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  1. Arnaud E, Laporte MA, Kim S, Aubert C, Leonelli S, Miro B, et al.
    Patterns (N Y), 2020 Oct 09;1(7):100105.
    PMID: 33205138 DOI: 10.1016/j.patter.2020.100105
    Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying innovative solutions that support quality data annotation. The Ontologies CoP stimulates knowledge sharing among stakeholders, such as researchers, data managers, domain experts, experts in ontology design, and platform development teams.
  2. Rizos G, Lawson J, Mitchell S, Shah P, Wen X, Banks-Leite C, et al.
    Patterns (N Y), 2024 Mar 08;5(3):100932.
    PMID: 38487806 DOI: 10.1016/j.patter.2024.100932
    Along with propagating the input toward making a prediction, Bayesian neural networks also propagate uncertainty. This has the potential to guide the training process by rejecting predictions of low confidence, and recent variational Bayesian methods can do so without Monte Carlo sampling of weights. Here, we apply sample-free methods for wildlife call detection on recordings made via passive acoustic monitoring equipment in the animals' natural habitats. We further propose uncertainty-aware label smoothing, where the smoothing probability is dependent on sample-free predictive uncertainty, in order to downweigh data samples that should contribute less to the loss value. We introduce a bioacoustic dataset recorded in Malaysian Borneo, containing overlapping calls from 30 species. On that dataset, our proposed method achieves an absolute percentage improvement of around 1.5 points on area under the receiver operating characteristic (AU-ROC), 13 points in F1, and 19.5 points in expected calibration error (ECE) compared to the point-estimate network baseline averaged across all target classes.
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