Learning techniques, the utilization of Deep Learning has not been fully explored. Additionally, such models are not easy to use because of the high-quality data used in their training, lack of computational power, and poor generalizability of the models. To this end, we create an open-source easy-to-use web application to address some of these issues which may help improve crop production. In particular, we support crop recommendation, fertilizer recommendation, plant disease prediction, and an interactive news-feed. In addition, we also use interpretability techniques in an attempt to explain the prediction made by our disease detection model.

Advances in deep learning and transfer learning have paved the way for various automation classification tasks in agriculture, including plant diseases, pests, weeds, and plant species detection. However, agriculture automation still faces various challenges, such as the limited size of datasets and the absence of plant-domain-specific pretrained models. Domain specific pretrained models have shown state of art performance in various computer vision tasks including face recognition and medical imaging diagnosis. In this paper, we propose AgriNet dataset, a collection of 160k agricultural images from more than 19 geographical locations, several images captioning devices, and more than 423 classes of plant species and diseases. We also introduce AgriNet models, a set of pretrained models on five ImageNet architectures: VGG16, VGG19, Inception-v3, InceptionResNet-v2, and Xception. AgriNet-VGG19 achieved the highest classification accuracy of 94 % and the highest F1-score of 92%. Additionally, all proposed models were found to accurately classify the 423 classes of plant species, diseases, pests, and weeds with a minimum accuracy of 87% for the Inception-v3 model.Finally, experiments to evaluate of superiority of AgriNet models compared to ImageNet models were conducted on two external datasets: pest and plant diseases dataset from Bangladesh and a plant diseases dataset from Kashmir.

Developing computer vision-based rice phenotyping techniques is crucial for precision field management and accelerating breeding, thereby continuously advancing rice production. Among phenotyping tasks, distinguishing image components is a key prerequisite for characterizing plant growth and development at the organ scale, enabling deeper insights into eco-physiological processes. However, due to the fine structure of rice organs and complex illumination within the canopy, this task remains highly challenging, underscoring the need for a high-quality training dataset. Such datasets are scarce, both due to a lack of large, representative collections of rice field images and the time-intensive nature of annotation. To address this gap, we established the first comprehensive multi-class rice semantic segmentation dataset, RiceSEG. We gathered nearly 50,000 high-resolution, ground-based images from five major rice-growing countries (China, Japan, India, the Philippines, and Tanzania), encompassing over 6,000 genotypes across all growth stages. From these original images, 3,078 representative samples were selected and annotated with six classes (background, green vegetation, senescent vegetation, panicle, weeds, and duckweed) to form the RiceSEG dataset. Notably, the sub-dataset from China spans all major genotypes and rice-growing environments from the northeast to the south. Both state-of-the-art convolutional neural networks and transformer-based semantic segmentation models were used as baselines. While these models perform reasonably well in segmenting background and green vegetation, they face difficulties during the reproductive stage, when canopy structures are more complex and multiple classes are involved. These findings highlight the importance of our dataset for developing specialized segmentation models for rice and other crops.

The number of people living in this agricultural nation of ours, which is surrounded by lush greenery, is growing on a daily basis. As a result of this, the level of arable land is decreasing, as well as residential houses and industrial factories. The food crisis is becoming the main threat for us in the upcoming days. Because on the one hand, the population is increasing, and on the other hand, the amount of food crop production is decreasing due to the attack of diseases. Rice is one of the most significant cultivated crops since it provides food for more than half of the world's population. Bangladesh is dependent on rice (Oryza sativa) as a vital crop for its agriculture, but it faces a significant problem as a result of the ongoing decline in rice yield brought on by common diseases. Early disease detection is the main difficulty in rice crop cultivation. In this paper, we proposed our own dataset, which was collected from the Bangladesh field, and also applied deep learning and transfer learning models for the evaluation of the datasets. We elaborately explain our dataset and also give direction for further research work to serve society using this dataset. We applied a light CNN model and pre-trained InceptionNet-V2, EfficientNet-V2, and MobileNet-V2 models, which achieved 91.5% performance for the EfficientNet-V2 model of this work. The results obtained assaulted other models and even exceeded approaches that are considered to be part of the state of the art. It has been demonstrated by this study that it is possible to precisely and effectively identify diseases that affect rice leaves using this unbiased datasets. After analysis of the performance of different models, the proposed datasets are significant for the society for research work to provide solutions for decreasing rice leaf disease.

We curate a dataset AgMMU for evaluating and developing vision-language models (VLMs) to produce factually accurate answers for knowledge-intensive expert domains. Our AgMMU concentrates on one of the most socially beneficial domains, agriculture, which requires connecting detailed visual observation with precise knowledge to diagnose, e.g., pest identification, management instructions, etc. As a core uniqueness of our dataset, all facts, questions, and answers are extracted from 116,231 conversations between real-world users and authorized agricultural experts. After a three-step dataset curation pipeline with GPT-4o, LLaMA models, and human verification, AgMMU features an evaluation set of 5,460 multiple-choice questions (MCQs) and open-ended questions (OEQs). We also provide a development set that contains 205,399 pieces of agricultural knowledge information, including disease identification, symptoms descriptions, management instructions, insect and pest identification, and species identification. As a multimodal factual dataset, it reveals that existing VLMs face significant challenges with questions requiring both detailed perception and factual knowledge. Moreover, open-source VLMs still demonstrate a substantial performance gap compared to proprietary ones. To advance knowledge-intensive VLMs, we conduct fine-tuning experiments using our development set, which improves LLaVA-1.5 evaluation accuracy by up to 3.1%. We hope that AgMMU can serve both as an evaluation benchmark dedicated to agriculture and a development suite for incorporating knowledge-intensive expertise into general-purpose VLMs.

Stomata play a crucial role in regulating plant physiological processes and reflecting environmental responses. However, accurate and high-throughput stomatal phenotyping remains challenging, as conventional approaches rely on destructive sampling and manual annotation, restricting large-scale and field deployment. To overcome these limitations, a noninvasive restoration-detection integrated framework, termed StomaD2, is developed to achieve accurate and fast stomatal phenotyping under complex imaging conditions. The framework incorporates a diffusion-based restoration module to recover degraded images and a specialized rotated object detection network tailored to the small, dense, and cluttered characteristics of stomata. The proposed network enhances feature representation through three key innovations: a column-wise structure for global feature interaction, context-aware resampling and reweighting mechanism to improve multi-scale consistency, and a feature reassembly module to boost discrimination against complex backgrounds. In extensive comparisons, StomaD2 demonstrated state-of-the-art performance. On public Maize and Wheat datasets, it achieved accuracies of 0.994 and 0.992, respectively, significantly outperforming existing benchmarks. When benchmarked against ten other advanced models, including Oriented Former and YOLOv12, StomaD2 achieved a top-tier F1-score/mAP of 0.989. The framework is integrated into a user-friendly, field-operable system that supports the fast extraction of eight stomatal phenotypes, such as density and conductance. Validated on more than 130 plant species, StomaD2's results highlight its strong generalizability and potential for large-scale phenotyping, plant physiology analysis, and precision agriculture applications.

This dataset represents almost all the harmful diseases for rice in Bangladesh. This dataset consists of 1106 image of five harmful diseases called Brown Spot, Leaf Scaled, Rice Blast, Rice Turngo, Steath Blight in two different background variation named field background picture and white background picture. Two different background variation helps the dataset to perform more accurately so that the user can use this data for field use as well as white background for decision making. The data is collected from rice field of Dhaka Division. This dataset can use for rice leaf diseases classification, diseases detection using Computer Vision and Pattern Recognition for different rice leaf disease.

Accurate maize seedling detection is crucial for precision agriculture, yet curated datasets remain scarce. We introduce MSDD, a high-quality aerial image dataset for maize seedling stand counting, with applications in early-season crop monitoring, yield prediction, and in-field management. Stand counting determines how many plants germinated, guiding timely decisions such as replanting or adjusting inputs. Traditional methods are labor-intensive and error-prone, while computer vision enables efficient, accurate detection. MSDD contains three classes-single, double, and triple plants-capturing diverse growth stages, planting setups, soil types, lighting conditions, camera angles, and densities, ensuring robustness for real-world use. Benchmarking shows detection is most reliable during V4-V6 stages and under nadir views. Among tested models, YOLO11 is fastest, while YOLOv9 yields the highest accuracy for single plants. Single plant detection achieves precision up to 0.984 and recall up to 0.873, but detecting doubles and triples remains difficult due to rarity and irregular appearance, often from planting errors. Class imbalance further reduces accuracy in multi-plant detection. Despite these challenges, YOLO11 maintains efficient inference at 35 ms per image, with an additional 120 ms for saving outputs. MSDD establishes a strong foundation for developing models that enhance stand counting, optimize resource allocation, and support real-time decision-making. This dataset marks a step toward automating agricultural monitoring and advancing precision agriculture.

We present two large datasets of labelled plant-images that are suited towards the training of machine learning and computer vision models. The first dataset encompasses as the day of writing over 1.2 million images of indoor-grown crops and weeds common to the Canadian Prairies and many US states. The second dataset consists of over 540,000 images of plants imaged in farmland. All indoor plant images are labelled by species and we provide rich etadata on the level of individual images. This comprehensive database allows to filter the datasets under user-defined specifications such as for example the crop-type or the age of the plant. Furthermore, the indoor dataset contains images of plants taken from a wide variety of angles, including profile shots, top-down shots, and angled perspectives. The images taken from plants in fields are all from a top-down perspective and contain usually multiple plants per image. For these images metadata is also available. In this paper we describe both datasets' characteristics with respect to plant variety, plant age, and number of images. We further introduce an open-access sample of the indoor-dataset that contains 1,000 images of each species covered in our dataset. These, in total 14,000 images, had been selected, such that they form a representative sample with respect to plant age and ndividual plants per species. This sample serves as a quick entry point for new users to the dataset, allowing them to explore the data on a small scale and find the parameters of data most useful for their application without having to deal with hundreds of thousands of individual images.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

Vision-driven field monitoring is central to digital agriculture, yet models built on general-domain pretrained backbones often fail to generalize across tasks, owing to the interaction of fine, variable canopy structures with fluctuating field conditions. We present FoMo4Wheat, one of the first crop-domain vision foundation model pretrained with self-supervision on ImAg4Wheat, the largest and most diverse wheat image dataset to date (2.5 million high-resolution images collected over a decade at 30 global sites, spanning >2,000 genotypes and >500 environmental conditions). This wheat-specific pretraining yields representations that are robust for wheat and transferable to other crops and weeds. Across ten in-field vision tasks at canopy and organ levels, FoMo4Wheat models consistently outperform state-of-the-art models pretrained on general-domain dataset. These results demonstrate the value of crop-specific foundation models for reliable in-field perception and chart a path toward a universal crop foundation model with cross-species and cross-task capabilities. FoMo4Wheat models and the ImAg4Wheat dataset are publicly available online: https://github.com/PheniX-Lab/FoMo4Wheat and https://huggingface.co/PheniX-Lab/FoMo4Wheat. The demonstration website is: https://fomo4wheat.phenix-lab.com/.

