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Motion Code

I. Introduction

In this work, we employ variational inference and stochastic process modeling to develop a framework called Motion Code.

1. Download datasets and trained models

The trained models for Motion Code is available in the folder saved_models due to their small sizes. However, for reproducibility, you need to download the datasets as we cannot store them directly in the repos due to limited storage. In addition to data, the trained attention-based benchmarking models are available through downloading. To download the datasets and attention-based benchmarking models, follow 3 steps:

  1. Go to the download link: https://www.swisstransfer.com/d/b3ff7a9a-52fc-49b4-a25c-1e584707bd18 and download the zip file.

    • Password: assets_for_motion_code

    Note that it can take up to 10 minutes to download the file. Additionally, the link is expired every month, but this repos is continuously updated and you can always check this README.md for updated link(s)

  2. Unzip the downloaded file. Inside the file is motion_code folder, which contains 2 sub-folders data and TSLibrary:

    • The data folder contains experiment data (basic noisy datasets, audio and parkinson data). Copy this folder to the repo root (if data folder already exists in the repo, then copy its content over).
    • TSLibrary contain 3 folders, and you need to add these 3 folders to the TSLibrary folder of the repo. These 3 folders include:
      • dataset: contains .ts version of data folder
      • checkpoints: contains trained attention-based models
      • results: contains classification results of attention-based models

  3. Please make sure that you have data, dataset, checkpoints, and results downloaded and stored in the correct location as instructed above. Once this is done, you're ready to run tutorial notebooks and other notebooks in the repo.

2. Basic usage

Please look at the tutorial notebook tutorial_notebook.ipynb to learn how to use Motion Code. To initialize the model, use the code:

from motion_code import MotionCode
model = MotionCode(m=10, Q=1, latent_dim=2, sigma_y=0.1)

For training the Motion Code, use:

model.fit(X_train, Y_train, labels_train, model_path)

Motion Code performs both classification and forecasting.

  • For the classification task, use: 
    model.classify_predict(X_test, Y_test)
  • For the forecasting task, use: 
    mean, covar = model.forecast_predict(test_time_horizon, label=0)

All package prerequisites are given in requirements.txt. You can install by

pip install -r requirements.txt

II. Interpretable Features

To learn how to generate interpretable features, please see Pronunciation_Audio.ipynb for further tutorial. This notebook gets the audio data, trains a Motion Code model on the data, and plots the interpretable features obtained from Motion Code's most informative timestamps.

Here are some examples of the most informative timestamps features extracted from Motion Code that captures different underlying dynamics:

Humidity sensor (MoteStrain) Temperature sensor (MoteStrain)
Winter power demand (ItalyPowerDemand) Spring power demand (ItalyPowerDemand)
Word "absortivity" (Pronunciation audio) Word "anything" (Pronunciation audio)



III. Benchmarking

The main benchmark file is benchmarks.py. For benchmarking models, we consider two types:

  • Non attention-based and our model
  • Attention-based model such as Informer or Autoformer

You can get all classification benchmarks in a highlighted manner by running the notebook collect_all_benchmarks.ipynb. Once the run is completed, the output out/all_classification_benchmark_results.html will contain all classification benchmark results. To further doing more customize steps, you can follow additional instructions below:

2. Non Attention-Based Method

Running Benchmarks:

  1. Classification benchmarking on basic dataset with noise: 
    python benchmarks.py --dataset_type="basics" --load_existing_model=True --load_existing_data=True --output_path="out/classify_basics.csv"
  2. Forecasting benchmarking on basic dataset with noise: 
    python benchmarks.py --dataset_type="basics" --forecast=True --load_existing_model=True --load_existing_data=True --output_path="out/forecast_basics.csv"
  3. Classification and forecasting benchmarking on (Pronunciation) Audio dataset: 
    python benchmarks.py --dataset_type="pronunciation" --load_existing_model=True --load_existing_data=True --output_path="out/classify_pronunciation.csv"
python benchmarks.py --dataset_type="pronunciation" --forecast=True --load_existing_model=True --load_existing_data=True --output_path="out/forecast_pronunciation.csv"
  4. Benchmarking on Parkinson data for either PD setting 1 or PD setting 2: 
    python benchmarks.py --dataset_type="parkinson_1" --load_existing_model=True --output_path="out/classify_parkinson_1.csv"
python benchmarks.py --dataset_type="parkinson_2" --load_existing_model=True --output_path="out/classify_parkinson_2.csv"

3. Attention-Based Method

We will use the Time Series Library (TSLibrary), stored in the TSLibrary folder. To rerun all training, execute the script:

bash TSLibrary/attention_benchmark.sh

For efficiency, it is recommended to use existing (already) trained models and run collect_all_benchmarks.ipynb to get the benchmark results.

4. Hyperparameter Details

Classification:

  • DTW: distance="dtw"
  • TSF: n_estimators=100
  • BOSS-E: max_ensemble_size=3
  • Shapelet: estimator=RotationForest(n_estimators=3), n_shapelet_samples=100, max_shapelets=10, batch_size=20
  • SVC: kernel=mean_gaussian_tskernel
  • LSTM-FCN: n_epochs=200
  • Rocket: num_kernels=500
  • Hive-Cote 2: time_limit_in_minutes=0.2
  • Attention-based parameters: Refer to TSLibrary/attention_benchmark.sh

Forecasting:

  • Exponential Smoothing: trend="add", seasonal="additive", sp=12
  • ARIMA: order=(1, 1, 0), seasonal_order=(0, 1, 0, 12)
  • State-space: level="local linear trend", freq_seasonal=[{"period": 12, "harmonics": 10}]
  • TBATS: use_box_cox=False, use_trend=False, use_damped_trend=False, sp=12, use_arma_errors=False, n_jobs=1

IV. Visualization

The main visualization file is visualize.py.

1. Motion Code Interpretability

To extract interpretable features from Motion Code, run:

python visualize.py --type="classify_motion_code" --dataset="PD setting 2"

Change the dataset argument as needed (e.g., Pronunciation Audio, PD setting 1, PD setting 2).

2. Forecasting Visualization

  1. To visualize forecasting with mean and variance: 
    python visualize.py --type="forecast_mean_var" --dataset="ItalyPowerDemand"
  2. To visualize forecasting with informative timestamps: 
    python visualize.py --type="forecast_motion_code" --dataset="ItalyPowerDemand"

V. File Structure

  1. Tutorial notebooks: tutorial_notebook.ipynb, Pronunciation_Audio.ipynb
  2. data folder: Contains three subfolders:
    • basics: Basic datasets with noise.
    • audio: Pronunciation Audio dataset.
    • parkinson: Parkinson sensor dataset.
  3. saved_models folder: Contains (already) trained Motion Code models for inference and benchmarking.
  4. Python files:
    • Data processing: data_processing.py, parkinson_data_processing.py, utils.py
    • Motion Code model: motion_code.py, motion_code_utils.py, sparse_gp.py
    • Benchmarking: benchmark.py (Non-attention), collect_all_benchmarks.ipynb (All)
    • Visualization: visualize.py
    • Other notebooks: Under notebooks folder are MotionCodeTSC_create.ipynb to convert .npy to .ts data and Pronunciation_Audio.ipynb for extracting intepretable feature from varying-length audio data
  5. Time Series Library TSLibrary folder : contains attention_benchmark.sh for re-running all attention-based benchmarking models training.