ROCHESTER(INSTITUTE(OF(TECHNOLOGY(
ENGL(582/782:(ADVANCED(TOPICS(IN(COMP(LING!
TIME:!TR!9:30(10:45!!!ROOM:!LBR(3244!
!
Instructor:!Emily!Prud'hommeaux!
Office:!LBR(1317!
Email:[email protected]!
Office!hours:!Thursday!11(12!or!by!appt.!!
!
Course(description:(This!course!explores!the!application!of!natural!language!processing!
algorithms!to!biomedical!data,!including!electronic!health!records,!clinically(elicited!language!
and!speech!data,!and!biomedical!literature.!In!this!seminar(!and!project(based!class,!students!will!
read!and!discuss!scholarly!articles!to!gain!exposure!to!the!field!and!explore!topics!and!techniques!
in!more!depth!in!a!laboratory!setting,!ultimately!designing!and!implementing!a!system!for!
analyzing!biomedical!text.!ENGL!782!is!a!graduate(level!counterpart!to!ENGL!582.!Students!
enrolled!under!the!graduate(level!number!will!be!required!to!complete!extra!course!components.!
Prerequisites:!ENGL!481/781!or!instructor’s!consent.!
!
Attendance(policy:(RIT!requires!students!to!attend!class.!Please!come!to!every!class!and!arrive!
on!time.!This!is!for!your!own!benefit!since!you!are!responsible!for!knowing!the!material!that!is!
covered!in!lectures,!readings,!peer!presentations,!exercises,!and!group!work.!If!you!have!to!miss!a!
class,!prepare!any!readings!and!assignments!for!that!class!and!borrow!class!notes!from!a!
classmate.!!Whenever!you!have!questions!about!the!material,!please!send!me!an!email,!stop!by!
my!office!hours,!and!set!up!an!appointment!to!talk!with!me.!
!
Course(topics:(The!topics!explored!in!this!class!include...!
• Review!of!natural!language!processing!(NLP)!and!computational!linguistics:!language!
models,!part(of(speech!tagging,!parsing,!semantic!analysis,!text!normalization.(
• Demonstration!of!and!hands(on!practice!with!available!NLP!tools!and!software!packages.(
• Analysis!of!clinically(elicited!spoken!language!data.(
• Analysis!of!electronic!health!records!for!data!mining.(
• Information!extraction!from!biomedical!literature.(
• Applications!of!NLP!for!assistive!communication!technology.(
!
Course(objectives:!Upon!completing!this!course,!you!should!be!able!to...!
• Understand!the!computational!techniques!and!approaches!for!analyzing!human!language.!
• Use!available!NLP!tools!and!software!to!extract!linguistic!information!from!texts.!
• Run!and!improve!an!existing!language!analysis!system.!
• Think!creatively!about!features!that!can!improve!performance!of!that!system.!
• Synthesize!and!present!a!critical!summary!of!journal!articles!about!NLP!in!biomedicine.!
!
Books(and(materials:!There!is!no!required!textbook!for!this!class.!Most!of!the!readings!will!
come!from!journals!and!conferences!and!will!be!made!available!on!myCourses.!For!students!
without!a!strong!background!in!NLP!and!computational!linguistics,!I!recommend!the!following!
introductory!textbooks,!which!I!will!be!putting!on!reserve!at!the!library.(
Jurafsky,!D.,!and!Martin,!J.!(2008).#Speech#and#Language#Processing,#2nd#Edition.!!
Manning,!C.,!and!Schütze,!H.!(1999).!Foundations#of#Statistical#Natural#Language#Processing.!!
!
Classroom(expectations:!This!class!takes!place!in!a!computing!lab,!and!we!will!regularly!use!the!
special!features!of!this!classroom!to!engage!in!hands(on!activities.!Please!be!professional!and!do!
not!use!the!computers!for!activities!not!directly!related!to!the!class!(e.g.,!chatting,!social!media,!
watching!cat!videos).!
!
Equal(access:(RIT!is!committed!to!providing!reasonable!accommodations!to!students!with!
disabilities.!If!you!would!like!to!request!accommodations!such!as!special!seating!or!testing!
modifications!due!to!a!disability,!please!contact!the!Disability!Services!Office.!It!is!located!in!the!
Student!Alumni!Union,!Room!1150;!the!Web!site!is!www.rit.edu/dso.!After!you!receive!
accommodation!approval,!it!is!imperative!that!you!see!me!during!office!hours!so!that!we!can!
work!out!whatever!arrangement!is!necessary.!!
!
Course(website:(All!necessary!materials!will!be!available!in!myCourses,!and!all!necessary!
software!and!data!will!be!available!either!in!myCourses!or!on!the!computers!in!the!lab.!You!will!
need!a!working!RIT!email!account!so!that!you!receive!any!announcements!though!myCourses.!!
