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Bioacoustic fundamental frequency estimation: a cross-species dataset and deep learning baseline. 生物声学基频估计:跨物种数据集和深度学习基线。
IF 2.1 4区 生物学 Q2 ZOOLOGY Pub Date : 2025-01-01 Epub Date: 2025-06-02 DOI: 10.1080/09524622.2025.2500380
Paul Best, Marcelo Araya-Salas, Axel G Ekström, Bárbara Freitas, Frants H Jensen, Arik Kershenbaum, Adriano R Lameira, Kenna D S Lehmann, Pavel Linhart, Robert C Liu, Malavika Madhavan, Andrew Markham, Marie A Roch, Holly Root-Gutteridge, Martin Šálek, Grace Smith-Vidaurre, Ariana Strandburg-Peshkin, Megan R Warren, Matthew Wijers, Ricard Marxer

The fundamental frequency (F0) is a key parameter for characterising structures in vertebrate vocalisations, for instance defining vocal repertoires and their variations at different biological scales ( e.g population dialects, individual signatures). However, the task is too laborious to perform manually, and its automation is complex. Despite significant advancements in the fields of speech and music for automatic F0 estimation, similar progress in bioacoustics has been limited. To address this gap, we compile and publish a benchmark dataset of over 250,000 calls from 14 taxa, each paired with ground truth F0 values. These vocalisations range from infra-sounds to ultra-sounds, from high to low harmonicity, and some include non-linear phenomena. Testing different algorithms on these signals, we demonstrate the potential of neural networks for F0 estimation, even for taxa not seen in training, or when trained without labels. Also, to inform on the applicability of algorithms to analyse signals, we propose spectral measurements of F0 quality which correlate well with performance. While current performance results are not satisfying for all studied taxa, they suggest that deep learning could bring a more generic and reliable bioacoustic F0 tracker, helping the community to analyse vocalisations via their F0 contours.

基本频率(F0)是表征脊椎动物发声结构的关键参数,例如定义声音库及其在不同生物尺度上的变化(例如种群方言,个体特征)。然而,这项任务过于费力,无法手动执行,而且自动化也很复杂。尽管语音和音乐领域在自动F0估计方面取得了重大进展,但生物声学方面的类似进展有限。为了解决这一差距,我们编译并发布了一个基准数据集,其中包含来自14个分类群的超过250,000个呼叫,每个呼叫都与地面真实F0值配对。这些发声范围从次音到超音,从高谐波到低谐波,有些还包括非线性现象。我们在这些信号上测试了不同的算法,证明了神经网络对F0估计的潜力,即使是在训练中没有看到的分类群,或者在没有标签的情况下训练。此外,为了了解算法分析信号的适用性,我们提出了与性能良好相关的F0质量的频谱测量。虽然目前的性能结果并不能让所有研究的分类群都满意,但他们认为,深度学习可以带来更通用、更可靠的生物声学F0跟踪器,帮助群落通过F0轮廓分析发声。
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引用次数: 0
Unsupervised discrimination of male Tawny owls ( Strix aluco ) individual calls using robust measurements of the acoustic signal 雄性黄褐色猫头鹰(Strix aluco)个体呼叫的无监督识别使用声学信号的鲁棒测量
4区 生物学 Q2 ZOOLOGY Pub Date : 2023-11-01 DOI: 10.1080/09524622.2023.2270486
Daniele Roccazzello, Orlando Tomassini, Elena Bernardini, Alessandro Massolo, Marco Dragonetti, Dimitri Giunchi
ABSTRACTVocal individuality has been widely documented in the Tawny owl (Strix aluco); however, all statistical tools employed thus far to discriminate individual vocalisations have relied on prior knowledge regarding number and identity of individuals. In this study, we tested the effectiveness of four unsupervised clustering algorithms in distinguishing among eight Tawny owl males, solely based on acoustic characteristics of their vocalisations. We also employed both traditional bound-based and robust measurements of acoustic signal to compare their efficacy. We finally evaluated the applicability of this method in identifying the number and distribution of the remaining males recorded in our study area. Three of the four unsupervised techniques had a high rate of success in discriminating among vocalisations of the eight males. In all