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Qianwen WANG, PhD
Postdoctoral Fellow
Department of Biomedical Informatics
Harvard Medical School
FromAI Models toAIApplications
Interpreting and Steering AI Explanations
with InteractiveVisualizations
Powerful AI Model
Usable and Useful AI Applications
1
2
About Me
Tenure-Track Assistant Professor
Aug 2023, CSE@UMN
Ph.D study at HKUST
with Prof. Huamin Qu
2015-2020
2015
2020
PostDoc at Harvard
with Prof. Nils Gehlenborg
2020-2023
Oxford
https://qianwen.info
•Awardee of the Harvard DSI Postdoctoral
Research Fund
•Abstract Chair for ISMB BioVis, Poster Chair for
PacificVis
•Program Committee members of IEEE VIS,
ACM IUI, ChinaVis.
•Honorable mention award from IEEE VIS 2022
•Best paper award from IMLH@ICML 2021
•Best abstract awards from BioVis ISMB 2021
and 2022
B.Eng at XJTU
2011-2015
3
We are Hiring
The Department of Computer Science and Engineering
University of Minnesota, Twin Cites (UMN)
I am seeking highly motivated students, RAs, interns, and visitors to be part of our
dynamic team at UMN CSE. Feel free to drop me an email if you are interested!
Twin cites, Minnesota
• Boasts 29 Nobel Laureates and 3 Pulitzer Prize winners
among its alumni.
• 44th in Academic Ranking of World University, 2022
• The CSE department is recognized for housing numerous
esteemed scholars, including Tian He, Vipin Kumar,
Joseph Konstan, etc
• One of the largest metropolitan areas in
the Midwestern US
• Land of 10,000 lakes
• Good public transportation, a thriving arts
scene, and teams in all four major
professional sports (NBA, NFL, MLB, NHL)
4
AI and Human
How can domain users apply AI to complete
desired tasks easily and efficiently
How can domain users apply AI to complete
desired tasks easily and efficiently
Adapt from Langer et al. 2021. What Do We Want From Explainable Artificial Intelligence
AI and Human
AI User
Developer
Deployer
Affected
Parties
Regulator
AI Application
5
Even if we were to make no further progress in the next decade,
deploying existing AI algorithms to every applicable problem would be a
game changer for most industries.
— Francois Chollet
6
The Importance of AI Application
Medical
Diagnosis
Drug Design Personalised
Medicine
Prognosis
Prediction
Healthcare
Chatbot
Epic’s AI algorithms are delivering
inaccurate information on
seriously ill patients
MIKE REDDY FOR STAT
https://www.statnews.com/2021/07/26/epic-hospital-algorithms-sepsis-investigation/?
utm_source=researcher_app&utm_medium=referral&utm_campaign=RESR_MRKT_Rese
archer_inbound
https://www.fiercehealthcare.com/practices/nearly-half-u-s-doctors-
say-they-are-anxious-about-using-ai-powered-software-survey
It is hard to achieve, especially in biomedical applications
7
The Challenges in AI Application
Why it is hard to achieve
The capabilities of AI The needs from users
8
AI Application
The gap needs
to be filled!
Abstract benchmark tasks
The capabilities of AI The needs from users
Complicated domain-specific tasks
9
Why it is hard to achieve
AI Application
Powerful AI Model
Usable and Useful AI Applications
10
Interactive Visualization
Explainable AI
Filling the Gap
Stages of the
Human Communication
Uijt!qbujfou!tipvme!cf!ejbhoptfe!
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dbo!cf!mjolfe!up!bopuifs!
ejtfbtf!◤
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11
Receive
Interpret
Feedback
InteractiveVisualizations + Explainable / Interactive AI
AI Applications
12
Receive
Interpret
Feedback
InteractiveVisualizations + Explainable / Interactive AI
13
Receive
Interpret
Feedback
AI Applications
Enable users to provide feedback and
steer AI models for the desired tasks
14
Help users interpret AI and generate
meaningful and actionable insights
Help users interpret AI and generate
meaningful and actionable insights
Present users explanations about the AI
for the desired tasks
Receive
Interpret
Feedback
My Studies
Drug Repurposing
Biomedical Knowledge Graph
Single-Cell Transcriptomics
Genomics
Genomics, Pathology
Cancer Genomics, Patent Cohort
15
• DNN Genealogy (TVCG 19)
• DiscriLens (VIS 20)
• GNNLens (TVCG 21)
• ATMSeer (CHI 19)
• HypoML (VIS 20)
• ThreadStates (VIS 21)
• GenoRec (VIS 22)
• DrugExplorer🏅(IMLH@ICML 21, VIS 22)
• Polyphony🏅(VIS 22, Biovis ISMB 22)
• Drava (CHI 2023)
Receive
Interpret
Feedback
My Studies
Drug Repurposing
Biomedical Knowledge Graph
Single-Cell Transcriptomics
Genomics
Genomics, Pathology
Cancer Genomics, Patent Cohort
16
• DNN Genealogy (TVCG 19)
• DiscriLens (VIS 20)
• GNNLens (TVCG 21)
• ATMSeer (CHI 19)
• HypoML (VIS 20)
• ThreadStates (VIS 21)
• GenoRec (VIS 22)
• DrugExplorer🏅(IMLH@ICML 21, VIS 22)
• Polyphony🏅(VIS 22, Biovis ISMB 22)
• Drava (CHI 2023)
Receive
Interpret
Feedback
My Studies
Receiving Explanations
DO NOT Guarantee Insights!
Receive
Interpret
Debugging Tests for Model Explanations,
NeurIPs 2020, Julius Adebayo, Michael Muelly, Ilaria Liccardi, Been Kim
Human subjects fail to identify defective models
using attribution-based explanations, but instead
rely, primarily, on model predictions.
Attribution-based Explanations
18
Receiving Explanations
DO NOT Guarantee Insights!
R
Natural Images
Attribution-based Explanations
19
Natural Images
Anshul Kundaje, Stanford University
Deep learning approaches to decode the human genome
Regulatory Genomic
Attribution-based Explanations
Insights from Explanations,
it depends…
21
How to Select and Present aVisual
Explanation that can lead to
actionable insights?
Designing InteractiveVisualizations
for User-Centric XAI
Payal Chandak
Kexin Huang
Nils Gehlenborg Marinka Zitnik
HARVARD-MIT
Qianwen Wang
Best Paper Award
IMLH@ICML 2021
Best Paper Honorable Mention
IEEE VIS Conference 2022
IEEE Transactions on Visualization and Computer Graphics
A Study on GNN-based Drug Repurposing
22
Nodes: drugs, diseases, proteins, etc
Edges: known relations among these nodes
Graph Neural Networks (GNNs)
for Drug Repurposing
23
13-15 YEARS
$2-3 BILLION
Develop a new drug from scratch and
get it to the market
< 1/2 time
~ 1/4 cost
Drug Repurposing
Identify new therapeutic uses of existing drugs
Hair loss
Hypertension
24
Graph Neural Networks (GNNs)
for Drug Repurposing
AI Algorithm:
Explain a GNN model
AI Application:
Explain a GNN model used for
drug repurposing to Domain Users
Hao Yuan et al. 2022 25
Wang, Danding, et al. "Designing theory-driven user-centric
explainable AI." Proceedings of the 2019 CHI conference on
human factors in computing systems. 2019.
