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Andersen PH, Broomé S, Rashid M, Lundblad J, Ask K, Li Z, Hernlund E, Rhodin M, Kjellström H. Towards Machine Recognition of Facial Expressions of Pain in Horses. Animals (Basel) 2021; 11:1643. [PMID: 34206077 PMCID: PMC8229776 DOI: 10.3390/ani11061643] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/30/2023] Open
Abstract
Automated recognition of human facial expressions of pain and emotions is to a certain degree a solved problem, using approaches based on computer vision and machine learning. However, the application of such methods to horses has proven difficult. Major barriers are the lack of sufficiently large, annotated databases for horses and difficulties in obtaining correct classifications of pain because horses are non-verbal. This review describes our work to overcome these barriers, using two different approaches. One involves the use of a manual, but relatively objective, classification system for facial activity (Facial Action Coding System), where data are analyzed for pain expressions after coding using machine learning principles. We have devised tools that can aid manual labeling by identifying the faces and facial keypoints of horses. This approach provides promising results in the automated recognition of facial action units from images. The second approach, recurrent neural network end-to-end learning, requires less extraction of features and representations from the video but instead depends on large volumes of video data with ground truth. Our preliminary results suggest clearly that dynamics are important for pain recognition and show that combinations of recurrent neural networks can classify experimental pain in a small number of horses better than human raters.
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Affiliation(s)
- Pia Haubro Andersen
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE 75007 Uppsala, Sweden; (J.L.); (K.A.); (E.H.); (M.R.)
| | - Sofia Broomé
- Division of Robotics, Perception and Learning, KTH Royal Institute of Technology, SE 100044 Stockholm, Sweden; (S.B.); (Z.L.)
| | - Maheen Rashid
- Department of Computer Science, University of California at Davis, California, CA 95616, USA;
| | - Johan Lundblad
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE 75007 Uppsala, Sweden; (J.L.); (K.A.); (E.H.); (M.R.)
| | - Katrina Ask
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE 75007 Uppsala, Sweden; (J.L.); (K.A.); (E.H.); (M.R.)
| | - Zhenghong Li
- Division of Robotics, Perception and Learning, KTH Royal Institute of Technology, SE 100044 Stockholm, Sweden; (S.B.); (Z.L.)
- Department of Computer Science, Stony Brook University, New York, NY 11794, USA
| | - Elin Hernlund
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE 75007 Uppsala, Sweden; (J.L.); (K.A.); (E.H.); (M.R.)
| | - Marie Rhodin
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE 75007 Uppsala, Sweden; (J.L.); (K.A.); (E.H.); (M.R.)
| | - Hedvig Kjellström
- Division of Robotics, Perception and Learning, KTH Royal Institute of Technology, SE 100044 Stockholm, Sweden; (S.B.); (Z.L.)
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Gaps in Live Inter-Observer Reliability Testing of Animal Behavior: A Retrospective Analysis and Path Forward. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2021. [DOI: 10.3390/jzbg2020014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Observational behavior research is an important activity for zoos and aquariums, often being conducted to provide insights into welfare and guide management decisions. This research relies on standardized protocols to ensure consistent data collection. Inter-observer reliability, where untrained observers are tested against the behavior identifications of an expert observer, represent a critical internal validation process. Recent software advances have made reliability testing easier and more accessible, but there is limited guidance on what constitutes a strong reliability test. In this study, we reviewed historic reliability test data from Lincoln Park Zoo’s on-going behavior monitoring program. Six representative species were chosen that included 645 live pairwise reliability tests conducted across 163 total project observers. We identified that observers were being tested on only approximately 25% of the behaviors listed and defined in the species ethograms. Observers did encounter a greater percent of the ethogram with successive reliability tests, but this gap remained large. While inactive behaviors were well-represented during reliability tests, social and other non-maintenance solitary behaviors (e.g., exploratory, scent marking, play, etc.) did not frequently occur during tests. While the ultimate implications of these gaps in testing are unclear, these results highlight the risks of live reliability testing as an inherently non-standardized process. We suggest several approaches to help address these limitations, including refining ethograms, reconsidering criteria, and supplementing live training with video. We hope this self-critique encourages others to critically examine their methods, enhance the quality of their behavioral data, and ultimately, strengthen conclusions drawn about animal behavior and welfare.
