skip to main content


Title: Tracking changes in behavioural dynamics using prediction error
Automated analysis of video can now generate extensive time series of pose and motion in freely-moving organisms. This requires new quantitative tools to characterise behavioural dynamics. For the model roundworm Caenorhabditis elegans , body pose can be accurately quantified from video as coordinates in a single low-dimensional space. We focus on this well-established case as an illustrative example and propose a method to reveal subtle variations in behaviour at high time resolution. Our data-driven method, based on empirical dynamic modeling, quantifies behavioural change as prediction error with respect to a time-delay-embedded ‘attractor’ of behavioural dynamics. Because this attractor is constructed from a user-specified reference data set, the approach can be tailored to specific behaviours of interest at the individual or group level. We validate the approach by detecting small changes in the movement dynamics of C. elegans at the initiation and completion of delta turns. We then examine an escape response initiated by an aversive stimulus and find that the method can track return to baseline behaviour in individual worms and reveal variations in the escape response between worms. We suggest that this general approach—defining dynamic behaviours using reference attractors and quantifying dynamic changes using prediction error—may be of broad interest and relevance to behavioural researchers working with video-derived time series.  more » « less
Award ID(s):
1655203 1660584
NSF-PAR ID:
10298679
Author(s) / Creator(s):
; ; ; ; ; ;
Editor(s):
Gilestro, Giorgio F
Date Published:
Journal Name:
PLOS ONE
Volume:
16
Issue:
5
ISSN:
1932-6203
Page Range / eLocation ID:
e0251053
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Significant advances in computational ethology have allowed the quantification of behaviour in unprecedented detail. Tracking animals in social groups, however, remains challenging as most existing methods can either capture pose or robustly retain individual identity over time but not both.

    To capture finely resolved behaviours while maintaining individual identity, we built NAPS (NAPS is ArUco Plus SLEAP), a hybrid tracking framework that combines state‐of‐the‐art, deep learning‐based methods for pose estimation (SLEAP) with unique markers for identity persistence (ArUco). We show that this framework allows the exploration of the social dynamics of the common eastern bumblebee (Bombus impatiens).

    We provide a stand‐alone Python package for implementing this framework along with detailed documentation to allow for easy utilization and expansion. We show that NAPS can scale to long timescale experiments at a high frame rate and that it enables the investigation of detailed behavioural variation within individuals in a group.

    Expanding the toolkit for capturing the constituent behaviours of social groups is essential for understanding the structure and dynamics of social networks. NAPS provides a key tool for capturing these behaviours and can provide critical data for understanding how individual variation influences collective dynamics.

     
    more » « less
  2. Abstract

    Host behaviour is known to influence disease dynamics. Additionally, hosts often change their behaviours in response to pathogen detection to resist and avoid disease. The capacity of wildlife populations to respond to pathogens using behavioural plasticity is critical for reducing the impacts of disease outbreaks. However, there is limited information regarding the ability of ectothermic vertebrates to resist diseases via behavioural plasticity.

    Here, we experimentally examine the effect of host behaviour on ranaviral infections, which affect at least 175 species of ectothermic vertebrates. We placed metamorphic (temporal block 1) or adult (block 2) southern toads (Anaxyrus terrestris) in thermal gradients, tested their temperature preferences before and after oral inoculation by measuring individual‐level body temperature over time, and measured ranaviral loads of viral‐exposed individuals.

    We found significant individual‐level variation in temperature preference and evidence for behavioural fever in both metamorphic and adultA. terrestrisduring the first 2 days after exposure. Additionally, we found that individual‐level change in temperature preference was negatively correlated with ranaviral load and a better predictor of load than average temperature preference or maximum temperature reached by an individual. In other words, an increase in baseline temperature preference was more important than simply reaching an absolute temperature.

    These results suggest that behavioural fever is an effective mechanism for resisting ranaviral infections.

