Update README.md (#2)

- Update README.md (03264fce1fb06e8e03e95f2d80e578b2da0667d6)
- Update README.md (57e3f36085a4c38e0fc67cb4ff092483292b589f)

README.md

@@ -1,25 +1,23 @@
 ---
-license: apache-2.0
 tags:
 - computer_vision
 - pose_estimation
+- animal_pose_estimation
+- deeplabcut
 ---
 
-Copyright 2021-2023 by Mackenzie Mathis, Alexander Mathis, Shaokai Ye and contributors. All rights reserved.
+# MODEL CARD:
 
+## Model Details
 
-- Please cite **Ye et al 2023** if you use this model in your work https://arxiv.org/abs/2203.07436v1 
-- If this license is not suitable for your business or project
-please contact EPFL-TTO (https://tto.epfl.ch/) for a full commercial license.
+• SuperAnimal-Quadruped model developed by the [M.W.Mathis Lab](http://www.mackenziemathislab.org/) in 2023, trained to predict quadruped pose from images. 
+Please see [Shaokai Ye et al. 2023](https://arxiv.org/abs/2203.07436) for details.
 
-This software may not be used to harm any animal deliberately!
+• The model is an HRNet-w32 trained on our Quadruped-80K dataset.
 
-
-**MODEL CARD:**
-
-This model was trained a dataset called "Quadrupred-40K." It was trained in Tensorflow 2 within the [DeepLabCut framework](www.deeplabcut.org). 
-Full training details can be found in Ye et al. 2023, but in brief, this was trained with **DLCRNet** as introduced in [Lauer et al 2022 Nature Methods](https://www.nature.com/articles/s41592-022-01443-0).
-You can use this model simply with our light-weight loading package called [DLCLibrary](https://github.com/DeepLabCut/DLClibrary). Here is an example useage:
+• It was trained within the DeepLabCut framework. Full training details can be found in Ye et al. 2023.
+You can use this model simply with our light-weight loading package called [DLCLibrary](https://github.com/DeepLabCut/DLClibrary). 
+Here is an example useage:
 
 ```python
 from pathlib import Path
@@ -31,60 +29,128 @@ model_dir.mkdir()
 download_huggingface_model("superanimal_quadruped", model_dir)
 ```
 
-**Training Data:**
+## Intended Use
+• Intended to be used for pose estimation of quadruped images taken from side-view. The model serves a better starting
+point than ImageNet weights in downstream datasets such as AP-10K.
+
+• Intended for academic and research professionals working in fields related to animal behavior, such as neuroscience
+and ecology.
+
+• Not suitable as a zeros-shot model for applications that require high keypiont precision, but can be fine-tuned with
+minimal data to reach human-level accuracy. Also not suitable for videos that look dramatically different from those
+we show in the paper.
+
+## Factors
+
+• Based on the known robustness issues of neural networks, the relevant factors include the lighting, contrast and
+resolution of the video frames. The present of objects might also cause false detections and erroneous keypoints.
+When two or more animals are extremely close, it could cause the top-down detectors to only detect only one animal,
+if used without further fine-tuning or with a method such as BUCTD (Zhou et al. 2023 ICCV).
+
+## Metrics
+• Mean Average Precision (mAP)
+
+## Evaluation Data
+• In the paper we benchmark on AP-10K, AnimalPose, Horse-10, and iRodent using a leave-one-out strategy. Here,
+we provide the model that has been trained on all datasets (see below), therefore it should be considered “fine-tuned"
+on all animal training data listed below. This model is meant for production and evaluation in downstream scientific
+applications.
+
+## Training Data:
 
 It consists of being trained together on the following datasets:
 
