Automated Pollen Classification via Subinstance Recognition: A Comprehensive Comparison of Classical and Deep Learning Architectures

Pollen identification is critical for melissopalynology (honey authentication), ecological monitoring, and allergen tracking, yet manual microscopic analysis remains labor-intensive, subjective, and error-prone when multiple grains overlap in realistic samples. Existing automated approaches often fail to address multi-grain scenarios or lack systematic comparison across classical and deep learning paradigms, limiting their practical deployment. This study proposes a subinstance-based classification framework combining YOLOv12n object detection for grain isolation, independent classification via classical machine learning (ML), convolutional neural networks (CNNs), or Vision Transformers (ViTs), and majority voting aggregation. Five classical classifiers with systematic feature selection, three CNN architectures (ResNet50, EfficientNet-B0, ConvNeXt-Tiny), and three ViT variants (ViT-B/16, ViT-B/32, ViT-L/16) are evaluated on four datasets (full images vs. isolated grains; raw vs. CLAHE-preprocessed) for four berry pollen species (Ribes nigrum, Ribes uva-crispa, Lonicera caerulea, and Amelanchier alnifolia). Stratified image-level splits ensure no data leakage, and explainable AI techniques (SHAP, Grad-CAM++, and gradient saliency) validate biological interpretability across all paradigms. Results demonstrate that grain isolation substantially improves classical ML performance (F1 from 0.83 to 0.91 on full images to 0.96–0.99 on isolated grains, +8–13 percentage points), while deep learning excels on both levels (CNNs: F1 = 1.000 on full images with CLAHE; ViTs: F1 = 0.99). At the instance level, all paradigms converge to near-perfect discrimination (F1 ≥ 0.96), indicating sufficient capture of morphological information. Majority voting aggregation provides +3–5% gains for classical methods but only +0.3–4.8% for deep models already near saturation. Explainable AI analysis confirms that models rely on biologically meaningful cues: blue channel moments and texture features for classical ML (SHAP), grain boundaries and exine ornamentation for CNNs (Grad-CAM++), and distributed attention across grain structures for ViTs (gradient saliency). Qualitative validation on 211 mixed-pollen images confirms robust generalization to realistic multi-species samples. The proposed framework (YOLOv12n + SVC/ResNet50 + majority voting) is practical for deployment in honey authentication, ecological surveys, and fine-grained biological image analysis.