Liao, Q. Vera, Daniel Gruen, and Sarah Miller. "Questioning the
AI: informing design practices for explainable AI user
experiences." Proceedings of the 2020 CHI Conference on
Human Factors in Computing Systems. 2020.
For General Users, not domain specific
For General Interfaces, little discussion about visualisation design
26
An Extended Nested Model
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1 2 2 drug gene/protein cellular_com.. gene/protein disease
2 drug drug disease disease disease
1 drug disease drug disease disease
Agalsidase beta chylomicron ret... Alipogene tipar... lysosomal acid l... Wolman disease
indication indication indication includes
1 drug disease gene/protein disease disease
1 drug disease gene/protein disease
Agalsidase beta
Avelumab
Idursulfase
Galsulfase
&#7/&
)-.&/0/*%#0
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XAI Design Considerations
27
Format of Explanations
28
CommonVisual Presentations
of GNN Explanations
29
Alzheimer
BCHE
ACHE
BCL2
BAX
endometriu...
Organopho...
Chlorpyrifos
Chlorpyrifos
Neurotrans...
nucleus
1-BENZYL...
Methylphos...
Ranitidine
Estrogen-de...
The NLRP1 ...
Activation o...
Estrogen-de...
Ibuprofen
Release of a...
TP53 Regul...
Transcriptio...
nucleus
Repaglinide
hypogonad...
ABCC8
PPARG
CYP2C8
Hypogonadi...
Betamethas...
Testosterone
monobutyl ...
Regulation ...
ATP sensitiv...
ATP
endometriu...
Diethylhexy...
Air Pollutants
Dibutyl Pht...
nucleus
nucleoplasm
alpha-Linol...
Vemurafenib
Diethylstilb...
Ibuprofen
Neighbor Nodes
a Subgraph
b
disease gene/protein anatomy gene/protein drug
Alzheimer BCHE endometrium e... ABCC8 Repaglinide
disease_protein absent absent drug targets
disease gene/protein cellular_com.. gene/protein drug
Alzheimer ACHE nucleus PPARG Repaglinide
disease_protein interact with interact with drug targets
BAX
disease_protein interact with interact with drug targets
disease gene/protein drug gene/protein drug
Alzheimer BCL2 Ibuprofen CYP2C8 Repaglinide
disease_protein drug targets drug targets drug targets
disease gene/protein drug
Alzheimer PPARG Repaglinide
disease_protein drug targets
Alzheimer nucleus PPARG Repaglinide
Paths
c
Meta Path
Path
CommonVisual Presentations
of GNN Explanations
30
CommonVisual Presentations
of GNN Explanations
31
CommonVisual Presentations
of GNN Explanations
32
CommonVisual Presentations
of GNN Explanations
more similar
less similar
33
ALS Ritonavir
NR1|2
Local Explanation: individual semantic paths in the
knowledge graph that reflects biomedical mechanisms
disease drug
gene/protein
Group Explanation: a meta-path that indicate a
sequence of node/relation types
disease A drug P
gene n
disease A drug O
gene j
disease A drug O
gene m
disease B drug P
gene n
disease C drug Q
gene j
Granularity of Explanations
34
A predicted drug
A Meta Path
Organize and compare path-based explanations at different levels of granularity
Meta Matrix
35
35
Use Case
antidiabetic drugs
expand/collapse hide/unhide
User Study
42
12 medical professionals who have worked related fields for more than five years,
five clinical researchers,
five practicing physicians,
two medical school students who used to work as pharmacists.
7 males, 5 females, the mean (SD) age was 34.25 (6.12) years
“important problem”
“Super helpful”
“Exactly why I would prescribe an off-label medication for chronic pain”
0.667
0.542
0.542
0.792
0.0 0.2 0.4 0.6 0.8 1.0
path subgraph node baseline
Accuracy
58.308
92.150
92.688
18.358
0 20 40 60 80 100 120
Time(second)
3.542
3.167
2.688
2.375
1.0 2.0 3.0 4.0 5.0
Confidence
F(3,33)=3.39
p<.05
F(3,33)=6.58
p<.05
F(3,33)=24.73
p<.05
more
accurate
less
accurate
quicker slower
more
confident
less
confident
b
a
c d Significant difference
Users are able to perform
tasks more accurately,
confidently, and quickly.
Format of explanations
User Study
43
0.667
0.542
0.542
0.792
0.0 0.2 0.4 0.6 0.8 1.0
path subgraph node baseline
Accuracy
58.308
92.150
92.688
18.358
0 20 40 60 80 100 120
Time(second)
3.542
3.167
2.688
2.375
1.0 2.0 3.0 4.0 5.0
Confidence
F(3,33)=3.39
p<.05
F(3,33)=6.58
p<.05
F(3,33)=24.73
p<.05
more
accurate
less
accurate
quicker slower
more
confident
less
confident
b
a
c d Significant difference
User Study
A poorly-designed visual
explanation is not necessarily
better than a non-explanation
baseline
44
Format of explanations
45
Best Paper Award
IMLH@ICML 2021
Best Paper Honorable Mention
IEEE VIS Conference 2022
c Path Explanation
E
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d
11 2 5 13 2
13 disease
gene/protein
molecular_function
drug
1 1 1 2 1
2
disease
gene/protein
drug
unipolar depres...
HTR7
Clozapine associated
targets
〃
HTR2C
〃
associated
targets
〃
〃
Clomipramine associated
targets
1
disease
gene/protein
pathway
drug
20 17 20 20 15 14 11 disease
gene/protein
anatomy
drug
Users can compare the
explanations of different
selected drugs
Users can hide ( ), unhide ( ), collapse ( ), or expand ( )
a group of explanation paths based on the meta-path
Drug Embedding
b
gene/protein
gene/protein
gene/protein
C3
C4
C2
Ditto mark (〃) indicates this
node is the same as the node
in the above path
a Control Panel
Select drugs
through lasso or click
M
o
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m
i
d
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5
8
3
1
1
C1 MetaMatrix provides an overview
of all predicted drugs in terms
of meta paths
C5
Ranked by scores or grouped
based on embeddings
DrugExplorer
How can user feedback steer AI?
>1,400 users from 64 countries
in the first month
http://txgnn.org
Steer AI
46
Can AI Explanations enable users to
Interpret and Steer AI at the same time?