Wheat management strategies play a critical role in determining yield. Traditional management decisions often rely on labour-intensive expert inspections, which are expensive, subjective and difficult to scale. Recently, Vision-Language Models (VLMs) have emerged as a promising solution to enable scalable, data-driven management support. However, due to a lack of domain-specific knowledge, directly applying VLMs to wheat management tasks results in poor quantification and reasoning capabilities, ultimately producing vague or even misleading management recommendations. In response, we propose WisWheat, a wheat-specific dataset with a three-layered design to enhance VLM performance on wheat management tasks: (1) a foundational pretraining dataset of 47,871 image-caption pairs for coarsely adapting VLMs to wheat morphology; (2) a quantitative dataset comprising 7,263 VQA-style image-question-answer triplets for quantitative trait measuring tasks; and (3) an Instruction Fine-tuning dataset with 4,888 samples targeting biotic and abiotic stress diagnosis and management plan for different phenological stages. Extensive experimental results demonstrate that fine-tuning open-source VLMs (e.g., Qwen2.5 7B) on our dataset leads to significant performance improvements. Specifically, the Qwen2.5 VL 7B fine-tuned on our wheat instruction dataset achieves accuracy scores of 79.2% and 84.6% on wheat stress and growth stage conversation tasks respectively, surpassing even general-purpose commercial models such as GPT-4o by a margin of 11.9% and 34.6%.

Deep learning models are transforming agricultural applications by enabling automated phenotyping, monitoring, and yield estimation. However, their effectiveness heavily depends on large amounts of annotated training data, which can be labor and time intensive. Recent advances in open-set object detection, particularly with models like Grounding-DINO, offer a potential solution to detect regions of interests based on text prompt input. Initial zero-shot experiments revealed challenges in crafting effective text prompts, especially for complex objects like individual leaves and visually similar classes. To address these limitations, we propose an efficient few-shot adaptation method that simplifies the Grounding-DINO architecture by removing the text encoder module (BERT) and introducing a randomly initialized trainable text embedding. This method achieves superior performance across multiple agricultural datasets, including plant-weed detection, plant counting, insect identification, fruit counting, and remote sensing tasks. Specifically, it demonstrates up to a sim24% higher mAP than fully fine-tuned YOLO models on agricultural datasets and outperforms previous state-of-the-art methods by sim10% in remote sensing, under few-shot learning conditions. Our method offers a promising solution for automating annotation and accelerating the development of specialized agricultural AI solutions.

UAVs emerge as the optimal carriers for visual weed iden?tification and integrated pest and disease management in crops. How?ever, the absence of specialized datasets impedes the advancement of model development in this domain. To address this, we have developed the Pests and Diseases Tree dataset (PDT dataset). PDT dataset repre?sents the first high-precision UAV-based dataset for targeted detection of tree pests and diseases, which is collected in real-world operational environments and aims to fill the gap in available datasets for this field. Moreover, by aggregating public datasets and network data, we further introduced the Common Weed and Crop dataset (CWC dataset) to ad?dress the challenge of inadequate classification capabilities of test models within datasets for this field. Finally, we propose the YOLO-Dense Pest (YOLO-DP) model for high-precision object detection of weed, pest, and disease crop images. We re-evaluate the state-of-the-art detection models with our proposed PDT dataset and CWC dataset, showing the completeness of the dataset and the effectiveness of the YOLO-DP. The proposed PDT dataset, CWC dataset, and YOLO-DP model are pre?sented at https://github.com/RuiXing123/PDT_CWC_YOLO-DP.

An early, non-invasive, and on-site detection of nutrient deficiencies is critical to enable timely actions to prevent major losses of crops caused by lack of nutrients. While acquiring labeled data is very expensive, collecting images from multiple views of a crop is straightforward. Despite its relevance for practical applications, unsupervised domain adaptation where multiple views are available for the labeled source domain as well as the unlabeled target domain is an unexplored research area. In this work, we thus propose an approach that leverages multiple camera views in the source and target domain for unsupervised domain adaptation. We evaluate the proposed approach on two nutrient deficiency datasets. The proposed method achieves state-of-the-art results on both datasets compared to other unsupervised domain adaptation methods. The dataset and source code are available at https://github.com/jh-yi/MV-Match.

In precision agriculture, the detection and recognition of insects play an essential role in the ability of crops to grow healthy and produce a high-quality yield. The current machine vision model requires a large volume of data to achieve high performance. However, there are approximately 5.5 million different insect species in the world. None of the existing insect datasets can cover even a fraction of them due to varying geographic locations and acquisition costs. In this paper, we introduce a novel ``Insect-1M'' dataset, a game-changing resource poised to revolutionize insect-related foundation model training. Covering a vast spectrum of insect species, our dataset, including 1 million images with dense identification labels of taxonomy hierarchy and insect descriptions, offers a panoramic view of entomology, enabling foundation models to comprehend visual and semantic information about insects like never before. Then, to efficiently establish an Insect Foundation Model, we develop a micro-feature self-supervised learning method with a Patch-wise Relevant Attention mechanism capable of discerning the subtle differences among insect images. In addition, we introduce Description Consistency loss to improve micro-feature modeling via insect descriptions. Through our experiments, we illustrate the effectiveness of our proposed approach in insect modeling and achieve State-of-the-Art performance on standard benchmarks of insect-related tasks. Our Insect Foundation Model and Dataset promise to empower the next generation of insect-related vision models, bringing them closer to the ultimate goal of precision agriculture.

The rapid advancement of transformer-based language models has catalyzed breakthroughs in biomedical and clinical natural language processing; however, plant science remains markedly underserved by such domain-adapted tools. In this work, we present PlantBert, a high-performance, open-source language model specifically tailored for extracting structured knowledge from plant stress-response literature. Built upon the DeBERTa architecture-known for its disentangled attention and robust contextual encoding-PlantBert is fine-tuned on a meticulously curated corpus of expert-annotated abstracts, with a primary focus on lentil (Lens culinaris) responses to diverse abiotic and biotic stressors. Our methodology combines transformer-based modeling with rule-enhanced linguistic post-processing and ontology-grounded entity normalization, enabling PlantBert to capture biologically meaningful relationships with precision and semantic fidelity. The underlying corpus is annotated using a hierarchical schema aligned with the Crop Ontology, encompassing molecular, physiological, biochemical, and agronomic dimensions of plant adaptation. PlantBert exhibits strong generalization capabilities across entity types and demonstrates the feasibility of robust domain adaptation in low-resource scientific fields. By providing a scalable and reproducible framework for high-resolution entity recognition, PlantBert bridges a critical gap in agricultural NLP and paves the way for intelligent, data-driven systems in plant genomics, phenomics, and agronomic knowledge discovery. Our model is publicly released to promote transparency and accelerate cross-disciplinary innovation in computational plant science.

Measuring soil health indicators is an important and challenging task that affects farmers' decisions on timing, placement, and quantity of fertilizers applied in the farms. Most existing methods to measure soil health indicators (SHIs) are in-lab wet chemistry or spectroscopy-based methods, which require significant human input and effort, time-consuming, costly, and are low-throughput in nature. To address this challenge, we develop an artificial intelligence (AI)-driven near real-time unmanned aerial vehicle (UAV)-based multispectral sensing (UMS) solution to estimate total nitrogen (TN) of the soil, an important macro-nutrient or SHI that directly affects the crop health. Accurate prediction of soil TN can significantly increase crop yield through informed decision making on the timing of seed planting, and fertilizer quantity and timing. We train two machine learning models including multi-layer perceptron and support vector machine to predict the soil nitrogen using a suite of data classes including multispectral characteristics of the soil and crops in red, near-infrared, and green spectral bands, computed vegetation indices, and environmental variables including air temperature and relative humidity. To generate the ground-truth data or the training data for the machine learning models, we measure the total nitrogen of the soil samples (collected from a farm) using laser-induced breakdown spectroscopy (LIBS).

This article presents GrowliFlower, a georeferenced, image-based UAV time series dataset of two monitored cauliflower fields of size 0.39 and 0.60 ha acquired in 2020 and 2021. The dataset contains RGB and multispectral orthophotos from which about 14,000 individual plant coordinates are derived and provided. The coordinates enable the dataset users the extraction of complete and incomplete time series of image patches showing individual plants. The dataset contains collected phenotypic traits of 740 plants, including the developmental stage as well as plant and cauliflower size. As the harvestable product is completely covered by leaves, plant IDs and coordinates are provided to extract image pairs of plants pre and post defoliation, to facilitate estimations of cauliflower head size. Moreover, the dataset contains pixel-accurate leaf and plant instance segmentations, as well as stem annotations to address tasks like classification, detection, segmentation, instance segmentation, and similar computer vision tasks. The dataset aims to foster the development and evaluation of machine learning approaches. It specifically focuses on the analysis of growth and development of cauliflower and the derivation of phenotypic traits to foster the development of automation in agriculture. Two baseline results of instance segmentation at plant and leaf level based on the labeled instance segmentation data are presented. The entire data set is publicly available.

Accurate identification of crop and weed species is critical for precision agriculture and sustainable farming. However, it remains a challenging task due to a variety of factors -- a high degree of visual similarity among species, environmental variability, and a continued lack of large, agriculture-specific image data. We introduce iNatAg, a large-scale image dataset which contains over 4.7 million images of 2,959 distinct crop and weed species, with precise annotations along the taxonomic hierarchy from binary crop/weed labels to specific species labels. Curated from the broader iNaturalist database, iNatAg contains data from every continent and accurately reflects the variability of natural image captures and environments. Enabled by this data, we train benchmark models built upon the Swin Transformer architecture and evaluate the impact of various modifications such as the incorporation of geospatial data and LoRA finetuning. Our best models achieve state-of-the-art performance across all taxonomic classification tasks, achieving 92.38\% on crop and weed classification. Furthermore, the scale of our dataset enables us to explore incorrect misclassifications and unlock new analytic possiblities for plant species. By combining large-scale species coverage, multi-task labels, and geographic diversity, iNatAg provides a new foundation for building robust, geolocation-aware agricultural classification systems. We release the iNatAg dataset publicly through AgML (https://github.com/Project-AgML/AgML), enabling direct access and integration into agricultural machine learning workflows.