cases, the best results were obtained using robust measurements. However, when extending the analysis to the remaining unknown males recorded, the highest rate of misclassification errors made results more difficult to interpret. Our study provided a useful tool to discriminate male Tawny owls when only their call recordings are available. Furthermore, this method could be extended to other nocturnal and vociferous species, representing one of the few existing approaches for unsupervised classification of individuals based on acoustic features.KEYWORDS: Hierarchical clusterindividual discriminationrobust signal measurementsunsupervised clusteringunsupervised classificationvocal individuality AcknowledgementsThe authors would like to thank the University of Pisa Working group (Tavolo Tecnico) for the Monte Pisano fires, which is dedicated to support the local community to study the effects of fires and to promote restoration of burnt areas. Moreover, we would like to thank Regione Toscana, the University of Pisa and the Department of Biology for funding the PhD scholarship for Tomassini Orlando following the recommendation provided by the Tavolo Tecnico. In particular, we would like to thank Gianni Bedini and Giulio Petroni for the financial support. Our thanks go to Elisabetta Palagi for providing us with the software Raven Pro. We extend our appreciation to Marta Berti, Giulia Cerritelli and Pietro Valente and for their help with data collection in the field. Additionally, we are grateful to Lorenzo Vanni and Luca Puglisi for their advice on data collection. Lastly, we are indebted to John Kastelic for his valuable assistance in refining the written content.Author contributionsDaniele Roccazzello, together with Orlando Tomassini, conducted the fieldwork, acoustical and statistical analyses, and wrote the manuscript. Elena Bernardini contributed to the fieldwork and acoustical analysis. Marco Dragonetti directed the acoustic analysis and edited the manuscript. Alessandro Massolo suggested statistical analyses and edited the manuscript. Dimitri Giunchi supervised and supported the overall study and also edited the
摘要褐鸮(Strix aluco)的声音个性已被广泛记载;然而,迄今为止,所有用于区分个体发声的统计工具都依赖于关于个体数量和身份的先验知识。在这项研究中,我们测试了四种无监督聚类算法的有效性,仅基于它们发声的声学特征来区分8只雄性黄褐色猫头鹰。我们还采用传统的基于边界的声信号测量和鲁棒的声信号测量来比较它们的效果。最后,我们评估了该方法在确定我们研究区域内记录的剩余雄性数量和分布方面的适用性。在四种无监督的方法中,有三种在区分八只雄性的叫声方面成功率很高。在所有情况下,使用稳健的测量获得了最佳结果。然而,当将分析扩展到剩余的未知男性记录时,最高的错误分类错误率使结果更难以解释。我们的研究提供了一个有用的工具来区分雄性茶色猫头鹰,当它们的呼叫记录是可用的。此外,这种方法可以扩展到其他夜行和吵闹的物种,代表了少数现有的基于声学特征的个体无监督分类方法之一。关键词:分层聚类、个体判别、鲁棒信号测量、监督聚类、无监督分类、声音个性致谢作者要感谢比萨大学工作小组(Tavolo Tecnico)对蒙特皮萨诺火灾的研究,他们致力于支持当地社区研究火灾的影响并促进烧伤地区的恢复。此外,我们要感谢托斯卡纳大区、比萨大学和生物系根据Tavolo Tecnico的建议为托马西尼·奥兰多提供博士奖学金。我们特别要感谢贝迪尼和佩特罗尼的财政支持。我们感谢Elisabetta Palagi为我们提供了Raven Pro软件。我们对Marta Berti、Giulia Cerritelli和Pietro Valente以及他们在实地数据收集方面的帮助表示感谢。此外,我们感谢Lorenzo Vanni和Luca Puglisi在数据收集方面的建议。最后,我们感谢John Kastelic在完善书面内容方面提供的宝贵帮助。作者贡献daniele Roccazzello和Orlando Tomassini一起进行了田野调查、声学和统计分析,并撰写了手稿。埃琳娜·贝尔纳迪尼为现场工作和声学分析做出了贡献。Marco Dragonetti指导了声学分析并编辑了手稿。亚历山德罗·马索罗建议进行统计分析,并编辑了手稿。Dimitri Giunchi监督和支持整个研究,并编辑了手稿。所有作者都认可了手稿的最终定稿。披露声明作者未报告潜在的利益冲突。补充材料本文的补充数据可在https://doi.org/10.1080/09524622.2023.2270486.Additional info网站上在线获取。
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引用次数: 0
The sound of hope: searching for critically endangered species using acoustic template matching 希望之声:利用声学模板匹配寻找极度濒危物种
4区 生物学 Q2 ZOOLOGY Pub Date : 2023-10-23 DOI: 10.1080/09524622.2023.2268579
C.B. De Araújo, J.P. Zurano, I.M.D. Torres, C.R.M.A. Simões, G.L.M. Rosa, A.G. Aguiar, W. Nogueira, H.A.L.S. Vilela, G. Magnago, B.T. Phalan, G.A. Zurita