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Uhlmann SS, Yochum N, Ampe B. Repeatability of flatfish reflex impairment assessments based on video recordings. PLoS One 2020; 15:e0229456. [PMID: 32101577 PMCID: PMC7043772 DOI: 10.1371/journal.pone.0229456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/06/2020] [Indexed: 12/04/2022] Open
Abstract
Using measures of reflex impairment and injury to quantify an aquatic organism’s vitality have gained popularity as survival predictors of discarded non-target fisheries catch. To evaluate the robustness of this method with respect to ‘rater’ subjectivity, we tested inter- and intra-rater repeatability and the role of ‘expectation bias’. From video clips, multiple raters determined impairment levels of four reflexes of beam-trawled common sole (Solea solea) intended for discard. Raters had a range of technical experience, including veterinary students, practicing veterinarians, and fisheries scientists. Expectation bias was evaluated by first assessing a rater’s assumption about the effect of air exposure on vitality, then comparing their reflex ratings of the same fish, once when the true air exposure duration was indicated and once when the time was exaggerated (by either 15 or 30 min). Inter-rater repeatability was assessed by having multiple raters evaluate those clips with true air exposure information; and intra- and inter-rater repeatability was determined by having individual raters evaluate a series of duplicated clips, all with true air exposure. Results indicate that inter- and intra-rater repeatability were high (intra-class correlation coefficients of 74% for both), and were not significantly affected by background type nor expectation bias related to assumed impact from prolonged air exposure. This suggests that reflex impairment as a metric for predicting fish survival is robust to involving multiple raters with diverse backgrounds. Bias is potentially more likely to be introduced through subjective reflexes than raters, given that consistency in scoring differed for some reflexes based on rater experience type. This study highlights the need to provide ample training for raters, and that no prior experience is needed to become a reliable rater. Moreover, before implementing reflexes in a vitality study, it is important to evaluate whether the determination of presence/absence is subjective.
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Affiliation(s)
- Sven Sebastian Uhlmann
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, Ostend, Belgium
- * E-mail:
| | - Noëlle Yochum
- NOAA, Alaska Fisheries Science Center, Seattle, United States of America
| | - Bart Ampe
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, Ostend, Belgium
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Cox TE, Ramsey DSL, Sawyers E, Campbell S, Matthews J, Elsworth P. The impact of RHDV-K5 on rabbit populations in Australia: an evaluation of citizen science surveys to monitor rabbit abundance. Sci Rep 2019; 9:15229. [PMID: 31645713 PMCID: PMC6811621 DOI: 10.1038/s41598-019-51847-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/30/2019] [Indexed: 11/08/2022] Open
Abstract
The increasing popularity of citizen science in ecological research has created opportunities for data collection from large teams of observers that are widely dispersed. We established a citizen science program to complement the release of a new variant of the rabbit biological control agent, rabbit haemorrhagic disease virus (RHDV), known colloquially as K5, across Australia. We evaluated the impact of K5 on the national rabbit population and compared citizen science and professionally-collected spotlight count data. Of the citizen science sites (n = 219), 93% indicated a decrease in rabbit abundance following the release of K5. The overall finite monthly growth rate in rabbit abundance was estimated as 0.66 (95%CI, 0.26, 1.03), averaging a monthly reduction of 34% at the citizen science sites one month after the release. No such declines were observed at the professionally monitored sites (n = 22). The citizen science data submissions may have been unconsciously biased or the number of professional sites may have been insufficient to detect a change. Citizen science participation also declined by 56% over the post-release period. Future programs should ensure the use of blinded trials to check for unconscious bias and consider how incentives and/or the good will of the participants can be maintained throughout the program.
