Last CFP: Automated clinical coding (ICD10) shared task: CodiEsp track (eHealth CLEF2020

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**** Call for Participation CodiEsp: Clinical Case Coding Task (eHealth
CLEF 2020) *** *



*CodiEsp (eHealth CLEF=E2=80=93 Multilingual Information Extraction) Shared=
 Task on
automatic assignment of ICD10 codes (procedures, diagnosis) track at CLEF
2020*

http://temu.bsc.es/codiesp



Plan TL Award for the CodiEsp Track



We are currently organizing a shared task on automated clinical coding
methods (CodiEsp) that will be part of the eHealth CLEF 2020.


Clinical coding is of critical importance to generate indicators related to
diagnoses in epidemiological studies (epidemiology/health trends) and
determine treatment effectiveness resulting in a direct impact in patient
healthcare.


The CodiEsp sub-tracks:

*1.CodiEsp Diagnosis Coding *sub-task* (CodiEsp-D)*: will require automatic
ICD10-CM [CIE10 Diagn=C3=B3stico] code assignment to each clinical case doc=
ument.

*2.CodiEsp Procedure Coding *sub-task* (CodiEsp-P):* will require automatic
ICD10-PCS [CIE10 Procedimiento] code assignment to each clinical case
document.

*3.CodiEsp Explainable AI *exploratory sub-task* (CodiEsp-X).* Systems are
required to extract the evidence text supporting the predicted codes (both
ICD10-CM and ICD10-PCS).



*Task description*

Clinical coding essentially requires the transformation (or classification)
of medical texts into a structured or coded format using internationally
recognized class codes.

These codes describe a patient=E2=80=99s diagnosis or treatment. Clinical c=
oding is
critical for standardizing electronic clinical records; enable aetiology
studies, monitor health trends, carry out epidemiology studies, clinical
and biomedical research, assist clinical decision-making or even
reimbursement.

As part of the eHealth CLEF (http://clef-ehealth.org) Multilingual
Information Extraction Shared Task we organize* CodiEsp: Clinical Case
Coding Task (http://temu.bsc.es/codiesp <http://temu.bsc.es/codiesp>). *The
CodiEsp task will address the automatic extraction and assignment of
clinical coding (diagnosis and procedures) to clinical case documents in
Spanish.

To enable participation of researches around the world, in addition to the
basic data in Spanish, we will also publish versions of the training,
development, and test set *automatically translated into English*.

Participating systems will be asked to automatically assign ICD10 codes (or
CIE-10, in Spanish) to clinical case documents. Evaluation is done through
comparison to manually assigned ICD10 codes.

*Publications and workshop*

As in previous eHealth CLEF efforts, there will be an *evaluation workshop
allocated at CLEF 2020* where participating teams can present their systems
and results. Moreover, participating teams will be invited to submit their
system description papers for publication at the *CLEF 2020 Working Notes
proceedings*. For previous working notes see: http://ceur-ws.org/Vol-2125/



*CodiEsp awards*

There will we three awards for the top-scoring teams promoted by the
Spanish Plan for the Advancement of Language Technology (Plan TL) and the
Barcelona Supercomputing Center (BSC).

--------------------------------------

*Participation and useful info*

--------------------------------------

   1. CodiEsp web, info & detailed description:http://temu.bsc.es/codiesp/
   2. Registration for CodiEsp (Multilingual Information Extraction eHealth
   track):http://temu.bsc.es/codiesp/index.php/registration/
   3. Datasets:https://zenodo.org/record/3693570
   <https://zenodo.org/record/3693570#.Xl5bK9-YU5k>
   4. Additional training resources:https://doi.org/10.5281/zenodo.3606662



------------------------

*Main CodiEsp Track organizers*

------------------------

   - *Martin Krallinger*, Barcelona Supercomputing Center.
   - *Antonio Miranda*, Barcelona Supercomputing Center.
   - *Aitor Gonzalez-Agirre*, Barcelona Supercomputing Center.
   - *Marta Villegas*, Barcelona Supercomputing Center.
   - *Jordi Armengol*, Barcelona Supercomputing Center.