Human society needs to increase food production by an estimated 70% by 2050 to feed an expected population size that is predicted to be over 9 billion people. Currently, infectious diseases reduce the potential yield by an average of 40% with many farmers in the developing world experiencing yield losses as high as 100%. The widespread distribution of smartphones among crop growers around the world with an expected 5 billion smartphones by 2020 offers the potential of turning the smartphone into a valuable tool for diverse communities growing food. One potential application is the development of mobile disease diagnostics through machine learning and crowdsourcing. Here we announce the release of over 50,000 expertly curated images on healthy and infected leaves of crops plants through the existing online platform PlantVillage. We describe both the data and the platform. These data are the beginning of an on-going, crowdsourcing effort to enable computer vision approaches to help solve the problem of yield losses in crop plants due to infectious diseases.

Mycotoxin contamination poses a significant risk to cereal crop quality, food safety, and agricultural productivity. Accurate prediction of mycotoxin levels can support early intervention strategies and reduce economic losses. This study investigates the use of neural networks and transfer learning models to predict mycotoxin contamination in Irish oat crops as a multi-response prediction task. Our dataset comprises oat samples collected in Ireland, containing a mix of environmental, agronomic, and geographical predictors. Five modelling approaches were evaluated: a baseline multilayer perceptron (MLP), an MLP with pre-training, and three transfer learning models; TabPFN, TabNet, and FT-Transformer. Model performance was evaluated using regression (RMSE, R^2) and classification (AUC, F1) metrics, with results reported per toxin and on average. Additionally, permutation-based variable importance analysis was conducted to identify the most influential predictors across both prediction tasks. The transfer learning approach TabPFN provided the overall best performance, followed by the baseline MLP. Our variable importance analysis revealed that weather history patterns in the 90-day pre-harvest period were the most important predictors, alongside seed moisture content.

Invasive plant species are detrimental to the ecology of both agricultural and wildland areas. Euphorbia esula, or leafy spurge, is one such plant that has spread through much of North America from Eastern Europe. When paired with contemporary computer vision systems, unmanned aerial vehicles, or drones, offer the means to track expansion of problem plants, such as leafy spurge, and improve chances of controlling these weeds. We gathered a dataset of leafy spurge presence and absence in grasslands of western Montana, USA, then surveyed these areas with a commercial drone. We trained image classifiers on these data, and our best performing model, a pre-trained DINOv2 vision transformer, identified leafy spurge with 0.84 accuracy (test set). This result indicates that classification of leafy spurge is tractable, but not solved. We release this unique dataset of labelled and unlabelled, aerial drone imagery for the machine learning community to explore. Improving classification performance of leafy spurge would benefit the fields of ecology, conservation, and remote sensing alike. Code and data are available at our website: leafy-spurge-dataset.github.io.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Foodborne gastrointestinal (GI) illness is a common cause of ill health in the UK. However, many cases do not interact with the healthcare system, posing significant challenges for traditional surveillance methods. The growth of publicly available online restaurant reviews and advancements in large language models (LLMs) present potential opportunities to extend disease surveillance by identifying public reports of GI illness. In this study, we introduce a novel annotation schema, developed with experts in GI illness, applied to the Yelp Open Dataset of reviews. Our annotations extend beyond binary disease detection, to include detailed extraction of information on symptoms and foods. We evaluate the performance of open-weight LLMs across these three tasks: GI illness detection, symptom extraction, and food extraction. We compare this performance to RoBERTa-based classification models fine-tuned specifically for these tasks. Our results show that using prompt-based approaches, LLMs achieve micro-F1 scores of over 90% for all three of our tasks. Using prompting alone, we achieve micro-F1 scores that exceed those of smaller fine-tuned models. We further demonstrate the robustness of LLMs in GI illness detection across three bias-focused experiments. Our results suggest that publicly available review text and LLMs offer substantial potential for public health surveillance of GI illness by enabling highly effective extraction of key information. While LLMs appear to exhibit minimal bias in processing, the inherent limitations of restaurant review data highlight the need for cautious interpretation of results.

Plant developmental plasticity, particularly in root system architecture, is fundamental to understanding adaptability and agricultural sustainability. ChronoRoot 2.0 builds upon established low-cost hardware while significantly enhancing software capabilities and usability. The system employs nnUNet architecture for multi-class segmentation, demonstrating significant accuracy improvements while simultaneously tracking six distinct plant structures encompassing root, shoot, and seed components: main root, lateral roots, seed, hypocotyl, leaves, and petiole. This architecture enables easy retraining and incorporation of additional training data without requiring machine learning expertise. The platform introduces dual specialized graphical interfaces: a Standard Interface for detailed architectural analysis with novel gravitropic response parameters, and a Screening Interface enabling high-throughput analysis of multiple plants through automated tracking. Functional Principal Component Analysis integration enables discovery of novel phenotypic parameters through temporal pattern comparison. We demonstrate multi-species analysis, with Arabidopsis thaliana and Solanum lycopersicum, both morphologically distinct plant species. Three use cases in Arabidopsis thaliana and validation with tomato seedlings demonstrate enhanced capabilities: circadian growth pattern characterization, gravitropic response analysis in transgenic plants, and high-throughput etiolation screening across multiple genotypes.ChronoRoot 2.0 maintains the low-cost, modular hardware advantages of its predecessor while dramatically improving accessibility through intuitive graphical interfaces and expanded analytical capabilities. The open-source platform makes sophisticated temporal plant phenotyping more accessible to researchers without computational expertise.

Large Multimodal Models (LMMs) has demonstrated capabilities across various domains, but comprehensive benchmarks for agricultural remote sensing (RS) remain scarce. Existing benchmarks designed for agricultural RS scenarios exhibit notable limitations, primarily in terms of insufficient scene diversity in the dataset and oversimplified task design. To bridge this gap, we introduce AgroMind, a comprehensive agricultural remote sensing benchmark covering four task dimensions: spatial perception, object understanding, scene understanding, and scene reasoning, with a total of 13 task types, ranging from crop identification and health monitoring to environmental analysis. We curate a high-quality evaluation set by integrating eight public datasets and one private farmland plot dataset, containing 25,026 QA pairs and 15,556 images. The pipeline begins with multi-source data preprocessing, including collection, format standardization, and annotation refinement. We then generate a diverse set of agriculturally relevant questions through the systematic definition of tasks. Finally, we employ LMMs for inference, generating responses, and performing detailed examinations. We evaluated 18 open-source LMMs and 3 closed-source models on AgroMind. Experiments reveal significant performance gaps, particularly in spatial reasoning and fine-grained recognition, it is notable that human performance lags behind several leading LMMs. By establishing a standardized evaluation framework for agricultural RS, AgroMind reveals the limitations of LMMs in domain knowledge and highlights critical challenges for future work. Data and code can be accessed at https://rssysu.github.io/AgroMind/.

Accurate plant counting provides valuable information for agriculture such as crop yield prediction, plant density assessment, and phenotype quantification. Vision-based approaches are currently the mainstream solution. Prior art typically uses a detection or a regression model to count a specific plant. However, plants have biodiversity, and new cultivars are increasingly bred each year. It is almost impossible to exhaust and build all species-dependent counting models. Inspired by class-agnostic counting (CAC) in computer vision, we argue that it is time to rethink the problem formulation of plant counting, from what plants to count to how to count plants. In contrast to most daily objects with spatial and temporal invariance, plants are dynamic, changing with time and space. Their non-rigid structure often leads to worse performance than counting rigid instances like heads and cars such that current CAC and open-world detection models are suboptimal to count plants. In this work, we inherit the vein of the TasselNet plant counting model and introduce a new extension, TasselNetV4, shifting from species-specific counting to cross-species counting. TasselNetV4 marries the local counting idea of TasselNet with the extract-and-match paradigm in CAC. It builds upon a plain vision transformer and incorporates novel multi-branch box-aware local counters used to enhance cross-scale robustness. Two challenging datasets, PAC-105 and PAC-Somalia, are harvested. Extensive experiments against state-of-the-art CAC models show that TasselNetV4 achieves not only superior counting performance but also high efficiency.Our results indicate that TasselNetV4 emerges to be a vision foundation model for cross-scene, cross-scale, and cross-species plant counting.

We propose a novel hybrid cable-based robot with manipulator and camera for high-accuracy, medium-throughput plant monitoring in a vertical hydroponic farm and, as an example application, demonstrate non-destructive plant mass estimation. Plant monitoring with high temporal and spatial resolution is important to both farmers and researchers to detect anomalies and develop predictive models for plant growth. The availability of high-quality, off-the-shelf structure-from-motion (SfM) and photogrammetry packages has enabled a vibrant community of roboticists to apply computer vision for non-destructive plant monitoring. While existing approaches tend to focus on either high-throughput (e.g. satellite, unmanned aerial vehicle (UAV), vehicle-mounted, conveyor-belt imagery) or high-accuracy/robustness to occlusions (e.g. turn-table scanner or robot arm), we propose a middle-ground that achieves high accuracy with a medium-throughput, highly automated robot. Our design pairs the workspace scalability of a cable-driven parallel robot (CDPR) with the dexterity of a 4 degree-of-freedom (DoF) robot arm to autonomously image many plants from a variety of viewpoints. We describe our robot design and demonstrate it experimentally by collecting daily photographs of 54 plants from 64 viewpoints each. We show that our approach can produce scientifically useful measurements, operate fully autonomously after initial calibration, and produce better reconstructions and plant property estimates than those of over-canopy methods (e.g. UAV). As example applications, we show that our system can successfully estimate plant mass with a Mean Absolute Error (MAE) of 0.586g and, when used to perform hypothesis testing on the relationship between mass and age, produces p-values comparable to ground-truth data (p=0.0020 and p=0.0016, respectively).

The need for higher agricultural productivity has demanded the intensive use of pesticides. However, their correct use depends on assessment methods that can accurately predict how well the pesticides' spraying covered the intended crop region. Some methods have been proposed in the literature, but their high cost and low portability harm their widespread use. This paper proposes and experimentally evaluates a new methodology based on the use of a smartphone-based mobile application, named DropLeaf. Experiments performed using DropLeaf showed that, in addition to its versatility, it can predict with high accuracy the pesticide spraying. DropLeaf is a five-fold image-processing methodology based on: (i) color space conversion, (ii) threshold noise removal, (iii) convolutional operations of dilation and erosion, (iv) detection of contour markers in the water-sensitive card, and, (v) identification of droplets via the marker-controlled watershed transformation. The authors performed successful experiments over two case studies, the first using a set of synthetic cards and the second using a real-world crop. The proposed tool can be broadly used by farmers equipped with conventional mobile phones, improving the use of pesticides with health, environmental and financial benefits.