Human Knowledge
about Classes
Human Knowledge
about Concepts
• Polyphony (VIS 22, Biovis ISMB 22)
• Drava (CHI 2023)
47
Can AI Explanations enable users to
Interpret and Steer AI at the same time?
Human Knowledge
about Classes
• Polyphony (VIS 22, Biovis ISMB 22)
Steer
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Model
Fine-tuning
Update
PolyPhony:
An Interactive Transfer Learning Framework
for Single-Cell Data Analysis
Mark Keller
Furui Cheng
Nils Gehlenborg
Huamin Qu
Qianwen Wang
Best Long Abstract Award
BioVis COSI, Conference on Intelligent System for Molecular Biology (ISMB)
IEEE VIS 2022
IEEE Transactions on Visualization and Computer Graphics
48
Training Dataset
AI Algorithm:
Classification
49
AI Tool:
Single Cell Annotation
50
Tissue
Cell-Type
Mapping
AI Algorithm:
Classification
AI Tool:
Single Cell Annotation
Cannot be directly applied
51
Cell Types
Labelled data
Unlabelled new data
Labelled data
Unlabelled new data
AI may not tell Technical Variations
(i.e., batch effect) from Biological
Variations (i.e., different cell types)
Human inputs are needed!
Cell Types
52
AI Tool for Single Cell Annotation
Automatic
Annotation
Manual
Validation
Workflow
AI Tool for Single Cell Annotation
How about asking users to manually label
some items?
Power to the People: The Role of Humans in Interactive Machine Learning
Saleema Amershi et al. 2014, AI Magazine
Previous studies show that
• Users do not want to be treated as an
oracle that simply label individual items
• Transparency about the AI system will help
users provide accurate feedback
53
Cell Types
Anchor
analogous cell populations across datasets
• Interpret AI in a way that is consistent with user
workflow and mental model
• Steer AI by integrating human knowledge
Interactive Anchors
Enable Simultaneous AI Interpretation and Steering
54
Cell Types
Anchor
analogous cell populations across datasets
• Interpret AI in a way that is consistent with user
workflow and mental model
• Steer AI by integrating human knowledge
Interactive Anchors
Enable Simultaneous AI Interpretation and Steering
55
Cell Types
Steer
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Interpret Anchor
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!%$%
! " #
$
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Model
Fine-tuning
Update
Generate Anchor
0
0
Polyphony
56
Generate Anchor Recommendations
Harmony (Korsunsky et al., Nature Methods, 2019)
One Anchor
Clusters
57
Polyphony
Similarity Matrix
Polyphony
Interpret Anchors
A
B C
Steer
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Fine-tuning
Update
Reference
Query
58
Polyphony
Steer Anchors: Edit
59
Use Cases
Before Refinement
The reference dataset
• a plate-based protocol
• contains 7,290 cells from 32 donors
• annotated with eleven cell types
The query dataset:
• generated using a droplet-based protocol
• contains 8,391 cells from 4 donors
• Has the same cell types as the reference
Pancreas Dataset
60
After Refinement
Six postdoc researchers and one assistant professor in single-cell analysis.
“intuitive and easy to use”
“more than just giving me an answer”
“I can fix undesired outcomes”
Evaluation
Simulation
61
62
Best Long Abstract Award
BioVis COSI, Conference on Intelligent System for Molecular Biology (ISMB)
Computational biology
Data Visualization
PolyPhony:
An Interactive Transfer Learning Framework
for Single-Cell Data Analysis
Knowledge can be more complicated than Classes
63
In Polyphony,
items form Clear Clusters based on their
overall similarity after Dimension Reduction
Knowledge can be more complicated than Classes
In Polyphony,
items form Clear Clusters based on their
overall similarity after Dimension Reduction
What if there is no clear clusters?
What if the users are interested in certain
aspect rather than the overall similarity?
64
Steer AI
65
Can AI Explanations enable users to
Interpret and Steer AI at the same time?
Human Knowledge
about Classes
Human Knowledge
about Concepts
• Polyphony (VIS 22, Biovis ISMB 22)
• Drava (CHI 2023)
DRAVA
for theVisual Exploration of Small Multiples
Aligning Human Concepts with Machine Learning Latent Dimensions
Qianwen Wang Nils Gehlenborg
Sehi L’Yi
BioVis COSI, Conference on Intelligent
System for Molecular Biology (ISMB’22)
ACM CHI Conference on Human Factors in
Computing Systems (CHI’23)
66
Harvard Data Science Initiative
Postdoctoral Fellow Research Fund
Concepts
Knowledge can be more complicated than Classes
One Class
(Zebra)
67
Multiple Concepts
(Horse, stripe, grass)
Concepts
Knowledge can be more complicated than Classes
68
One Class
(Zebra)
Multiple Concepts
(Horse, stripe, grass)
Concepts
Knowledge can be more complicated than Classes
69
One Class
(Zebra)
Multiple Concepts
(Horse, stripe, grass)
Pink-
Purple
Tissue
Density
Extract Concepts from AI
70
Been Kim et al. TCAV, 2018
Zhenge Zhao et al. Concept Extract, 2021
Extract Concepts from AI
encoder decoder
input: x latent
vector: z
!"
output: x
#"
• Learn concepts without labels
• Show what a concept looks like
Disentangled Representation Learning
!"#$%#&'("
71
UMAP
AI Algorithm:
Disentangled
Representation Learning
AI Tool:
Concept-driven
Visual Exploration
encoder decoder
input: x latent
vector: z
!"
output: x
#"
72
!"#$%&'(&)#*+&,-./% 01%12/*1&31)&
,-./%&4%5)"16$1
latent
dimensions
synthesized
images
data
items
7%*12821*&95%:18*;
modify
items
modify
groups
split merge
investigated dim
assistant
dim
assign
distribution
locate items
of interest
reveal
association
a b c
assign
DRAVA
A Three-Step Workflow
73
TADs in Genomic Contact Matrices
Each row represents a latent dimension (a potential concept)
Ranked by a saliency score
Interpret Concepts
via synthesised images
74
nested structure
thickness of diagonal
asymmetric structure
Interpret Concepts
via synthesised images
75
nested structure
thickness of diagonal
asymmetric structure
Interpret Concepts
via synthesised images
76
Data Items
Partial Compression See-Through Item
Label
Group
Label
a c
label 1 label2
b
1D grouping
2D grouping
Representative Average
label1
22
Interpret Concepts
via data items
77
Lekschas et al.