------------------------

*Important Dates*

------------------------

Jan 13: Training and development set release
March 2: Test and background set release
May 3: End of evaluation
May 5: Results notified
May  24: Paper submission
Jun 28: Camera-ready paper submission
Sep 22-25: CLEF 2020 Conference (Thessaloniki, Greece)

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<div dir=3D"ltr"><p style=3D"text-align:center"><b>*** Call for Participati=
on <span><span>CodiEsp</span></span>: Clinical Case Coding Task (eHealth CL=
EF 2020) *** <br></b></p><p style=3D"text-align:center">=C2=A0</p><p style=
=3D"text-align:center"><b><span><span>CodiEsp</span></span>
 (eHealth CLEF=E2=80=93 Multilingual Information Extraction) Shared Task on=
=20
automatic assignment of ICD10 codes (procedures, diagnosis) track at=20
CLEF 2020</b></p><p style=3D"text-align:center"><a href=3D"http://temu.bsc.=
es/codiesp" target=3D"_blank">http://temu.bsc.es/<span><span>codiesp</span>=
</span></a></p><p style=3D"text-align:center"><b>=C2=A0</b></p><p style=3D"=
text-align:center">Plan TL Award for the <span><span>CodiEsp</span></span> =
Track</p><p>=C2=A0</p><p class=3D"MsoNormal" style=3D"margin:0cm 0cm 0.0001=
pt;font-size:12pt;font-family:Cambria"><span style=3D"color:black">We are c=
urrently organizing a
shared task on automated clinical coding methods (<span>CodiEsp</span>) tha=
t will be part of
the eHealth CLEF 2020. <br></span></p><p class=3D"MsoNormal" style=3D"margi=
n:0cm 0cm 0.0001pt;font-size:12pt;font-family:Cambria"><br></p><p class=3D"=
MsoNormal" style=3D"margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:Camb=
ria">Clinical
 coding is of critical importance to generate indicators related to=20
diagnoses in epidemiological studies (epidemiology/health trends) and=20
determine treatment effectiveness resulting in a direct impact in=20
patient healthcare.</p><p><br></p><p>The <span><span>CodiEsp</span></span> =
sub-tracks:</p><p><b>1.<span><span>CodiEsp</span></span> Diagnosis Coding=
=C2=A0</b>sub-task<b>=C2=A0(<span><span>CodiEsp</span></span>-D)</b>: will =
require automatic ICD10-CM [CIE10 Diagn=C3=B3stico] code assignment to each=
 clinical case document.<b><br></b></p><p><b>2.<span><span>CodiEsp</span></=
span> Procedure Coding=C2=A0</b>sub-task<b>=C2=A0(<span><span>CodiEsp</span=
></span>-P):</b>=C2=A0will require automatic ICD10-PCS [CIE10 Procedimiento=
] code assignment to each clinical case document.</p><p><b>3.<span><span>Co=
diEsp</span></span> Explainable AI=C2=A0</b>exploratory sub-task<b>=C2=A0(<=
span><span>CodiEsp</span></span>-X).</b>=C2=A0Systems are required to extra=
ct the evidence text supporting the predicted codes (both ICD10-CM and ICD1=
0-PCS).</p><p>=C2=A0</p><p><b>Task description</b></p><p>Clinical
 coding essentially requires the transformation (or classification) of=20
medical texts into a structured or coded format using internationally=20
recognized class codes.</p><p>These codes describe a patient=E2=80=99s diag=
nosis
 or treatment. Clinical coding is critical for=C2=A0standardizing electroni=
c=20
clinical records; enable aetiology studies, monitor health trends, carry
 out epidemiology studies,=C2=A0clinical and biomedical research, assist=20
clinical decision-making or even reimbursement.</p><p>As part of the eHealt=
h CLEF (<a href=3D"http://clef-ehealth.org/" target=3D"_blank">http://clef-=
ehealth.org</a>) Multilingual Information Extraction Shared Task we organiz=
e<b>=C2=A0<span><span>CodiEsp</span></span>: Clinical Case Coding Task (<a =
href=3D"http://temu.bsc.es/codiesp" target=3D"_blank">http://temu.bsc.es/<s=