!
Course(requirements(and(grading(
!
Undergraduate(
Graduate(
Class!participation!and!attendance!
20%!
10%!
Lab!competition!participation!
10%!
10%!
Article!presentations!
10%!!
15%!!
Evaluation!of!peer!presentations!
5%!
5%!
Problem!set!
10%!
5%!
Quiz!
10%!
10%!
Final!project!proposal!
5%!
5%!
Final!project!presentation!
15%!
15%!
Final!project!written!report!
15%!
15%!
Annotated!bibliography!
N/A!
10%!
!
Class#participation#and#attendance:!You!are!expected!to!participate!actively!in!class!by!showing!
up,!looking!interested,!asking!questions,!and!making!insightful!comments!whenever!possible.!It!is!
your!job!to!demonstrate!that!you!are!making!an!effort!to!process!and!understand!the!material,!
whether!it!is!a!lecture,!a!peer!presentation,!a!demonstration,!or!a!lab!activity.!
!
Lab#competition#participation:#During!several!class!periods,!you!will!be!working!in!groups!to!
improve!two!language!analysis!systems:!(1)!a!system!that!identifies!patients!with!Alzheimer's!
Disease,!and!(2)!a!system!that!extracts!information!from!biomedical!journal!articles.!The!groups!
will!be!competing!to!see!which!ideas!yield!the!largest!accuracy!improvements.!(Currently(
scheduled(for(Tuesday(10/7,(and(Thursday(11/6.)(
!
Article#presentations:#Every!student!will!be!responsible!for!reading!an!article!from!a!provided!list!
(or!of!his/her!own!choosing!with!instructor!approval),!presenting!the!article!to!the!class!using!
slides,!and!facilitating!a!discussion!about!the!article.!Undergraduates!will!present!2!articles!over!
the!course!of!the!semester.!Graduate!students!will!present!3!articles.!An!article!presentation!
should!take!about!10!minutes!with!5!additional!minutes!for!questions!and!discussion.!We!will!
work!out!the!scheduling!of!the!presentations!during!the!first!few!weeks!of!class.!(Currently(
scheduled(for(Tuesday(9/30,(Thursday(10/30,(Thursday(11/13,(and(Thursday(11/20.)(
!
Evaluation#of#peer#presentations:!Periodically!I!will!ask!you!to!evaluate!the!presentations!of!your!
peers.!I!will!provide!the!evaluation!form,!and!you!will!complete!the!form!during!class!after!the!
presentation.!You!will!be!graded!on!how!thoughtfully!and!carefully!you!evaluate!your!peers.!Your!
peers'!evaluations!of!you!will!not!affect!your!grade.!
!
Problem#set:#!There!will!be!one!problem!set!that!will!guide!you!through!using!some!of!the!NLP!
tools!available!to!you!in!the!lab.!The!goal!is!to!understand!how!to!use!these!tools!well!enough!to!
be!able!to!apply!them!in!the!lab!competitions!and!in!your!final!project.!You!will!have!two!class!
periods!to!complete!the!lab,!and!you!can!return!to!the!lab!at!your!convenience!to!continue!
working.!(Tentatively(due(via(myCourses,(Friday(9/19(at(11:59pm(Rochester(time.)!
!
Quiz:!There!will!be!one!quiz!on!the!NLP!review!material.!The!purpose!of!this!quiz!is!to!ensure!
that!everyone!understands!enough!about!NLP!to!continue!with!the!course!as!I!have!planned!it.!If!
it!seems!like!we!need!more!review,!I!will!adjust!the!schedule!accordingly.!(Currently(scheduled(
for(Thursday(9/11.)!
!
Final#project:#A!large!part!of!your!grade!will!come!from!your!final!project.!The!topic!of!your!final!
project!can!be!anything!related!to!NLP!in!the!biomedical!domain.!I!will!be!presenting!several!
ideas!for!topics!during!the!first!few!weeks!of!class.!For!undergraduates,!I!recommend!an!
independent!continuation!or!extension!of!the!first!lab!competition,!using!either!new!techniques!
or!a!new!dataset!or!both.!Graduate!students!should!try!to!involve!their!current!research!program!
in!some!way,!if!possible.!
!!
• Final!project!proposal:!A!5(minute!presentation!and!a!1(page!summary!will!be!required.!
(Presentations(currently(scheduled(for(Thursday(10/9.(Written(summary(
tentatively(due(that(same(day(via(myCourses(at(11:59pm(Rochester(time.)!
• Final!project!presentation:!A!15(minute!presentation!with!5!minutes!for!questions.!
(Presentations(currently(scheduled(for(Tues.(12/2,(Thurs.(12/4,(Tues.(12/9.)!
