Visualization of Public Health Data - GitHub Pages · · 2019-10-22Visualization of public health...
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Visualization of Public Health DataAnamaria CrisanPhD Student at UBC in Computer ScienceSupervisors: Jennifer Gardy , Population and Public HealthTamara Munzner, Computer Science
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WHAT ARE PUBLIC HEALTH DATA?
Person
PlaceTime
(FOR INFECTIOUS DISEASE MANAGEMENT)
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Genomic
Contact NetworkPatient Data
Outcomes
Geography /Location
Time
Treatment
PersonPlaceTime
WHAT ARE PUBLIC HEALTH DATA?(FOR INFECTIOUS DISEASE MANAGEMENT)
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YOU
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NursesCliniciansMedical Health Officers Researchers Community Leaders
• Public health has multidisciplinary decision making teams• More data & diverse data types = more informed decision making• BUT - not all stakeholders can interpret / understand data
• Support needed for decision making with heterogeneous data
SUPPORT FOR DATA DRIVEN DECISIONS
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PROPOSAL
Visualization of public health data can improve knowledge sharing and decision making in infectious disease prevention and control
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60%
Probability Frequency Visualization6 in 10
< <
Whiting (2015) “How well do health professionals interpret diagnostic information? A systematic review”
• Numeracy : the ability to reason with numbers§ Individuals with low numeracy have a difficulty interpreting
numbers and probabilities§ Also true amongst educated professionals
• Visualization can make data more accessible to diverse stakeholders on decision making teams
WHY VISUALIZATION?Least Understandable Most Understandable
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Baseline Visualization
Alternative 1 Alternative 2
BUT! VISUAL DESIGN ALSO MATTERS
Zikmund-Fisher (2013). A demonstration of ''less can be more'' in risk graphics.
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EXAMPLE OF GUIDANCE : WWW. VIZHEALTH.ORG
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APPLICATION TO PUBLIC HEALTH• Lots of interest in Visualization in Public Health
• But - mainly developing ad hoc solutions • Visualization designers usually bioinformaticians (high numeracy,
lack stakeholder context)
• Stakeholders relying on Excel for visualizations
• Need to make a case for better visualizations• Need to treat data visualization as a research
process
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VISUALIZATION DESIGN & ANALYSIS
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Steps for visual design1. Partner with a group of stakeholders that have a
problem
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Steps for visual design1. Partner with a group of stakeholders that have a
problem2. Ask what data stakeholders use (is it available)?
VISUALIZATION DESIGN & ANALYSIS
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Steps for visual design1. Partner with a group of stakeholders that have a
problem2. Ask what data stakeholders use (is it available)?
3. Ask what stakeholders do with the data [tasks]
VISUALIZATION DESIGN & ANALYSIS
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Steps for visual design1. Partner with a group of stakeholders that have a
problem2. Ask what data stakeholders use (is it available)?
3. Ask what stakeholders do with the data [tasks]
4. Explore if other visualizations have addressed this problem and set of tasks
VISUALIZATION DESIGN & ANALYSIS
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Steps for visual design1. Partner with a group of stakeholders that have a
problem2. Ask what data stakeholders use (is it available)?
3. Ask what stakeholders do with the data [tasks]
4. Explore if other visualizations have addressed this problem and set of tasks
5. Test multiple alternatives (including new ones you develop) with stakeholders
VISUALIZATION DESIGN & ANALYSIS
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Steps for visual design1. Partner with a group of stakeholders that have a
problem2. Ask what data stakeholders use (is it available)?
3. Ask what stakeholders do with the data [tasks]
4. Explore if other visualizations have addressed this problem and set of tasks
5. Test multiple alternatives (including new ones you develop) with stakeholders
6. Gather qualitative & quantitative evaluation data
VISUALIZATION DESIGN & ANALYSIS
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Steps for visual design1. Partner with a group of stakeholders that have a
problem2. Ask what data stakeholders use (is it available)?