ABSTRACTPassive acoustic monitoring (PAM) has become increasingly popular in monitoring biodiversity. It produces large amounts of data and can provide a foundation for understanding the long-term consequences of environmental degradation. However, extracting biological information from such extensive datasets can be challenging and requires advanced computational skills. Herein, we introduce a streamlined workflow for detecting acoustic signals of three critically endangered birds: Cherry-throated Tanager (Nemosia rourei), Alagoas Antwren (Myrmotherula snowi), and Blue-eyed Ground-dove (Columbina cyanopis). As these species are among the world’s most endangered birds, locating new populations is a top priority. We chose potential templates based on the acoustic parameters of the vocal repertoire and evaluated their performance using soundscapes with known composition (gold standard data). To evaluate the efficiency of the templates, we used precision and recall metrics and found that achieving high precision rates comes at the cost of recall rates. Although we used gold standard data to calibrate our algorithm, large-scale validations have revealed the limitations as some templates have exhibited significantly lower precision values. The use of binomial models helped reset precision values to 90%. Our workflow can process large amounts of data efficiently, helping to monitor populations of these critically endangered species, locate new populations and evaluate population dynamics.KEYWORDS: PAMbioacousticsconservationNemosia roureiMyrmotherula snowiColumbina cyanopis AcknowledgementsWe wish to thank all field personnel that work hard to keep the lights on. CONICET provided a post-doc fellowship to CBdA.Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThe work was supported by the Consejo Nacional de Investigaciones Científicas y Técnicas.
摘要被动声监测(PAM)在生物多样性监测中越来越受欢迎。它产生了大量的数据,可以为了解环境退化的长期后果提供基础。然而,从如此广泛的数据集中提取生物信息可能具有挑战性,并且需要先进的计算技能。本文介绍了一种简化的工作流程,用于检测三种极度濒危鸟类:樱桃喉塔纳ager (Nemosia rourei), Alagoas Antwren (Myrmotherula snowi)和蓝眼斑鸠(Columbina cyanopis)的声音信号。由于这些物种是世界上最濒危的鸟类之一,寻找新的种群是当务之急。我们根据声乐曲目的声学参数选择潜在模板,并使用已知成分的音景(金标准数据)评估它们的表现。为了评估模板的效率,我们使用了精确率和召回率指标,并发现实现高精确率是以召回率为代价的。尽管我们使用了金标准数据来校准我们的算法,但大规模验证已经揭示了一些模板的局限性,因为一些模板显示出明显较低的精度值。使用二项式模型帮助将精度值重置为90%。我们的工作流程可以有效地处理大量数据,帮助监测这些极度濒危物种的种群,定位新的种群并评估种群动态。关键词:pambioacoustic conservationnemosia rouroureimymmotherula snowolbibiina cyanopis致谢我们要感谢所有辛勤工作的现场工作人员。CONICET为CBdA提供博士后奖学金。披露声明作者未报告潜在的利益冲突。补充资料经费这项工作得到了全国调查委员会Científicas的支助。
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引用次数: 0
Parselmouth for bioacoustics: automated acoustic analysis in Python 生物声学的蛇佬腔:Python中的自动声学分析
4区 生物学 Q2 ZOOLOGY Pub Date : 2023-10-13 DOI: 10.1080/09524622.2023.2259327
Yannick Jadoul, Bart de Boer, Andrea Ravignani
Bioacoustics increasingly relies on large datasets and computational methods. The need to batch-process large amounts of data and the increased focus on algorithmic processing require software tools. To optimally assist in a bioacoustician’s workflow, software tools need to be as simple and effective as possible. Five years ago, the Python package Parselmouth was released to provide easy and intuitive access to all functionality in the Praat software. Whereas Praat is principally designed for phonetics and speech processing, plenty of bioacoustics studies have used its advanced acoustic algorithms. Here, we evaluate existing usage of Parselmouth and discuss in detail several studies which used the software library. We argue that Parselmouth has the potential to be used even more in bioacoustics research, and suggest future directions to be pursued with the help of Parselmouth.
