The PhysioNet/Computing in Cardiology Challenge 2010:
Mind the Gap

In settings ranging from sleep studies to surgery to sports medicine to intensive care, real-time monitoring of a variety of physiologic signals has become an essential tool for clinicians and researchers. Transient corruption or loss of one or more signals, common in all of these settings, can be disruptive, especially when continuous observations are required in order to rule out rare events or as a basis for forecasting. Signal corruption can be particularly challenging when it mimics features that are associated with pathologic states.

Humans can be remarkably adept at dealing with transient noise and signal loss in these settings. Filling in gaps, and making use of context to recognize and ignore noise, are processes that our sensory and cognitive abilities leave us well-equipped to do. Can algorithmic solutions that take account of the same data, in broader contexts and without fatigue, do as well?

The aim of this year's challenge is to develop robust methods for filling in gaps in multiparameter physiologic data (including ECG signals, continuous blood pressure waveforms, and respiration), and for recognizing intervals of signal corruption in these data. In event 1, participants are asked to reconstruct, using any combination of available prior and concurrent information, segments of signals that have been removed from multiparameter recordings of patients in intensive care units. In event 2, segments of the signals to be reconstructed have been corrupted with noise, and the task is to locate the corrupted segments as well as to estimate the original signals.

Data for the Challenge

Participants are provided with three data sets, each containing segments of missing and corrupted signals that replace the target signals (the original uncorrupted signals that are to be reconstructed):

• Set A is a small set of records for participants' use as a training set. The target signals are provided for the records in this set. Additional training data can easily be constructed from any of the multiparameter data available in PhysioBank, such as the MIMIC II Waveform Database.
• Set B is a large set of records for which the target signals are withheld until the conclusion of the challenge. Participants may submit reconstructions of the target signals in this set once per day for the duration of the challenge; they will receive scores (which will also be posted on this web site) for each submission.
• Set C is also a large set of records, with the target signals withheld. Participants may submit reconstructions of the target signals at any time for the duration of the challenge, but they will not receive scores except for their final submissions, which will determine the final rankings and the winners of the challenge.

Since the target signals are known, the accuracy of the reconstruction can be measured directly as the RMS difference between the target and the reconstructed signals.

The data sets will be posted beginning on 1 December 2009, along with information on how to submit reconstructions for scoring. To download them efficiently, use rsync as described here (retrieve the challenge-2010 "module").

Entering the Challenge

The Challenge will begin on 1 January 2010, and entries will be accepted until 1 September 2010.

To be eligible for an award:

• Submit at least one valid entry (to either event) no later than noon GMT on Friday, 30 April 2010.
• Submit an abstract (about 300 words) describing your work on the Challenge to Computing in Cardiology (CinC) by 1 May 2010. Please select "PhysioNet/CinC Challenge" as the topic of your abstract, so it can be identified easily by the abstract review committee.
• Attend Computing in Cardiology in Belfast, Northern Ireland, 26-29 September.

If your abstract is accepted, you will be expected to prepare a four-page paper for publication in Computing in Cardiology, and to present a talk or poster about your work at CinC.

During a plenary session of Computing in Cardiology in September, four awards will be presented to the eligible participants in attendance with the best final scores as follows:

1. Best open source entry in event 1
2. Best entry in event 1
3. Best open-source entry in event 2
4. Best entry in event 2

As in previous years, the Challenge includes an open source division. You may enter the open source division by sending the source code for your challenge entry by email, before noon GMT on Wednesday, 1 September 2010, to PhysioNet. Use the subject line "Challenge 2010 entry source", and be sure to include:

• Your name and email address
• All sources needed to produce a working version of your software (except for readily available standard libraries and header files)
• A note describing how to produce a working version of your software (a commented Makefile is ideal), and how to run your software

Each source file submitted should begin with a comment block containing the names of its authors and a reference to the open source license you have chosen for it, if any; for example:

     /* fill.c - fill signal gaps using large wads of duct tape
        Copyright (C) 2010  Herman Foobar <hbar@uncertain.org>
        This software is released under the terms of the GNU General
        Public License (http://www.gnu.org/copyleft/gpl.html).
     */

Source files in C, C++, Fortran, or Matlab m-code are preferred; other languages may be acceptable, but please ask first. Do not submit any code that cannot be freely redistributed. Following the conclusion of the Challenge, selected entries will be posted, with full credit to their authors, on PhysioNet.

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Updated Tuesday, 01-Dec-2009 12:54:47 EST