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Affiliation(s)
- Tarnya E Cox
- Vertebrate Pest Research Unit, New South Wales Department of Primary Industries, 1447 Forest Road Orange, New South Wales, 2800, Australia.
- Centre for Invasive Species Solutions, Building 22, University of Canberra, University Drive South, Bruce, Australian Capital Territory, 2617, Australia.
| | - David S L Ramsey
- Arthur Rylah Institute for Environmental Research, Department of Environment, Land, Water and Planning, PO Box 137, Heidelberg, Victoria, 3084, Australia
- Centre for Invasive Species Solutions, Building 22, University of Canberra, University Drive South, Bruce, Australian Capital Territory, 2617, Australia
- School of Biological Sciences, Molecular Life Sciences Building, University of Adelaide, North Terrace, Adelaide, 5005, Australia
| | - Emma Sawyers
- Vertebrate Pest Research Unit, New South Wales Department of Primary Industries, 1447 Forest Road Orange, New South Wales, 2800, Australia
- Centre for Invasive Species Solutions, Building 22, University of Canberra, University Drive South, Bruce, Australian Capital Territory, 2617, Australia
| | - Susan Campbell
- Biosecurity and Sustainability, Department of Primary Industries and Regional Development, 444 Albany Hwy, Albany, Western Australia, 6330, Australia
| | - John Matthews
- Department of Economic Development, Jobs, Transport and Resources, 147 Bahgallah Road, Casterton, Victoria, 3311, Australia
| | - Peter Elsworth
- Pest Animal Research Centre, Department of Agriculture and Fisheries, PO Box 102, Toowoomba, Queensland, 4350, Australia
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McLennan KM, Miller AL, Dalla Costa E, Stucke D, Corke MJ, Broom DM, Leach MC. Conceptual and methodological issues relating to pain assessment in mammals: The development and utilisation of pain facial expression scales. Appl Anim Behav Sci 2019. [DOI: 10.1016/j.applanim.2019.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Pierard M, McGreevy P, Geers R. Reliability of a descriptive reference ethogram for equitation science. J Vet Behav 2019. [DOI: 10.1016/j.jveb.2018.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dyson S, Van Dijk J. Application of a ridden horse ethogram to video recordings of 21 horses before and after diagnostic analgesia: Reduction in behaviour scores. EQUINE VET EDUC 2018. [DOI: 10.1111/eve.13029] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- S. Dyson
- Centre for Equine StudiesAnimal Health TrustNewmarket UK
| | - J. Van Dijk
- Centre for Preventative Medicine Animal Health Trust Newmarket UK
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Wicherts JM. The Weak Spots in Contemporary Science (and How to Fix Them). Animals (Basel) 2017; 7:E90. [PMID: 29186879 PMCID: PMC5742784 DOI: 10.3390/ani7120090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 01/17/2023] Open
Abstract
In this review, the author discusses several of the weak spots in contemporary science, including scientific misconduct, the problems of post hoc hypothesizing (HARKing), outcome switching, theoretical bloopers in formulating research questions and hypotheses, selective reading of the literature, selective citing of previous results, improper blinding and other design failures, p-hacking or researchers' tendency to analyze data in many different ways to find positive (typically significant) results, errors and biases in the reporting of results, and publication bias. The author presents some empirical results highlighting problems that lower the trustworthiness of reported results in scientific literatures, including that of animal welfare studies. Some of the underlying causes of these biases are discussed based on the notion that researchers are only human and hence are not immune to confirmation bias, hindsight bias, and minor ethical transgressions. The author discusses solutions in the form of enhanced transparency, sharing of data and materials, (post-publication) peer review, pre-registration, registered reports, improved training, reporting guidelines, replication, dealing with publication bias, alternative inferential techniques, power, and other statistical tools.
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Affiliation(s)
- Jelte M Wicherts
- Department of Methodology and Statistics, Tilburg University, Warandelaan 2, 5037 AB, Tilburg, The Netherlands.
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