PhenoNEST: A Neuro-Symbolic Framework for Ontology-Aware Multimodal Plant Phenotyping and Trait Discovery

High-throughput plant phenotyping, the quantitative measurement of observable plant traits, is critical for modern breeding but remains constrained by a "phenotyping bottleneck," where manual data collection is labor-intensive and prone to observer bias. Conventional closed-set computer vision systems fail to address this challenge, as they require extensive species-specific annotation and lack the flexibility to handle diverse breeding populations. To bridge this gap, we present CropVLM, a Vision-Language Model (VLM) adapted for the agricultural domain via Domain-Specific Semantic Alignment (DSSA). Trained on 52,987 manually selected image-caption pairs covering 37 species in natural field conditions, CropVLM effectively maps agronomic terminology to fine-grained visual features. We further introduce the Hybrid Open-Set Localization Network (HOS-Net), an architecture that integrates CropVLM to enable the detection of novel crops solely from natural language descriptions without retraining. By eliminating the reliance on species-specific training data, CropVLM provides a scalable solution for high-throughput phenotyping, accelerating genetic gain and facilitating large-scale biodiversity research essential for sustainable agriculture. The trained model weights and complete pipeline implementation are publicly available at: https://github.com/boudiafA/CropVLM. In comprehensive evaluations, CropVLM achieves 72.51% zero-shot classification accuracy, outperforming seven CLIP-style baselines. Our detection pipeline demonstrates superior zero-shot generalization to novel species, achieving 49.17 AP50 on our CVTCropDet benchmark and 50.73 AP50 on tropical fruit species, compared to 34.89 and 48.58 for the next-best method, respectively.

High-throughput plant phenotyping now generates image derived datasets far faster than scientists can analyze them. At Oak Ridge National Laboratory's Advanced Plant Phenotyping Laboratory (APPL), automated stations image hundreds of plants daily across multiple remote sensing modalities; yet, trait extraction and interpretation remain manual, expert-bound, and strictly post-hoc, making analysis, not acquisition, the binding constraint on discovery. We present an end-to-end agentic AI framework that turns the facility from a data factory into an interactive autonomous, discovery platform, where scientists partner with AI agents to accelerate time to insight. A conversational Co-Scientist Agent translates a scientist's natural-language question into a structured analysis plan, and a headless Compute Agent dispatches Vision Transformer segmentation and trait extraction on the Frontier exascale supercomputer. The two agents run in separate security and resource domains and communicate over a secure, token-authenticated streaming channel, a design that accounts for the federation, data-movement, and provenance realities cloud-native agentic frameworks ignore, ensuring end-to-end provenance is captured for every interaction. The framework turns a days- to weeks-long analysis process into an interactive loop where agents reason over results, recommend next analyses, and respond to follow-up questions in seconds.

Agricultural image understanding requires fine-grained recognition of plant diseases, pests, crop structures, and botanical species under complex real-world conditions. Despite recent advances in Multimodal Large Language Models (MLLMs), existing models remain limited to text-only outputs and lack pixel-level visual grounding capabilities. In this work, we introduce AgriScope, a unified pixel-grounded multimodal framework for agricultural image understanding. AgriScope jointly supports image-level, region-level, and pixel-level understanding within a unified framework, enabling tasks such as grounded caption generation, referring expression segmentation, and multi-turn multimodal interaction for agricultural imagery. AgriScope integrates biologically specialized semantic representations with dense spatial grounding through biological-semantic encoding, dense spatial representations, and pixel decoding. To support large-scale grounded learning, we introduce AgriGround, a large-scale pixel-grounded agricultural multimodal instruction-tuning dataset containing over 500K images and 11M instruction-following samples spanning plant disease analysis, crop and weed identification, insect pest recognition, and fine-grained botanical understanding. AgriGround is constructed through a multi-stage automatic annotation pipeline that integrates multimodal caption generation, phrase-level grounding, segmentation mask generation, and task-oriented instruction synthesis to produce densely grounded supervision. Extensive experiments across multiple agricultural vision-language tasks demonstrate the effectiveness of AgriScope in pixel-grounded multimodal understanding, establishing a strong benchmark for agricultural vision-language learning and visual grounding. The dataset and code will be made publicly available at (https://github.com/boudiafA/AgriScope)