• Final!project!written!report:!A!3(5!page!summary!of!your!project!containing!the!following!
components:!introduction!and!background,!data,!methods,!results,!conclusions!and!future!
work.!(Written(reports(due(Tuesday(12/9(at(11:59pm(Rochester(time.)!
#
Annotated#bibliography#(graduate#students#only):!Graduate!students!will!be!required!to!submit!an!
annotated!bibliography!to!accompany!their!final!project.!The!bibliography!must!contain!a!2(to(3!
sentence!summary!for!5!journal!or!conference!articles!related!to!the!topic!of!the!final!project.!
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Grade(conversion:(At!the!end!of!the!semester,!your!letter!grade!will!be!assigned!based!on!the!
following!scale:!
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Collaboration(Policy:(Collaboration!with!fellow!students!is!required!for!the!lab!competitions.!
Collaboration!with!fellow!students!is!encouraged!in!preparing!readings!and!in!working!on!the!
problem!set.!All!other!work!must!be!completed!individually.!
!
Code(of(Academic(Integrity:!As!an!institution!of!higher!learning,!RIT!expects!students!to!behave!
honestly!and!ethically!at!all!times,!especially!when!submitting!work!for!evaluation!in!conjunction!
with!any!course!or!degree!requirement.!The!Department!of!English!encourages!all!students!to!
become!familiar!with!the!RIT!Honor!Code!and!with!RIT’s!Academic!Integrity!Policy.!As!an!
additional!resource!on!specifically!the!appropriate!practices!for!citing!work!considered!for!your!
assignments!in!this!course,!see!http://infoguides.rit.edu/content.php?pid=170660.!!
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Tentative(Weekly(Outline(
!
The!course!schedule!is!tentative!and!subject!to!change!at!any!time!in!accordance!with!the!needs!
of!the!students!or!in!response!to!disruptions!due!to!unforeseen!circumstances.!
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Week( Date(
Topic(
Notes(
1!
8/26/14!
Intro!to!NLP!in!Biomedicine!
!!
8/28/14!
Review!of!NLP!
!
!!
2!
9/2/14!
Review!of!NLP!
!!
!!
9/4/14!
Review!of!NLP!
!!
3!
9/9/14!
Review!of!NLP!
!!
!!
9/11/14!
Quiz!+!NLP!Tools!Demo!
Quiz!in!class!
4!
9/16/14!
NLP!Lab!
!!
9/18/14!
NLP!Lab!+!free!time!for!exploring!
final!project!topics!
5!
9/23/14!
Analyzing!clinically!elicited!language!
!!
9/25/14!
One!paragraph!summary!of!
Analyzing!clinically!elicited!language! final!project!idea!by!
11:59pm.!
6!
9/30/14!
Article!Presentations!
Joe,!Ravdeep,!Qiyun,!Ben,!
Zach!
10/2/14!
System!Demonstration!and!!
Lab!Competition!
!!
10/7/14!
Lab!Competition!
10/9/14!
Final!Project!Proposals!
10/14/14!
No!class!(!RIT!on!Monday!schedule!
10/16/14!
Analyzing!biomedical!journal!
articles!
10/21/14!
Analyzing!biomedical!journal!
articles!
!
10/23/14!
No!class!(!Must!attend!Dan!Roth!
lecture!
More!info!on!Dan!Roth!
lecture!TBA!
!
7!
!
8!
!
9!
!
!
!
Problem!set!due!9/19!at!
11:59pm!
!
Final!project!proposal!
written!summary!due!10/9!
at!11:59pm!
!
!!
10!
!
11!
!
12!
!
13!
!
14!
!
15!
!
16!
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(
10/28/14!
Dan!Roth!discussion!and!article!
presentations!
Preethi,!Joe!
10/30/14!
Article!presentations!
Ravdeep,!Zach,!Ben,!Quiyun!
11/4/14!
System!Demonstration!and!!
Lab!Competition!
!
11/6/14!
Lab!Competition!
11/11/14!
Analyzing!electronic!health!records:!
Intro!and!article!presentations!
11/13/14!
Article!Presentations!
11/18/14!
NLP!in!assistive!communication!
technology!
11/20/14!
Article!Presentations!
!
Zach,!Alf,!Dan,!Preethi!!
11/25/14!
Summary,!Discussion,!Future!
Directions!
!
11/27/14!
No!class!(!Thanksgiving!
12/2/14!
Final!Project!Presentations!
12/4/14!
Final!Project!Presentations!
12/9/14!
Final!Project!Presentations!
!
Dan,!Preethi,!Alf!
!Qiyun,!Ben,!Ravdeep,!Joe!
!
!
!
Final!project!written!report!
due!12/9!at!11:59pm!