生物声学越来越依赖于大型数据集和计算方法。批量处理大量数据的需求以及对算法处理的日益关注需要软件工具。为了最佳地协助生物声学家的工作流程,软件工具需要尽可能简单有效。五年前,Python包Parselmouth发布,提供了对Praat软件中所有功能的简单和直观的访问。尽管Praat主要是为语音和语音处理设计的,但许多生物声学研究都使用了其先进的声学算法。在此,我们评估了Parselmouth的现有使用情况,并详细讨论了几个使用该软件库的研究。我们认为蛇佬腔在生物声学研究中有更多的应用潜力,并建议在蛇佬腔的帮助下追求未来的方向。
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引用次数: 0
Sound production in sea turtle nests and hatchlings ( Eretmochelys imbricata and Caretta caretta ) in Northeast Brazil 巴西东北部海龟巢和幼龟(Eretmochelys imbricata和Caretta Caretta)的声音生产
4区 生物学 Q2 ZOOLOGY Pub Date : 2023-09-18 DOI: 10.1080/09524622.2023.2251936
Safira Núbia Dias de Melo, Matheus Felipe de Souza Dias da Silva, Paulo Jorge Parreira dos Santos, Vívian Chimendes da Silva Neves, Bruna Martins Bezerra
ABSTRACTSea turtles have been considered the least vocal of living reptiles, but recent studies are changing this perception. Here, we aimed to investigate the acoustics of hatchlings of, Eretmochelys imbricata and Caretta caretta in Northeast Brazil, to describe their acoustic signals and compare sound structure within and between species. We monitored 13 km in Ipojuca, southern coast of Pernambuco State. We recorded five nests of each species and the hatchlings’ walk to the sea in 2020/2021. We recorded 12 sonotypes in C. caretta and 5 in E. imbricata, increasing the number of described signals. Nevertheless, not all sonotypes were produced by all or in the different developmental stages. Some of the sounds for both species reached ultrasonic frequencies. The sound structure varied between C. caretta nests, suggesting a potential vocal signature, but the sound structure had no variation between E. imbricata nests. The sound structure varied between species. Despite their reputation for being silent, this study shows a diverse acoustic repertoire in the target species, further supporting speculations of acoustic signals mediating the potential synchronisation of hatchlings’ departure to the sea. Our signal descriptions could be used for future passive acoustic monitoring of the target species. Future studies should focus on understanding the functionality of acoustic signals in the different life stages.KEYWORDS: Vocal signaturebioacousticsincubationTestudinesvocalisation AcknowledgementsWe thank the staff at the NGO Ecoassociados, who provided logistical support for the development of this work. We also thank professors Pedro Murilo Sales Nunes, Ednilza Maranhão dos Santos, Thyara Noely Simões, Artur Campos Dália Maia and Frederico Simão Hintze de Oliveira, for fruitful discussion during the Master dissertation defence and the comments on an earlier version of this manuscript. This study complied with Brazilian law and data collection was conducted under the SISBIO Licence number 75658. SM is supported by a Capes scholarship (Financial code: 001). BMB and the study were supported through FACEPE grants (BFT-01602.04/17; BFT-0014-2.05/20; APQ-1230-2.05/22) and CNPq productive grant (Grant number 309256/2019-4).Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData can be made available upon reasonable request.Supplementary materialSupplemental data for this article can be accessed online at https://doi.org/10.1080/09524622.2023.2251936.Additional informationFundingThis work was supported by CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) through a scholarship to SM (Financial code 001), and grants from FACEPE (Fundação de Amparo a Ciência e Tecnologia do Estado de Pernambuco; grant codes: [BFT-01602.04/17; BFT-0014-2.05/20]) and from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico; Grant number [309256/2019-4]) to BMB.