-- **AwA-Pose** Quadruped dataset, see full details at (9).
-- **AnimalPose** See full details at (10).
-- **AcinoSet** See full details at (11).
-- **Horse-30** Horse-30 dataset, benchmark task is called Horse-10; See full details at (12).
-- **StanfordDogs** See full details at (13, 14).
-- **AP-10K** See full details at (15).
+- **AwA-Pose** Quadruped dataset, see full details at (1).
+- **AnimalPose** See full details at (2).
+- **AcinoSet** See full details at (3).
+- **Horse-30** Horse-30 dataset, benchmark task is called Horse-10; See full details at (4).
+- **StanfordDogs** See full details at (5, 6).
+- **AP-10K** See full details at (7).
 - **iRodent** We utilized the iNaturalist API functions for scraping observations
-with the taxon ID of Suborder Myomorpha (16). The functions allowed us to filter the large amount of observations down to the
+with the taxon ID of Suborder Myomorpha (8). The functions allowed us to filter the large amount of observations down to the
 ones with photos under the CC BY-NC creative license. The most common types of rodents from the collected observations are
 Muskrat (Ondatra zibethicus), Brown Rat (Rattus norvegicus), House Mouse (Mus musculus), Black Rat (Rattus rattus), Hispid
 Cotton Rat (Sigmodon hispidus), Meadow Vole (Microtus pennsylvanicus), Bank Vole (Clethrionomys glareolus), Deer Mouse
 (Peromyscus maniculatus), White-footed Mouse (Peromyscus leucopus), Striped Field Mouse (Apodemus agrarius). We then
 generated segmentation masks over target animals in the data by processing the media through an algorithm we designed that
-uses a Mask Region Based Convolutional Neural Networks(Mask R-CNN) (17) model with a ResNet-50-FPN backbone (18),
-pretrained on the COCO datasets (19). The processed 443 images were then manually labeled with both pose annotations and
-segmentation masks.
-
-Here is an image with the keypoint guide, the distribution of images per dataset, and examples from the datasets inferenced with a model trained with less data for benchmarking as in Ye et al 2023. 
-Thereby note that performance of this model we are releasing has comporable or higher performance. 
-
-Please note that each dataest was labeled by separate labs & seperate individuals, therefore while we map names
-to a unified pose vocabulary, there will be annotator bias in keypoint placement (See Ye et al. 2023 for our Supplementary Note on annotator bias). 
-You will also note the dataset is highly diverse across species, but collectively has more representation of domesticated animals like dogs, cats, horses, and cattle. 
-We recommend if performance is not as good as you need it to be, first try video adaptation (see Ye et al. 2023), 
-or fine-tune these weights with your own labeling. 
+uses a Mask Region Based Convolutional Neural Networks(Mask R-CNN) (8) model with a ResNet-50-FPN backbone (9),
+pretrained on the COCO datasets (10). The processed 443 images were then manually labeled with both pose annotations and
+segmentation masks. iRodent data is banked at https://zenodo.org/record/8250392.
 
+Here is an image with the keypoint guide:
 <p align="center">
 <img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1690988780004-AG00N6OU1R21MZ0AU9RE/modelcard-SAQ.png?format=1500w" width="95%">
 </p>
 