Pining.js. InfoVIS 2020
The model confuses the
diagonal thickness with the
nested structure
Interpret Concepts
via data items
78
User Refinement
Refine Concepts
79
!"#$%&'( )#*$#
a b
a
selected
metric
+,"-%#
c
!"#$%&!$'()*+
,)-+!(&.)/
!0#$%&!$&12-
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drag & drop
lasso
Depile All
Extract
Browse Separately
Magnify
Depile All
Extract
Browse Separately
Magnify
drag &
drop
extract
Input
feature
map
Encoder
conv
block
conv
block
flatten
FC
reparametrize
…
conv
block
Concept A
Decoder
Transposed
conv
block
resize
FC
…
Transposed
conv
block
a c
b
z
conv
block
global
maxpool
softmax
Concept Adaptor
Decoder
Transposed
conv
block
resize
FC
…
Transposed
conv
block
c
b
80
Refine Concepts
Model Structure
Bangs
Smiling
Scale
N=5%
N=2%
N=1%
Ours Baseline
81
Refine Concepts
Evaluation
Concept-drivenVisual Exploration
Image patches of
breast cancer specimens
82
Hard to interpret
Purple Pink
Tissue
Density
Strong correlation with the
presence of cancer cells
Strong correlation with the
presence of cancer cells
Filter items to investigate confident
false-negative predictions
They are more likely fatty tissues
surrounded by cancer cells
These items are mostly loose purple
tissues
89
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Interpret and Steer Concept-based Explanations
More accurate concepts
More interpretable and flexible visual exploration
DRAVA Harvard Data Science Initiative
Postdoctoral Fellow Research Fund
A NSF-sponsored workshop on interactive visualization
and analysis of high-dimensional scientific data
https://qianwen.info/DRAVA/#/use-cases
Summary
Usable and Useful AI Applications through interactive visual explanations
that imitate the communication process between humans
90
Help users interpret AI and generate
meaningful and actionable insights
Enable users to provide feedback and
steer AI for the desired tasks
Present users explanations about AI
Summary
User-Centric
Design Considerations
Data
Format
Human
Knowledge
Solutions
Graph
Biological
Mechanisms
Increased speed, accuracy,
and confidence in validating
predictions
High-
dimensional
Vectors
Classes
Improved user satisfaction
level & annotation accuracy
Concepts
Reveal and fix concept
mismatches that are hidden
in previous methods
Steer
!"#$%&'()"&
$*()+%$(&$
#,%'(
#*%-(!
.(%$/-(#
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$(#$"&4)
!%$%
! " #
$
$
Model
Fine-tuning
Update
Partial Compression See-Through
Item
Label
Group
Label
label 1
label2
1D grouping
2D grouping
Representative Average
label1
22
Path Explanation
E
s
c
i
t
a
l
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p
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I
s
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a
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d
b
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x
a
z
i
d
11 2 5 13 2
13 disease
gene/protein
molecular_function
drug
1 1 1 2 1
2
disease
gene/protein
drug
unipolar depres...
HTR7
Clozapine associated
targets
〃
HTR2C
〃
associated
targets
〃
〃
Clomipramine associated
targets
1
disease
gene/protein
pathway
drug
20 17 20 20 15 14 11 disease
gene/protein
anatomy
drug
Users can compare the
explanations of different
selected drugs
Users can hide ( ), unhide ( ), collapse ( ), or expand ( )
a group of explanation paths based on the meta-path
gene/protein
gene/protein
gene/protein
2
3
1
Ditto mark (〃) indicates this
node is the same as the node
in the above path
Interpreting and Steering AI Explanations
91
Usable and Useful AI Applications through interactive visual explanations
that imitate the communication process between humans
Summary
User-Centric
Design Considerations
Data
Format
Human
Knowledge
Solutions
Graph
Biological
Mechanisms
Increased speed, accuracy,
and confidence in validating
predictions
High-
dimensional
Vectors
Classes
Improved user satisfaction
level & annotation accuracy
Concepts
Reveal and fix concept
mismatches that are hidden
in previous methods
Steer
!"#$%&'()"&
$*()+%$(&$
#,%'(
#*%-(!
.(%$/-(#
Interpret Anchor
0''(,$
1(2('$
0!!
1(3&(
$-%"&"&4
!%$%
$(#$"&4)
!%$%
! " #
$
$
Model
Fine-tuning
Update
Partial Compression See-Through
Item
Label
Group
Label
label 1
label2
1D grouping
2D grouping
Representative Average
label1
22
Path Explanation
E
s
c
i
t
a
l
o
p
r
a
m
D
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s
v
e
n
l
a
f
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a
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C
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C
l
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i
p
r
a
m
i
n
e
I
s
o
c
a
r
d
b
o
x
a
z
i
d
11 2 5 13 2
13 disease
gene/protein
molecular_function
drug
1 1 1 2 1
2
disease
gene/protein
drug
unipolar depres...
HTR7
Clozapine associated
targets
〃
HTR2C
〃
associated
targets
〃
〃
Clomipramine associated
targets
1
disease
gene/protein
pathway
drug
20 17 20 20 15 14 11 disease
gene/protein
anatomy
drug
Users can compare the
explanations of different
selected drugs
Users can hide ( ), unhide ( ), collapse ( ), or expand ( )
a group of explanation paths based on the meta-path
gene/protein
gene/protein
gene/protein
2
3
1
Ditto mark (〃) indicates this
node is the same as the node
in the above path
92
Interpreting and Steering AI Explanations
Usable and Useful AI Applications through interactive visual explanations
that imitate the communication process between humans
Beyond Publications
Open-Source Real-World Users Media Coverage
93
Users of ML4VIS
Over 3,000 visits
across 40+ countries
Users of Gosling
Over 15,000 NPM
downloads across 120+
countries
Research Agenda
Previous Studies
94
Design Frameworks and Guidelines
Narvis (VIS 18)
ML4VIS (TVCG 2021)
User-Centric XAI🏅(VIS 22)
SineStream (VIS 20)
Visualization Techniques/Tools for
Human-AI Collaboration
HypoML (VIS 20) DiscriLens (VIS 20)
ATMSeer (CHI 19) GNNLens (TVCG 21)
DNN Genealogy (TVCG 19)
ThreadStates (VIS 21) DrugExplorer🏅(VIS 22)
Polyphony🏅(VIS 22, Biovis ISMB 22)
PapARVis (CHI 20)
Biomedical Applications
OncoThreads (Bioinformatics 21)
Polyphony🏅(VIS 22, Biovis ISMB 22)
Gosling🏅(VIS 21, Biovis ISMB 21)
GenoRec (VIS 22) ThreadStates (VIS 21)
DrugExplorer🏅(VIS 22, Biovis ISMB 21)
Future Research Agenda
Towards
Multimodality
https://storyset.com/illustration/data-points/rafiki
8
txt
Safeguards for
Interaction
https://storyset.com/illustration/warning/rafiki
Hypothesis for
New Biological
Knowledge
https://storyset.com/illustration/stem-cell-research/rafiki
Research Agenda
95
Human-AI Teaming:
Safeguards for Interaction
https://storyset.com/illustration/warning/
AI is imperfect, so are humans
• When and Why do users give biased/inconsistent
feedback for AI explanations?
• How to help users provide informed and accurate
feedback?
• How to detect biased/inconsistent user feedback in
Human-AI collaboration?