海龟一直被认为是现存爬行动物中声音最小的,但最近的研究正在改变这种看法。在此,我们研究了巴西东北部的Eretmochelys imbricata和Caretta Caretta幼龟的声学特征,以描述它们的声音信号,并比较物种内和物种间的声音结构。我们在伯南布哥州南部海岸的伊波茹卡监测了13公里。我们在2020/2021年记录了每个物种的5个巢穴和幼仔走向大海的过程。我们分别记录了12个和5个声型,增加了描述信号的数量。然而,并非所有的声型都是由所有人或在不同的发育阶段产生的。这两个物种的一些声音达到了超声波频率。不同巢间的声音结构不同,表明可能存在发声特征,但不同巢间的声音结构没有变化。声音结构因物种而异。尽管它们以沉默著称,但这项研究显示了目标物种的多种声音曲目,进一步支持了声音信号介导幼体出海的潜在同步的猜测。我们的信号描述可用于未来目标物种的被动声监测。未来的研究应着重于了解不同生命阶段声信号的功能。我们感谢非政府组织Ecoassociados的工作人员,他们为这项工作的开展提供了后勤支持。我们还要感谢Pedro Murilo Sales Nunes、Ednilza maranh o dos Santos、Thyara Noely Simões、Artur Campos Dália Maia和Frederico sim o Hintze de Oliveira教授在硕士论文答辩期间进行的富有成效的讨论和对本文早期版本的评论。这项研究符合巴西法律,数据收集是在SISBIO许可证编号75658下进行的。SM由Capes奖学金支持(财务代码:001)。BMB和该研究由FACEPE资助(BFT-01602.04/17;bft - 0014 - 2.05/20;APQ-1230-2.05/22)和CNPq生产补助金(批准号309256/2019-4)。披露声明作者未报告潜在的利益冲突。数据可用性声明应合理要求,可提供数据。本研究由CAPES (ordindena ode aperfeiamento de Pessoal de Nível Superior)通过SM奖学金(财务代码001)和FACEPE (fundao de Amparo a Ciência e Tecnologia do Estado de Pernambuco)资助;授权代码:[BFT-01602.04/17;BFT-0014-2.05/20])和CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico;资助编号[309256/2019-4])
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引用次数: 0
Threat vocalisations are acoustically similar between humans (Homo sapiens) and chimpanzees (Pan troglodytes) 人类(智人)和黑猩猩(类人猿)发出威胁的声音在声学上是相似的。
IF 1.8 4区 生物学 Q2 ZOOLOGY Pub Date : 2023-08-29 DOI: 10.1080/09524622.2023.2250320
Roza G. Kamiloğlu, Cantay Caliskan, K. Slocombe, D. Sauter
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引用次数: 0
Evaluating factors affecting species detection using passive acoustic monitoring in neotropical forests: a playback experiment 评估影响新热带森林被动声学监测物种检测的因素:回放实验
IF 1.8 4区 生物学 Q2 ZOOLOGY Pub Date : 2023-08-25 DOI: 10.1080/09524622.2023.2246413
Anja Hutschenreiter, J. Sosa-López, F. González-García, F. Aureli
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引用次数: 1
The functions and evolution of graded complex calls in a treefrog 树蛙分级复呼的功能及其进化
IF 1.8 4区 生物学 Q2 ZOOLOGY Pub Date : 2023-08-03 DOI: 10.1080/09524622.2023.2241707
Bicheng Zhu, Xiaomeng Zhao, Haodi Zhang, Jichao Wang, Jianguo Cui
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引用次数: 0
What do we know about advertisement calls of Mexican anurans? A bibliographic review 我们对墨西哥阿努兰人的广告电话了解多少?书目综述
IF 1.8 4区 生物学 Q2 ZOOLOGY Pub Date : 2023-08-02 DOI: 10.1080/09524622.2023.2241046
Samantha Ordóñez-Flores, Atziri Alicia Ibarra-Reyes, L. Ochoa-Ochoa
{"title":"What do we know about advertisement calls of Mexican anurans? A bibliographic review","authors":"Samantha Ordóñez-Flores, Atziri Alicia Ibarra-Reyes, L. Ochoa-Ochoa","doi":"10.1080/09524622.2023.2241046","DOIUrl":"https://doi.org/10.1080/09524622.2023.2241046","url":null,"abstract":"","PeriodicalId":55385,"journal":{"name":"Bioacoustics-The International Journal of Animal Sound and Its Recording","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44430020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chasing the bird: 3D acoustic tracking of aerial flight displays with a minimal planar microphone array 追逐鸟:用最小平面麦克风阵列对空中飞行显示器进行三维声学跟踪
IF 1.8 4区 生物学 Q2 ZOOLOGY Pub Date : 2023-08-02 DOI: 10.1080/09524622.2023.2241420
G. Dutilleux, B. Sandercock, J. Kålås
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引用次数: 1
期刊
Bioacoustics-The International Journal of Animal Sound and Its Recording
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