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7th Place Solution for the Cornell Birdcall Identification Kaggle Challenge

Implementation of the submission of team "[CP-JKU] Three Geese and a GAN" of the Institute of Computational Perception at Johannes-Kepler-University Linz, Austria, to the Cornell Birdcall Identification Challenge run at Kaggle from July to September 2020.

This submission reached place 7 of 1390 on the private leaderboard, and can be modified to score between places 1 and 2.

For a detailed explanation of the methods employed here, please see the 7th place solution writeup as posted on Kaggle.

Prerequisites

Software

You will need Python 3 with at least the following modules:

  • numpy
  • scikit-learn
  • torch>=1.5.1
  • tqdm
  • pandas

For some features, additional modules are required:

  • tensorboard
  • apex
  • matplotlib

With pip, prerequisites can be installed with:

pip3 install numpy scikit-learn tqdm pandas matplotlib

Similar with conda:

conda install numpy scikit-learn tqdm pandas matplotlib

Pytorch should be installed following the instructions on pytorch.org. You will need Pytorch 1.5.1 or later.

Tensorboard can be installed with pip3 install tensorboard or conda install -c conda-forge tensorboard.

Apex currently needs to be installed via pip (even when using conda):

TORCH_CUDA_ARCH_LIST="6.1;7.5" pip3 install -v --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" https://github.com/NVIDIA/apex/archive/master.zip

TORCH_CUDA_ARCH_LIST lists the compute capabilities to compile for; it only needs to be set if the installation is shared across multiple machines with different GPUs (by default, it compiles for all GPUs on the current machine).

Apart from Python, you will need ffmpeg. On Debian and Ubuntu, this can be installed with sudo apt install ffmpeg libavcodec-extra.

Dataset

To prepare the dataset for training, follow the instructions in definitions/datasets/kagglebirds2020/README.md.

PANN weights

To prepare the pretrained PANN model for training, follow the instructions in definitions/models/pann/README.md.

Training

To train the models needed for one of the submissions, run:

OMP_NUM_THREADS=1 experiments/train_kagglebirds2020.sh --cuda-device=0

Append --var data.num_workers=4 --var data.pin_memory=1 to parallelize data loading over multiple subprocesses if your GPU is not fully utilized. If you do not want to log experiments with TensorBoard, append --logdir=''. To run experiments in parallel on multiple GPUs, simply run the script multiple times with different CUDA device indices (the ones already running or finished will be skipped).

The training script contains all experiments ran up to the submission deadline, but has most of them commented out.

Prediction

It is possible to compute predictions locally for a test set following the challenge's test set layout (for example, the birdcall-check or birdcall-check-2 dataset). To do so, run the predict_kagglebirds2020.py script, pointing it to the location of the dataset and all the model files you want to ensemble:

OMP_NUM_THREADS=1 ./predict_kagglebirds2020.py --threshold=0.5 \
  --threshold-convert=logit --var data.len_max=20 --local-then-global \
  --local-then-global-overlap=0.5 --filter-local-by-global \
  --filtered-threshold=0.1 --var model.pretrained_weights= \
  --train-csv=definitions/datasets/kagglebirds2020/train.csv \
  --test-csv=/share/cp/datasets/birds_kaggle_2020/external/birdcall_check2/test.csv \
  --test-audio=/share/cp/datasets/birds_kaggle_2020/external/birdcall_check2/test_audio \
  results/kagglebirds2020/pann/rnddownmix_noiseprob10_noisemaxfact10_blocks6_log1px_negprob001_r1.mdl \
  results/kagglebirds2020/pann/rnddownmix_noiseprob10_noisemaxfact10_noisemaxamp10_blocks6_log1px_negprob001_r1.mdl \
  results/kagglebirds2020/pann/rnddownmix_noiseprob10_noisemaxfact10_blocks6_log1px_r1.mdl \
  /tmp/predictions.csv

This includes several options for the inference. The most important one seems to be --filtered-threshold=...: Lowering it will allow more local detections to come through for the species that were found to be present in the recording with the larger global --threshold=... and longer pooling window of length --var data.len_max=... (in seconds). The challenge submissions were done with --filtered-threshold=0.3, but a value of 0.2, 0.1 or 0.05 gives a progressively better balance of precision and recall, and a higher f1-score.

Evaluation

It is also possible to evaluate predictions produced as above against a ground truth "perfect submission" as included in the birdcall-check-2 dataset:

./eval_kagglebirds2020.py \
  --train-csv=definitions/datasets/kagglebirds2020/train.csv \
  /share/cp/datasets/birds_kaggle_2020/external/birdcall_check2/perfect_submission.csv \
  /tmp/predictions.csv

Submission

The submission to Kaggle is based on the same prediction script used above. The idea is to upload the code and model weights as a private dataset, then have a simple Kaggle kernel extract them and run the prediction script. Two shell scripts are included to help with this. The first one just collects the files:

./kaggle_pack.sh \
  results/kagglebirds2020/pann/rnddownmix_noiseprob10_noisemaxfact10_blocks6_log1px_negprob001_r1.mdl \
  results/kagglebirds2020/pann/rnddownmix_noiseprob10_noisemaxfact10_noisemaxamp10_blocks6_log1px_negprob001_r1.mdl \
  results/kagglebirds2020/pann/rnddownmix_noiseprob10_noisemaxfact10_blocks6_log1px_r1.mdl

The code is stored in kaggle_upload/kaggle_py.tgz and the model weights and configurations in kaggle_upload/kaggle_mdl.tgz.

You can either directly upload them as a private dataset, or automate this even further: Install the Kaggle API client (pip3 install kaggle), create an API token (see https://www.kaggle.com/docs/api), create a private dataset on Kaggle, then update the kaggle_upload/dataset-metadata.json file. Once done, you can call kaggle_upload.sh "some comment" to create a new version of the dataset using what's in the kaggle_upload/ directory.

Finally, create a new Notebook on Kaggle, add both your own dataset and the birdcall-check dataset, import the notebook from kaggle_submit.ipynb (or copy/paste the commands), and do "Save version and run all". Afterwards it should be ready for submission. Whenever you have a new ensemble, just rerun ./kaggle_pack.sh and ./kaggle_upload.sh, open the notebook, check for a new version for your private dataset, then do "Save version and run all" again.