Bioacoustic sensors, sometimes known as autonomous recording units (ARUs), can record sounds of wildlife over long periods of time in scalable and minimally invasive ways. Deriving per-species ...abundance estimates from these sensors requires detection, classification, and quantification of animal vocalizations as individual acoustic events. Yet, variability in ambient noise, both over time and across sensors, hinders the reliability of current automated systems for sound event detection (SED), such as convolutional neural networks (CNN) in the time-frequency domain. In this article, we develop, benchmark, and combine several machine listening techniques to improve the generalizability of SED models across heterogeneous acoustic environments. As a case study, we consider the problem of detecting avian flight calls from a ten-hour recording of nocturnal bird migration, recorded by a network of six ARUs in the presence of heterogeneous background noise. Starting from a CNN yielding state-of-the-art accuracy on this task, we introduce two noise adaptation techniques, respectively integrating short-term (60 ms) and long-term (30 min) context. First, we apply per-channel energy normalization (PCEN) in the time-frequency domain, which applies short-term automatic gain control to every subband in the mel-frequency spectrogram. Secondly, we replace the last dense layer in the network by a context-adaptive neural network (CA-NN) layer, i.e. an affine layer whose weights are dynamically adapted at prediction time by an auxiliary network taking long-term summary statistics of spectrotemporal features as input. We show that PCEN reduces temporal overfitting across dawn vs. dusk audio clips whereas context adaptation on PCEN-based summary statistics reduces spatial overfitting across sensor locations. Moreover, combining them yields state-of-the-art results that are unmatched by artificial data augmentation alone. We release a pre-trained version of our best performing system under the name of BirdVoxDetect, a ready-to-use detector of avian flight calls in field recordings.
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Aim
Ecological data collected by the general public are valuable for addressing a wide range of ecological research and conservation planning, and there has been a rapid increase in the scope and ...volume of data available. However, data from eBird or other large‐scale projects with volunteer observers typically present several challenges that can impede robust ecological inferences. These challenges include spatial bias, variation in effort and species reporting bias.
Innovation
We use the example of estimating species distributions with data from eBird, a community science or citizen science (CS) project. We estimate two widely used metrics of species distributions: encounter rate and occupancy probability. For each metric, we critically assess the impact of data processing steps that either degrade or refine the data used in the analyses. CS data density varies widely across the globe, so we also test whether differences in model performance are robust to sample size.
Main conclusions
Model performance improved when data processing and analytical methods addressed the challenges arising from CS data; however, the degree of improvement varied with species and data density. The largest gains we observed in model performance were achieved with 1) the use of complete checklists (where observers report all the species they detect and identify, allowing non‐detections to be inferred) and 2) the use of covariates describing variation in effort and detectability for each checklist. Occupancy models were more robust to a lack of complete checklists. Improvements in model performance with data refinement were more evident with larger sample sizes. In general, we found that the value of each refinement varied by situation and we encourage researchers to assess the benefits in other scenarios. These approaches will enable researchers to more effectively harness the vast ecological knowledge that exists within CS data for conservation and basic research.
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How do you successfully engage an audience in a citizen-science project? The processes developed by eBird (www.ebird.org), a fast-growing web-based tool that now gathers millions of bird observations ...per month, offers a model.
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Citizen science data are increasingly making valuable contributions to ecological studies. However, many citizen science surveys are also designed to encourage wide participation and therefore the ...participants have a range of natural history expertise, leading to variation and potentially bias in the data.
We assessed a recently proposed measure of observer expertise, calculated based on the average numbers of species recorded by observers. We investigated if this observer expertise score is associated with how often an observer reports any individual species. Species reporting rates increased monotonically with the observer's expertise score for 197 of 200 species, suggesting that this expertise score describes inter‐observer variation in the detectability of individual species.
Expertise scores were incorporated into single‐species occupancy models as a covariate, to explain inter‐observer variation in detectability. Including expertise as a detectability covariate led to improved model fit and improved predictive performance on validation data. The expertise score had a large effect on the estimated detectability, comparable in magnitude to the effect of the duration of the observation period.
Expertise scores were also included into single‐species occupancy models that estimated seasonal patterns in species occupancy and seasonal expertise effects. The addition of a seasonal effect of expertise led to improved model fit and increased predictive performance on validation data. The seasonal expertise accounted for bias that may be introduced by seasonal differences in the effect of expertise, caused by changes in the environment or species behaviour.
Measures of observer expertise included in models as a covariate can account for heterogeneity and bias introduced by variable expertise, although in this example the differences in estimated occupancy were small. This method of incorporating observer expertise can be used in any regression model of species occurrence, occupancy, abundance, or density to produce more reliable ecological inference and may be most important where citizen science schemes encourage wide participation. Overall, the results highlight the value of recording observer identity and other detectability covariates, to control for sources of bias associated with the observation process.
