Tutorial for the PSB2015 session on "Crowdsourcing and learning from Crowd Data" Slides created by Robert Leaman, Benjamin Good, and Andrew Su.

1. Robert Leaman Benjamin Good
Zhiyong Lu Andrew Su
http://slideshare.net/andrewsu

2.  The aggregated decisions of a group
are often better than the those of any
single member
 Requirements:
 Diversity
 Independence
 Decentralization
 Aggregation
2[Surowiecki, 2004]
Sir Francis Galton

3.  An undefined group of people
 Typically ‘large’
 Diverse skills and abilities
 Typically no special skills assumed
3
[Estelles-Arolas, 2012]

4.  Computational power
 Distributed computing
 Content
 Web searches, social media
updates, blogs
 Observations
 Online surveys
 Personal data
4[Good & Su, 2013]

5.  Cognitive power
 Visual reasoning, language
processing
 Creative effort
 Resource creation, algorithm
development
 Funding: $$$
5[Good & Su, 2013]

6.  Crowd data
 Content
 Search logs
 Crowdsourcing
 Observations
 Cognitive power
 Creative effort
 Not a focus in this
tutorial
 Distributed
computing
 Crowdfunding
6

7.  Access
 To the data; to the crowd
▪ 1 in 5 people have a smartphone worldwide
 Engagement
 Getting contributors’ attention
 Incentive
 Quality control
7

8.  Information reflects health
 Disease status
 Disease associations
 Health related behaviors
 Information also drives health
 Knowledge and beliefs regarding prevention and
treatment
 Quality monitoring of health information
available to public 8
“Infodemiology”
[Eysenbach, 2006]

9.  Key challenge: text
 Variability: tired, wiped, pooped  somnolence
 Ambiguity: numb  sensory or cognition?
 Two levels
 Keyword: locate specific terms + synonyms
 Concept: attempt to normalize mentions to
specific entities
 Measurement
 Disproportionality analysis
 Separating signal from noise
9

10.  Objective: predict flu
outbreaks from internet
search trends
 Access to search data via
direct access to logs or via
ad clicks
 High correlation between
clicks one week and cases
the next
 Caveats!
 Many potential confounders
10
[Eysenbach, 2006]
[Eysenbach, 2009]
[Ginsberg et al., 2009]
2004 2005 2006 2007
searches
cases

11.  Objective: Mine social media
forums for ADR reports
 Lexicon based on UMLS
Metathesaurus, SIDER,
MedEffect, and a set of
colloquial phrases (“zonked”,
misspellings)
 Demonstrated viability of
text mining (73.9% f-
measure)
 Revealed known ADRs and
putatively novel ADRs
Olanzapine Known
incidence
Corpus
Frequency
Weight gain 65% 30.0%
Fatigue 26% 15.9%
Increased
cholesterol
22% -
Increased
appetite
- 4.9%
Depression - 3.1%
Tremor - 2.7%
Diabetes 2% 2.6%
Anxiety - 1.4%
11
[Leaman et al., 2010]

12.  Objective: identify DDI from
internet search logs
 DDI reports difficult to find
 Focused on a DDI unknown at
time data collected
▪ Paroxetine + pravastatin 
hyperglycemia
 Synonyms
 Web searches
 Disproportionality analysis
 Results
 Significant association
 Classifying 31TP & 31TN pairs
▪ AUC = 0.82 12
[White et al., 2013]

13.  Outsourcing
 Tasks normally performed in-house
 To a large, diverse, external group
 Via an open call
13
[Estelles-Arolas, 2012]

14. EXPERT LABOR
 Must be found
 Expensive
 Often slow
 High quality
 Ambiguity OK
 Hard to use for
experiments
 Must be retained
CROWD LABOR
 Readily available
 Inexpensive
 Fast
 Quality variable
 Instructions must be clear
 Easy prototyping and
experimentation
 Retention less important
14

15.  Humans (even unskilled) simply better than
computers at some tasks
 Allows workflows to include an “HPU”
 Highly scalable
 Rapid turn-around
 High throughput
 Diverse solutions
 Low risk
 Low cost
15
[Quinn & Bederson, 2011]

16.  Microtask: low difficulty, large in number
 Observations or data processing
 Surveying, text or image annotation
 Validation: redundancy and aggregation
 Megatask: high difficulty, low in number
 Problem solving, creative effort
 Validation: manually, with metrics or rubric
16
[Good & Su, 2013]

17. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
content creation
17
[Good & Su, 2013]

18. 18
Requester
Tasks
Amazon
Tasks
Tasks
TasksTasks
Tasks
Tasks
Aggregation
function
Workers
http://www.thesheepmarket.com/

19.  Automatically tag all genes (NCBI’s gene tagger), all
mutations (UMBC’s EMU)
 Highlight candidate gene-mutation pairs in context
 Frame task as simple yes/no questions
Slide courtesy: L. Hirschman [Burger et al., 2012]

20. 20

21. 21
[Mea 2014]
Tagging cells for
breast cancer
based on stain

22. 22
Requester
Tasks
Amazon
Tasks
Tasks
TasksTasks
Tasks
Tasks
Aggregation
function
Workers

23.  Baseline: majority vote
 Can we do better?
 Separate annotator bias and error
 Model annotator quality
▪ Measure with labeled data or reputation
 Model difficulty of each task
 Sometimes disagreement is informative
23
[Ipeirotis et al., 2010]
[Raykar et al., 2010]
[Arroyo &Welty, 2013]

24. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
content creation
24
[Good & Su, 2013]

25.  Volunteers label images of cell biopsies from
cancer patients
 Estimate presence and number of cancer cells
 Incentive
 Altruism, sense of mastery
 Quality
 training, redundancy
 Analyzed 2.4 million images as of 11/2014
25
[cellslider.net]

26. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
framework
26
[Good & Su, 2013]

27. EXAMPLE: RECAPTCHA,
 Workflow:
logging into a
website
 Sequestration:
performing
optical
character
recognition
27

28. EXAMPLE: PROBLEM-TREATMENT KNOWLEDGE BASE CREATION
 Workflow: prescribing medication
 Sequestration:entering reason for prescription
into ordering system
28
[Mccoy 2012]

29. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
content creation
29
[Good & Su, 2013]

30. 30
MalariaSpot: Luengo-Ortiz 2012
MOLT: Mavandadi 2012

31. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
content creation
31
[Good & Su, 2013]

32.  Bioinformatics students simultaneously learn
and perform metagenome annotation
 Incentive:
educational
 Quality:
aggregation,
instructor
evaluation
32[Hingamp et al., 2008]

33. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
content creation
33
[Good & Su, 2013]

34. OPEN PROFESSIONAL PLATFORMS ($$$)
 Innocentive
 TopCoder
 Kaggle
ACADEMIC (PUBLICATIONS..)
 DREAM (see invited opening talk at crowdsourcing session)
 CASP
34

35. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
content creation
35
[Good & Su, 2013]

36.  Players manipulate proteins to find the 3D
shape with the lowest calculated free energy
 Competitive and collaborative
 Incentive
 Altruism, fun, community
 Quality
 Automated scoring
 High performance, found
a difficult key retroviral structure
36
[Khatib, et al., 2011]

37. MICROTASK
 Microtask market
 Citizen science
 Workflow
sequestration
 Casual game
 Educational
MEGATASK
 Innovation contest
 Hard game
 Collaborative
content creation
37

38.  Aims to provide a
Wikipedia page for
every notable human
gene
 Repository of
functional knowledge
 10K distinct genes
 50M views & 15K edits
per year
38
[Huss et al., 2008]
[Good et al., 2011]

39.  Means many different things
 Fundamental points:
 Humans (even unskilled) simply better than
computers at some tasks
 There are a lot of humans available
 There are many approaches for accessing their
talents
39

40. INTRINSIC
 Altruism
 Fun
 Education
 Sense of mastery
 Resource creation
EXTRINSIC
 Money
 Recognition
 Community
40

41.  Define problem & goal
 Decide platform
 Decompose problem into tasks
 Separate: expert, crowdsourced & automatable
 Refine crowdsourced tasks
 Simple, clear, self-contained, engaging
 Design: instructions and user interface
41
[Hetmank, 2013]
[Alonso & Lease, 2011]
[Eickhoff & deVries, 2011]

42.  Iterate
 Test internally
 Calibrate with small crowdsourced sample
 Verify understanding, timing, pricing & quality
 Incorporate feedback
 Run production
 Scale on data before workers
 Validate results
42
[Hetmank, 2013]
[Alonso & Lease, 2011]
[Eickhoff & deVries, 2011]

43.  Automatic evaluation
 If possible
 Direct quality assessment
 Expensive
▪ Microtask: Include tasks with known answers
▪ Megatask: Evaluate tasks after completion (rubric)
 Aggregate redundant responses
43

