Community forum for the 2008 PhysioNet/CinC Challenge (Sept. 23, 2008, 2:46 p.m.)
If you have any questions or comments regarding this challenge, please post it directly in our Community Discussion Forum. This will increase transparency (benefiting all the competitors) and ensure that all the challenge organizers see your question.
Results from the PhysioNet/CinC Challenge 2008 (Sept. 22, 2008, midnight)
Congratulations to the winners of the PhysioNet/CinC Challenge 2008 on the subject of T-wave alternans. Final results are now available: scores, reference rankings of the Challenge 2008 data set, and the open source software contributed by participants in the open source division of the Challenge.
PhysioNet/CinC Challenge 2008 (March 17, 2008, midnight)
The PhysioNet/Computers in Cardiology Challenge 2008 is underway. The topic of this, the ninth open challenge in our annual series, is detection and quantification of T-wave alternans.
When using this resource, please cite the following publications:
The ninth annual PhysioNet/Computers in Cardiology Challenge aims to improve understanding of methods for identification and analysis of T-wave alternans in the ECG.
One hundred years after the first observation of T-wave alternans was reported by HE Hering , the phenomenon is widely understood to be an important indicator of risk of sudden cardiac death. Yet for most of that time TWA was believed to be rare. In 1981, at the eighth annual meeting of Computers in Cardiology, Dan Adam, Solange Akselrod, and Richard Cohen first reported the existence of microvolt-level T-wave alternans , too small in amplitude to be detected visually at standard display scales.
T-wave alternans (TWA) is a pattern in the ECG characterized by two (rarely more) distinct forms of T-waves appearing in alternation, at or above a patient-specific heart rate generally in the range of 90 to 120 beats per minute. Although the mechanisms have not been fully elucidated, a large amount of empirical evidence collected during the past 25 years has demonstrated an association between the amount of TWA, the heart rate at which it appears, and the risk of sudden cardiac death (SCD). In particular, the absence of significant TWA in a patient with congestive heart failure, low ejection fraction, or a recent myocardial infarction is strongly predictive of a low risk of SCD. A positive finding in such a patient, though less specific, may indicate that an implantable cardiac defibrillator would be appropriate, an indication that can be confirmed using invasive testing. Since TWA analysis is performed on the surface ECG, it is an inexpensive and non-invasive test. In clinical applications, TWA analysis can be done as part of an exercise stress test, but there is interest in the research community in using conventional long-term (Holter) ECG recordings to observe TWA in the context of activities of daily living. A review by Armoundas, Tomaselli, and Esperer discusses mechanisms that may account for the associations among TWA and other risk factors for SCD, as well as clinical applications of TWA .
A variety of algorithms for detecting and quantifying TWA have been proposed, employing techniques from linear and nonlinear signal processing such as spectral analysis, complex demodulation, counting zero-crossings in a series of correlation coefficients, periodogram and complex demodulation analysis of T-wave principal components, Capon filtering, Poincaré maps, periodicity transforms, statistical tests, moving averages, maximum likelihood estimators and generalized likelihood ratio tests, and more. For a comprehensive and systematic discussion of methods for TWA detection and analysis, see the review by Martínez and Olmos .
PhysioNet has a wide variety of data that might be appropriate for this challenge. Visitors were invited to nominate some of these data for inclusion in the challenge data set, from among those in these databases:
A good challenge data set should include not only clear-cut cases, but also a sampling of cases that might be expected to pose problems (for example, because of changes in conduction patterns, ectopy, or noise).
Participants were asked send a list of the records they wished to nominate for inclusion in the official challenge data set by email to email@example.com with the subject “Challenge 2008 data nomination”, no later than noon GMT on Thursday, 17 April 2008. Those who wished to nominate records other than those in the databases listed above were asked to state briefly why they believed their choices are particularly appropriate for this challenge. Participants also were invited to contribute data to PhysioNet to be considered for this challenge, and several did so. Thanks to all who participated in this process.
We have compiled all nominations and selected the most promising cases for inclusion in the official data set, together with new cases that have not been available previously. The official PhysioNet/Computers in Cardiology Challenge 2008 data set is now available (as individual files) and, for convenience, it is also available as a tarball.
Scores will be determined by the following procedure, once a minimum number of entries have been received:
You will receive your score by return email. The first scores will be sent on or about 27 April 2008; scores for entries received after that date will usually be sent within a day of receipt.
The reference rankings are initially determined by the entries received. Final reference rankings will be compiled in August. Scores reported before that time are preliminary and are subject to change. Final scores used to determine the winners of the challenge will be sent to all participants shortly after the deadline for entries (1 September 2008).
