├── LICENSE ├── .gitignore └── README.md /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Yann Bayle 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | wheels/ 24 | *.egg-info/ 25 | .installed.cfg 26 | *.egg 27 | 28 | # PyInstaller 29 | # Usually these files are written by a python script from a template 30 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 31 | *.manifest 32 | *.spec 33 | 34 | # Installer logs 35 | pip-log.txt 36 | pip-delete-this-directory.txt 37 | 38 | # Unit test / coverage reports 39 | htmlcov/ 40 | .tox/ 41 | .coverage 42 | .coverage.* 43 | .cache 44 | nosetests.xml 45 | coverage.xml 46 | *.cover 47 | .hypothesis/ 48 | 49 | # Translations 50 | *.mo 51 | *.pot 52 | 53 | # Django stuff: 54 | *.log 55 | local_settings.py 56 | 57 | # Flask stuff: 58 | instance/ 59 | .webassets-cache 60 | 61 | # Scrapy stuff: 62 | .scrapy 63 | 64 | # Sphinx documentation 65 | docs/_build/ 66 | 67 | # PyBuilder 68 | target/ 69 | 70 | # Jupyter Notebook 71 | .ipynb_checkpoints 72 | 73 | # pyenv 74 | .python-version 75 | 76 | # celery beat schedule file 77 | celerybeat-schedule 78 | 79 | # SageMath parsed files 80 | *.sage.py 81 | 82 | # dotenv 83 | .env 84 | 85 | # virtualenv 86 | .venv 87 | venv/ 88 | ENV/ 89 | 90 | # Spyder project settings 91 | .spyderproject 92 | .spyproject 93 | 94 | # Rope project settings 95 | .ropeproject 96 | 97 | # mkdocs documentation 98 | /site 99 | 100 | # mypy 101 | .mypy_cache/ 102 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Awesome Bioacoustic 2 | 3 | By [Yann Bayle](http://yannbayle.fr/english/index.php) ([Website](http://yannbayle.fr/english/index.php), [GitHub](https://github.com/ybayle)) from LaBRI ([Website](http://www.labri.fr/), [Twitter](https://twitter.com/labriOfficial/)), Univ. Bordeaux ([Website](https://www.u-bordeaux.fr/), [Twitter](https://twitter.com/univbordeaux)), CNRS ([Website](http://www.cnrs.fr/), [Twitter](https://twitter.com/CNRS)) and SCRIME ([Website](https://scrime.u-bordeaux.fr/)). 4 | 5 | Very personal list of references on bioacoustic, which is **under construction**. 6 | It references mostly signal processing and machine learning scientific articles and datasets but also contains media-related post. 7 | The list is for my academic work but feel free to contribute! 8 | 9 | ### Birds 10 | 11 | - [BirdVox Projet](https://wp.nyu.edu/birdvox) 12 | - [[PDF](http://www.justinsalamon.com/uploads/4/3/9/4/4394963/salamon_fusinglearning_bioacoustics_icassp2017.pdf)][[Datasets](https://wp.nyu.edu/birdvox/codedata/#datasets)] - Fusing Shallow and Deep Learning for Bioacoustic Bird Species Classification, J. Salamon, J. P. Bello, A. Farnsworth and S. Kelling. ICASSP 2017. 13 | - [Bird detection in audio: A survey and a challenge](https://arxiv.org/pdf/1608.03417.pdf) 14 | - Bardeli, R., Wolff, D., Kurth, F., Koch, M., Tauchert, K. H., & Frommolt, K. H. (2010). Detecting bird sounds in a complex acoustic environment and application to bioacoustic monitoring. Pattern Recognition Letters, 31(12), 1524-1534. 15 | - [[PDF](https://www.researchgate.net/profile/Justin_Salamon/publication/323369757_Birdvox-Full-Night_A_Dataset_And_Benchmark_For_Avian_Flight_Call_Detection/links/5a909cf4aca2721405623123/Birdvox-Full-Night-A-Dataset-And-Benchmark-For-Avian-Flight-Call-Detection.pdf)][[Dataset](https://wp.nyu.edu/birdvox/birdvox-full-night/)] Vincent Lostanlen and Justin Salamon and Andrew Farnsworth and Andrew Farnsworth and Juan Pablo Bello. Birdvox-full-night: A Dataset And Benchmark For Avian Flight Call Detection, ICASSP 2018. 