Automatic monitoring of tree plantations plays a crucial role in agriculture. Flawless monitoring of tree health helps farmers make informed decisions regarding their management by taking appropriate action. Use of drone images for automatic plantation monitoring can enhance the accuracy of the monitoring process, while still being affordable to small farmers in developing countries such as India. Small, low cost drones equipped with an RGB camera can capture high-resolution images of agricultural fields, allowing for detailed analysis of the well-being of the plantations. Existing methods of automated plantation monitoring are mostly based on satellite images, which are difficult to get for the farmers. We propose an automated system for plantation health monitoring using drone images, which are becoming easier to get for the farmers. We propose a dataset of images of trees with three categories: ``Good health", ``Stunted", and ``Dead". We annotate the dataset using CVAT annotation tool, for use in research purposes. We experiment with different well-known CNN models to observe their performance on the proposed dataset. The initial low accuracy levels show the complexity of the proposed dataset. Further, our study revealed that, depth-wise convolution operation embedded in a deep CNN model, can enhance the performance of the model on drone dataset. Further, we apply state-of-the-art object detection models to identify individual trees to better monitor them automatically.

Accurately detecting rice flowering time is crucial for timely pollination in hybrid rice seed production. This not only enhances pollination efficiency but also ensures higher yields. However, due to the complexity of field environments and the characteristics of rice spikelets, such as their small size and short flowering period, automated and precise recognition remains challenging. To address this, this study proposes a rice spikelet flowering recognition method based on an improved YOLOv8 object detection model. First, a Bidirectional Feature Pyramid Network (BiFPN) replaces the original PANet structure to enhance feature fusion and improve multi-scale feature utilization. Second, to boost small object detection, a p2 small-object detection head is added, using finer feature mapping to reduce feature loss commonly seen in detecting small targets. Given the lack of publicly available datasets for rice spikelet flowering in field conditions, a high-resolution RGB camera and data augmentation techniques are used to construct a dedicated dataset, providing reliable support for model training and testing. Experimental results show that the improved YOLOv8s-p2 model achieves an mAP@0.5 of 65.9%, precision of 67.6%, recall of 61.5%, and F1-score of 64.41%, representing improvements of 3.10%, 8.40%, 10.80%, and 9.79%, respectively, over the baseline YOLOv8. The model also runs at 69 f/s on the test set, meeting practical application requirements. Overall, the improved YOLOv8s-p2 offers high accuracy and speed, providing an effective solution for automated monitoring in hybrid rice seed production.

Knowledge distillation (KD) remains challenging due to the opaque nature of the knowledge transfer process from a Teacher to a Student, making it difficult to address certain issues related to KD. To address this, we proposed UniCAM, a novel gradient-based visual explanation method, which effectively interprets the knowledge learned during KD. Our experimental results demonstrate that with the guidance of the Teacher's knowledge, the Student model becomes more efficient, learning more relevant features while discarding those that are not relevant. We refer to the features learned with the Teacher's guidance as distilled features and the features irrelevant to the task and ignored by the Student as residual features. Distilled features focus on key aspects of the input, such as textures and parts of objects. In contrast, residual features demonstrate more diffused attention, often targeting irrelevant areas, including the backgrounds of the target objects. In addition, we proposed two novel metrics: the feature similarity score (FSS) and the relevance score (RS), which quantify the relevance of the distilled knowledge. Experiments on the CIFAR10, ASIRRA, and Plant Disease datasets demonstrate that UniCAM and the two metrics offer valuable insights to explain the KD process.

A database of images of approximately 960 unique plants belonging to 12 species at several growth stages is made publicly available. It comprises annotated RGB images with a physical resolution of roughly 10 pixels per mm. To standardise the evaluation of classification results obtained with the database, a benchmark based on f_{1} scores is proposed. The dataset is available at https://vision.eng.au.dk/plant-seedlings-dataset

The recent 'Mpox' outbreak, formerly known as 'Monkeypox', has become a significant public health concern and has spread to over 110 countries globally. The challenge of clinically diagnosing mpox early on is due, in part, to its similarity to other types of rashes. Computer-aided screening tools have been proven valuable in cases where Polymerase Chain Reaction (PCR) based diagnosis is not immediately available. Deep learning methods are powerful in learning complex data representations, but their efficacy largely depends on adequate training data. To address this challenge, we present the "Mpox Skin Lesion Dataset Version 2.0 (MSLD v2.0)" as a follow-up to the previously released openly accessible dataset, one of the first datasets containing mpox lesion images. This dataset contains images of patients with mpox and five other non-mpox classes (chickenpox, measles, hand-foot-mouth disease, cowpox, and healthy). We benchmark the performance of several state-of-the-art deep learning models, including VGG16, ResNet50, DenseNet121, MobileNetV2, EfficientNetB3, InceptionV3, and Xception, to classify mpox and other infectious skin diseases. In order to reduce the impact of racial bias, we utilize a color space data augmentation method to increase skin color variability during training. Additionally, by leveraging transfer learning implemented with pre-trained weights generated from the HAM10000 dataset, an extensive collection of pigmented skin lesion images, we achieved the best overall accuracy of 83.59pm2.11%. Finally, the developed models are incorporated within a prototype web application to analyze uploaded skin images by a user and determine whether a subject is a suspected mpox patient.

Weed management represents a critical challenge in agriculture, significantly impacting crop yields and requiring substantial resources for control. Effective weed monitoring and analysis strategies are crucial for implementing sustainable agricultural practices and site-specific management approaches. We introduce WeedSense, a novel multi-task learning architecture for comprehensive weed analysis that jointly performs semantic segmentation, height estimation, and growth stage classification. We present a unique dataset capturing 16 weed species over an 11-week growth cycle with pixel-level annotations, height measurements, and temporal labels. WeedSense leverages a dual-path encoder incorporating Universal Inverted Bottleneck blocks and a Multi-Task Bifurcated Decoder with transformer-based feature fusion to generate multi-scale features and enable simultaneous prediction across multiple tasks. WeedSense outperforms other state-of-the-art models on our comprehensive evaluation. On our multi-task dataset, WeedSense achieves mIoU of 89.78% for segmentation, 1.67cm MAE for height estimation, and 99.99% accuracy for growth stage classification while maintaining real-time inference at 160 FPS. Our multitask approach achieves 3times faster inference than sequential single-task execution and uses 32.4% fewer parameters. Please see our project page at weedsense.github.io.

Plant traits such as leaf carbon content and leaf mass are essential variables in the study of biodiversity and climate change. However, conventional field sampling cannot feasibly cover trait variation at ecologically meaningful spatial scales. Machine learning represents a valuable solution for plant trait prediction across ecosystems, leveraging hyperspectral data from remote sensing. Nevertheless, trait prediction from hyperspectral data is challenged by label scarcity and substantial domain shifts (\eg across sensors, ecological distributions), requiring robust cross-domain methods. Here, we present GreenHyperSpectra, a pretraining dataset encompassing real-world cross-sensor and cross-ecosystem samples designed to benchmark trait prediction with semi- and self-supervised methods. We adopt an evaluation framework encompassing in-distribution and out-of-distribution scenarios. We successfully leverage GreenHyperSpectra to pretrain label-efficient multi-output regression models that outperform the state-of-the-art supervised baseline. Our empirical analyses demonstrate substantial improvements in learning spectral representations for trait prediction, establishing a comprehensive methodological framework to catalyze research at the intersection of representation learning and plant functional traits assessment. All code and data are available at: https://github.com/echerif18/HyspectraSSL.

In orchard automation, dense foliage during the canopy season severely occludes tree structures, minimizing visibility to various canopy parts such as trunks and branches, which limits the ability of a machine vision system. However, canopy structure is more open and visible during the dormant season when trees are defoliated. In this work, we present an information fusion framework that integrates multi-seasonal structural data to support robotic and automated crop load management during the entire growing season. The framework combines high-resolution RGB-D imagery from both dormant and canopy periods using YOLOv9-Seg for instance segmentation, Kinect Fusion for 3D reconstruction, and Fast Generalized Iterative Closest Point (Fast GICP) for model alignment. Segmentation outputs from YOLOv9-Seg were used to extract depth-informed masks, which enabled accurate 3D point cloud reconstruction via Kinect Fusion; these reconstructed models from each season were subsequently aligned using Fast GICP to achieve spatially coherent multi-season fusion. The YOLOv9-Seg model, trained on manually annotated images, achieved a mean squared error (MSE) of 0.0047 and segmentation mAP@50 scores up to 0.78 for trunks in dormant season dataset. Kinect Fusion enabled accurate reconstruction of tree geometry, validated with field measurements resulting in root mean square errors (RMSE) of 5.23 mm for trunk diameter, 4.50 mm for branch diameter, and 13.72 mm for branch spacing. Fast GICP achieved precise cross-seasonal registration with a minimum fitness score of 0.00197, allowing integrated, comprehensive tree structure modeling despite heavy occlusions during the growing season. This fused structural representation enables robotic systems to access otherwise obscured architectural information, improving the precision of pruning, thinning, and other automated orchard operations.

Accurate crop yield prediction is of utmost importance for informed decision-making in agriculture, aiding farmers, and industry stakeholders. However, this task is complex and depends on multiple factors, such as environmental conditions, soil properties, and management practices. Combining heterogeneous data views poses a fusion challenge, like identifying the view-specific contribution to the predictive task. We present a novel multi-view learning approach to predict crop yield for different crops (soybean, wheat, rapeseed) and regions (Argentina, Uruguay, and Germany). Our multi-view input data includes multi-spectral optical images from Sentinel-2 satellites and weather data as dynamic features during the crop growing season, complemented by static features like soil properties and topographic information. To effectively fuse the data, we introduce a Multi-view Gated Fusion (MVGF) model, comprising dedicated view-encoders and a Gated Unit (GU) module. The view-encoders handle the heterogeneity of data sources with varying temporal resolutions by learning a view-specific representation. These representations are adaptively fused via a weighted sum. The fusion weights are computed for each sample by the GU using a concatenation of the view-representations. The MVGF model is trained at sub-field level with 10 m resolution pixels. Our evaluations show that the MVGF outperforms conventional models on the same task, achieving the best results by incorporating all the data sources, unlike the usual fusion results in the literature. For Argentina, the MVGF model achieves an R2 value of 0.68 at sub-field yield prediction, while at field level evaluation (comparing field averages), it reaches around 0.80 across different countries. The GU module learned different weights based on the country and crop-type, aligning with the variable significance of each data source to the prediction task.

