Methods
Purpose of models in biology
Dornhaus A, Smith B, Hristova K, Buckley L 2021 ‘How can we fully realize the potential of mathematical and biological models to reintegrate biology?’, Integrative and Comparative Biology: icab142 - pdf - outcome of an NSF-sponsored workshop on ‘Reintegrating Biology’; argues that many researchers (modelers and empiricists alike) would benefit from more clearly defining what the purpose of (their) models is and can be, and distinguishing between explanatory, forecast, and statistical models (which have and need different levels of detail/generality, and where in each case the word ‘predicts’ means a qualitatively different thing)
See also Masel & Dornhaus 2026 (in Education) on this topic
Network analysis
Blonder B, Wey TW, Dornhaus A, James R, Sih A 2012 ‘Temporal dynamics and network analysis’, Methods in Ecology and Evolution 3: 958-972 - pdf - review paper on the benefits of adding a time component to network analysis, and review of existing analysis tools as well as an accompanying package particularly geared towards animal social network analysis (analysis of dynamical, time-ordered interactions, such as directional information flow through a network)
Tracking objects on video
Rice L, Tate S, Farynyk D, Sun J, Chism G, Charbonneau D, Fasciano T, Dornhaus A, Shin MC 2020 ‘ABCTracker: an easy-to-use, cloud-based application for tracking multiple objects’, arXiv preprint - pdf - ABCTracker newest iteration & description
Nguyen H, Fasciano T, Charbonneau D, Dornhaus A, Shin MC 2014 ‘Data Association Based Ant Tracking with Interactive Error Correction’; WACV 2014: IEEE Winter Conference on Applications of Computer Vision (peer reviewed conference paper) - pdf - ABCTracker development - this tracker has the unique advance of allowing user corrections after tracking with an easy-to-use graphical interface, and with ML help in identifying the most crucial/uncertain places to be checked by the user first, to effectively make use of the user’s manual time investment
Rice L, Dornhaus A, Shin MC 2015 ‘Efficient Training of Multiple Ant Tracking’, WACV 2015: IEEE Winder Conference on Applications of Computer Vision (peer-reviewed conference paper) - pdf - ABCTracker advances, now particularly better tracking with much less training data
Fasciano T, Dornhaus A, Shin MC 2015 ‘Multiple Insect Tracking with Occlusion Sub-tunnels’, WACV 2015: IEEE Winder Conference on Applications of Computer Vision (peer-reviewed conference paper) - pdf -
Fasciano T, Dornhaus A, Shin MC 2014 ‘Ant Tracking with Occlusion Tunnels’; WACV 2014: IEEE Winter Conference on Applications of Computer Vision (peer reviewed conference paper) - pdf - improved tracking in ABCTracker
Fasciano T, Nguyen H, Dornhaus A, Shin MC 2013 ‘Tracking multiple ants in a colony’, Applications of Computer Vision (WACV), 2013 IEEE Workshop pp.534-540 (peer reviewed conference paper) - pdf - ABCTracker advances
Fletcher M, Dornhaus A, Shin MC 2011 ‘Multiple Ant Tracking with Global Foreground Maximization and Variable Target Proposal Distribution’, WACV '11 Proceedings of the 2011 IEEE Workshop on Applications of Computer Vision WACV p570-576 (peer reviewed conference paper) - pdf - initial ABCTracker paper focusing on the task of tracking large numbers of often-occluded and similar-looking ants