3. Ask what stakeholders do with the data [tasks]
4. Explore if other visualizations have addressed this problem and set of tasks
5. Test multiple alternatives (including new ones you develop) with stakeholders
6. Gather qualitative & quantitative evaluation data
AN ITERAVTIVE PROCESS
VISUALIZATION DESIGN & ANALYSIS
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EXAMPLE: TB GENOMIC CLINICAL REPORTCurrent Report
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DESIGN PROCESS OVERVIEWQuestion: Can we improve upon the existing report design
Note: Not a data vis project, but uses data vis methods and result will feed into other data vis projects
Phase 1: Expert consultations
Phase 2: Task Questionnaire
Design Sprint
Phase 3: Design choice Questionnaire
Phase 4: Evaluation of final report design
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DESIGN PROCESS OVERVIEWQuestion: Can we improve upon the existing report design
Note: Not a data vis project, but uses data vis methods and result will feed into other data vis projects
Phase 1: Expert consultations
Phase 2: Task Questionnaire
Design Sprint
Phase 3: Design choice Questionnaire
Phase 4: Evaluation of final report design
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PHASE 1EXPERT CONSULTATIONSParticipants: 7 = physicians (clinical & laboratory), public health researchers
Key Findings
• Different needs between physicians and researchers
• Physicians had greater time pressure
• Trust in lab and procedures
• Some data on report not necessary, other data confusing
• Constraints on delivery report due EHR
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PHASE 2TASK QUESTIONNAIRE
Participants: 17 = physicians (clinical & laboratory), nurses, public health researchers, surveillance experts
Key findings
• Quantitative support for earlier qualitative findings
• Better granularity of data used, and confidence performing, different tasks
Q: What could improve the efficiency of using molecular data?
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PHASE 2DESIGN SPRINT
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PHASE 2DESIGN SPRINT
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PHASE 3DESIGN CHOICE QUESTIONNAIREParticipants: 42Goal: Compare control (existing report) with options developed in the design sprint
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PHASE 3DESIGN CHOICE QUESTIONNAIREKey finding #1: Comparing whole reports not very useful
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PHASE 3DESIGN CHOICE QUESTIONNAIREKey finding #2: Generally strong preference patterns, consistent between clinicians and non-clinicians
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PHASE 3DESIGN CHOICE QUESTIONNAIREKey finding #2: Generally strong preference patterns, consistent between clinicians and non-clinicians
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PHASE 3DESIGN CHOICE QUESTIONNAIREKey finding #2: Generally strong preference patterns, consistent between clinicians and non-clinicians
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PHASE 3DESIGN CHOICE QUESTIONNAIREKey finding #2: Generally strong preference patterns, consistent between clinicians and non-clinicians
“If you can combine the phylogenetic tree with some kind of graph showing temporal spread that would be perfect. Adding geographical data would be a really helpful bonus too.”
“I like tree best but I like tree formats in general so I am biased. C;A and F are of equal value to me.”
“Not useful for clinician. you need to refer this question to public health officials who do contact tracing”
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Problem & task data will be used to construct more complex visualizations in future* *like my PhD work
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Genomic
Contact NetworkPatient Data
Outcomes
Geography /Location
time
Treatment
PersonPlaceTime
Tuberculosis Whole Genome Sequence
WHERE IS MY WORK HEADED?
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EpiCOGShttps://amcrisan.shinyapps.io/EpiCOGSDEMO/
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DECOMPOSING VIS TO TWO LEVELSPROBLEM & TASK BASED DESIGNWorking with stakeholders to solve relevant problems & provide workable solutions
ABSTRACTIONS & VISUAL ENCODINGSCommon terminology to describe & compare visualizations
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Contact Info
http://cs.ubc.ca/~acrisan
@amcrisan Dr. James Johnston, Dr. Maureen Mayhew, Dr. Victoria Cook, Nash Dahlla, Dr. Jason Wong, Dr. James Brooks, Johnathan Spence, Laura MacDougall, Michael Coss, Ciaran Aiken, and David Roth, Matthew Brehmer, Madison Elliott, Zipeng Liu, Dylan Dong, and Kimberly Dextras-Romagnino
Thanks
IN CONCLUSION• Data visualization can support decision making in diverse
stakeholder groups
• Visual design, not just presence of visualization, matters
• Visualization is a research process in design
• Consider and evaluate alternative choices
• Stay tuned for future developments!
