{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T18:00:03Z","timestamp":1776103203723,"version":"3.50.1"},"reference-count":47,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2009,11,18]],"date-time":"2009-11-18T00:00:00Z","timestamp":1258502400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Algorithms"],"abstract":"<jats:p>Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks.<\/jats:p>","DOI":"10.3390\/a2041410","type":"journal-article","created":{"date-parts":[[2009,11,19]],"date-time":"2009-11-19T02:20:40Z","timestamp":1258597240000},"page":"1410-1428","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["A Framework for Bioacoustic Vocalization Analysis Using Hidden Markov Models"],"prefix":"10.3390","volume":"2","author":[{"given":"Yao","family":"Ren","sequence":"first","affiliation":[{"name":"Electrical and Computer Engineering, Marquette University, Milwaukee, WI 53201, USA"}]},{"given":"Michael T.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Electrical and Computer Engineering, Marquette University, Milwaukee, WI 53201, USA"}]},{"given":"Patrick J.","family":"Clemins","sequence":"additional","affiliation":[{"name":"American Association for the Advancement of Science, Washington, DC 20005, USA"}]},{"given":"Michael","family":"Darre","sequence":"additional","affiliation":[{"name":"Animal Sciences, University of Connecticut, Storrs, CT 06269, USA"}]},{"given":"Sharon Stuart","family":"Glaeser","sequence":"additional","affiliation":[{"name":"Oregon Zoo, Portland, OR 97221, USA"}]},{"given":"Tomasz S.","family":"Osiejuk","sequence":"additional","affiliation":[{"name":"Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Pozna\u0144, Poland"}]},{"given":"Ebenezer","family":"Out-Nyarko","sequence":"additional","affiliation":[{"name":"Animal Sciences, University of Connecticut, Storrs, CT 06269, USA"}]}],"member":"1968","published-online":{"date-parts":[[2009,11,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1111\/j.1439-0310.1987.tb00676.x","article-title":"Quantitative analysis of animal vocal phonology: An application to swamp sparrow song","volume":"76","author":"Clark","year":"1987","journal-title":"Ethology"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1111\/j.1439-0310.1988.tb00195.x","article-title":"A quantitative technique to compare and classify humpback whale (Megaptera novaeangliae) sounds","volume":"77","author":"Chabot","year":"1988","journal-title":"Ethology"},{"key":"ref_3","unstructured":"Mellinger, D.K., and Clark, C.W. (, January October). Recognizing transient low-frequency whale sounds by spectrogram correlation. Proceedings of the IEEE Oceans '93, Victoria, BC, Canada."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3616","DOI":"10.1121\/1.423944","article-title":"Long-range acoustic detection and localization of blue whale calls in the northeast Pacific Ocean","volume":"104","author":"Stafford","year":"1998","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1109\/48.180305","article-title":"Fish detection and identification using neural networks","volume":"17","author":"Ramani","year":"1992","journal-title":"IEEE J. Ocean Eng."},{"key":"ref_6","unstructured":"Gaetz, W., Jantzen, K., Weinberg, H., Spong, P., and Symonds, H. (, January October). A neural network mechanism for recognition of indivudual Orcinus orca based on their acoustic behavior: Phase 1. Proceedings of the IEEE Oceans '93, Victoria, BC, Canada."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/0893-6080(91)90051-6","article-title":"Recognizing successive dolphin echoes with an integrator gateway network","volume":"4","author":"Moore","year":"1991","journal-title":"Neural Netw."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2497","DOI":"10.1121\/1.407385","article-title":"A quantitative measure of similarity for tursiops truncatus signature whistles","volume":"94","author":"Buck","year":"1993","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1121\/1.1847850","article-title":"Automatic classification and speaker idenfication of African elephant (Loxodonta africana) vocalizations","volume":"117","author":"Clemins","year":"2005","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_10","unstructured":"Clemins, P.J., Trawicki, M.B., Adi, K., Tao, J., and Johnson, M.T. (, January May). Generalized perceptual features for vocalization and analysis across multiple species. Proceedings of the IEEE International Conference on Acoustic, Speech and Signal Processing, Toulouse, France."