Beat-PD challenge

https://www.synapse.org/#!Synapse:syn20825169

Yidi Huang, Mark Keller, Mohammed Saqib

This repository contains our submission for the BEAT-PD challenge. Our pipeline is presented as a set of two Jupyter notebooks: feature extraction.ipynb and personalized.ipynb, respectively handling feature extraction and model fitting/evaluation. The final_sub branch (default) contains a cleaned up copy of our code, consisting of the minimum necessary files to reproduce our final pipeline. Other approaches we tried can be found in the other branches.

Pipeline overview

• Extract tsfresh features from windowed observations
  • Computed feature representations are saved to extracted_features/
• Randomized hyperparameter search with CV
  • Scores from hyperparameter search are saved to performance/
• Re-fit with winning hyperparameters
  • Fitted models are saved to models/
• Predict test data
  • Final test set predictions are saved to test_predictions/

The first three steps can be resource intensive. Cached results from the hyperparameter search and model fitting are available in this repository, and extracted feature representations are available for download here.

Prerequisites

• Python3.6+
• Anaconda - env.yml contains an anaconda environment specification
• A SLURM cluster - fitted models can be evaluated without a cluster, but feature extraction and fitting will be greatly accelerated using a cluster, and the hyperparameter search is infeasible on a single computer.
  • Easily switch between local and distributed execution by uncommenting either SLURMCluster or LocalCluster in the initialization cells at the top of the notebooks
  • If running on a SLURM cluster, the arguments to SLURMCluster() and cluster.adapt() may need tuning. More information on the dask scheduler here and available parameters here.

Pipeline in detail

The test set predictions can be regenerated using our pre-trained models following the directions in the last section below and downloading the extracted feature representations from here.

Preconditions

The feature extraction step, first in the pipeline, expects to find the raw data files in the data/ directory. Specifically, it looks for raw sensor csv files in data/cis-pd/training_data/*.csv for CIS-PD and data/real_pd/training_data/*/*.csv for REAL-PD. It also expects to find the test set sensor files under data/test_set/{cis,real}-pd/testing_data/{*.csv,*/*.csv}.

Feature extraction

The feature extraction.ipynb notebook iterates through the supplied raw data directories and extracts a collection of feature vectors. For each raw sensor file, it computes a composite signal that is the root mean square of the supplied axes. It then extracts 10s data windows for every 5s of signal, and uses the tsfresh library to compute a feature vector for each window. This process is parallelized over data files using a distributed Dask cluster. The outputs of this step are written to the extracted_features/ensem/ directory, organized by dataset. A copy of these files is also made available for download here.

Hyperparameter search

The hyperparameter search takes place in the Model eval h2 heading in personalized.ipynb. It can be started by running the notebook as shown through the end of the Model eval heading to perform the search for all CIS-PD models, and by replacing dataset='cis-tsfeatures' with dataset='real_watch_accel-tsfeatures' under the Load data h1 heading, and replacing for subj in cis_subjs with for subj in real_subjs under Model eval. The search process can be intensive. The search parameters and cluster configuration shown were feasible given our time and resource constraints, but may not be on a different cluster. The results from the search are saved in performance/cv_paramsweeps/

Re-fit on train data

The best performing hyperparameters for each model were used to initialize a new model, which was fitted on all of the available training data. This requires the data be loaded and the model specified by running personalized.ipynb through the end of the Model spec heading. The first two cells under Train final model params perform the model fits in distributed fashion and serializes the fitted models to be saved under models/final_fitted. As saved, the notebook is configured for CIS-PD, but can be changed for REAL-PD by making the changes described in the previous section.

Predict test data

The set of models used to generate our final test set predictions are saved in the models/final_fitted/ directory following an intuitive naming scheme. Additionally, the windowed feature vector representations of the test set data can be generated following the feature extraction section above. These can be loaded in order to reproduce our final test set predictions. This step can be reproduced by first running personalized.ipynb through the first cell under Load data, then running the cells under Predictions on test set. Assuming that the files are found in their expected locations, this step will generate a prediction for each sample using the personalized model for that subject, making a naive guess using the subject-specific mean if the model was unable to make a prediction on that sample.