Research Agenda
96
Human-AI Teaming:
Safeguards for Interaction
https://storyset.com/illustration/warning/
AI is imperfect, so are humans
• When and Why do users give biased/
inconsistent feedback for AI
explanations?
• How to help users provide informed
and accurate feedback?
• How to detect biased/inconsistent
user feedback in Human-AI
collaboration?
My previous study:
Framework of designing interactive
visual explanations
Testbeds
Drava, Polyphony, DrugExplorer,
TheadStates, etc
Partial Compression See-Through
Item
Label
Group
Label
label 1
label2
1D grouping
2D grouping
Representative Average
label1
22
Path Explanation
E
s
c
i
t
a
l
o
p
r
a
m
D
e
s
v
e
n
l
a
f
a
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i
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e
F
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u
o
x
e
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M
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t
a
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a
p
i
n
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C
l
o
z
a
p
i
n
e
C
l
o
m
i
p
r
a
m
i
n
e
I
s
o
c
a
r
d
b
o
x
a
z
i
d
11 2 5 13 2
13 disease
gene/protein
molecular_function
drug
1 1 1 2 1
2
disease
gene/protein
drug
unipolar depres...
HTR7
Clozapine associated
targets
〃
HTR2C
〃
associated
targets
〃
〃
Clomipramine associated
targets
1
disease
gene/protein
pathway
drug
20 17 20 20 15 14 11 disease
gene/protein
anatomy
drug
Users can compare the
explanations of different
selected drugs
Users can hide ( ), unhide ( ), collapse ( ), or expand ( )
a group of explanation paths based on the meta-path
gene/protein
gene/protein
gene/protein
2
3
1
Ditto mark (〃) indicates this
node is the same as the node
in the above path
Towards Relatable Explainable AI with the Perceptual Process, Zhang et al. 2022
Research Agenda
97
Human-AI Communication:
Towards Multimodality
https://storyset.com/illustration/data-points/rafiki
8
txt
Multimodality enables
• Comprehensive Analysis: highlight patterns that might
be missed by using a single modality.
• Effective Communication: improve visual representations
through the integration of other modalities (e.g., text).
Research Agenda
98
Human-AI Communication:
Towards Multimodality
https://storyset.com/illustration/data-points/rafiki
8
txt
Multimodality enables
• Comprehensive Analysis: highlight patterns that might
be missed by using a single modality.
• Effective Communication: improve visual representations
through the integration of other modalities (e.g., text).
Pathology Radiology
Genomic
Data
Electronic
Medical Record
Diagnosis and
Treatment
Research Agenda
99
AI for Science:
Hypothesis Generation
and Validation
https://storyset.com/illustration/stem-cell-research/rafiki
Learning new knowledge from AI
• How to evaluate AI explanations when there is
no ground truth?
• How to systematically generate hypotheses
from AI explanations?
Consistent with the off-label prescription decisions made
by clinicians in a large healthcare system (1,272,085
patients, 480 diseases, and 1,290 drugs)
Acknowledgement
Icons & Images
Thanks!
Data
Format
Human
Knowledge
Solutions
Graph
Biological
Mechanisms
Increased speed, accuracy,
and confidence in validating
AI predictions
DrugExplorer🏅
(VIS 22, IMLH@ICML 21)
High-
dimensional
Vectors
Classes
Improved user satisfaction
level & annotation accuracy
Polyphony🏅
(VIS 22, Biovis ISMB 22)
Concepts
Reveal and fix concept
mismatches that are hidden
in previous methods
Drava
(ACM CHI 23)
Steer
!"#$%&'()"&
$*()+%$(&$
#,%'(
#*%-(!
.(%$/-(#
Interpret Anchor
0''(,$
1(2('$
0!!
1(3&(
$-%"&"&4
!%$%
$(#$"&4)
!%$%
! " #
$
$
Model
Fine-tuning
Update
Partial Compression See-Through
Item
Label
Group
Label
label 1
label2
1D grouping
2D grouping
Representative Average
label1
22
Path Explanation
E
s
c
i
t
a
l
o
p
r
a
m
D
e
s
v
e
n
l
a
f
a
x
i
n
e
F
l
u
o
x
e
t
i
n
e
M
i
r
t
a
z
a
p
i
n
e
C
l
o
z
a
p
i
n
e
C
l
o
m
i
p
r
a
m
i
n
e
I
s
o
c
a
r
d
b
o
x
a
z
i
d
11 2 5 13 2
13 disease
gene/protein
molecular_function
drug
1 1 1 2 1
2
disease
gene/protein
drug
unipolar depres...
HTR7
Clozapine associated
targets
〃
HTR2C
〃
associated
targets
〃
〃
Clomipramine associated
targets
1
disease
gene/protein
pathway
drug
20 17 20 20 15 14 11 disease
gene/protein
anatomy
drug
Users can compare the
explanations of different
selected drugs
Users can hide ( ), unhide ( ), collapse ( ), or expand ( )
a group of explanation paths based on the meta-path
gene/protein
gene/protein
gene/protein
2
3
1
Ditto mark (〃) indicates this
node is the same as the node
in the above path
Present users
explanations
Help users
generate insights
Enable users to
steer AI
Usable and Useful AI Applications through interactive visual
explanations that imitate the communication process between humans
https://qianwen.info
qianwen@umn.edu

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Interpreting and Steering AI Explanations Via Interactive Visualizations

  • 1. Qianwen WANG, PhD Postdoctoral Fellow Department of Biomedical Informatics Harvard Medical School FromAI Models toAIApplications Interpreting and Steering AI Explanations with InteractiveVisualizations Powerful AI Model Usable and Useful AI Applications 1
  • 2. 2 About Me Tenure-Track Assistant Professor Aug 2023, CSE@UMN Ph.D study at HKUST with Prof. Huamin Qu 2015-2020 2015 2020 PostDoc at Harvard with Prof. Nils Gehlenborg 2020-2023 Oxford https://qianwen.info •Awardee of the Harvard DSI Postdoctoral Research Fund •Abstract Chair for ISMB BioVis, Poster Chair for PacificVis •Program Committee members of IEEE VIS, ACM IUI, ChinaVis. •Honorable mention award from IEEE VIS 2022 •Best paper award from IMLH@ICML 2021 •Best abstract awards from BioVis ISMB 2021 and 2022 B.Eng at XJTU 2011-2015
  • 3. 3 We are Hiring The Department of Computer Science and Engineering University of Minnesota, Twin Cites (UMN) I am seeking highly motivated students, RAs, interns, and visitors to be part of our dynamic team at UMN CSE. Feel free to drop me an email if you are interested! Twin cites, Minnesota • Boasts 29 Nobel Laureates and 3 Pulitzer Prize winners among its alumni. • 44th in Academic Ranking of World University, 2022 • The CSE department is recognized for housing numerous esteemed scholars, including Tian He, Vipin Kumar, Joseph Konstan, etc • One of the largest metropolitan areas in the Midwestern US • Land of 10,000 lakes • Good public transportation, a thriving arts scene, and teams in all four major professional sports (NBA, NFL, MLB, NHL)
  • 5. How can domain users apply AI to complete desired tasks easily and efficiently How can domain users apply AI to complete desired tasks easily and efficiently Adapt from Langer et al. 2021. What Do We Want From Explainable Artificial Intelligence AI and Human AI User Developer Deployer Affected Parties Regulator AI Application 5
  • 6. Even if we were to make no further progress in the next decade, deploying existing AI algorithms to every applicable problem would be a game changer for most industries. — Francois Chollet 6 The Importance of AI Application Medical Diagnosis Drug Design Personalised Medicine Prognosis Prediction Healthcare Chatbot
