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IDOBE: Infectious Disease Outbreak forecasting Benchmark Ecosystem

Overview

IDOBE is a curated collection of epidemiological time series focused on outbreak forecasting. IDOBE compiles from multiple data repositories spanning over a century of surveillance and across U.S. states and global locations. This repository provides

  • Over 10000 outbreak timeseries corresponding to different diseases
  • Scripts for extracting analytical measures to analyze outbreaks
  • A suite of trained baseline forecasting models (statistical and DNN models)
  • Evaluation scripts of probabilistic forecasts

Data

  • raw_data/outbreaks_disease_location.csv

Data statistics

  • stats/output/ - consists of entropy, permutation entropy, and shape statistics for the different outbreaks
  • stats/stats_compute.ipynb - notebook for computing the different statistics

Baseline models

  • baselines/src/ - folder contains different classes of models