A Dataset-Centric Benchmark of Deep Learning Methods for Grape Leaf Disease Classification and Detection

Public datasets for agricultural disease detection are usually judged fit for use from reported metrics, which say nothing about whether the annotation scheme is internally consistent. On one public grape disease dataset (3288 images, 11995 boxes, 6 classes), varying model capacity, input resolution and detection paradigm yields a test-set mAP50 range comparable to seed-to-seed noise, with the bottleneck at small objects across all five architectures. The finding lies on the data side: one class is annotated at whole-leaf level (median box area 43.16% of the image) while the other five are annotated at lesion level. On 5156 cross-species images containing no grape, 65.7% of the false-positive boxes fall into that one class, an over-representation of 13.41x relative to its share of the training annotations. Counterfactual retraining establishes a causal effect of granularity on the magnitude of the shortcut: shrinking only that class's boxes cuts its cross-species false positives by 66%, and a placebo control confirms the effect is specific to the manipulated class. A manipulation in the opposite direction, with criteria registered in advance, returns a negative result: coarsening the finest class to whole-leaf level (0.57% to 40.37%), matched in box count and share of annotations and with higher in-distribution AP, still leaves its cross-species false positives at zero boxes, while the unmanipulated original class holds 50.0% of them. Annotation granularity is therefore a modulator of this shortcut, not its cause: it can amplify or attenuate a sink that already exists, but cannot create one, and what fixes the destination remains open. We also give a granularity screening statistic requiring neither images nor training, and show airborne lesion-level detection to be optically out of reach. The failure mode is invisible to in-distribution evaluation.

Deep learning models for crop leaf disease recognition routinely report near-perfect accuracy yet are typically trained and evaluated on a single dataset collected under controlled laboratory conditions, leaving their behavior under realistic cross-region domain shift poorly understood. We introduce MLD (Multi-crop Leaf Disease) dataset, a unified multi-region benchmark that combines six public crop-disease datasets from the USA, Asia, and Africa into a shared hierarchical taxonomy spanning 18 crops, 56 crop-disease classes (including one healthy class per crop) making 167,427 images. We define standardized single-source and pooled multi-source evaluation protocols that explicitly probe cross-region generalization. We also investigate whether exploiting the inherent crop-to-disease dependency via a hierarchical formulation (HiLeaD) that conditions disease prediction on the predicted crop improves recognition under cross-region shift. Under the HiLeaD, the model trained on PlantVillage achieves 99.07% in-domain disease F1 but collapses to 12.88% when tested on PlantDoc, exposing a severe cross-region domain gap. The model trained on the pooled MLD dataset partly recovers cross-region disease F1 from 12.88% to 39.64% on PlantDoc (HiLeaD), achieving a 26.76 percentage point improvement. The hierarchical formulation provides a consistent additional gain, ranging from 1.71 to 4.88 percentage points in disease F1 over the flat baseline under the MLD dataset indicating that progress in this area is currently limited more by data coverage and diversity than by model design.

Cluster closure, defined as the progressive filling of gaps between the berries in a grape bunch, is a key trait in vineyard management, impacting disease risk. However, traditional visual scoring methods are labor-intensive, subjective, and lack temporal resolution. Existing datasets rarely support fine-grained berry-level analysis, limiting the development of robust deep learning models. In this work, we present ViViD-5k, a large-scale in-field Vineyard Vision Dataset containing 5,000 images with dense annotations, including over 648,000 berry centroids and cluster segmentation masks spanning 13 grape varieties. Building on this dataset, we introduce GrapeSAM, a two-stage visual pipeline that combines point-based berry localization with prompt-based segmentation using Segment Anything, followed by transformer-based cluster segmentation. The pipeline enables automated, in-field estimation of cluster closure with minimal supervision. Quantitative results demonstrate strong segmentation and counting accuracy across diverse conditions, while visualizations confirm robustness on both in-domain and out-of-domain samples. This work provides a scalable and objective alternative to manual compactness scoring and supports high-throughput grape phenotyping with enhanced spatial detail.