  • 7. Epic’s AI algorithms are delivering inaccurate information on seriously ill patients MIKE REDDY FOR STAT https://www.statnews.com/2021/07/26/epic-hospital-algorithms-sepsis-investigation/? utm_source=researcher_app&utm_medium=referral&utm_campaign=RESR_MRKT_Rese archer_inbound https://www.fiercehealthcare.com/practices/nearly-half-u-s-doctors- say-they-are-anxious-about-using-ai-powered-software-survey It is hard to achieve, especially in biomedical applications 7 The Challenges in AI Application
  • 8. Why it is hard to achieve The capabilities of AI The needs from users 8 AI Application
  • 9. The gap needs to be filled! Abstract benchmark tasks The capabilities of AI The needs from users Complicated domain-specific tasks 9 Why it is hard to achieve AI Application
  • 10. Powerful AI Model Usable and Useful AI Applications 10 Interactive Visualization Explainable AI Filling the Gap
  • 11. Stages of the Human Communication Uijt!qbujfou!tipvme!cf!ejbhoptfe! xjui!Ejtfbtf!B! ◥Cfdbvtf!pg!uif!sftvmut!pg! uftu!N!!boe!!uftu!O◤ ◥Pi-!sjhiu-!uif!sftvmu!pg! uftu!N!joejdbuft!uibu1/◤ ◥Cvu!uif!sftvmu!pg!uftu!O! dbo!cf!mjolfe!up!bopuifs! ejtfbtf!◤ Nbz!J!lopx!zpvs! tvhhftujpot@ 11 Receive Interpret Feedback
  • 12. InteractiveVisualizations + Explainable / Interactive AI AI Applications 12 Receive Interpret Feedback
  • 13. InteractiveVisualizations + Explainable / Interactive AI 13 Receive Interpret Feedback AI Applications
  • 14. Enable users to provide feedback and steer AI models for the desired tasks 14 Help users interpret AI and generate meaningful and actionable insights Help users interpret AI and generate meaningful and actionable insights Present users explanations about the AI for the desired tasks Receive Interpret Feedback My Studies
  • 15. Drug Repurposing Biomedical Knowledge Graph Single-Cell Transcriptomics Genomics Genomics, Pathology Cancer Genomics, Patent Cohort 15 • DNN Genealogy (TVCG 19) • DiscriLens (VIS 20) • GNNLens (TVCG 21) • ATMSeer (CHI 19) • HypoML (VIS 20) • ThreadStates (VIS 21) • GenoRec (VIS 22) • DrugExplorer🏅(IMLH@ICML 21, VIS 22) • Polyphony🏅(VIS 22, Biovis ISMB 22) • Drava (CHI 2023) Receive Interpret Feedback My Studies
  • 16. Drug Repurposing Biomedical Knowledge Graph Single-Cell Transcriptomics Genomics Genomics, Pathology Cancer Genomics, Patent Cohort 16 • DNN Genealogy (TVCG 19) • DiscriLens (VIS 20) • GNNLens (TVCG 21) • ATMSeer (CHI 19) • HypoML (VIS 20) • ThreadStates (VIS 21) • GenoRec (VIS 22) • DrugExplorer🏅(IMLH@ICML 21, VIS 22) • Polyphony🏅(VIS 22, Biovis ISMB 22) • Drava (CHI 2023) Receive Interpret Feedback My Studies
  • 17. Receiving Explanations DO NOT Guarantee Insights! Receive Interpret
  • 18. Debugging Tests for Model Explanations, NeurIPs 2020, Julius Adebayo, Michael Muelly, Ilaria Liccardi, Been Kim Human subjects fail to identify defective models using attribution-based explanations, but instead rely, primarily, on model predictions. Attribution-based Explanations 18 Receiving Explanations DO NOT Guarantee Insights!
  • 20. Natural Images Anshul Kundaje, Stanford University Deep learning approaches to decode the human genome Regulatory Genomic Attribution-based Explanations Insights from Explanations, it depends…
  • 21. 21 How to Select and Present aVisual Explanation that can lead to actionable insights?
  • 22. Designing InteractiveVisualizations for User-Centric XAI Payal Chandak Kexin Huang Nils Gehlenborg Marinka Zitnik HARVARD-MIT Qianwen Wang Best Paper Award IMLH@ICML 2021 Best Paper Honorable Mention IEEE VIS Conference 2022 IEEE Transactions on Visualization and Computer Graphics A Study on GNN-based Drug Repurposing 22
  • 23. Nodes: drugs, diseases, proteins, etc Edges: known relations among these nodes Graph Neural Networks (GNNs) for Drug Repurposing 23
  • 24. 13-15 YEARS $2-3 BILLION Develop a new drug from scratch and get it to the market < 1/2 time ~ 1/4 cost Drug Repurposing Identify new therapeutic uses of existing drugs Hair loss Hypertension 24 Graph Neural Networks (GNNs) for Drug Repurposing
  • 25. AI Algorithm: Explain a GNN model AI Application: Explain a GNN model used for drug repurposing to Domain Users Hao Yuan et al. 2022 25
  • 26. Wang, Danding, et al. "Designing theory-driven user-centric explainable AI." Proceedings of the 2019 CHI conference on human factors in computing systems. 2019. Liao, Q. Vera, Daniel Gruen, and Sarah Miller. "Questioning the AI: informing design practices for explainable AI user experiences." Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems. 2020. For General Users, not domain specific For General Interfaces, little discussion about visualisation design 26
  • 27. An Extended Nested Model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drug gene/protein cellular_com.. gene/protein disease 2 drug drug disease disease disease 1 drug disease drug disease disease Agalsidase beta chylomicron ret... Alipogene tipar... lysosomal acid l... Wolman disease indication indication indication includes 1 drug disease gene/protein disease disease 1 drug disease gene/protein disease Agalsidase beta Avelumab Idursulfase Galsulfase &#7/& )-.&/0/*%#0 94#'. )-.&/0/*%#0 XAI Design Considerations 27
  • 29. CommonVisual Presentations of GNN Explanations 29 Alzheimer BCHE ACHE BCL2 BAX endometriu... Organopho... Chlorpyrifos Chlorpyrifos Neurotrans... nucleus 1-BENZYL... Methylphos... Ranitidine Estrogen-de... The NLRP1 ... Activation o... Estrogen-de... Ibuprofen Release of a... TP53 Regul... Transcriptio... nucleus Repaglinide hypogonad... ABCC8 PPARG CYP2C8 Hypogonadi... Betamethas... Testosterone monobutyl ... Regulation ... ATP sensitiv... ATP endometriu... Diethylhexy... Air Pollutants Dibutyl Pht... nucleus nucleoplasm alpha-Linol... Vemurafenib Diethylstilb... Ibuprofen Neighbor Nodes a Subgraph b disease gene/protein anatomy gene/protein drug Alzheimer BCHE endometrium e... ABCC8 Repaglinide disease_protein absent absent drug targets disease gene/protein cellular_com.. gene/protein drug Alzheimer ACHE nucleus PPARG Repaglinide disease_protein interact with interact with drug targets BAX disease_protein interact with interact with drug targets disease gene/protein drug gene/protein drug Alzheimer BCL2 Ibuprofen CYP2C8 Repaglinide disease_protein drug targets drug targets drug targets disease gene/protein drug Alzheimer PPARG Repaglinide disease_protein drug targets Alzheimer nucleus PPARG Repaglinide Paths c Meta Path Path
  • 33. CommonVisual Presentations of GNN Explanations more similar less similar 33
  • 34. ALS Ritonavir NR1|2 Local Explanation: individual semantic paths in the knowledge graph that reflects biomedical mechanisms disease drug gene/protein Group Explanation: a meta-path that indicate a sequence of node/relation types disease A drug P gene n disease A drug O gene j disease A drug O gene m disease B drug P gene n disease C drug Q gene j Granularity of Explanations 34
  • 35. A predicted drug A Meta Path Organize and compare path-based explanations at different levels of granularity Meta Matrix 35 35
  • 37.