44. PRO
 Reduced cost  more
data
 Fast turn-around time
 High throughput
 “Real world”
environment
 Public participation &
awareness
CON
 Potentially poor quality
 Spammers
 Potentially low
retention
 Privacy concerns for
sensitive data
 Lax protections for
workers
44

45.  Potentially poor quality: discussed previously
 Low retention
 Complicates quality estimation due to sparsity
 Do workers build task-specific expertise?
 Privacy
 Sensitive data requires trusted workers
45

46.  Protection for workers
 Low pay, no protections, benefits, or career path
 Potential to cause harm
▪ E.g. exposure to anti-vaccine information
 Is IRB approval needed?
 Can be addressed
 Responsibility of the researcher
▪ “[opportunity to] deliberately value ethics above cost
savings”
46
[Graber & Graber, 2013]
[Fort, Adda and Cohen, 2011]
[Fort, Adda and Cohen, 2011]

47.  Demographics:
 Shift from mostly US to US/India mix
 Average pay is <$2.00 / hour
 Over 30% rely on MTurk for basic income
 Workers not anonymous
 However:
 Tools can be used ethically or unethically
 Crowdsourcing ≠ AMT
47
[Ross et al., 2009]
[Lease et al., 2013]

48.  Improved predictability
 Pricing, quality, retention
 Improved infrastructure
 Data analysis, validation & aggregation
 Improved trust mechanisms
 Matching workers and tasks
 Relevant characteristics for matching each
 Increased mobility
48

49.  Crowdsourcing and learning from crowd data
offer distinct advantages
 Scalability
 Rapid turn-around
 Throughput
 Low cost
 Must be carefully planned and managed
49

50.  Wide variety of approaches and platforms
available
 Resources section lists several
 Many questions still open
 Science using crowdsourcing
 Science of crowdsourcing
50

51.  Thanks to the members of the crowd who make this
methodology possible
 Questions: robert.leaman@nih.gov,
bgood@scripps.edu, asu@scripps.edu
 Support:
 Robert Leaman & Zhiyong Lu:
▪ Intramural Research Program of National Library of Medicine, NIH
 Benjamin Good & Andrew Su:
▪ National Institute of General Medical Sciences, NIH: R01GM089820
and R01GM083924
▪ NationalCenter for AdvancingTranslational Sciences, NIH:
UL1TR001114
51

52.  Distributed computing: BOINC
 Microtask markets: Amazon MechanicalTurk,
Clickworker, SamaSource, many others
 Meta services: Crowdflower, Crowdsource
 Educational: annotathon.org
 Innovation contest: Innocentive,TopCoder
 Crowdfunding: Rockethub, Petridish
52

53.  Adar E:Why I hate MechanicalTurk research (and workshops). In: CHI: 2011;
Vancouver, BC, Canada. Citeseer.
 Alonso O, Lease M: Crowdsourcing for Information Retrieval: Principles, Methods
and Applications.Tutorial at ACM-SIGIR 2011.
 Aroyo L,Welty C: CrowdTruth: Harnessing disagreement in crowdsourcing a
relation extraction gold standard. In:WebSci2013 ACM 2013. 2013.
 Burger J, Doughty E, Bayer S,Tresner-Kirsch D,Wellner B, Aberdeen J, Lee K,
Kann M, Hirschman L:Validating Candidate Gene-Mutation Relations in MEDLINE
Abstracts via Crowdsourcing. In: Data Integration in the Life Sciences.vol. 7348:
Springer Berlin Heidelberg; 2012: 83-91.
 Eickhoff C, deVries A: How Crowdsourceable is yourTask? In:WSDM 2011
Workshop on Crowdsourcing for Search and Data Mining; Hong Kong, China. 2011:
11-14.
 Estelles-Arolas E, Gonzalez-Ladron-de-Guevara F:Towards an integrated
crowdsourcing definition. Journal of Information Science 2012, 38(189).
 Fort K, Adda G, Cohen KB: Amazon MechanicalTurk: Gold Mine or Coal Mine?
Computational Linguistics 2011, 37(2).
 Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, Brilliant L:
Detecting influenza epidemics using search engine query data. Nature 2009,
457(7232):1012-1014.
53