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Garcia-Retamero et. al (2013) “Visual representation of statistical information improves diagnostic inferences in doctors and their patients”
RANDOMIZE
Probability
Frequency
RND
Visual Aid
No Visual Aid
RND
Visual Aid
No Visual Aid
Patients+
Doctors
STUDY DESIGN RESULTSVisualization improved comprehension of both doctors and patientsVisualization improved concordance between doctors and patients
Quasi-randomized trial with four conditionsOutcome : correctly calculating the risk (essentially a math test)
EXAMPLE : SHARED DECISION MAKING
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DECOMPOSING VIS TO TWO LEVELSPROBLEM & TASK BASED DESIGNWorking with stakeholders to solve relevant problems & provide workable solutions
ABSTRACTIONS & VISUAL ENCODINGSCommon terminology to describe & compare visualizations
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PROBLEM & TASK BASED DESIGN
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Why is data being visualized?Different stakeholders have different needs!
“How is a pathogen changing over time?” “Are there clusters of disease?”
? ?
Understanding Disease DynamicsProblem:
Tasks:
Example
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DECOMPOSING VIS TO TWO LEVELSPROBLEM & TASK BASED DESIGNWorking with stakeholders to solve relevant problems & provide workable solutions
ABSTRACTIONS & VISUAL ENCODINGSCommon terminology to describe & compare visualizations
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ABSTRACTIONS & VISUAL ENCODINGS
40Munzner (2014) “Visualization Analysis and Design”
Decomposition Visualizations into geometric shapes & properties
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Munzner (2014) “Visualization Analysis and Design”
Vertical Position Vertical Position Vertical Position Vertical PositionHorizontal Position Horizontal Position Horizontal Position
Colour ColourSize
DESCRIBING VISUALIZATIONSUsing geometric marks and their properties (channels)
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DESCRIBING DISEASE DYNAMICS
Horizontal PositionTransmission Timing
SNP Absent
Horizontal Pos.Genetic Similarity
Red Dot Transmission event
Colour = cluster
SNP Present
EXAMPLE 1: PHYLOGENETIC TREE + DOT PLOT
Colour + DotVertical Pos.
Case Similarity
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EXAMPLE 2: NETWORK DIAGRAM
Horizontal + Vertical Position
Thickness of lineProbability of transmissions
Colour = cluster
Chain of transmissionsCase Similarity
DESCRIBING DISEASE DYNAMICS
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What information does the visualization show?How does the visualization show that information?
WHAT HOW TREE NETWORKTransmissionTiming
Horizontal pos.
Colored Dot
Transmission Confidence
Thickness
Color
CaseSimilarity
Horizontal + Vertical pos.
Black/White Dot
Colored Shape
SNP presence Black/White Dot
(line) (square)
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DESCRIBING DISEASE DYNAMICCOMPARING VISUALIZATIONS
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LINKING VIS ABSTRACTIONS TO BIOINFORMATIC ONTOLOGIES
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• Can connect ontologies to visualizations through abstractions
• Suggest visualizations based on available data
• Need to know what kinds of visualizations are suitable for different research questions§ Currently working on this
§ Similar idea to www.vizhealth.org☝
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PROBLEM & TASK BASED DESIGN
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Transmission timing & genetic similarity Transmission between & within clusters of related cases
Why is data being visualized?
“How is a pathogen changing over time?” “Are there clusters of disease?”