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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#1F497D">Apologies for multiple posts
</span><span style="font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Announcement of Data Release and Call for Participation<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">2014 i2b2/UTHealth Shared-Tasks and Workshop<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">on Challenges in Natural Language Processing for Clinical Data<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><a href="https://www.i2b2.org/NLP/">https://www.i2b2.org/NLP/</a></span></span><span style="font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Tentative Timeline<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Registration: begins March 14, 2014<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Training Data Release: 1 May, 2014<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Test Data Release: 1 July, 2014<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">System Outputs Due: 3 July, 2014<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Systems Due: 15 July, 2014<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Paper Submission: 1 August, 2014<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Workshop: TBA<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">The 2014 i2b2/UTHealth challenge consists of two traditional NLP tracks:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Track 1: De-identification: Removing protected health information (PHI) is a critical step in making medical records accessible to more people, yet it is a very difficult and nuanced task.
This track addresses the problem of de-identifying medical records over a new set of over 1300 patient records, with surrogate PHI for participants to identify.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Track 2: Identifying risk factors for heart disease over time: Medical records for diabetic patients contain information about heart disease risk factors such as high blood pressure and cholesterol
levels, obesity, smoking status, etc. This track aims to identify the information that is medically relevant to identifying heart disease risk, and track their progression over sets of longitudinal patient records.<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">The data for this task is provided by Partners HealthCare. All records have been fully de-identified and manually annotated for risk factors related to diabetes and heart disease risk factors.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Data for the challenge will be released under a Rules of Conduct and Data Use Agreement. Obtaining the data requires completing a registration, which will start March 14, 2014.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">For either track, i2b2 will give the participants the option to submit their system software in addition to their system output for evaluation. Teams that submit software will be evaluated
separately from teams that submit only system output.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">In addition, the i2b2 organizing committee is currently considering hosting a general "i2b2 Software for Clinical NLP" track that allows all past and current i2b2 challenge participants to
submit and share with the community any software developed for any i2b2 shared-task.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Evaluation Dates, File Formats, and Evaluation Metrics<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">The evaluation for the NLP tracks will be conducted using withheld test data. Participating teams are asked to stop development as soon as they download the test data. Each team is allowed
to upload (through this website) up to three system runs for each of the tasks. System output is expected in the form of standoff annotations, following the exact format of the ground truth annotations to be provided by the organizers.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Evaluation of submitted software will be evaluated by the program committee on factors such as ease of installation and ease of use.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Participants are asked to submit a short paper describing their system and analyzing their performance. Papers should be in AMIA style and should not exceed five pages. Authors of top performing
systems and of particularly novel approaches will be invited to present or demo their systems at the workshop. Submitted software can be presented at the final workshop in the form of a poster or live demo.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Tentative Schedule:<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">March 14, 2014<span class="apple-tab-span">
</span> Registration Opens<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">May 1, 2014<span class="apple-tab-span">
</span>Training Data Release<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">July 1, 2014<span class="apple-tab-span">
</span>Test Data Release<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">July 3, 2014<span class="apple-tab-span">
</span>System Outputs on Test Data Due at 11:59pm Eastern Time<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">July 15, 2014<span class="apple-tab-span">
</span> Systems Due<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">August 1, 2014<span class="apple-tab-span">
</span> Paper Submissions<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">TBA<span class="apple-tab-span">
</span>Workshop<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Organizing Committee:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Ozlem Uzuner, co-chair,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">SUNY at Albany<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Amber Stubbs, co-chair,<span class="apple-tab-span"><o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">SUNY at Albany<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Hua Xu, co-chair,<span class="apple-tab-span">
</span> University of Texas, Houston<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">John Aberdeen,<span class="apple-tab-span">
</span> MITRE<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Susanne Churchill,<span class="apple-tab-span">
</span> Partners Healthcare<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Cheryl Clark,<span class="apple-tab-span">
</span> MITRE<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Dina Demner Fushman,<span class="apple-tab-span">
</span> NIH/NLM<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Joshua Denny,<span class="apple-tab-span">
</span> Vanderbilt University<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Bill Hersh,<span class="apple-tab-span">
</span>Oregon Health and Science University<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Lynette Hirschman,<span class="apple-tab-span">
</span> MITRE<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Issac Kohane,<span class="apple-tab-span">
</span> Partners Healthcare<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Vishesh Kumar,<span class="apple-tab-span">
</span> Massachusetts General Hospital<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Anna Rumshisky,<span class="apple-tab-span">
</span> UMass Lowell<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Stanley Shaw,<span class="apple-tab-span">
</span> Massachusetts General Hospital<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Peter Szolovits,<span class="apple-tab-span">
</span> MIT<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Meliha Yetisgen,<span class="apple-tab-span">
</span> University of Washington<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif"">Please see the announcements for more information. Questions on the challenge can be addressed to Ozlem Uzuner, <a href="mailto:i2b2nlp@albany.edu">i2b2nlp@albany.edu</a>.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif""><br>
<o:p></o:p></span></p>
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