Vegetation indices allow to efficiently monitor vegetation growth and agricultural activities. Previous generations of satellites were capturing a limited number of spectral bands, and a few expert-designed vegetation indices were sufficient to harness their potential. New generations of multi- and hyperspectral satellites can however capture additional bands, but are not yet efficiently exploited. In this work, we propose an explainable-AI-based method to select and design suitable vegetation indices. We first train a deep neural network using multispectral satellite data, then extract feature importance to identify the most influential bands. We subsequently select suitable existing vegetation indices or modify them to incorporate the identified bands and retrain our model. We validate our approach on a crop classification task. Our results indicate that models trained on individual indices achieve comparable results to the baseline model trained on all bands, while the combination of two indices surpasses the baseline in certain cases.

Foodborne illness is a serious but preventable public health problem -- with delays in detecting the associated outbreaks resulting in productivity loss, expensive recalls, public safety hazards, and even loss of life. While social media is a promising source for identifying unreported foodborne illnesses, there is a dearth of labeled datasets for developing effective outbreak detection models. To accelerate the development of machine learning-based models for foodborne outbreak detection, we thus present TWEET-FID (TWEET-Foodborne Illness Detection), the first publicly available annotated dataset for multiple foodborne illness incident detection tasks. TWEET-FID collected from Twitter is annotated with three facets: tweet class, entity type, and slot type, with labels produced by experts as well as by crowdsource workers. We introduce several domain tasks leveraging these three facets: text relevance classification (TRC), entity mention detection (EMD), and slot filling (SF). We describe the end-to-end methodology for dataset design, creation, and labeling for supporting model development for these tasks. A comprehensive set of results for these tasks leveraging state-of-the-art single- and multi-task deep learning methods on the TWEET-FID dataset are provided. This dataset opens opportunities for future research in foodborne outbreak detection.

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..

Agricultural applications such as yield prediction, precision agriculture and automated harvesting need systems able to infer the crop state from low-cost sensing devices. Proximal sensing using affordable cameras combined with computer vision has seen a promising alternative, strengthened after the advent of convolutional neural networks (CNNs) as an alternative for challenging pattern recognition problems in natural images. Considering fruit growing monitoring and automation, a fundamental problem is the detection, segmentation and counting of individual fruits in orchards. Here we show that for wine grapes, a crop presenting large variability in shape, color, size and compactness, grape clusters can be successfully detected, segmented and tracked using state-of-the-art CNNs. In a test set containing 408 grape clusters from images taken on a trellis-system based vineyard, we have reached an F 1 -score up to 0.91 for instance segmentation, a fine separation of each cluster from other structures in the image that allows a more accurate assessment of fruit size and shape. We have also shown as clusters can be identified and tracked along video sequences recording orchard rows. We also present a public dataset containing grape clusters properly annotated in 300 images and a novel annotation methodology for segmentation of complex objects in natural images. The presented pipeline for annotation, training, evaluation and tracking of agricultural patterns in images can be replicated for different crops and production systems. It can be employed in the development of sensing components for several agricultural and environmental applications.

Commercial plant phenotyping systems using fixed cameras cannot perceive many plant details due to leaf occlusion. In this paper, we present Botany-Bot, a system for building detailed "annotated digital twins" of living plants using two stereo cameras, a digital turntable inside a lightbox, an industrial robot arm, and 3D segmentated Gaussian Splat models. We also present robot algorithms for manipulating leaves to take high-resolution indexable images of occluded details such as stem buds and the underside/topside of leaves. Results from experiments suggest that Botany-Bot can segment leaves with 90.8% accuracy, detect leaves with 86.2% accuracy, lift/push leaves with 77.9% accuracy, and take detailed overside/underside images with 77.3% accuracy. Code, videos, and datasets are available at https://berkeleyautomation.github.io/Botany-Bot/.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.

Studying and analyzing cropland is a difficult task due to its dynamic and heterogeneous growth behavior. Usually, diverse data sources can be collected for its estimation. Although deep learning models have proven to excel in the crop classification task, they face substantial challenges when dealing with multiple inputs, named Multi-View Learning (MVL). The methods used in the MVL scenario can be structured based on the encoder architecture, the fusion strategy, and the optimization technique. The literature has primarily focused on using specific encoder architectures for local regions, lacking a deeper exploration of other components in the MVL methodology. In contrast, we investigate the simultaneous selection of the fusion strategy and encoder architecture, assessing global-scale cropland and crop-type classifications. We use a range of five fusion strategies (Input, Feature, Decision, Ensemble, Hybrid) and five temporal encoders (LSTM, GRU, TempCNN, TAE, L-TAE) as possible configurations in the MVL method. We use the CropHarvest dataset for validation, which provides optical, radar, weather time series, and topographic information as input data. We found that in scenarios with a limited number of labeled samples, a unique configuration is insufficient for all the cases. Instead, a specialized combination should be meticulously sought, including an encoder and fusion strategy. To streamline this search process, we suggest identifying the optimal encoder architecture tailored for a particular fusion strategy, and then determining the most suitable fusion strategy for the classification task. We provide a methodological framework for researchers exploring crop classification through an MVL methodology.

Large Language Models (LLMs) have exhibited remarkable capabilities in understanding and interacting with natural language across various sectors. However, their effectiveness is limited in specialized areas requiring high accuracy, such as plant science, due to a lack of specific expertise in these fields. This paper introduces PLLaMa, an open-source language model that evolved from LLaMa-2. It's enhanced with a comprehensive database, comprising more than 1.5 million scholarly articles in plant science. This development significantly enriches PLLaMa with extensive knowledge and proficiency in plant and agricultural sciences. Our initial tests, involving specific datasets related to plants and agriculture, show that PLLaMa substantially improves its understanding of plant science-related topics. Moreover, we have formed an international panel of professionals, including plant scientists, agricultural engineers, and plant breeders. This team plays a crucial role in verifying the accuracy of PLLaMa's responses to various academic inquiries, ensuring its effective and reliable application in the field. To support further research and development, we have made the model's checkpoints and source codes accessible to the scientific community. These resources are available for download at https://github.com/Xianjun-Yang/PLLaMa.

Early detection of highly pathogenic avian influenza (HPAI) and endemic poultry diseases is critical for global food security. While computer vision models excel at classifying diseases from fecal imaging, deploying these systems at scale is bottlenecked by farm data privacy concerns and institutional data silos. Furthermore, existing open-source agricultural datasets frequently suffer from severe, undocumented data contamination. In this paper, we introduce FecalFed, a privacy-preserving federated learning framework for poultry disease classification. We first curate and release poultry-fecal-fl, a rigorously deduplicated dataset of 8,770 unique images across four disease classes, revealing and eliminating a 46.89% duplication rate in popular public repositories. To simulate realistic agricultural environments, we evaluate FecalFed under highly heterogeneous, non-IID conditions (Dirichlet α=0.5). While isolated single-farm training collapses under this data heterogeneity, yielding only 64.86% accuracy, our federated approach recovers performance without centralizing sensitive data. Specifically, utilizing server-side adaptive optimization (FedAdam) with a Swin-Small architecture achieves 90.31% accuracy, closely approaching the centralized upper bound of 95.10\%. Furthermore, we demonstrate that an edge-optimized Swin-Tiny model maintains highly competitive performance at 89.74%, establishing a highly efficient, privacy-first blueprint for on-farm avian disease monitoring.

Precise crop yield prediction is essential for improving agricultural practices and ensuring crop resilience in varying climates. Integrating weather data across the growing season, especially for different crop varieties, is crucial for understanding their adaptability in the face of climate change. In the MLCAS2021 Crop Yield Prediction Challenge, we utilized a dataset comprising 93,028 training records to forecast yields for 10,337 test records, covering 159 locations across 28 U.S. states and Canadian provinces over 13 years (2003-2015). This dataset included details on 5,838 distinct genotypes and daily weather data for a 214-day growing season, enabling comprehensive analysis. As one of the winning teams, we developed two novel convolutional neural network (CNN) architectures: the CNN-DNN model, combining CNN and fully-connected networks, and the CNN-LSTM-DNN model, with an added LSTM layer for weather variables. Leveraging the Generalized Ensemble Method (GEM), we determined optimal model weights, resulting in superior performance compared to baseline models. The GEM model achieved lower RMSE (5.55% to 39.88%), reduced MAE (5.34% to 43.76%), and higher correlation coefficients (1.1% to 10.79%) when evaluated on test data. We applied the CNN-DNN model to identify top-performing genotypes for various locations and weather conditions, aiding genotype selection based on weather variables. Our data-driven approach is valuable for scenarios with limited testing years. Additionally, a feature importance analysis using RMSE change highlighted the significance of location, MG, year, and genotype, along with the importance of weather variables MDNI and AP.

Crop detection is integral for precision agriculture applications such as automated yield estimation or fruit picking. However, crop detection, e.g., apple detection in orchard environments remains challenging due to a lack of large-scale datasets and the small relative size of the crops in the image. In this work, we address these challenges by reformulating the apple detection task in a semi-supervised manner. To this end, we provide the large, high-resolution dataset MAD comprising 105 labeled images with 14,667 annotated apple instances and 4,440 unlabeled images. Utilizing this dataset, we also propose a novel Semi-Supervised Small Apple Detection system S^3AD based on contextual attention and selective tiling to improve the challenging detection of small apples, while limiting the computational overhead. We conduct an extensive evaluation on MAD and the MSU dataset, showing that S^3AD substantially outperforms strong fully-supervised baselines, including several small object detection systems, by up to 14.9%. Additionally, we exploit the detailed annotations of our dataset w.r.t. apple properties to analyze the influence of relative size or level of occlusion on the results of various systems, quantifying current challenges.

California is a global leader in agricultural production, contributing 12.5% of the United States total output and ranking as the fifth-largest food and cotton supplier in the world. Despite the availability of extensive historical yield data from the USDA National Agricultural Statistics Service, accurate and timely crop yield forecasting remains a challenge due to the complex interplay of environmental, climatic, and soil-related factors. In this study, we introduce a comprehensive crop yield benchmark dataset covering over 70 crops across all California counties from 2008 to 2022. The benchmark integrates diverse data sources, including Landsat satellite imagery, daily climate records, monthly evapotranspiration, and high-resolution soil properties. To effectively learn from these heterogeneous inputs, we develop a multi-modal deep learning model tailored for county-level, crop-specific yield forecasting. The model employs stratified feature extraction and a timeseries encoder to capture spatial and temporal dynamics during the growing season. Static inputs such as soil characteristics and crop identity inform long-term variability. Our approach achieves an overall R2 score of 0.76 across all crops of unseen test dataset, highlighting strong predictive performance across California diverse agricultural regions. This benchmark and modeling framework offer a valuable foundation for advancing agricultural forecasting, climate adaptation, and precision farming. The full dataset and codebase are publicly available at our GitHub repository.

