All thresholds barred: direct estimation of call density in bioacoustic data

Abstract

Passive acoustic monitoring (PAM) studies generate thousands of hours of audio, which may be used to monitor specific animal populations, conduct broad biodiversity surveys, detect threats such as poachers, and more. Machine learning classifiers for species identification are increasingly being used to process the vast amount of audio generated by bioacoustic surveys, expediting analysis and increasing the utility of PAM as a management tool. In common practice, a threshold is applied to classifier output scores, and scores above the threshold are aggregated into a detection count. The choice of threshold produces biased counts of vocalizations, which are subject to false positive/negative rates that may vary across subsets of the dataset. In this work, we advocate for directly estimating call density: The proportion of detection windows containing the target vocalization, regardless of classifier score. We propose a validation scheme for estimating call density in a body of data and obtain, through Bayesian reasoning, probability distributions of confidence scores for both the positive and negative classes. We use these distributions to predict site-level call densities, which may be subject to distribution shifts (when the defining characteristics of the data distribution change). These methods may be applied to the outputs of any binary detection classifier operating on fixed-size audio input windows. We test our proposed methods on a real-world study of Hawaiian birds and provide simulation results leveraging existing fully annotated datasets, demonstrating robustness to variations in call density and classifier model quality.