Colin McCormick’s research while affiliated with Georgetown University and other places

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Publications (1)


Monarch butterflies (adult shown to right) proceed through five developmental instars as juveniles. In the field, size is a useful factor in instar-identification, combined with other morphological differences that can be easily learned. However, since photograph sources almost never have scale bars and background features that could be used for scale, such as host plant leaves, vary a great deal in size, only morphological features can be used to distinguish caterpillar stages using field photographs. Photo credit: Karen Oberhauser (printed with permission).
Monarch caterpillars progress through five developmental stages (instars), depicted in panels (a–p). These images are representative samples of 1 photos used in the test set. Our team of experts annotated each image, providing both the caterpillar’s location (bounding box) and its respective instar assignment. Photo credit: (a) 25,650,687 © Norman Murray, all rights reserved, (b) 31,420,666 © Rodrigo Solis Sosa, some rights reserved (CC-BY-NC), (c) 15,569,693 © Kim Smith, some rights reserved (CC-BY-NC-ND), (d) 31,790,764 © Emma Horrigan, all rights reserved, (e) 6,909,852 © Mark Kluge, some rights reserved (CC-BY-NC), (f) 19,541,839 © Even Dankowicz, some rights reserved (CC-BY), (g) 52,506,640 © Lyell Slade, lls, some rights reserved(CC-BY-NC), (h) 69,162,508 © Michael (Mike) Ostrowski, some rights reserved (CC-BY-SA), (i) 33,171,148 © David Weisenbeck, some rights reserved (CC-BY), (j) 78,138,914 © Ian Shelburne, all rights reserved, (k) 121,456,617 © Chris Buelow, some rights reserved (CC-BY-NC), (l) 41,213,164 © Lauren J. Simpson, some rights reserved (CC-BY-NC), (m) 38,839,028 © Meghan Pierce, some rights reserved (CC-BY-NC), (n) 18,690,481 © Royce J. Bitzer (iowabiologist), some rights reserved (CC-BY-NC). Each number corresponds to an iNaturalist observation ID, accessible via the base URL https://www.inaturalist.org/observations/followed by the respective observation number. The photos are printed with permission from the photographer.
Evolution of the box loss, object loss, class loss, mAP50, and mAP50-95 for the large model on the validation set, during the 256 epochs of training. Box loss represents the mean of IoU loss, objectness loss represents the mean of the object detection loss, and classification loss represents the mean of classification loss in the validation dataset. In all three metrics of losses, the loss curves become stable, with small fluctuations after about 200 epochs. This means, after about 200 epochs the model is fully trained, indicating that further epochs are not likely to improve performance. Based on this, we trained the model with 256 epochs.
The confusion matrix displays the classification accuracy for the fully trained large model, on (a) the validation set (left) and (b) the hold-out test set (right). The validation set comprised 383 (18%) images, while the holdout test set contained 213 (10%) images of instars from categories 1–5.Monarch caterpillars (larvae) go through five developmental stages, known as instar 1 to instar 5. The size ranges for each stage are as follows: 1st instar (2–6 mm), 2nd instar (6–9 mm), 3rd instar (10–14 mm), 4th instar (13–25 mm), and 5th instar (25–45 mm) (for details, see Supplementary A⁵¹). In instances where the predicted label matches the true label, the value along the diagonal becomes 1.
F1 score curve of a YOLOV5 large weight model. F1 score is a measure of model’s accuracy and it is the harmonic mean of precision and recall. Higher F1 score signifies superior performance, with the optimal threshold for the model prediction identified where the F1 score peaks. Notably, this YOLOv5 large model averaged for all classes achieves significantly high confidence (0.9), while concurrently optimizing the F1 (0.81) score.

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Artificial intelligence correctly classifies developmental stages of monarch caterpillars enabling better conservation through the use of community science photographs
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November 2024

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75 Reads

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1 Citation

Naresh Neupane

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Rhea Goswami

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Kyle Harrison

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Colin McCormick

Rapid technological advances and growing participation from amateur naturalists have made countless images of insects in their natural habitats available on global web portals. Despite advances in automated species identification, traits like developmental stage or health remain underexplored or manually annotated, with limited focus on automating these features. As a proof-of-concept, we developed a computer vision model utilizing the YOLOv5 algorithm to accurately detect monarch butterfly caterpillars in photographs and classify them into their five developmental stages (instars). The training data were obtained from the iNaturalist portal, and the photographs were first classified and annotated by experts to allow supervised training of models. Our best trained model demonstrates excellent performance on object detection, achieving a mean average precision score of 95% across all five instars. In terms of classification, the YOLOv5l version yielded the best performance, reaching 87% instar classification accuracy for all classes in the test set. Our approach and model show promise in developing detection and classification models for developmental stages for insects, a resource that can be used for large-scale mechanistic studies. These photos hold valuable untapped information, and we’ve released our annotated collection as an open dataset to support replication and expansion of our methods.

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Citations (1)


... Beyond species-level identification, aquatic biodiversity research requires the assessment of habitat quality, the prediction of ecological changes, and the evaluation of environmental risks. The biological research questions in this domain focus on whether machine learning can reliably model habitat suitability, forecast ecosystem changes, and assess risks posed by pollution, invasive species, and land-use alterations [56][57][58][59][60][61][62][63]. Computationally, these challenges are formalized primarily as regression and classification problems, often requiring spatial prediction and risk categorization. ...

Reference:

Artificial Intelligence in Aquatic Biodiversity Research: A PRISMA-Based Systematic Review
Artificial intelligence correctly classifies developmental stages of monarch caterpillars enabling better conservation through the use of community science photographs