Meeting the increasing global demand for food security and sustainable farming requires intelligent crop recommendation systems that operate in real time. Traditional soil analysis techniques are often slow, labor-intensive, and not suitable for on-field decision-making. To address these limitations, we introduce AgroSense, a deep-learning framework that integrates soil image classification and nutrient profiling to produce accurate and contextually relevant crop recommendations. AgroSense comprises two main components: a Soil Classification Module, which leverages ResNet-18, EfficientNet-B0, and Vision Transformer architectures to categorize soil types from images; and a Crop Recommendation Module, which employs a Multi-Layer Perceptron, XGBoost, LightGBM, and TabNet to analyze structured soil data, including nutrient levels, pH, and rainfall. We curated a multimodal dataset of 10,000 paired samples drawn from publicly available Kaggle repositories, approximately 50,000 soil images across seven classes, and 25,000 nutrient profiles for experimental evaluation. The fused model achieves 98.0% accuracy, with a precision of 97.8%, a recall of 97.7%, and an F1-score of 96.75%, while RMSE and MAE drop to 0.32 and 0.27, respectively. Ablation studies underscore the critical role of multimodal coupling, and statistical validation via t-tests and ANOVA confirms the significance of our improvements. AgroSense offers a practical, scalable solution for real-time decision support in precision agriculture and paves the way for future lightweight multimodal AI systems in resource-constrained environments.

Visually cataloging and quantifying the natural world requires pushing the boundaries of both detailed visual classification and counting at scale. Despite significant progress, particularly in crowd and traffic analysis, the fine-grained, taxonomy-aware plant counting remains underexplored in vision. In contrast to crowds, plants exhibit nonrigid morphologies and physical appearance variations across growth stages and environments. To fill this gap, we present TPC-268, the first plant counting benchmark incorporating plant taxonomy. Our dataset couples instance-level point annotations with Linnaean labels (kingdom -> species) and organ categories, enabling hierarchical reasoning and species-aware evaluation. The dataset features 10,000 images with 678,050 point annotations, includes 268 countable plant categories over 242 plant species in Plantae and Fungi, and spans observation scales from canopy-level remote sensing imagery to tissue-level microscopy. We follow the problem setting of class-agnostic counting (CAC), provide taxonomy-consistent, scale-aware data splits, and benchmark state-of-the-art regression- and detection-based CAC approaches. By capturing the biodiversity, hierarchical structure, and multi-scale nature of botanical and mycological taxa, TPC-268 provides a biologically grounded testbed to advance fine-grained class-agnostic counting. Dataset and code are available at https://github.com/tiny-smart/TPC-268.

Heart disease, also known as cardiovascular disease, is a prevalent and critical medical condition characterized by the impairment of the heart and blood vessels, leading to various complications such as coronary artery disease, heart failure, and myocardial infarction. The timely and accurate detection of heart disease is of paramount importance in clinical practice. Early identification of individuals at risk enables proactive interventions, preventive measures, and personalized treatment strategies to mitigate the progression of the disease and reduce adverse outcomes. In recent years, the field of heart disease detection has witnessed notable advancements due to the integration of sophisticated technologies and computational approaches. These include machine learning algorithms, data mining techniques, and predictive modeling frameworks that leverage vast amounts of clinical and physiological data to improve diagnostic accuracy and risk stratification. In this work, we propose to detect heart disease from ECG images using cutting-edge technologies, namely vision transformer models. These models are Google-Vit, Microsoft-Beit, and Swin-Tiny. To the best of our knowledge, this is the initial endeavor concentrating on the detection of heart diseases through image-based ECG data by employing cuttingedge technologies namely, transformer models. To demonstrate the contribution of the proposed framework, the performance of vision transformer models are compared with state-of-the-art studies. Experiment results show that the proposed framework exhibits remarkable classification results.

The application of artificial intelligence (AI) in three-dimensional (3D) agricultural research, particularly for maize, has been limited by the scarcity of large-scale, diverse datasets. While 2D image datasets are abundant, they fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present AgriField3D (https://baskargroup.github.io/AgriField3D/), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset comprises over 1,000 high-quality point clouds collected using a Terrestrial Laser Scanner, complemented by procedural models that provide structured, parametric representations of maize plants. These procedural models, generated using Non-Uniform Rational B-Splines (NURBS) and optimized via a two-step process combining Particle Swarm Optimization (PSO) and differentiable programming, enable precise, scalable reconstructions of leaf surfaces and plant architectures. To enhance usability, we performed graph-based segmentation to isolate individual leaves and stalks, ensuring consistent labeling across all samples. We also conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset further includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled versions (100k, 50k, 10k points) optimized for various computational needs. By integrating point cloud data of field grown plants with high-fidelity procedural models and ensuring meticulous manual validation, AgriField3D provides a comprehensive foundation for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research.

This paper introduces a synthetic benchmark to evaluate the performance of vision language models (VLMs) in generating plant simulation configurations for digital twins. While functional-structural plant models (FSPMs) are useful tools for simulating biophysical processes in agricultural environments, their high complexity and low throughput create bottlenecks for deployment at scale. We propose a novel approach that leverages state-of-the-art open-source VLMs -- Gemma 3 and Qwen3-VL -- to directly generate simulation parameters in JSON format from drone-based remote sensing images. Using a synthetic cowpea plot dataset generated via the Helios 3D procedural plant generation library, we tested five in-context learning methods and evaluated the models across three categories: JSON integrity, geometric evaluations, and biophysical evaluations. Our results show that while VLMs can interpret structural metadata and estimate parameters like plant count and sun azimuth, they often exhibit performance degradation due to contextual bias or rely on dataset means when visual cues are insufficient. Validation on a real-world drone orthophoto dataset and an ablation study using a blind baseline further characterize the models' reasoning capabilities versus their reliance on contextual priors. To the best of our knowledge, this is the first study to utilize VLMs to generate structural JSON configurations for plant simulations, providing a scalable framework for reconstruction 3D plots for digital twin in agriculture.

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs in diagnostic tasks. Despite the increasing attention in this field, a holistic view is still lacking. Many critical aspects remain unclear, such as the diseases and clinical data to which LLMs have been applied, the LLM techniques employed, and the evaluation methods used. In this article, we perform a comprehensive review of LLM-based methods for disease diagnosis. Our review examines the existing literature across various dimensions, including disease types and associated clinical specialties, clinical data, LLM techniques, and evaluation methods. Additionally, we offer recommendations for applying and evaluating LLMs for diagnostic tasks. Furthermore, we assess the limitations of current research and discuss future directions. To our knowledge, this is the first comprehensive review for LLM-based disease diagnosis.

Agricultural pest management increasingly relies on timely and accurate access to expert knowledge, yet high quality labeled data and continuous expert support remain limited, particularly for farmers operating in rural regions with unstable/no internet connectivity. At the same time, the rapid growth of AI and LLMs has created new opportunities to deliver practical decision support tools directly to end users in agriculture through compact and deployable systems. This work addresses (i) generating a structured insect information dataset, and (ii) adapting a lightweight LLM model (leq 7B) by fine tuning it for edge device uses in agricultural pest management. The textual data collection was done by reviewing and collecting information from available pest databases and published manuscripts on nine selected pest species. These structured reports were then reviewed and validated by a domain expert. From these reports, we constructed Q/A pairs to support model training and evaluation. A LoRA-based fine-tuning approach was applied to multiple lightweight LLMs and evaluated. Initial evaluation shows that Mistral 7B achieves an 88.9\% pass rate on the domain-specific Q/A task, substantially outperforming Qwen 2.5 7B (63.9\%), and LLaMA 3.1 8B (58.7\%). Notably, Mistral demonstrates higher semantic alignment (embedding similarity: 0.865) despite lower lexical overlap (BLEU: 0.097), indicating that semantic understanding and robust reasoning are more predictive of task success than surface-level conformity in specialized domains. By combining expert organized data, well-structured Q/A pairs, semantic quality control, and efficient model adaptation, this work contributes towards providing support for farmer facing agricultural decision support tools and demonstrates the feasibility of deploying compact, high-performing language models for practical field-level pest management guidance.

Identification of tree species plays a key role in forestry related tasks like forest conservation, disease diagnosis and plant production. There had been a debate regarding the part of the tree to be used for differentiation, whether it should be leaves, fruits, flowers or bark. Studies have proven that bark is of utmost importance as it will be present despite seasonal variations and provides a characteristic identity to a tree by variations in the structure. In this paper, a deep learning based approach is presented by leveraging the method of computer vision to classify 50 tree species, on the basis of bark texture using the BarkVN-50 dataset. This is the maximum number of trees being considered for bark classification till now. A convolutional neural network(CNN), ResNet101 has been implemented using transfer-learning based technique of fine tuning to maximise the model performance. The model produced an overall accuracy of >94% during the evaluation. The performance validation has been done using K-Fold Cross Validation and by testing on unseen data collected from the Internet, this proved the model's generalization capability for real-world uses.

Dengue fever presents a substantial challenge in developing countries where sanitation infrastructure is inadequate. The absence of comprehensive healthcare systems exacerbates the severity of dengue infections, potentially leading to life-threatening circumstances. Rapid response to dengue outbreaks is also challenging due to limited information exchange and integration. While timely dengue outbreak forecasts have the potential to prevent such outbreaks, the majority of dengue prediction studies have predominantly relied on data that impose significant burdens on individual countries for collection. In this study, our aim is to improve health equity in resource-constrained countries by exploring the effectiveness of high-resolution satellite imagery as a nontraditional and readily accessible data source. By leveraging the wealth of publicly available and easily obtainable satellite imagery, we present a scalable satellite extraction framework based on Sentinel Hub, a cloud-based computing platform. Furthermore, we introduce DengueNet, an innovative architecture that combines Vision Transformer, Radiomics, and Long Short-term Memory to extract and integrate spatiotemporal features from satellite images. This enables dengue predictions on an epi-week basis. To evaluate the effectiveness of our proposed method, we conducted experiments on five municipalities in Colombia. We utilized a dataset comprising 780 high-resolution Sentinel-2 satellite images for training and evaluation. The performance of DengueNet was assessed using the mean absolute error (MAE) metric. Across the five municipalities, DengueNet achieved an average MAE of 43.92. Our findings strongly support the efficacy of satellite imagery as a valuable resource for dengue prediction, particularly in informing public health policies within countries where manually collected data is scarce and dengue virus prevalence is severe.