54.  Good BM, Clarke EL, de Alfaro L, Su AI: Gene Wiki in 2011: community
intelligence applied to human gene annotation. Nucleic Acids Res 2011, 40:D1255-
1261.
 Good BM, Su AI: Crowdsourcing for bioinformatics. Bioinformatics 2013,
29(16):1925-1933.
 Graber MA, Graber A: Internet-based crowdsourcing and research ethics: the
case for IRB review. Journal of medical ethics 2013, 39(2):115-118.
 Halevy A, Norvig P, Pereira F:The Unreasonable Effectiveness of Data. IEEE
Intelligent Systems 2009, 9:8-12.
 Harpaz R, Callahan A,Tamang S, LowY, Odgers D, Finlayson S, Jung K, LePendu
P, Shah NH:Text Mining for Adverse Drug Events: the Promise,Challenges, and
State of the Art. Drug Safety 2014, 37(10):777-790.
 Hetmank L: Components and Functions of Crowdsourcing Systems - A
Systematic Literature Review. In: 11th International Conference on
Wirtschaftsinformatik; Leipzip,Germany. 2013.
 Hingamp P, Brochier C,Talla E, Gautheret D,Thieffry D, Herrmann C:
Metagenome annotation using a distributed grid of undergraduate students. PLoS
biology 2008, 6(11):e296.
 Howe J: Crowdsourcing:Why the power of the crowd is driving the future of
business:Crown Business; 2009.
54

55.  Huss JW, Orozco D, Goodale J,Wu C, Batalov S,VickersTJ,Valafar F, Su AI:A
GeneWiki for Community Annotation of Gene Function. PLoS biology 2008,
6(7):e175.
 Ipeirotis P: Managing Crowdsourced Human Computation.Tutorial at WWW2011.
 Ipeirotis PG, Provost F,Wang J: Quality Management on Amazon Mechanical
Turk. In: KDD-HCOMP;Washington DC, USA. 2010.
 Khatib F, DiMaio F, Foldit Contenders G, FolditVoid Crushers G, Cooper S,
Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I et al: Crystal structure
of a monomeric retroviral protease solved by protein folding game players. Nature
structural & molecular biology 2011, 18(10):1175-1177.
 Leaman R,Wojtulewicz L, Sullivan R, Skariah A,Yang J, Gonzalez G:Towards
Internet-Age Pharmacovigilance: Extracting Adverse Drug Reactions from User
Posts to Health-Related Social Networks. In: BioNLPWorkshop; 2010: 117-125.
 Lease M, Hullman J, Bingham JP, Bernstein M, Kim J, LaseckiWS, Bakhshi S,
MitraT, Miller RC: MechanicalTurk is Not Anonymous. In.: Social Science Research
Network; 2013.
 Nakatsu RT, Grossman EB, Iacovou CL: A taxonomy of crowdsourcing based on
task complexity. Journal of Information Science 2014.
 Nielsen J: Usability Engineering:Academic Press; 1993.
55

56.  Pustejovsky J, Stubbs A: Natural Language Annotation for Machine Learning:
O'Reilly Media; 2012.
 Quinn AJ, Bederson BB: Human Computation: A Survey andTaxonomy of a
Growing Field. In: CHI;Vancouver, BC, Canada. 2011.
 Ranard BL, HaYP, Meisel ZF, Asch DA, Hill SS, Becker LB, Seymour AK, Merchant
RM: Crowdsourcing--harnessing the masses to advance health and medicine, a
systematic review. Journal ofGeneral Internal Medicine 2014, 29(1):187-203.
 RaykarVC,Yu S, Zhao LH,Valadez GH, Florin C, Bogoni L, Moy L: Learning from
Crowds. Journal of Machine Learning Research 2010, 11:1297-1332.
 Ross J, Zaldivar A, Irani L:Who are theTurkers?Worker demographics in Amazon
MechanicalTurk. In.: Department of Informatics, UC Irvine USA; 2009.
 Surowiecki J:The Wisdom of Crowds: Doubleday; 2004.
 Vakharia D, Lease M: Beyond AMT: AnAnalysis of Crowd Work Platforms. arXiv;
2013.
 Von Ahn L: Games with a Purpose.Computer 2006, 39(6):92-94.
 White R,Tatonetti NP, Shah NH, Altman RB, Horvitz E:Web-scale
pharmacovigilance: listening to signals from the crowd. J Am Med InformAssoc
2013, 20:404-408.
 Yuen M-C, King I, Leung K-S:A Survey of Crowdsourcing Systems. In: IEEE
International Conference on Privacy, Security, Risk andTrust. 2011.
56