Dataset Information

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2.

ABSTRACT: Motion-activated wildlife cameras (or "camera traps") are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists. We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the "species model," and one that determines if an image is empty or if it contains an animal, the "empty-animal model." Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36%-91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91%-94% on out-of-sample datasets from different continents. Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (MLWIC2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths.

SUBMITTER: Tabak MA

PROVIDER: S-EPMC7548173 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2.

Tabak Michael A MA Norouzzadeh Mohammad S MS Wolfson David W DW Newton Erica J EJ Boughton Raoul K RK Ivan Jacob S JS Odell Eric A EA Newkirk Eric S ES Conrey Reesa Y RY Stenglein Jennifer J Iannarilli Fabiola F Erb John J Brook Ryan K RK Davis Amy J AJ Lewis Jesse J Walsh Daniel P DP Beasley James C JC VerCauteren Kurt C KC Clune Jeff J Miller Ryan S RS

Ecology and evolution 20200916 19

Motion-activated wildlife cameras (or "camera traps") are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as we ...[more]

PMID: 33072266

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Project description:Wild animals are essential for ecosystem structuring and stability, and thus they are important for ecological research. Since most wild animals have high athletic or concealable abilities or both, it is used to be relatively difficult to acquire evidence of animal appearances before applications of camera traps in ecological researches. However, a single camera trap may produce thousands of animal images in a short period of time and inevitably ends up with millions of images requiring classification. Although there have been many methods developed for classifying camera trap images, almost all of them follow the pattern of a very deep convolutional neural network processing all camera trap images. Consequently, the corresponding surveillance area may need to be delicately controlled to match the network capability, and it may be difficult to expand the area in the future. In this study, we consider a scenario in which camera traps are grouped into independent clusters, and images produced by a cluster are processed by an edge device installed with a customized network. Accordingly, edge devices in this scenario may be highly heterogeneous due to cluster scales. Resultantly, networks popular in the classification of camera trap images may not be deployable for edge devices without modifications requiring the expertise which may be hard to obtain. This motivates us to automatize network design via neural architecture search for edge devices. However, the search may be costly due to the evaluations of candidate networks, and its results may be infeasible without considering the resource limits of edge devices. Accordingly, we propose a search method using regression trees to evaluate candidate networks to lower search costs, and candidate networks are built based on a meta-architecture automatically adjusted regarding to the resource limits. In experiments, the search consumes 6.5 hours to find a network applicable to the edge device Jetson X2. The found network is then trained on camera trap images through a workstation and tested on Jetson X2. The network achieves competitive accuracies compared with the automatically and the manually designed networks.

Project description:Tumor markers are used to screen tens of millions of individuals worldwide at annual health check-ups, especially in East Asia. Machine learning (ML)-based algorithms that improve the diagnostic accuracy and clinical utility of these tests can have substantial impact leading to the early diagnosis of cancer. ML-based algorithms, including a cancer screening algorithm and a secondary organ of origin algorithm, were developed and validated using a large real world dataset (RWD) from asymptomatic individuals undergoing routine cancer screening at a Taiwanese medical center between May 2001 and April 2015. External validation was performed using data from the same period from a separate medical center. The data set included tumor marker values, age, and gender from 27,938 individuals, including 342 subsequently confirmed cancer cases. Separate gender-specific cancer screening algorithms were developed. For men, a logistic regression-based algorithm outperformed single-marker and other ML-based algorithms, with a mean area under the receiver operating characteristic curve (AUROC) of 0.7654 in internal and 0.8736 in external cross validation. For women, a random forest-based algorithm attained a mean AUROC of 0.6665 in internal and 0.6938 in external cross validation. The median time to cancer diagnosis (TTD) in men was 451.5, 204.5, and 28 days for the mild, moderate, and high-risk groups, respectively; for women, the median TTD was 229, 132, and 125 days for the mild, moderate, and high-risk groups. A second algorithm was developed to predict the most likely affected organ systems for at-risk individuals. The algorithm yielded 0.8120 sensitivity and 0.6490 specificity for men, and 0.8170 sensitivity and 0.6750 specificity for women. ML-derived algorithms, trained and validated by using a RWD, can significantly improve tumor marker-based screening for multiple types of early stage cancers, suggest the tissue of origin, and provide guidance for patient follow-up.

Project description:BackgroundAnemia is one of the global public health problems that affect children and pregnant women. Anemia occurs when the level of red blood cells within the body decreases or when the structure of the red blood cells is destroyed or when the Hb level in the red blood cell is below the normal threshold, which results from one or more increased red cell destructions, blood loss, defective cell production or a depleted sum of Red Blood Cells.MethodsThe method used in this study is divided into three phases: the datasets were gathered, which is the palm, pre-processed the image, which comprised; Extracted images, and augmented images, segmented the Region of Interest of the images and acquired their various components of the CIE L*a*b* colour space (also referred to as the CIELAB), and finally developed the proposed models for the detection of anemia using the various algorithms, which include CNN, k-NN, Nave Bayes, SVM, and Decision Tree. The experiment utilized 527 initial datasets, rotation, flipping and translation were utilized and augmented the dataset to 2635. We randomly divided the augmented dataset into 70%, 10%, and 20% and trained, validated and tested the models respectively.ResultsThe results of the study justify that the models performed appropriately when the palm is used to detect anemia, with the Naïve Bayes achieving a 99.96% accuracy while the SVM achieved the lowest accuracy of 96.34%, as the CNN also performed better with an accuracy of 99.92% in detecting anemia.ConclusionsThe invasive method of detecting anemia is expensive and time-consuming; however, anemia can be detected through the use of non-invasive methods such as machine learning algorithms which is efficient, cost-effective and takes less time. In this work, we compared machine learning models such as CNN, k-NN, Decision Tree, Naïve Bayes, and SVM to detect anemia using images of the palm. Finally, the study supports other similar studies on the potency of the Machine Learning Algorithm as a non-invasive method in detecting iron deficiency anemia.

Dataset Information

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2.

Publications

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2.

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