In recent years, Deep Learning (DL) models are becoming important due to their demonstrated success at overcoming complex learning problems. DL models have been applied effectively for different Natural Language Processing (NLP) tasks such as part-of-Speech (PoS) tagging and Machine Translation (MT). Disease Named Entity Recognition (Disease-NER) is a crucial task which aims at extracting disease Named Entities (NEs) from text. In this paper, a DL model for Disease-NER using dictionary information is proposed and evaluated on National Center for Biotechnology Information (NCBI) disease corpus and BC5CDR dataset. Word embeddings trained over general domain texts as well as biomedical texts have been used to represent input to the proposed model. This study also compares two different Segment Representation (SR) schemes, namely IOB2 and IOBES for Disease-NER. The results illustrate that using dictionary information, pre-trained word embeddings, character embeddings and CRF with global score improves the performance of Disease-NER system.

Analyzing and detecting cannabis seed variants is crucial for the agriculture industry. It enables precision breeding, allowing cultivators to selectively enhance desirable traits. Accurate identification of seed variants also ensures regulatory compliance, facilitating the cultivation of specific cannabis strains with defined characteristics, ultimately improving agricultural productivity and meeting diverse market demands. This paper presents a study on cannabis seed variant detection by employing a state-of-the-art object detection model Faster R-CNN. This study implemented the model on a locally sourced cannabis seed dataset in Thailand, comprising 17 distinct classes. We evaluate six Faster R-CNN models by comparing performance on various metrics and achieving a mAP score of 94.08\% and an F1 score of 95.66\%. This paper presents the first known application of deep neural network object detection models to the novel task of visually identifying cannabis seed types.

The success of deep learning in visual recognition tasks has driven advancements in multiple fields of research. Particularly, increasing attention has been drawn towards its application in agriculture. Nevertheless, while visual pattern recognition on farmlands carries enormous economic values, little progress has been made to merge computer vision and crop sciences due to the lack of suitable agricultural image datasets. Meanwhile, problems in agriculture also pose new challenges in computer vision. For example, semantic segmentation of aerial farmland images requires inference over extremely large-size images with extreme annotation sparsity. These challenges are not present in most of the common object datasets, and we show that they are more challenging than many other aerial image datasets. To encourage research in computer vision for agriculture, we present Agriculture-Vision: a large-scale aerial farmland image dataset for semantic segmentation of agricultural patterns. We collected 94,986 high-quality aerial images from 3,432 farmlands across the US, where each image consists of RGB and Near-infrared (NIR) channels with resolution as high as 10 cm per pixel. We annotate nine types of field anomaly patterns that are most important to farmers. As a pilot study of aerial agricultural semantic segmentation, we perform comprehensive experiments using popular semantic segmentation models; we also propose an effective model designed for aerial agricultural pattern recognition. Our experiments demonstrate several challenges Agriculture-Vision poses to both the computer vision and agriculture communities. Future versions of this dataset will include even more aerial images, anomaly patterns and image channels. More information at https://www.agriculture-vision.com.

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation. In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Traditionally, AI research in medical diagnosis has largely centered on image analysis. While this has led to notable advancements, the absence of patient-reported symptoms continues to hinder diagnostic accuracy. To address this, we propose a Pre-Consultation Dialogue Framework (PCDF) that mimics real-world diagnostic procedures, where doctors iteratively query patients before reaching a conclusion. Specifically, we simulate diagnostic dialogues between two vision-language models (VLMs): a DocVLM, which generates follow-up questions based on the image and dialogue history, and a PatientVLM, which responds using a symptom profile derived from the ground-truth diagnosis. We additionally conducted a small-scale clinical validation of the synthetic symptoms generated by our framework, with licensed clinicians confirming their clinical relevance, symptom coverage, and overall realism. These findings indicate that the resulting DocVLM-PatientVLM interactions form coherent, multi-turn consultations paired with images and diagnoses, which we then use to fine-tune the DocVLM. This dialogue-based supervision leads to substantial gains over image-only training, highlighting the value of realistic symptom elicitation for diagnosis.

WHO has declared that more than 2.2 billion people worldwide are suffering from visual disorders, such as media haze, glaucoma, and drusen. At least 1 billion of these cases could have been either prevented or successfully treated, yet they remain unaddressed due to poverty, a lack of specialists, inaccurate ocular fundus diagnoses by ophthalmologists, or the presence of a rare disease. To address this, the research has developed the Hybrid Trio-Network Model Algorithm for accurately diagnosing 12 distinct common and rare eye diseases. This algorithm utilized the RFMiD dataset of 3,200 fundus images and the Binary Relevance Method to detect diseases separately, ensuring expandability and avoiding incorrect correlations. Each detector, incorporating finely tuned hyperparameters to optimize performance, consisted of three feature components: A classical transfer learning CNN model, a two-stage CNN model, and a Siamese Network. The diagnosis was made using features extracted through this Trio-Model with Ensembled Machine Learning algorithms. The proposed model achieved an average accuracy of 97% and an AUC score of 0.96. Compared to past benchmark studies, an increase of over 10% in the F1-score was observed for most diseases. Furthermore, using the Siamese Network, the model successfully made predictions in diseases like optic disc pallor, which past studies failed to predict due to low confidence. This diagnostic tool presents a stable, adaptive, cost-effective, efficient, accessible, and fast solution for globalizing early detection of both common and rare diseases.

In this work we introduce Sen4AgriNet, a Sentinel-2 based time series multi country benchmark dataset, tailored for agricultural monitoring applications with Machine and Deep Learning. Sen4AgriNet dataset is annotated from farmer declarations collected via the Land Parcel Identification System (LPIS) for harmonizing country wide labels. These declarations have only recently been made available as open data, allowing for the first time the labeling of satellite imagery from ground truth data. We proceed to propose and standardise a new crop type taxonomy across Europe that address Common Agriculture Policy (CAP) needs, based on the Food and Agriculture Organization (FAO) Indicative Crop Classification scheme. Sen4AgriNet is the only multi-country, multi-year dataset that includes all spectral information. It is constructed to cover the period 2016-2020 for Catalonia and France, while it can be extended to include additional countries. Currently, it contains 42.5 million parcels, which makes it significantly larger than other available archives. We extract two sub-datasets to highlight its value for diverse Deep Learning applications; the Object Aggregated Dataset (OAD) and the Patches Assembled Dataset (PAD). OAD capitalizes zonal statistics of each parcel, thus creating a powerful label-to-features instance for classification algorithms. On the other hand, PAD structure generalizes the classification problem to parcel extraction and semantic segmentation and labeling. The PAD and OAD are examined under three different scenarios to showcase and model the effects of spatial and temporal variability across different years and different countries.

Pre-trained large vision-language models (VLMs) like CLIP have revolutionized visual representation learning using natural language as supervisions, and demonstrated promising generalization ability. In this work, we propose ViP, a novel visual symptom-guided prompt learning framework for medical image analysis, which facilitates general knowledge transfer from CLIP. ViP consists of two key components: a visual symptom generator (VSG) and a dual-prompt network. Specifically, VSG aims to extract explicable visual symptoms from pre-trained large language models, while the dual-prompt network utilizes these visual symptoms to guide the training on two learnable prompt modules, i.e., context prompt and merge prompt, which effectively adapts our framework to medical image analysis via large VLMs. Extensive experimental results demonstrate that ViP can outperform state-of-the-art methods on two challenging datasets.

We present WeedRepFormer, a lightweight multi-task Vision Transformer designed for simultaneous waterhemp segmentation and gender classification. Existing agricultural models often struggle to balance the fine-grained feature extraction required for biological attribute classification with the efficiency needed for real-time deployment. To address this, WeedRepFormer systematically integrates structural reparameterization across the entire architecture - comprising a Vision Transformer backbone, a Lite R-ASPP decoder, and a novel reparameterizable classification head - to decouple training-time capacity from inference-time latency. We also introduce a comprehensive waterhemp dataset containing 10,264 annotated frames from 23 plants. On this benchmark, WeedRepFormer achieves 92.18% mIoU for segmentation and 81.91% accuracy for gender classification using only 3.59M parameters and 3.80 GFLOPs. At 108.95 FPS, our model outperforms the state-of-the-art iFormer-T by 4.40% in classification accuracy while maintaining competitive segmentation performance and significantly reducing parameter count by 1.9x.

Weed control is a critical challenge in modern agriculture, as weeds compete with crops for essential nutrient resources, significantly reducing crop yield and quality. Traditional weed control methods, including chemical and mechanical approaches, have real-life limitations such as associated environmental impact and efficiency. An emerging yet effective approach is laser weeding, which uses a laser beam as the stem cutter. Although there have been studies that use deep learning in weed recognition, its application in intelligent laser weeding still requires a comprehensive understanding. Thus, this study represents the first empirical investigation of weed recognition for laser weeding. To increase the efficiency of laser beam cut and avoid damaging the crops of interest, the laser beam shall be directly aimed at the weed root. Yet, weed stem detection remains an under-explored problem. We integrate the detection of crop and weed with the localization of weed stem into one end-to-end system. To train and validate the proposed system in a real-life scenario, we curate and construct a high-quality weed stem detection dataset with human annotations. The dataset consists of 7,161 high-resolution pictures collected in the field with annotations of 11,151 instances of weed. Experimental results show that the proposed system improves weeding accuracy by 6.7% and reduces energy cost by 32.3% compared to existing weed recognition systems.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

Seed science is essential for modern agriculture, directly influencing crop yields and global food security. However, challenges such as interdisciplinary complexity and high costs with limited returns hinder progress, leading to a shortage of experts and insufficient technological support. While large language models (LLMs) have shown promise across various fields, their application in seed science remains limited due to the scarcity of digital resources, complex gene-trait relationships, and the lack of standardized benchmarks. To address this gap, we introduce SeedBench -- the first multi-task benchmark specifically designed for seed science. Developed in collaboration with domain experts, SeedBench focuses on seed breeding and simulates key aspects of modern breeding processes. We conduct a comprehensive evaluation of 26 leading LLMs, encompassing proprietary, open-source, and domain-specific fine-tuned models. Our findings not only highlight the substantial gaps between the power of LLMs and the real-world seed science problems, but also make a foundational step for research on LLMs for seed design.

At present, the identification of agricultural pests and diseases has the problem that the model is not lightweight enough and difficult to apply. Based on MobileNetV3, this paper introduces the Coordinate Attention block. The parameters of MobileNetV3-large are reduced by 22%, the model size is reduced by 19.7%, and the accuracy is improved by 0.92%. The parameters of MobileNetV3-small are reduced by 23.4%, the model size is reduced by 18.3%, and the accuracy is increased by 0.40%. In addition, the improved MobileNetV3-small was migrated to Jetson Nano for testing. The accuracy increased by 2.48% to 98.31%, and the inference speed increased by 7.5%. It provides a reference for deploying the agricultural pest identification model to embedded devices.