  • 38.
  • 41.
  • 42. User Study 42 12 medical professionals who have worked related fields for more than five years, five clinical researchers, five practicing physicians, two medical school students who used to work as pharmacists. 7 males, 5 females, the mean (SD) age was 34.25 (6.12) years “important problem” “Super helpful” “Exactly why I would prescribe an off-label medication for chronic pain”
  • 43. 0.667 0.542 0.542 0.792 0.0 0.2 0.4 0.6 0.8 1.0 path subgraph node baseline Accuracy 58.308 92.150 92.688 18.358 0 20 40 60 80 100 120 Time(second) 3.542 3.167 2.688 2.375 1.0 2.0 3.0 4.0 5.0 Confidence F(3,33)=3.39 p<.05 F(3,33)=6.58 p<.05 F(3,33)=24.73 p<.05 more accurate less accurate quicker slower more confident less confident b a c d Significant difference Users are able to perform tasks more accurately, confidently, and quickly. Format of explanations User Study 43
  • 44. 0.667 0.542 0.542 0.792 0.0 0.2 0.4 0.6 0.8 1.0 path subgraph node baseline Accuracy 58.308 92.150 92.688 18.358 0 20 40 60 80 100 120 Time(second) 3.542 3.167 2.688 2.375 1.0 2.0 3.0 4.0 5.0 Confidence F(3,33)=3.39 p<.05 F(3,33)=6.58 p<.05 F(3,33)=24.73 p<.05 more accurate less accurate quicker slower more confident less confident b a c d Significant difference User Study A poorly-designed visual explanation is not necessarily better than a non-explanation baseline 44 Format of explanations
  • 45. 45 Best Paper Award IMLH@ICML 2021 Best Paper Honorable Mention IEEE VIS Conference 2022 c Path Explanation E s c i t a l o p r a m D e s v e n l a f a x i n e F l u o x e t i n e M i r t a z a p i n e C l o z a p i n e C l o m i p r a m i n e I s o c a r d b o x a z i d 11 2 5 13 2 13 disease gene/protein molecular_function drug 1 1 1 2 1 2 disease gene/protein drug unipolar depres... HTR7 Clozapine associated targets 〃 HTR2C 〃 associated targets 〃 〃 Clomipramine associated targets 1 disease gene/protein pathway drug 20 17 20 20 15 14 11 disease gene/protein anatomy drug Users can compare the explanations of different selected drugs Users can hide ( ), unhide ( ), collapse ( ), or expand ( ) a group of explanation paths based on the meta-path Drug Embedding b gene/protein gene/protein gene/protein C3 C4 C2 Ditto mark (〃) indicates this node is the same as the node in the above path a Control Panel Select drugs through lasso or click M o c l o b e m i d e A g o m e l a t i n e 33 11 28 2 3 10 4 3 1 2 1 T r i m i p r a m i n e N e f a z o d o n e T r a z o d o n e 22 5 5 27 11 7 11 10 8 2 1 1 1 N o r t r i p t y l i n e E s c i t a l o p r a m 29 23 23 27 12 13 1 1 1 2 C l o m i p r a m i n e 5 8 3 1 1 C1 MetaMatrix provides an overview of all predicted drugs in terms of meta paths C5 Ranked by scores or grouped based on embeddings DrugExplorer How can user feedback steer AI? >1,400 users from 64 countries in the first month http://txgnn.org
  • 46. Steer AI 46 Can AI Explanations enable users to Interpret and Steer AI at the same time? Human Knowledge about Classes Human Knowledge about Concepts • Polyphony (VIS 22, Biovis ISMB 22) • Drava (CHI 2023)
  • 47. 47 Can AI Explanations enable users to Interpret and Steer AI at the same time? Human Knowledge about Classes • Polyphony (VIS 22, Biovis ISMB 22)
  • 48. Steer !"#$%&'()"& $*()+%$(&$ #,%'( #*%-(! .(%$/-(# Interpret Anchor 0''(,$ 1(2('$ 0!! 1(3&( $-%"&"&4 !%$% $(#$"&4) !%$% ! " # $ $ Model Fine-tuning Update PolyPhony: An Interactive Transfer Learning Framework for Single-Cell Data Analysis Mark Keller Furui Cheng Nils Gehlenborg Huamin Qu Qianwen Wang Best Long Abstract Award BioVis COSI, Conference on Intelligent System for Molecular Biology (ISMB) IEEE VIS 2022 IEEE Transactions on Visualization and Computer Graphics 48
  • 50. AI Tool: Single Cell Annotation 50 Tissue Cell-Type Mapping
  • 51. AI Algorithm: Classification AI Tool: Single Cell Annotation Cannot be directly applied 51 Cell Types Labelled data Unlabelled new data Labelled data Unlabelled new data AI may not tell Technical Variations (i.e., batch effect) from Biological Variations (i.e., different cell types)
  • 52. Human inputs are needed! Cell Types 52 AI Tool for Single Cell Annotation Automatic Annotation Manual Validation Workflow
  • 53. AI Tool for Single Cell Annotation How about asking users to manually label some items? Power to the People: The Role of Humans in Interactive Machine Learning Saleema Amershi et al. 2014, AI Magazine Previous studies show that • Users do not want to be treated as an oracle that simply label individual items • Transparency about the AI system will help users provide accurate feedback 53 Cell Types
  • 54. Anchor analogous cell populations across datasets • Interpret AI in a way that is consistent with user workflow and mental model • Steer AI by integrating human knowledge Interactive Anchors Enable Simultaneous AI Interpretation and Steering 54 Cell Types
  • 55. Anchor analogous cell populations across datasets • Interpret AI in a way that is consistent with user workflow and mental model • Steer AI by integrating human knowledge Interactive Anchors Enable Simultaneous AI Interpretation and Steering 55 Cell Types
  • 57. Generate Anchor Recommendations Harmony (Korsunsky et al., Nature Methods, 2019) One Anchor Clusters 57 Polyphony Similarity Matrix