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Citizen science enlists the public in collecting large quantities of data across an array of habitats and locations over long spans of time. Citizen science projects have been remarkably successful ...in advancing scientific knowledge, and contributions from citizen scientists now provide a vast quantity of data about species occurrence and distribution around the world. Most citizen science projects also strive to help participants learn about the organisms they are observing and to experience the process by which scientific investigations are conducted. Developing and implementing public data-collection projects that yield both scientific and educational outcomes requires significant effort. This article describes the model for building and operating citizen science projects that has evolved at the Cornell Lab of Ornithology over the past two decades. We hope that our model will inform the fields of biodiversity monitoring, biological research, and science education while providing a window into the culture of citizen science.
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New technologies are rapidly changing the way we collect, archive, analyze, and share scientific data. For example, over the next several years it is estimated that more than one billion autonomous ...sensors will be deployed over large spatial and temporal scales, and will gather vast quantities of data. Networks of human observers play a major role in gathering scientific data, and whether in astronomy, meteorology, or observations of nature, they continue to contribute significantly. In this paper we present an innovative use of the Internet and information technologies that better enhances the opportunity for citizens to contribute their observations to science and the conservation of bird populations. eBird is building a web-enabled community of bird watchers who collect, manage, and store their observations in a globally accessible unified database. Through its development as a tool that addresses the needs of the birding community, eBird sustains and grows participation. Birders, scientists, and conservationists are using eBird data worldwide to better understand avian biological patterns and the environmental and anthropogenic factors that influence them. Developing and shaping this network over time, eBird has created a near real-time avian data resource producing millions of observations per year.
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7.
Convergence of broad-scale migration strategies in terrestrial birds La Sorte, Frank A.; Fink, Daniel; Hochachka, Wesley M. ...
Proceedings - Royal Society. Biological sciences/Proceedings - Royal Society. Biological Sciences,
01/2016, Volume:
283, Issue:
1823
Journal Article
Peer reviewed
Open access
Migration is a common strategy used by birds that breed in seasonal environments. Selection for greater migration efficiency is likely to be stronger for terrestrial species whose migration ...strategies require non-stop transoceanic crossings. If multiple species use the same transoceanic flyway, then we expect the migration strategies of these species to converge geographically towards the most optimal solution. We test this by examining population-level migration trajectories within the Western Hemisphere for 118 migratory species using occurrence information from eBird. Geographical convergence of migration strategies was evident within specific terrestrial regions where geomorphological features such as mountains or isthmuses constrained overland migration. Convergence was also evident for transoceanic migrants that crossed the Gulf of Mexico or Atlantic Ocean. Here, annual population-level movements were characterized by clockwise looped trajectories, which resulted in faster but more circuitous journeys in the spring and more direct journeys in the autumn. These findings suggest that the unique constraints and requirements associated with transoceanic migration have promoted the spatial convergence of migration strategies. The combination of seasonal atmospheric and environmental conditions that has facilitated the use of similar broad-scale migration strategies may be especially prone to disruption under climate and land-use change.
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Automatic classification of animal vocalizations has great potential to enhance the monitoring of species movements and behaviors. This is particularly true for monitoring nocturnal bird migration, ...where automated classification of migrants' flight calls could yield new biological insights and conservation applications for birds that vocalize during migration. In this paper we investigate the automatic classification of bird species from flight calls, and in particular the relationship between two different problem formulations commonly found in the literature: classifying a short clip containing one of a fixed set of known species (N-class problem) and the continuous monitoring problem, the latter of which is relevant to migration monitoring. We implemented a state-of-the-art audio classification model based on unsupervised feature learning and evaluated it on three novel datasets, one for studying the N-class problem including over 5000 flight calls from 43 different species, and two realistic datasets for studying the monitoring scenario comprising hundreds of thousands of audio clips that were compiled by means of remote acoustic sensors deployed in the field during two migration seasons. We show that the model achieves high accuracy when classifying a clip to one of N known species, even for a large number of species. In contrast, the model does not perform as well in the continuous monitoring case. Through a detailed error analysis (that included full expert review of false positives and negatives) we show the model is confounded by varying background noise conditions and previously unseen vocalizations. We also show that the model needs to be parameterized and benchmarked differently for the continuous monitoring scenario. Finally, we show that despite the reduced performance, given the right conditions the model can still characterize the migration pattern of a specific species. The paper concludes with directions for future research.
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ABSTRACT
Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential ...Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a ‘Big Data’ approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence‐only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi‐source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter‐ or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi‐source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA‐based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.
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