Parameter Efficient Fine Tuning (PEFT) techniques have recently experienced significant growth and have been extensively employed to adapt large vision and language models to various domains, enabling satisfactory model performance with minimal computational needs. Despite these advances, more research has yet to delve into potential PEFT applications in real-life scenarios, particularly in the critical domains of remote sensing and crop monitoring. The diversity of climates across different regions and the need for comprehensive large-scale datasets have posed significant obstacles to accurately identify crop types across varying geographic locations and changing growing seasons. This study seeks to bridge this gap by comprehensively exploring the feasibility of cross-area and cross-year out-of-distribution generalization using the State-of-the-Art (SOTA) wheat crop monitoring model. The aim of this work is to explore PEFT approaches for crop monitoring. Specifically, we focus on adapting the SOTA TSViT model to address winter wheat field segmentation, a critical task for crop monitoring and food security. This adaptation process involves integrating different PEFT techniques, including BigFit, LoRA, Adaptformer, and prompt tuning. Using PEFT techniques, we achieved notable results comparable to those achieved using full fine-tuning methods while training only a mere 0.7% parameters of the whole TSViT architecture. The in-house labeled data-set, referred to as the Beqaa-Lebanon dataset, comprises high-quality annotated polygons for wheat and non-wheat classes with a total surface of 170 kmsq, over five consecutive years. Using Sentinel-2 images, our model achieved a 84% F1-score. We intend to publicly release the Lebanese winter wheat data set, code repository, and model weights.

Rice is one of the most widely cultivated crops globally and has been developed into numerous varieties. The quality of rice during cultivation is primarily determined by its cultivar and characteristics. Traditionally, rice classification and quality assessment rely on manual visual inspection, a process that is both time-consuming and prone to errors. However, with advancements in machine vision technology, automating rice classification and quality evaluation based on its cultivar and characteristics has become increasingly feasible, enhancing both accuracy and efficiency. This study proposes a real-time evaluation mechanism for comprehensive rice grain assessment, integrating a one-stage object detection approach, a deep convolutional neural network, and traditional machine learning techniques. The proposed framework enables rice variety identification, grain completeness grading, and grain chalkiness evaluation. The rice grain dataset used in this study comprises approximately 20,000 images from six widely cultivated rice varieties in China. Experimental results demonstrate that the proposed mechanism achieves a mean average precision (mAP) of 99.14% in the object detection task and an accuracy of 97.89% in the classification task. Furthermore, the framework attains an average accuracy of 97.56% in grain completeness grading within the same rice variety, contributing to an effective quality evaluation system.

Users of social platforms often perceive these sites as supportive spaces to post about their mental health issues. Those conversations contain important traces about individuals' health risks. Recently, researchers have exploited this online information to construct mental health detection models, which aim to identify users at risk on platforms like Twitter, Reddit or Facebook. Most of these models are centred on achieving good classification results, ignoring the explainability and interpretability of the decisions. Recent research has pointed out the importance of using clinical markers, such as the use of symptoms, to improve trust in the computational models by health professionals. In this paper, we propose using transformer-based architectures to detect and explain the appearance of depressive symptom markers in the users' writings. We present two approaches: i) train a model to classify, and another one to explain the classifier's decision separately and ii) unify the two tasks simultaneously using a single model. Additionally, for this latter manner, we also investigated the performance of recent conversational LLMs when using in-context learning. Our natural language explanations enable clinicians to interpret the models' decisions based on validated symptoms, enhancing trust in the automated process. We evaluate our approach using recent symptom-based datasets, employing both offline and expert-in-the-loop metrics to assess the quality of the explanations generated by our models. The experimental results show that it is possible to achieve good classification results while generating interpretable symptom-based explanations.

Skin diseases affect over a third of the global population, yet their impact is often underestimated. Automating skin disease classification to assist doctors with their prognosis might be difficult. Nevertheless, due to efficient feature extraction pipelines, deep learning techniques have shown much promise for various tasks, including dermatological disease identification. This study uses a skin disease dataset with 31 classes and compares it with all versions of Vision Transformers, Swin Transformers and DivoV2. The analysis is also extended to compare with benchmark convolution-based architecture presented in the literature. Transfer learning with ImageNet1k weights on the skin disease dataset contributes to a high test accuracy of 96.48\% and an F1-Score of 0.9727 using DinoV2, which is almost a 10\% improvement over this data's current benchmark results. The performance of DinoV2 was also compared for the HAM10000 and Dermnet datasets to test the model's robustness, and the trained model overcomes the benchmark results by a slight margin in test accuracy and in F1-Score on the 23 and 7 class datasets. The results are substantiated using explainable AI frameworks like GradCAM and SHAP, which provide precise image locations to map the disease, assisting dermatologists in early detection, prompt prognosis, and treatment.

Our research is motivated by the urgent global issue of a large population affected by retinal diseases, which are evenly distributed but underserved by specialized medical expertise, particularly in non-urban areas. Our primary objective is to bridge this healthcare gap by developing a comprehensive diagnostic system capable of accurately predicting retinal diseases solely from fundus images. However, we faced significant challenges due to limited, diverse datasets and imbalanced class distributions. To overcome these issues, we have devised innovative strategies. Our research introduces novel approaches, utilizing hybrid models combining deeper Convolutional Neural Networks (CNNs), Transformer encoders, and ensemble architectures sequentially and in parallel to classify retinal fundus images into 20 disease labels. Our overarching goal is to assess these advanced models' potential in practical applications, with a strong focus on enhancing retinal disease diagnosis accuracy across a broader spectrum of conditions. Importantly, our efforts have surpassed baseline model results, with the C-Tran ensemble model emerging as the leader, achieving a remarkable model score of 0.9166, surpassing the baseline score of 0.9. Additionally, experiments with the IEViT model showcased equally promising outcomes with improved computational efficiency. We've also demonstrated the effectiveness of dynamic patch extraction and the integration of domain knowledge in computer vision tasks. In summary, our research strives to contribute significantly to retinal disease diagnosis, addressing the critical need for accessible healthcare solutions in underserved regions while aiming for comprehensive and accurate disease prediction.

Automated pollen recognition is vital to paleoclimatology, biodiversity monitoring, and public health, yet conventional methods are hampered by inefficiency and subjectivity. Existing deep learning models often struggle to achieve the requisite localization accuracy for microscopic targets like pollen, which are characterized by their minute size, indistinct edges, and complex backgrounds. To overcome this limitation, we introduce HieraEdgeNet, a multi-scale edge-enhancement framework. The framework's core innovation is the introduction of three synergistic modules: the Hierarchical Edge Module (HEM), which explicitly extracts a multi-scale pyramid of edge features that corresponds to the semantic hierarchy at early network stages; the Synergistic Edge Fusion (SEF) module, for deeply fusing these edge priors with semantic information at each respective scale; and the Cross Stage Partial Omni-Kernel Module (CSPOKM), which maximally refines the most detail-rich feature layers using an Omni-Kernel operator - comprising anisotropic large-kernel convolutions and mixed-domain attention - all within a computationally efficient Cross-Stage Partial (CSP) framework. On a large-scale dataset comprising 120 pollen classes, HieraEdgeNet achieves a mean Average Precision (mAP@.5) of 0.9501, significantly outperforming state-of-the-art baseline models such as YOLOv12n and RT-DETR. Furthermore, qualitative analysis confirms that our approach generates feature representations that are more precisely focused on object boundaries. By systematically integrating edge information, HieraEdgeNet provides a robust and powerful solution for high-precision, high-efficiency automated detection of microscopic objects.

Large language models (LLMs) offer a promising pre-screening tool, improving early disease detection and providing enhanced healthcare access for underprivileged communities. The early diagnosis of various diseases continues to be a significant challenge in healthcare, primarily due to the nonspecific nature of early symptoms, the shortage of expert medical practitioners, and the need for prolonged clinical evaluations, all of which can delay treatment and adversely affect patient outcomes. With impressive accuracy in prediction across a range of diseases, LLMs have the potential to revolutionize clinical pre-screening and decision-making for various medical conditions. In this work, we study the diagnostic capability of LLMs for Rheumatoid Arthritis (RA) with real world patients data. Patient data was collected alongside diagnoses from medical experts, and the performance of LLMs was evaluated in comparison to expert diagnoses for RA disease prediction. We notice an interesting pattern in disease diagnosis and find an unexpected misalignment between prediction and explanation. We conduct a series of multi-round analyses using different LLM agents. The best-performing model accurately predicts rheumatoid arthritis (RA) diseases approximately 95\% of the time. However, when medical experts evaluated the reasoning generated by the model, they found that nearly 68\% of the reasoning was incorrect. This study highlights a clear misalignment between LLMs high prediction accuracy and its flawed reasoning, raising important questions about relying on LLM explanations in clinical settings. LLMs provide incorrect reasoning to arrive at the correct answer for RA disease diagnosis.

Visual Language Models (VLMs) have demonstrated impressive capabilities in visual grounding tasks. However, their effectiveness in the medical domain, particularly for abnormality detection and localization within medical images, remains underexplored. A major challenge is the complex and abstract nature of medical terminology, which makes it difficult to directly associate pathological anomaly terms with their corresponding visual features. In this work, we introduce a novel approach to enhance VLM performance in medical abnormality detection and localization by leveraging decomposed medical knowledge. Instead of directly prompting models to recognize specific abnormalities, we focus on breaking down medical concepts into fundamental attributes and common visual patterns. This strategy promotes a stronger alignment between textual descriptions and visual features, improving both the recognition and localization of abnormalities in medical images.We evaluate our method on the 0.23B Florence-2 base model and demonstrate that it achieves comparable performance in abnormality grounding to significantly larger 7B LLaVA-based medical VLMs, despite being trained on only 1.5% of the data used for such models. Experimental results also demonstrate the effectiveness of our approach in both known and previously unseen abnormalities, suggesting its strong generalization capabilities.

With a rapidly increasing amount and diversity of remote sensing (RS) data sources, there is a strong need for multi-view learning modeling. This is a complex task when considering the differences in resolution, magnitude, and noise of RS data. The typical approach for merging multiple RS sources has been input-level fusion, but other - more advanced - fusion strategies may outperform this traditional approach. This work assesses different fusion strategies for crop classification in the CropHarvest dataset. The fusion methods proposed in this work outperform models based on individual views and previous fusion methods. We do not find one single fusion method that consistently outperforms all other approaches. Instead, we present a comparison of multi-view fusion methods for three different datasets and show that, depending on the test region, different methods obtain the best performance. Despite this, we suggest a preliminary criterion for the selection of fusion methods.