As in previous years, the Challenge will include an open source division. You may enter the open source division by sending your source code by email, before noon GMT on Monday, 1 September 2008, to PhysioNet. Use the subject line “Challenge 2008 entry source”, and be sure to include:
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:
/* twarng.c - Detect and measure T-wave alternans using a random number generator Copyright (C) 2008 Herman Foobar <firstname.lastname@example.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.
If you submit an abstract describing your work on the challenge no later than 1 May 2008 to Computers in Cardiology, and a challenge entry no later than 1 September 2008 at noon GMT, you may be eligible for one or more awards that will be presented during the final plenary session of the conference on Wednesday, 17 September 2008.
The Board of Directors of Computers in Cardiology provides an annual grant of US$1000 for challenge awards. This year, a matching contribution from Electrogram, Inc. has allowed us to double the prize fund. We are deeply grateful for the generosity and enthusiastic support of Electrogram and Computers in Cardiology.
An award of US$1000 will be received by the eligible participant who achieves the best final score overall in this year’s Challenge.
An additional award of US$1000 will be given to the winner of the open source division. Participants in the open source division are eligible for both awards.
Regarding the estimate of the peak T-wave alternans magnitude, in what units it should be expressed? Does the estimate include the T-wave magnitude or only the added alternans?
You may use whatever units you wish. Estimate the magnitude of the alternans, not the magnitude of the T-waves. (Some methods involve expressing alternans magnitude or power as a fraction of total T-wave magnitude or power; it’s fine to do this, or not to do this, as you wish — but don’t add a T-wave measurement to your alternans estimate.)
The scoring is based on how your estimates rank the records (from least to most TWA) compared with a reference ranking of the records. Thus the units you choose don’t matter, so long as you use the same units for all of your measurements.
This is a hard problem, and I won’t be able to get final results in time for the abstract deadline. What needs to be submitted in the abstract?
Briefly, you will need to submit a short (~300 words) abstract, which may not include illustrations, by 1 May. Abstracts must be submitted on-line.
It would be ideal if you have submitted rough results for the Challenge problem no later than 27 April, so they can be scored and so that you can report your preliminary score in your abstract. If this is not possible, please discuss in your abstract relevant studies you have performed to date, touching on any novel aspects of your methods and quoting whatever results you have. Generally abstracts containing only “we will show ...” without any results are not accepted, so it is very important that you demonstrate in the abstract that you have actually accomplished something already. Given the complexity of the challenge and the short time available for working on it, the abstract reviewers will certainly make some allowance for those who are unable to obtain results on the challenge problem by the abstract deadline, if it appears they will be able to do so before the conference in September.
May I revise my entry?
You may submit entries at any time until the final deadline of noon GMT on 1 September. Each entry will be scored, and you may attempt to improve your score by submitting up to four revised entries (five in all).
You may choose any of your (up to five) entries as the basis for ranking, by sending an email specifying your choice to email@example.com, on or before noon GMT on 1 September. Please remember that it may take up to 24 hours after submitting an entry to receive scores, so try to submit your last entry at least a day before the deadline if you think you may want to exercise your choice. Your last entry will be used for ranking unless you specify otherwise.
If my abstract is accepted, what else must I do?
In September, if your abstract is accepted, you will be expected to submit a four-page paper, which may be illustrated, for publication in Computers in Cardiology on-line and in print. You will also be expected to attend the conference (14-17 September 2008 in Bologna, Italy) and to present your work in one of the scientific sessions of the conference, either as a poster or as a 10-minute oral presentation. Your paper and presentation should include your final results.
Why don’t you have a challenge about ...?
Each year, we receive many suggestions for challenge topics. We encourage you to contact us with further suggestions.
Final results are now available: papers presented by participants at CinC 2008, scores, reference rankings and additional details for the Challenge 2008 data set, and the open source software contributed by participants in the open source division of the Challenge.
The papers below were presented at Computers in Cardiology 2008. Please cite this publication when referencing any of these papers. These papers have been made available by their authors under the terms of the Creative Commons Attribution License 2.5 (CCAL). We wish to thank all of the authors for their contributions.
The first of these papers is an introduction to the challenge topic, with a summary of the challenge results and a discussion of their implications.
The remaining papers were presented by participants in the Challenge, who describe their approaches to the challenge problem.
An Open-Source Standard T-Wave Alternans Detector for
A Khaustov, S Nemati, GD Clifford
Anyone can access the files, as long as they conform to the terms of the specified license.
Download the ZIP file (81.1 MB)
Access the files using the Google Cloud Storage Browser here. Login with a Google account is required.
Access the data using the Google Cloud command line tools (please refer to the gsutil documentation for guidance):
gsutil -m -u YOUR_PROJECT_ID cp -r gs://challenge-2008-1.0.0.physionet.org DESTINATION
Download the files using your terminal:
wget -r -N -c -np https://physionet.org/files/challenge-2008/1.0.0/
Supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) under NIH grant number R01EB030362.