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    <p>Interesting question, but quite broad. I do recommend looking at some existing literature on automatic bird song identification. (Yup, there are a bunch of people working on it.)</p> <p>This paper (edit: sorry, dead link, but <a href="http://www.researchgate.net/profile/Olivier_Dufour2/publication/273079015_Clusterized_Mel_Filter_Cepstral_Coefficients_and_Support_Vector_Machines_for_Bird_Song_Identification/links/54f6cfa60cf27d8ed71ee492.pdf" rel="nofollow noreferrer">this chapter by Dufour et al. 2014</a> might be even clearer) uses a basic two-stage pattern recognition method that I would recommend trying first: feature extraction (the paper uses MFCCs), then classification (the paper uses a GMM). For each frame in the input signal, you get a vector of MFCCs (between 10 to 30). These MFCC vectors are used to train a GMM (or SVM) along with the corresponding bird species labels. Then, during testing, you submit a query MFCC vector to the GMM, and it will tell you which species it thinks it is.</p> <p>Although some have applied image processing techniques to audio classification/fingerprinting problems (e.g., <a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.4830&amp;rep=rep1&amp;type=pdf" rel="nofollow noreferrer">this paper by Google Research</a>), I hesitate to recommend these techniques for your problem or ones like it because of the annoying <em>temporal variations</em>. </p> <p>"What tools should I use for this analysis?" Among many others:</p> <ol> <li>feature extraction: MFCCs, onset detection</li> <li>classification: GMM, SVM</li> <li>Google</li> </ol> <p>Sorry for the incomplete answer, but it's a broad question, and there is more to this problem than can be answered here briefly.</p>
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