Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap).
House mice communicate through ultrasonic vocalizations (USVs), which are above the range of human hearing (>20 kHz), and several automated methods have been developed for USV detection and classification. Here we evaluate their advantages and disadvantages in a full, systematic comparison, while...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2022-05-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010049&type=printable |
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| author | Reyhaneh Abbasi Peter Balazs Maria Adelaide Marconi Doris Nicolakis Sarah M Zala Dustin J Penn |
| author_facet | Reyhaneh Abbasi Peter Balazs Maria Adelaide Marconi Doris Nicolakis Sarah M Zala Dustin J Penn |
| author_sort | Reyhaneh Abbasi |
| collection | DOAJ |
| description | House mice communicate through ultrasonic vocalizations (USVs), which are above the range of human hearing (>20 kHz), and several automated methods have been developed for USV detection and classification. Here we evaluate their advantages and disadvantages in a full, systematic comparison, while also presenting a new approach. This study aims to 1) determine the most efficient USV detection tool among the existing methods, and 2) develop a classification model that is more generalizable than existing methods. In both cases, we aim to minimize the user intervention required for processing new data. We compared the performance of four detection methods in an out-of-the-box approach, pretrained DeepSqueak detector, MUPET, USVSEG, and the Automatic Mouse Ultrasound Detector (A-MUD). We also compared these methods to human visual or 'manual' classification (ground truth) after assessing its reliability. A-MUD and USVSEG outperformed the other methods in terms of true positive rates using default and adjusted settings, respectively, and A-MUD outperformed USVSEG when false detection rates were also considered. For automating the classification of USVs, we developed BootSnap for supervised classification, which combines bootstrapping on Gammatone Spectrograms and Convolutional Neural Networks algorithms with Snapshot ensemble learning. It successfully classified calls into 12 types, including a new class of false positives that is useful for detection refinement. BootSnap outperformed the pretrained and retrained state-of-the-art tool, and thus it is more generalizable. BootSnap is freely available for scientific use. |
| format | Article |
| id | doaj-art-3a2c2e8b6a124e46bdf9e5d14e7ce6d5 |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2022-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-3a2c2e8b6a124e46bdf9e5d14e7ce6d52025-08-20T02:33:26ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582022-05-01185e101004910.1371/journal.pcbi.1010049Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap).Reyhaneh AbbasiPeter BalazsMaria Adelaide MarconiDoris NicolakisSarah M ZalaDustin J PennHouse mice communicate through ultrasonic vocalizations (USVs), which are above the range of human hearing (>20 kHz), and several automated methods have been developed for USV detection and classification. Here we evaluate their advantages and disadvantages in a full, systematic comparison, while also presenting a new approach. This study aims to 1) determine the most efficient USV detection tool among the existing methods, and 2) develop a classification model that is more generalizable than existing methods. In both cases, we aim to minimize the user intervention required for processing new data. We compared the performance of four detection methods in an out-of-the-box approach, pretrained DeepSqueak detector, MUPET, USVSEG, and the Automatic Mouse Ultrasound Detector (A-MUD). We also compared these methods to human visual or 'manual' classification (ground truth) after assessing its reliability. A-MUD and USVSEG outperformed the other methods in terms of true positive rates using default and adjusted settings, respectively, and A-MUD outperformed USVSEG when false detection rates were also considered. For automating the classification of USVs, we developed BootSnap for supervised classification, which combines bootstrapping on Gammatone Spectrograms and Convolutional Neural Networks algorithms with Snapshot ensemble learning. It successfully classified calls into 12 types, including a new class of false positives that is useful for detection refinement. BootSnap outperformed the pretrained and retrained state-of-the-art tool, and thus it is more generalizable. BootSnap is freely available for scientific use.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010049&type=printable |
| spellingShingle | Reyhaneh Abbasi Peter Balazs Maria Adelaide Marconi Doris Nicolakis Sarah M Zala Dustin J Penn Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap). PLoS Computational Biology |
| title | Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap). |
| title_full | Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap). |
| title_fullStr | Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap). |
| title_full_unstemmed | Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap). |
| title_short | Capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations (BootSnap). |
| title_sort | capturing the songs of mice with an improved detection and classification method for ultrasonic vocalizations bootsnap |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010049&type=printable |
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