Huyt/arabica-coffee-leaf-disease-efficientnet-b0

Arabica Coffee Leaf Disease Classification — efficientnet_b0

A efficientnet_b0 (4.0M params) fine-tuned to classify 5 arabica coffee leaf conditions from close-up RGB crops.

⚠️ Read this before comparing to published numbers

The source dataset lists 58,549 images. It contains 3,756 unique images — 93.6% of the rows are exact byte-for-byte duplicates. One Healthy image appears 520 times. After also grouping near-duplicate crops of the same leaf (perceptual hash, hamming <= 5), only 2,891 independent images remain.

Class counts collapse dramatically, and the balance inverts — Healthy is the largest class as listed and the smallest in reality:

Class	Listed rows	Byte-unique	Independent groups
Cerscospora	7,681	322	317
Healthy	18,983	62	48
Leaf_rust	8,336	1,042	918
Miner	16,978	1,639	923
Phoma	6,571	691	685
TOTAL	58,549	3,756	2,891

This model is trained and evaluated on the deduplicated, group-disjoint data, so no near-duplicate crop appears in more than one split.

The obvious expectation is that removing this much duplication should crater the score. It does not — and reporting that honestly matters more than a tidy story:

Split protocol	n train	Test accuracy	Test macro-F1
Naive random split over all 58,549 rows (leaky)	40,981	1.0000	1.0000
Group-aware split over 2,891 independent images (honest)	2,628	0.9911	0.9941

The leaky protocol buys only +0.0089 accuracy / +0.0059 macro-F1. So on this dataset the duplication inflates the apparent size (58,549 vs ~2,891 real images) far more than it inflates the score. These five classes are simply easy to separate: a model trained on 2,628 images with no duplicate leakage still reaches 99.11%.

Do not read this as "leakage is harmless" in general — it is a property of this dataset's easy class boundaries. Read it as: this dataset is ~20x smaller than its row count suggests, and its headline accuracies are not evidence of much.

Results (honest split, test n=564)

Metric	Score
Accuracy	0.9911
Macro-F1	0.9941

Measured with timm's canonical inference transform (224px, crop_pct=0.875, bicubic), i.e. exactly the preprocessing the Usage snippet produces.

Per-class

Class	Precision	Recall	F1	Test support	Train images
Cerscospora	1.000	1.000	1.000	48	226
Healthy	1.000	1.000	1.000	9	43
Leaf_rust	1.000	0.981	0.990	156	729
Miner	0.980	1.000	0.990	246	1147
Phoma	1.000	0.981	0.990	105	483

Intended use

Research and educational use only. Not a substitute for agronomist diagnosis. The Healthy class is supported by only 43 training images from 48 independent sources — treat its predictions with particular suspicion.

Training

• Backbone: efficientnet_b0 (ImageNet-pretrained, via timm)
• Data: 2628 train / 564 val / 564 test, split by near-duplicate group (70/15/15), verified zero group overlap
• Resolution: 224x224 (source crops are mostly 128x128, so they are upscaled)
• Optimiser: AdamW, OneCycle LR (max 3e-4), weight decay 0.05, 20 epochs, batch 64
• Loss: cross-entropy, label smoothing 0.1, no class weighting (uniform)
• Augmentation: random resized crop (0.6-1.0), h/v flip, colour jitter, random erasing
• Precision: bf16 autocast. Selection: best val macro-F1.

Usage

import timm, torch
from PIL import Image

model = timm.create_model("hf-hub:Huyt/arabica-coffee-leaf-disease-efficientnet-b0", pretrained=True).eval()
cfg = timm.data.resolve_data_config({}, model=model)
tf = timm.data.create_transform(**cfg)

img = Image.open("leaf.jpg").convert("RGB")
with torch.no_grad():
    probs = model(tf(img).unsqueeze(0)).softmax(-1)[0]

idx = int(probs.argmax())
print(model.pretrained_cfg["label_names"][idx], float(probs[idx]))

Class order (index -> label):

['Cerscospora', 'Healthy', 'Leaf_rust', 'Miner', 'Phoma']

Limitations

• The dataset is ~20x smaller than advertised. 2,891 independent images, not 58,549. Everything below follows from that.
• Healthy is critically under-supported: 48 independent images total. Its metrics rest on 9 test images and are not trustworthy.
• Crops, not leaves. Inputs are close-up patches (mostly 128x128), not whole leaves. The model expects similar close-ups; it is not a whole-plant or field classifier.
• Near-duplicate grouping is a lower bound. Perceptual hashing at hamming <= 5 catches tight crops of the same lesion. Wider crops of the same leaf may survive as separate groups, so residual same-source optimism may remain even in the honest number. A nearest-neighbour probe (ImageNet embeddings, test vs train) found the honest split's residual-similarity signal to be no worse than a comparably-built rice split (+0.42 vs +0.52 excess over the same-class baseline), but that probe cannot cleanly separate leakage from a genuinely low-diversity dataset. Treat 99.11% as an upper bound on real-world performance.
• The test set is small. 564 images; at 99.11% accuracy that is ~5 errors total. Per-class figures rest on tens of images and carry wide error bars.
• Single-source dataset (JMuBEN / JMuBEN2, Kenya). No external validation; the lab->field gap is unmeasured.

Reproduction

coffee_dedup.py (hashing + grouping), coffee_split.py (both splits), coffee_train.py (training), coffee_eval_final.py (canonical-transform eval) are included in this repo.

Dataset citation

@article{jepkoech2021arabica,
  title={Arabica coffee leaf images dataset for coffee leaf disease detection and classification},
  author={Jepkoech, Jennifer and Mugo, David Muchangi and Kenduiywo, Benson K and Too, Edna Chebet},
  journal={Data in brief}, volume={36}, pages={107142}, year={2021}, publisher={Elsevier}
}