Decision letter for "Sashimi : A toolkit for facilitating high‐throughput organismal image segmentation using deep learning"
Bibliographic record
Abstract
Deep learning methods for computer vision tasks show promise for automating the data analysis of camera trap images.Ecological camera traps are a common approach for monitoring an ecosystem's animal population, as they provide continual insight into an environment without being intrusive.However, the analysis of camera trap images is expensive, labour intensive, and time consuming.Recent advances in the field of deep learning for object detection show promise towards automating the analysis of camera trap images.Here, we demonstrate their capabilities by training and comparing two deep learning object detection classifiers, Faster R-CNN and YOLO v2.0, to identify, quantify, and localize animal species within camera trap images using the Reconyx Camera Trap and the self-labeled Gold Standard Snapshot Serengeti data sets.When trained on large labeled datasets, object recognition methods have shown success.We demonstrate their use, in the context of realistically sized ecological data sets, by testing if object detection methods are applicable for ecological research scenarios when utilizing transfer learning.Faster R-CNN outperformed YOLO v2.0 with average accuracies of 93.0% and 76.7% on the two data sets, respectively.Our findings show promising steps towards the automation of the labourious task of labeling camera trap images, which can be used to improve our understanding of the population dynamics of ecosystems across the planet.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.006 | 0.057 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.004 | 0.003 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.008 | 0.005 |
| Insufficient payload (model declined to judge) | 0.393 | 0.248 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".