pan><span>codiesp</span></span></a>).=C2=A0</b>The <span><span>CodiEsp</spa=
n></span>
 task will address the automatic extraction and assignment of clinical=20
coding (diagnosis and procedures) to clinical case documents in Spanish.</p=
><p>To
 enable participation of researches around the world, in addition to the
 basic data in Spanish, we will also publish versions of the training,=20
development, and test set=C2=A0<b>automatically translated into English</b>=
.</p><p>Participating
 systems will be asked to automatically assign ICD10 codes (or CIE-10,=20
in Spanish) to clinical case documents. Evaluation is done through=20
comparison to manually assigned ICD10 codes.</p><p><b>Publications and work=
shop</b></p><p>As in previous eHealth CLEF efforts, there will be an=C2=A0<=
b>evaluation workshop allocated at CLEF 2020</b>=C2=A0where
 participating teams can present their systems and results. Moreover,=20
participating teams will be invited to submit their system description=20
papers for publication at the=C2=A0<b>CLEF 2020 Working Notes proceedings</=
b>. For previous working notes see:=C2=A0<a href=3D"http://ceur-ws.org/Vol-=
2125/" target=3D"_blank">http://ceur-ws.org/Vol-2125/</a></p><p>=C2=A0</p><=
p><b><span><span>CodiEsp</span></span> awards</b></p><p>There
 will we three awards for the top-scoring teams promoted by the Spanish=20
Plan for the Advancement of Language Technology (Plan TL) and the=20
Barcelona Supercomputing Center (BSC).</p><p>------------------------------=
--------</p><p><b>Participation and useful info</b></p><p>-----------------=
---------------------</p><ol><li><span><span>CodiEsp</span></span> web, inf=
o &amp; detailed description:<a href=3D"http://temu.bsc.es/codiesp/" target=
=3D"_blank">http://temu.bsc.es/<span><span>codiesp</span></span>/</a></li><=
li>Registration for <span><span>CodiEsp</span></span> (Multilingual Informa=
tion Extraction eHealth track):<a href=3D"http://temu.bsc.es/codiesp/index.=
php/registration/" target=3D"_blank">http://temu.bsc.es/<span><span>codi</s=
pan><span>esp</span></span>/index.php/registration/</a></li><li>Datasets:<a=
 href=3D"https://zenodo.org/record/3693570#.Xl5bK9-YU5k" target=3D"_blank">=
https://zenodo.org/record/3693570</a></li><li>Additional training resources=
:<a href=3D"https://doi.org/10.5281/zenodo.3606662" target=3D"_blank">https=
://doi.org/10.5281/zenodo.3606662</a></li></ol><p>=C2=A0</p><p>------------=
------------</p><p><b>Main <span><span>CodiEsp</span></span> Track organize=
rs</b></p><p>------------------------</p><ul><li><b>Martin Krallinger</b>, =
Barcelona Supercomputing Center.</li><li><b>Antonio Miranda</b>, Barcelona =
Supercomputing Center.</li><li><b>Aitor Gonzalez-Agirre</b>, Barcelona Supe=
rcomputing Center.</li><li><b>Marta Villegas</b>, Barcelona Supercomputing =
Center.</li><li><b>Jordi Armengol</b>, Barcelona Supercomputing Center.</li=
></ul><p>=C2=A0</p><p>------------------------</p><p><b>Important Dates</b>=
</p><p>------------------------</p><table width=3D"550">
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</tr></tbody></table><p class=3D"MsoNormal" style=3D"margin:0cm 0cm 0.0001p=
t;font-size:12pt;font-family:Cambria"><span></span></p>Jan 13: Training and=
 development set release<br>March 2: Test and background set release <br>Ma=
y 3: End of evaluation<br>May 5: Results notified<br>May =C2=A024: Paper su=
bmission<br>Jun 28: Camera-ready paper submission<br><div>Sep 22-25: CLEF 2=
020 Conference (Thessaloniki, Greece)</div></div>

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