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neural network that segments and labels birdsong

Project description

TweetyNet

tweetynet image

A hybrid convolutional-recurrent neural network that segments and labels birdsong and other vocalizations.

sample annotation Canary song segmented into phrases

Installation

To install, run the following command at the command line:
pip install tweetynet

Before you install, you'll want to set up a virtual environment (for an explanation of why, see https://www.geeksforgeeks.org/python-virtual-environment/). Creating a virtual environment is not as hard as it might sound; here's a primer on Python tools: https://realpython.com/python-virtual-environments-a-primer/
For many scientific packages that depend on libraries written in
languages besides Python, you may find it easier to use a platform dedicated to managing those dependencies, such as Anaconda (which is free). You can use the conda command-line tool that they develop
to create environments and install the scientific libraries that this package depends on. In addition, using conda to install the dependencies may give you some performance gains (see https://www.anaconda.com/blog/developer-blog/tensorflow-in-anaconda/).
Here's how you'd set up a conda environment:
/home/you/code/ $ conda create -n tweetyenv python=3.5 numpy scipy joblib tensorflow-gpu ipython jupyter
/home/you/code/ $ source activate tweetyenv
(You don't have to source on Windows: > activate tweetyenv)

You can then use pip inside a conda environment:
(tweetyenv)/home/you/code/ $ pip install tweetynet

You can also work with a local copy of the code. It's possible to install the local copy with pip so that you can still edit the code, and then have its behavior as an installed library reflect those edits.

  • Clone the repo from Github using the version control tool git:
    (tweetyenv)/home/you/code/ $ git clone https://github.com/yardencsGitHub/tf_syllable_segmentation_annotation
    (you can install git from Github or using conda.)
  • Install the package with pip using the -e flag (for editable).
    $ (tweetyenv)/home/you/code/ $ cd tf_syllable_segmentation_annotation
    $ (tweetyenv) pip install -e .

Usage

Training tweetynet models to segment and label birdsong

To train models, use the command line interface, tweetynet-cli. You run it with config.ini files, using one of a handful of command-line flags. Here's the help text that prints when you run $ tweetynet-cli --help:

main script

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        run learning curve experiment with a single config.ini file, by passing the name of that file.
                        $ cnn-bilstm --config ./config_bird1.ini
  -g GLOB, --glob GLOB  string to use with glob function to search for config files fitting some pattern.
                        $ cnn-bilstm --glob ./config_finches*.ini
  -p PREDICT, --predict PREDICT
                        predict segments and labels for song, using a trained model specified in a single config.ini file
                        $ cnn-bilstm --predict ./predict_bird1.ini
  -s SUMMARY, --summary SUMMARY
                        runs function that summarizes results from generatinga learning curve, using a single config.ini file
                        $ cnn-bilstm --summary ./config_bird1.ini
  -t TXT, --txt TXT     name of .txt file containing list of config files to run
                        $ cnn-bilstm --text ./list_of_config_filenames.txt

As an example, you can run tweetynet-cli with a single config.ini file by using the --config flag and passing the name of the config.ini file as an argument:
(tweetyenv)$ tweetynet-cli --config ./configs/config_bird0.ini

For more details on how training works, see experiments.md, and for more details on the config.ini files, see README_config.md.

Data and folder structures

To train models, you must supply training data in the form of audio files or spectrograms, and annotations for each spectrogram.

Spectrograms and labels

The package can generate spectrograms from .wav files or .cbin files. It can also accept spectrograms in the form of Matlab .mat files. The locations of these files are specified in the config.ini file as explained in experiments.md and README_config.md.

Important model parameters

  • The following parameters must be correctly defined in the configuration .ini file.
    • input_vec_size - Must match the number of frequency bins in the spectrograms (current value is 513).
    • n_syllables - Must be the correct number of tags, including zero for non-syllable.
    • time_steps - The number of bins in a training snippet (current value is 87). The code concatenates all training data and trains the deep network using batches, containing snippets of length 'time_steps' from different points in the data. It is recommended to set 'time_steps' such that the snippets are of about 1 second.
  • The following parameters can be changed if needed:
    • n_max_iter - The maximal number of training steps (currently 18001).
    • batch_size - The number of snippets in each training batch (currently 11)
    • learning_rate - The training step rate coefficient (currently 0.001) Other parameters that specify the network itself can be changed in the code but require knowledge of tensorflow.

Preparing training files

It is possible to train on any manually annotated data but there are some useful guidelines:

  • Use as many examples as possible - The results will just be better. Specifically, this code will not label correctly syllables it did not encounter while training and will most probably generalize to the nearest sample or ignore the syllable.
  • Use noise examples - This will make the code very good in ignoring noise.
  • Examples of syllables on noise are important - It is a good practice to start with clean recordings. The code will not perform miracles and is most likely to fail if the audio is too corrupt or masked by noise. Still, training with examples of syllables on the background of cage noises will be beneficial.

Results of running the code

It is recommended to apply post processing when extracting the actual syllable tag and onset and offset timesfrom the estimates.

Predicting new labels

You can predict new labels by adding a [PREDICT] section to the config.ini file, and then running the command-line interface with the --predict flag, like so:
(tweetyenv)$ tweetynet-cli --predict ./configs/config_bird0.ini An example of what a config.ini file with a [PREDICT] section is in the doc folder here.

For users with some scripting / Tensorflow experience, you can reload a saved model using a checkpoint file saved by the Tensorflow checkpoint saver. Here's an example of how to do this, taken from the tweetynet.train_utils.learn_curve function:

meta_file = glob(os.path.join(training_records_dir, 'checkpoint*meta*'))[0]
data_file = glob(os.path.join(training_records_dir, 'checkpoint*data*'))[0]

model = TweetyNet(n_syllables=n_syllables,
                  input_vec_size=input_vec_size,
                  batch_size=batch_size)

with tf.Session(graph=model.graph) as sess:
    model.restore(sess=sess,
                  meta_file=meta_file,
                  data_file=data_file)

Model architecture

The architecture of this deep neural network is based on these papers:

The deep net. structure, used in this code, contains 3 elements:

  • 2 convolutional and max pooling layers - A convolutional layer convolves the spectrogram with a set of tunable features and the max pooling is used to limit the number of parameters. These layers allow extracting local spectral and temporal features of syllables and noise.
  • A long-short-term-memory recurrent layer (LSTM) - This layer allows the model to incorporate the temporal dependencies in the signal, such as canary trills and the duration of various syllables. The code contains an option to adding more LSTM layers but, since it isn't needed, those are not used.
  • A projection layer - For each time bin, this layer projects the previous layer's output on the set of possible syllables.

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