},{"key":"ref_11","unstructured":"Adi, K., Sonstrom, K.E., Scheifele, P.M., and Johnson, M.T. (, January April). Unsupervised validity measures for vocalization clustering. Proceedings of the Internatinal Conference on Acoustics Speech and Signal Processing, Las Vegas, NV, USA."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1121\/1.2837487","article-title":"Acoustic model adaptation for ortolan bunting (Emberiza Hortulana L.) song type classification","volume":"123","author":"Tao","year":"2008","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Weisburn, B.A., Mitchell, S.G., Clark, C.W., and Parks, T.W. (, January April). Isolating biological acoustic transient signals. Proceedings of the 1993 International Conference on Acoustics, Speech, and Signal Processing, Minneapolis, MN, USA.","DOI":"10.1109\/ICASSP.1993.319107"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2130","DOI":"10.1121\/1.428011","article-title":"Speech recognition meets bird song: A comparison of statistics-based and template-based techniques","volume":"106","author":"Anderson","year":"1999","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3626","DOI":"10.1121\/1.423945","article-title":"The neural network classification of false killer whale (Pseudorca crassidents) vocalizations","volume":"104","author":"Murray","year":"1998","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_16","unstructured":"Mellinger, D.K. (2002). Ishmael 1.0 User's Guide, Pacific Marine Enviromental Laboratory."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3412","DOI":"10.1121\/1.1623787","article-title":"Acoustic variability and distinguishability among mouse ultrasound vocalizations","volume":"114","author":"Liu","year":"2003","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1109\/TASSP.1985.1164550","article-title":"Speech Enhancement using a minimum mean-square error log-spectral amplitude estimator","volume":"ASSP\u201333","author":"Ephraim","year":"1985","journal-title":"IEEE Trans Acoust"},{"key":"ref_19","unstructured":"Alvarez, B.D., and Garcia, C.F. (, January September). System architecture for pattern recognition in eco systems. Proceedings of the ESA-EUSC, Madrid, Spain."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1121\/1.2202885","article-title":"Background noise cancellation of manatee vocalizations using an adaptive line enhancer","volume":"120","author":"Yan","year":"2006","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1121\/1.2932070","article-title":"Perceptually motivated wavelet packet transform for bioacoustic signal enhancement","volume":"124","author":"Ren","year":"2008","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Deller, J.R., Hansen, J.H.L., and Proakis, J.G. (2000). Discrete-Time Processing of Speech Signals, IEEE.","DOI":"10.1109\/9780470544402"},{"key":"ref_23","unstructured":"Department, C.U.E. (2002). Hidden Markov Model Toolkit (HTK) Version 3.2.1 User's Guide, Cambridge."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1214\/aoms\/1177697196","article-title":"A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains","volume":"41","author":"Baum","year":"1970","journal-title":"Ann. Math. Stat."},{"key":"ref_25","first-page":"1","article-title":"An inequality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes","volume":"3","author":"Baum","year":"1972","journal-title":"Inequalities"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1109\/PROC.1973.9030","article-title":"The viterbi algorithm","volume":"61","author":"Forney","year":"1973","journal-title":"IEEE"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1109\/TASSP.1980.1163420","article-title":"Comparison of parametric representations for monosyllabic word recognition in continuously spoken sentences","volume":"28","author":"Davis","year":"1980","journal-title":"IEEE Trans. Acoust."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1121\/1.399423","article-title":"Perceptual Linear predictive (PLP) analysis for speech recognition","volume":"87","author":"Hermansky","year":"1990","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_29","unstructured":"Clemins, P.J. (2005). Automatic Speaker Identification and Classification of Animal Vocalizations. [Dissertation, Electrical and Computer Engineering Department, Marquette University]."