 
-9. Prianka Banik, Lin Li, and Xishuang Dong. A novel dataset for keypoint detection of quadruped animals from images. ArXiv, abs/2108.13958, 2021
-10. Jinkun Cao, Hongyang Tang, Haoshu Fang, Xiaoyong Shen, Cewu Lu, and Yu-Wing Tai. Cross-domain adaptation for animal pose estimation.
+## Ethical Considerations
+
+• No experimental data was collected for this model; all datasets used are cited.
+
+## Caveats and Recommendations
+
+• The model may have reduced accuracy in scenarios with extremely varied lighting conditions or atypical animal
+characteristics not well-represented in the training data.
+
+• Please note that each dataest was labeled by separate labs & separate individuals, therefore while we map names to a
+unified pose vocabulary, there will be annotator bias in keypoint placement (See Ye et al. 2023 for our Supplementary
+Note on annotator bias). 
+
+• Note the dataset is highly diverse across species, but collectively has more
+representation of domesticated animals like dogs, cats, horses, and cattle. 
+
+• We recommend if performance is not as
+good as you need it to be, first try video adaptation (see Ye et al. 2023), or fine-tune these weights with your own
+labeling.
+
+## License
+
+Modified MIT.
+
+Copyright 2023 by Mackenzie Mathis, Shaokai Ye, and contributors. 
+
+Permission is hereby granted to you (hereafter "LICENSEE") a fully-paid, non-exclusive,
+and non-transferable license for academic, non-commercial purposes only (hereafter “LICENSE”)
+to use the "MODEL" weights (hereafter "MODEL"), subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial
+portions of the Software:
+
+This software may not be used to harm any animal deliberately.
+
+LICENSEE acknowledges that the MODEL is a research tool. 
+THE MODEL IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING 
+BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE MODEL
+OR THE USE OR OTHER DEALINGS IN THE MODEL.
+
+If this license is not appropriate for your application, please contact Prof. Mackenzie W. Mathis 
+(mackenzie@post.harvard.edu) and/or the TTO office at EPFL (tto@epfl.ch) for a commercial use license.
+
+Please cite **Ye et al** if you use this model in your work https://arxiv.org/abs/2203.07436v2.
+
+
+## References
+
+1. Prianka Banik, Lin Li, and Xishuang Dong. A novel dataset for keypoint detection of quadruped animals from images. ArXiv, abs/2108.13958, 2021
+2. Jinkun Cao, Hongyang Tang, Haoshu Fang, Xiaoyong Shen, Cewu Lu, and Yu-Wing Tai. Cross-domain adaptation for animal pose estimation.
 2019 IEEE/CVF International Conference on Computer Vision (ICCV), pages 9497–9506, 2019.
-11. Daniel Joska, Liam Clark, Naoya Muramatsu, Ricardo Jericevich, Fred Nicolls, Alexander Mathis, Mackenzie W. Mathis, and Amir Patel. Acinoset:
+3. Daniel Joska, Liam Clark, Naoya Muramatsu, Ricardo Jericevich, Fred Nicolls, Alexander Mathis, Mackenzie W. Mathis, and Amir Patel. Acinoset:
 A 3d pose estimation dataset and baseline models for cheetahs in the wild. 2021 IEEE International Conference on Robotics and Automation
 (ICRA), pages 13901–13908, 2021.
-12. Alexander Mathis, Thomas Biasi, Steffen Schneider, Mert Yuksekgonul, Byron Rogers, Matthias Bethge, and Mackenzie W Mathis. Pretraining
+4. Alexander Mathis, Thomas Biasi, Steffen Schneider, Mert Yuksekgonul, Byron Rogers, Matthias Bethge, and Mackenzie W Mathis. Pretraining
 boosts out-of-domain robustness for pose estimation. In Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision,
 pages 1859–1868, 2021.
-13. Aditya Khosla, Nityananda Jayadevaprakash, Bangpeng Yao, and Li Fei-Fei. Novel dataset for fine-grained image categorization. In First Workshop
+5. Aditya Khosla, Nityananda Jayadevaprakash, Bangpeng Yao, and Li Fei-Fei. Novel dataset for fine-grained image categorization. In First Workshop
 on Fine-Grained Visual Categorization, IEEE Conference on Computer Vision and Pattern Recognition, Colorado Springs, CO, June 2011.
-14. Benjamin Biggs, Thomas Roddick, Andrew Fitzgibbon, and Roberto Cipolla. Creatures great and smal: Recovering the shape and motion of
+6. Benjamin Biggs, Thomas Roddick, Andrew Fitzgibbon, and Roberto Cipolla. Creatures great and smal: Recovering the shape and motion of
 animals from video. In Asian Conference on Computer Vision, pages 3–19. Springer, 2018.
-15. Hang Yu, Yufei Xu, Jing Zhang, Wei Zhao, Ziyu Guan, and Dacheng Tao. Ap-10k: A benchmark for animal pose estimation in the wild. In Thirty-fifth
+7. Hang Yu, Yufei Xu, Jing Zhang, Wei Zhao, Ziyu Guan, and Dacheng Tao. Ap-10k: A benchmark for animal pose estimation in the wild. In Thirty-fifth
 Conference on Neural Information Processing Systems Datasets and Benchmarks Track (Round 2), 2021.
-16. iNaturalist. OGBIF Occurrence Download. https://doi.org/10.15468/dl.p7nbxt. iNaturalist, July 2020
-17. Kaiming He, Georgia Gkioxari, Piotr Dollár, and Ross Girshick. Mask r-cnn. In Proceedings of the IEEE international conference on computer
+8. iNaturalist. OGBIF Occurrence Download. https://doi.org/10.15468/dl.p7nbxt. iNaturalist, July 2020
+9. Kaiming He, Georgia Gkioxari, Piotr Dollár, and Ross Girshick. Mask r-cnn. In Proceedings of the IEEE international conference on computer
 vision, pages 2961–2969, 2017.
-18. Tsung-Yi Lin, Piotr Dollár, Ross Girshick, Kaiming He, Bharath Hariharan, and Serge Belongie. Feature pyramid networks for object detection, 2016.
-19. Tsung-Yi Lin, Michael Maire, Serge J. Belongie, Lubomir D. Bourdev, Ross B. Girshick, James Hays, Pietro Perona, Deva Ramanan, Piotr Doll’ar,
-and C. Lawrence Zitnick. Microsoft COCO: common objects in context. CoRR, abs/1405.0312, 2014
-
+10. Tsung-Yi Lin, Piotr Dollár, Ross Girshick, Kaiming He, Bharath Hariharan, and Serge Belongie. Feature pyramid networks for object detection, 2016.
+11. Tsung-Yi Lin, Michael Maire, Serge J. Belongie, Lubomir D. Bourdev, Ross B. Girshick, James Hays, Pietro Perona, Deva Ramanan, Piotr Doll’ar,
+and C. Lawrence Zitnick. Microsoft COCO: common objects in context. CoRR, abs/1405.0312, 2014