16 | - [Towards the Automatic Classification of Avian Flight Calls for Bioacoustic Monitoring](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166866) 17 | - [Bird Migration Interactive Maps](https://www.nationalgeographic.com/magazine/2018/03/bird-migration-interactive-maps/) 18 | - [Audio-only Bird Species Automated Identification Method with Limited Training Data Based on Multi-Channel Deep Convolutional Neural Networks](https://arxiv.org/abs/1803.01107) 19 | - [Bird species identification via transfer learning from music genres](https://www.sciencedirect.com/science/article/pii/S1574954117302467) 20 | - [See the Millions of Places Migrating Birds Have Gone—in One Gif](http://www.audubon.org/news/see-millions-places-migrating-birds-have-gone-one-gif) 21 | - [Scalable Preprocessing of High Volume Bird Acoustic Data](https://arxiv.org/abs/1802.00535) 22 | - [Red-winged blackbirds](https://twitter.com/paigebyerly/status/948568989952806912) 23 | - [Bird Audio Detection Challenge (BADC)](http://machine-listening.eecs.qmul.ac.uk/bird-audio-detection-challenge/) 24 | - [Code for one submission to the BADC by Karol J. Piczak](https://github.com/karoldvl/BADC-2017) 25 | - [LifeCLEF Bird Identification Task](https://www.researchgate.net/publication/278802086_LifeCLEF_Bird_Identification_Task_2014) 26 | - [Deciphering the dawn chorus](https://www.youtube.com/watch?v=9madFjojRGg) 27 | - [Evaluation of various feature sets and feature selection towards automatic recognition of bird species](https://www.inderscienceonline.com/doi/abs/10.1504/IJCAT.2017.088197) 28 | - [Computational Bioacoustic Scene Analysis](https://link.springer.com/chapter/10.1007%2F978-3-319-63450-0_11) 29 | - [GPU-based Training of Autoencoders for Bird Sound Data Processing](https://www.researchgate.net/publication/315738586_GPU-based_Training_of_Autoencoders_for_Bird_Sound_Data_Processing) 30 | - [Active Learning for Bird Sounds Classification](http://www.ingentaconnect.com/contentone/dav/aaua/2017/00000103/00000003/art00002) 31 | - [Birdify: le projet d'un Shazam pour les chants d'oiseaux](http://www.huffingtonpost.fr/2013/10/11/birdify-shazam-chants-oiseaux_n_4076487.html#slide=2711042) 32 | - [A Shazam but for bird calls?](https://twitter.com/MaconBlair/status/866102531717570560) 33 | - [Stacked Convolutional and Recurrent Neural Networks for Bird Audio Detection](https://arxiv.org/pdf/1706.02047.pdf) 34 | - [[Code](https://github.com/jaron/deep-listening)][[PDF](https://github.com/jaron/deep-listening/blob/master/ProjectReport.pdf)] Using deep learning to build an audio classifier to recognise birdsong 35 | 36 | ### Underwater bioacoustic 37 | 38 | - [Extreme diversity in the songs of Spitsbergen's bowhead whales](https://www.researchgate.net/publication/324202381_Extreme_diversity_in_the_songs_of_Spitsbergen%27s_bowhead_whales) 39 | - [DCLDE from SABIOD](http://sabiod.univ-tln.fr/DCLDE/) 40 | - [Sound samples from Youtube](https://www.youtube.com/watch?time_continue=45&v=UVy8bgD5Pbg) 41 | - [Humpback Whale Baby Boom Near Antarctica](https://www.nytimes.com/2018/05/01/science/humpback-whale-antarctica.html) (May 2018) - On why it is important to track whales with bioacoustics 42 | - [Click reception in the harbor porpoise (Phocoena phocoena): Effects of electrode and contact transducer location on the auditory brainstem response](https://asa.scitation.org/doi/10.1121/1.5030921) (April 2018) 43 | - [Unknown beaked whale echolocation signals recorded off eastern New Zealand](https://asa.scitation.org/doi/10.1121/1.5032127) (April 2018) 44 | - [Song recorded near a super-group of humpback whales on a mid-latitude feeding ground off South Africa ](https://asa.scitation.org/doi/10.1121/1.5032126) (April 2018) 45 | - [Comparison of passive acoustic soniferous fish monitoring with supervised and unsupervised approaches](https://asa.scitation.org/doi/10.1121/1.5034169) (April 2018) 46 | 47 | ### Human medical 48 | 49 | - [Lung sounds classification using convolutional neural networks](https://www.sciencedirect.com/science/article/pii/S0933365717302051) (May 2018) - CNN > MFCCs 50 | 51 | ### Other useful resources 52 | 53 | - [Six Ways Sound Data is Changing Conservation](https://blog.nature.org/science/2018/04/25/six-ways-sound-data-is-changing-conservation/) 54 | - [Metrics for Polyphonic Sound Event Detection](http://www.mdpi.com/2076-3417/6/6/162) 55 | --------------------------------------------------------------------------------