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1121\/1.1908437","article-title":"Critical bandwidth and the frequency coordinates of the basilar membrane","volume":"33","author":"Greenwood","year":"1961","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_31","unstructured":"Trawicki, M.B., and Johnson, M.T. Automatic song-type classification and speaker identification of Norwegian Ortolan Bunting (Emberiza Hurtulana). Proceedings of the IEEE International Conference on Machine Learning in Signal Processing (MLSP), Mystic, CT, USA."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1002\/1098-2361(2000)19:5<425::AID-ZOO11>3.0.CO;2-A","article-title":"Elephant communication","volume":"19","author":"Langbauer","year":"2000","journal-title":"Zoo Biol."},{"key":"ref_33","first-page":"193","article-title":"Reproductive behavior of the Asiatic elephant (Elephas maximus)","volume":"38","author":"Eisenberg","year":"1971","journal-title":"Behav. Ecol. Sociobiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1111\/j.1365-2028.1973.tb00101.x","article-title":"On the ecology and behaviour of the Lake Manyara elephants","volume":"11","year":"1973","journal-title":"E Afr. Wildl. J."},{"key":"ref_35","first-page":"775","article-title":"Do Asian elephants, especially males in musth, chemically signal via volatiles in breath?","volume":"22","author":"Rasmussen","year":"1997","journal-title":"Chem. Sens."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1006\/anbe.1999.1092","article-title":"Signal-receiver interplay in the communication of male condition by Asian elephants","volume":"57","author":"Schulte","year":"1999","journal-title":"Anim. Behav."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1006\/anbe.1999.1117","article-title":"Signal and Assessment in African Elephants: Evidence from playback experiments","volume":"58","author":"Poole","year":"1999","journal-title":"Anim. Behav."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.5479\/si.00810282.125","article-title":"Behavior and ecology of the Asiatic elephant in Southeastern Ceylon","volume":"125","author":"McKay","year":"1973","journal-title":"Smithsonian Contrib. Zool."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1007\/BF00300007","article-title":"Infrasonic calls of the Asian elephant","volume":"18","author":"Payne","year":"1986","journal-title":"Behav. Ecol. Sociobiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2710","DOI":"10.1121\/1.4784383","article-title":"A vocal repertoire of Asian elephant and comparison of call classification methods","volume":"125","author":"Glaeser","year":"2009","journal-title":"J. Acoust. Soc. Am."},{"key":"ref_41","unstructured":"Glaeser, S.S. (2009). Analysis and Classification of Sounds Produced by Asian Elephants (Elephas Maximus). [MSc Thesis, Department of Biology, Portland State University]."},{"key":"ref_42","unstructured":"Cramp, S., and Perrins, C.M. (1994). The birds of the western palearctic, Oxford University Press."},{"key":"ref_43","unstructured":"Steinberg, B.D. (1983). Microwave Imaging with Large Antenna Arrays, John Wiley & Sons."},{"key":"ref_44","unstructured":"Dale, S. Causes of Population Decline in Ortolan Bunting in Norway. Proceedings of the 3rd International Ortolan Symposium, Poznan, Poland."},{"key":"ref_45","unstructured":"Losak, K. (2007). A Comparative Analysis of Song Variation in Ortolan Bunting (Emberiza Hortulana) from Populations of Different Status and Quality. [Dissertation, Adam Mickiewicz University]."},{"key":"ref_46","first-page":"3","article-title":"Song structure and repertoire variation in ortolan bunting (Emberiza hortulana L.) from isolated Norwegian population","volume":"40","author":"Osiejuk","year":"2003","journal-title":"Ann Zool Fenn"},{"key":"ref_47","unstructured":"Michael, C.A., Joy, A.M., and Hughes, B.O. (2004). Poultry Behaviour and Welfare, CABI."}],"container-title":["Algorithms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4893\/2\/4\/1410\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T22:11:42Z","timestamp":1760220702000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4893\/2\/4\/1410"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,11,18]]},"references-count":47,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2009,12]]}},"alternative-id":["a2041410"],"URL":"https:\/\/doi.org\/10.3390\/a2041410","relation":{},"ISSN":["1999-4893"],"issn-type":[{"value":"1999-4893","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,11,18]]}}}