    A freePlain Language Summarycan be found within the Supporting Information of this article.

     
    more » « less
  3. SUMMARY Mantle convection and long-term lithosphere dynamics in the Earth and other planets can be treated as the slow deformation of a highly viscous fluid, and as such can be described using the compressible Navier–Stokes equations. Since on Earth-sized planets the influence of compressibility is not a dominant effect, density deviations from a reference profile are at most on the order of a few percent and using the full governing equations poses numerical challenges, most modelling studies have simplified the governing equations. Common approximations assume a temporally constant, but depth-dependent reference profile for the density (the anelastic liquid approximation), or drop compressibility altogether and use a constant reference density (the Boussinesq approximation). In most previous studies of mantle convection and crustal dynamics, one can assume that the error introduced by these approximations was small compared to the errors that resulted from poorly constrained material behaviour and limited numerical accuracy. However, as model parametrizations have become more realistic, and model resolution has improved, this may no longer be the case and the error due to using simplified conservation equations might no longer be negligible: while such approximations may be reasonable for models of mantle plumes or slabs traversing the whole mantle, they may be unsatisfactory for layered materials experiencing phase transitions or materials undergoing significant heating or cooling. For example, at boundary layers or close to dynamically changing density gradients, the error arising from the use of the aforementioned compressibility approximations can be the dominant error source, and common approximations may fail to capture the physical behaviour of interest. In this paper, we discuss new formulations of the continuity equation that include dynamic density variations due to temperature, pressure and composition without using a reference profile for the density. We quantify the improvement in accuracy relative to existing formulations in a number of benchmark models and evaluate for which practical applications these effects are important. Finally, we consider numerical aspects of the new formulations. We implement and test these formulations in the freely available community software aspect, and use this code for our numerical experiments. 
    more » « less
  4. Abstract

    Habitat conversion to farmland has increased human‐wildlife interactions, which often lead to conflict, injury or death for people and animals. Understanding the behavioural and landscape drivers of human‐wildlife conflict is critical for managing wildlife populations. Staging behaviour prior to crop incursions has been described across multiple taxa and offers potential utility in managing conflict, but few quantitative assessments of staging have been undertaken. Animal movement data can provide valuable, fine‐scale information on such behaviour with opportunities for application to real‐time management for conflict prediction.

    We developed an approach to assess the efficacy of six widely used metrics of animal movement to identify staging behaviour prior to agricultural incursions. We applied this approach to GPS data from 55 African elephants in the Serengeti‐Mara ecosystem and found tortuosity and HMM‐derived behavioural states to be the most effective for identifying staging events. We then assessed temporal patterns of defined staging at daily and seasonal scales and explored environmental and anthropogenic drivers of staging from spatial generalized logistic mixed models. Finally, we tested the viability of combining movement and simple spatial metrics to predict crop incursions based on GPS data.

    Our approach identified staging behaviour that appeared to be driven largely by human activity and diurnal availability of protective cover from forest, riverine vegetation, and topography. Staging also varied substantially by season. Tortuosity and behavioural state metrics identified different staging strategies with distinct spatial distributions and anthropogenic drivers, and appeared to be linked to the juxtaposition between protected and cultivated lands. Tortuosity‐based staging combined with distance‐to‐agriculture produced promising results for pre‐event prediction of crop incursion.

    Synthesis and applications. Our study found staging by elephants prior to crop use could be identified from GPS tracking data, indicating that a better understanding of movement behaviour can inform targeted and proactive human‐wildlife conflict management and inform spatial planning efforts. Our approach is extendable to other conflict‐prone species to assess pre‐conflict behaviours and space use and demonstrates some of the challenges and advantages of using animal behaviour to assess temporal and spatial heterogeneity in human‐wildlife conflict.

     
    more » « less
  5. Recovering 3D phase features of complex biological samples traditionally sacrifices computational efficiency and processing time for physical model accuracy and reconstruction quality. Here, we overcome this challenge using an approximant-guided deep learning framework in a high-speed intensity diffraction tomography system. Applying a physics model simulator-based learning strategy trained entirely on natural image datasets, we show our network can robustly reconstruct complex 3D biological samples. To achieve highly efficient training and prediction, we implement a lightweight 2D network structure that utilizes a multi-channel input for encoding the axial information. We demonstrate this framework on experimental measurements of weakly scattering epithelial buccal cells and strongly scatteringC. elegansworms. We benchmark the network’s performance against a state-of-the-art multiple-scattering model-based iterative reconstruction algorithm. We highlight the network’s robustness by reconstructing dynamic samples from a living worm video. We further emphasize the network’s generalization capabilities by recovering algae samples imaged from different experimental setups. To assess the prediction quality, we develop a quantitative evaluation metric to show that our predictions are consistent with both multiple-scattering physics and experimental measurements.

     
    more » « less