This repository contains scripts to replicate the experiments in Bioacoustic classification of avian calls from raw sound waveforms with an open source deep learning architecture. Part I describes the experiment with default settings, while Part II uses modified code to apply enhanced settings.

NIPS4Bplus provides detailed tags for the training dataset of the 2013 Neural Information Processing Scaled for Bioacoustics (NIPS4B) challenge for bird song classification. To use the data in SincNet with the default settings, we first prepare the files by cutting them according to the tags and then generate train, test and label lists.

The first step is to cut the original training NIPS4B wavefiles according to the NIPS4Bplus csv annotations. Run the script cut_nips4bplus_files.py as follows:

python cut_nips4bplus_files.py nips4b_bird_wav_folder nips4bplus_csv_folder output_path

where:

• nips4b_bird_wav_folder is the folder with the original training NIPS4B wavefiles
• nips4bplus_csv_folder is the folder with the NIPS4Bplus csv annotation files
• output_path is the output path for the cut files

This generates new (short) wavefiles from the tag dimensions and stores them in the output_path.

Then we generate lists of files and labels running generate_file_lists.py with:

pyton generate_file_lists.py nips4bplus_csv_folder nips4b_birdchallenge_espece_list.csv output_path

where:

• nips4bplus_csv_folder is the folder with the NIPS4Bplus csv annotation files
• nips4b_birdchallenge_espece_list.csv is the NIPS4B species list (csv) within the NIPS4B train labels
• output_path is the output path for the lists of files and labels

This generates lists of train and test files, and dictionary label files. The dictionary files list three class selections: All Classes, Bird Classes and Bird Species. But, there are only two sets of random train and test files: all_classes and bird. The set bird is combined with both the Bird Classes and Bird Species dictionaries for the respective experiments. Samples of these files are included under data_lists

Use the SincNet code from: https://github.com/mravanelli/SincNet. Follow the instructions in the SincNet repository but instead of using the Timit experiment settings, use one of the cfg files corresponding to your choice of experiment to run: all classes, bird classes or bird species. The cfg files maintain the settings of the Timit experiment in the SincNet repository except for the changes required for this dataset and each individual experiment. Modify the [data] section of the corresponding cfg file (ie. cfg/nips4bplus_all_classes.cfg) according to your paths.

• tr_lst is the "all_classes_train_files.scp" generated in b) above
• te_lst is the "all_classes_test_files.scp" generated in b) above
• lab_dict is the "all_classes_labels.npy" generated in b) above
• data_folder is the folder with the cut files generated in a) above
• output_path is the output path for the training results and model files

Then run speaker_id.py from SincNet as follows:

python speaker_id.py -–cfg=cfg/nips4bplus_all_classes.cfg

You may need to modify "cfg/nips4bplus_all_classes.cfg" according to your path and choice of experiment. Note that you would need data_io.py and dnn_models.py from SincNet in the same directory.

In order to process NIPS4Bplus tagged calls that are shorter than the frame length (cw_len) we have modified the SincNet code. The code utilises the original whole NIPS4B training files, but they need prior normalisation.

Run the code to normalise the original training NIPS4B wavefiles as follows:

python nips4b_normalise_files.py nips4b_bird_wav_folder output_folder

where:

• nips4b_bird_wav_folder is the folder of the original training NIPS4B wavefiles
• output_folder is the output folder for the normalised files

Generate csv lists of files acording to the NIPS4Bplus csv annotations running generate_mod_file_lists.py with:

pyton generate_mod_file_lists.py nips4bplus_csv_folder nips4b_birdchallenge_espece_list.csv output_path

where:

• nips4bplus_csv_folder is the folder with the NIPS4Bplus csv annotation files
• nips4b_birdchallenge_espece_list.csv is the NIPS4B species list (csv) within the NIPS4B train labels
• output_path is the output path for the lists of files and labels

This generates random train and test lists (that include the tag labels) as csv files for three selections of classes: All Classes, Bird Classes and Bird Species. Samples of these csv files are included under mod_data_lists.

The script call_id.py is a modified version of the speaker_id.py script from SincNet. First modify the [data] section, according to your paths, of one of the mod_cfg files corresponding to your choice of experiment to run: all classes, bird classes or bird species (ie. mod_cfg/mod_nips4bplus_all_classes.cfg).

• tr_lst is the "mod_all_classes_train_files.csv" generated in step 2 above
• te_lst is the "mod_all_classes_test_files.csv" generated in step 2 above
• lab_dict is not needed
• data_folder is the folder with the normalised files generated in step 1 above
• output_path is the output path for the training results and model files

Each mod_cfg file includes the best settings that we found for each experiment.

Then run call_id.py as follows:

python call_id.py --cfg=mod_cfg/mod_nips4bplus_all_classes.cfg

You may need to modify "mod_cfg/mod_nips4bplus_all_classes.cfg" according to your path and choice of experiment. Note that you would need data_io.py and dnn_models.py from SincNet in the same directory.

The requirements of the code are those of SincNet (https://github.com/mravanelli/SincNet#prerequisites) as well as the libraries glob, pandas and sklearn.

We would like to acknowledge the authors of NIPS4Bplus and SincNet, and their contribution to open science.

Bravo Sanchez, F., Hossain, R., English, N., Moore, S. Bioacoustic classification of avian calls from raw sound waveforms with an open-source deep learning architecture. Sci Rep (2021) https://www.nature.com/articles/s41598-021-95076-6

Morfi, V., Bas, Y., Pamuła, H., Glotin, H. & Stowell, D. NIPS4Bplus: a richly annotated birdsong audio dataset. PeerJ Computer Science 5, e223 (2019). http://doi.org/10.7717/peerj-cs.223

Ravanelli, M. & Bengio, Y. Speaker Recognition from Raw Waveform with SincNet. in 2018 IEEE Spoken Language Technology Workshop (SLT) 1021–1028 (IEEE, 2018). https://arxiv.org/abs/1808.00158

Source of NIPS4B train labels http://sabiod.univ-tln.fr/nips4b/media/birds/NIPS4B_BIRD_CHALLENGE_TRAIN_LABELS.tar

Source of NIPS4B wav files: http://sabiod.univ-tln.fr/nips4b/media/birds/NIPS4B_BIRD_CHALLENGE_TRAIN_TEST_WAV.tar.gz

Source of NIPS4Bplus transcriptions: https://doi.org/10.6084/m9.figshare.6798548