  • 58. Polyphony Interpret Anchors A B C Steer !"#$%&'()"& $*()+%$(&$ #,%'( #*%-(! .(%$/-(# Interpret Anchor 0''(,$ 1(2('$ 0!! 1(3&( $-%"&"&4 !%$% $(#$"&4) !%$% ! " # $ $ Model Fine-tuning Update Reference Query 58
  • 60. Use Cases Before Refinement The reference dataset • a plate-based protocol • contains 7,290 cells from 32 donors • annotated with eleven cell types The query dataset: • generated using a droplet-based protocol • contains 8,391 cells from 4 donors • Has the same cell types as the reference Pancreas Dataset 60 After Refinement Six postdoc researchers and one assistant professor in single-cell analysis. “intuitive and easy to use” “more than just giving me an answer” “I can fix undesired outcomes”
  • 62. 62 Best Long Abstract Award BioVis COSI, Conference on Intelligent System for Molecular Biology (ISMB) Computational biology Data Visualization PolyPhony: An Interactive Transfer Learning Framework for Single-Cell Data Analysis
  • 63. Knowledge can be more complicated than Classes 63 In Polyphony, items form Clear Clusters based on their overall similarity after Dimension Reduction
  • 64. Knowledge can be more complicated than Classes In Polyphony, items form Clear Clusters based on their overall similarity after Dimension Reduction What if there is no clear clusters? What if the users are interested in certain aspect rather than the overall similarity? 64
  • 65. Steer AI 65 Can AI Explanations enable users to Interpret and Steer AI at the same time? Human Knowledge about Classes Human Knowledge about Concepts • Polyphony (VIS 22, Biovis ISMB 22) • Drava (CHI 2023)
  • 66. DRAVA for theVisual Exploration of Small Multiples Aligning Human Concepts with Machine Learning Latent Dimensions Qianwen Wang Nils Gehlenborg Sehi L’Yi BioVis COSI, Conference on Intelligent System for Molecular Biology (ISMB’22) ACM CHI Conference on Human Factors in Computing Systems (CHI’23) 66 Harvard Data Science Initiative Postdoctoral Fellow Research Fund
  • 67. Concepts Knowledge can be more complicated than Classes One Class (Zebra) 67 Multiple Concepts (Horse, stripe, grass)
  • 68. Concepts Knowledge can be more complicated than Classes 68 One Class (Zebra) Multiple Concepts (Horse, stripe, grass)
  • 69. Concepts Knowledge can be more complicated than Classes 69 One Class (Zebra) Multiple Concepts (Horse, stripe, grass) Pink- Purple Tissue Density
  • 70. Extract Concepts from AI 70 Been Kim et al. TCAV, 2018 Zhenge Zhao et al. Concept Extract, 2021
  • 71. Extract Concepts from AI encoder decoder input: x latent vector: z !" output: x #" • Learn concepts without labels • Show what a concept looks like Disentangled Representation Learning !"#$%#&'(" 71 UMAP
  • 72. AI Algorithm: Disentangled Representation Learning AI Tool: Concept-driven Visual Exploration encoder decoder input: x latent vector: z !" output: x #" 72
  • 73. !"#$%&'(&)#*+&,-./% 01%12/*1&31)& ,-./%&4%5)"16$1 latent dimensions synthesized images data items 7%*12821*&95%:18*; modify items modify groups split merge investigated dim assistant dim assign distribution locate items of interest reveal association a b c assign DRAVA A Three-Step Workflow 73 TADs in Genomic Contact Matrices
  • 74. Each row represents a latent dimension (a potential concept) Ranked by a saliency score Interpret Concepts via synthesised images 74
  • 75. nested structure thickness of diagonal asymmetric structure Interpret Concepts via synthesised images 75
  • 76. nested structure thickness of diagonal asymmetric structure Interpret Concepts via synthesised images 76
  • 77. Data Items Partial Compression See-Through Item Label Group Label a c label 1 label2 b 1D grouping 2D grouping Representative Average label1 22 Interpret Concepts via data items 77 Lekschas et al. Pining.js. InfoVIS 2020
  • 78. The model confuses the diagonal thickness with the nested structure Interpret Concepts via data items 78
  • 79. User Refinement Refine Concepts 79 !"#$%&'( )#*$# a b a selected metric +,"-%# c !"#$%&!$'()*+ ,)-+!(&.)/ !0#$%&!$&12- +(2%&23 !4#$%&!$-21(&,. 5"#$-)%26-2('2 50#$.+7&1 54#$,8!/'2$'()*+ ,"#$7),!7 ,0#$'7)5!7 drag & drop lasso Depile All Extract Browse Separately Magnify Depile All Extract Browse Separately Magnify drag & drop extract
  • 82. Concept-drivenVisual Exploration Image patches of breast cancer specimens 82
  • 85. Strong correlation with the presence of cancer cells
  • 86. Strong correlation with the presence of cancer cells
  • 87. Filter items to investigate confident false-negative predictions
  • 88. They are more likely fatty tissues surrounded by cancer cells These items are mostly loose purple tissues
  • 89. 89 !"##$%&'%(#"!) *&+,#"!",( )&+,#"!",( #-"."(/ 0%1'&1(/.% +$2+.%&3&+"(4 !"##$%&'%(#"!) Interpret and Steer Concept-based Explanations More accurate concepts More interpretable and flexible visual exploration DRAVA Harvard Data Science Initiative Postdoctoral Fellow Research Fund A NSF-sponsored workshop on interactive visualization and analysis of high-dimensional scientific data https://qianwen.info/DRAVA/#/use-cases
  • 90. Summary Usable and Useful AI Applications through interactive visual explanations that imitate the communication process between humans 90 Help users interpret AI and generate meaningful and actionable insights Enable users to provide feedback and steer AI for the desired tasks Present users explanations about AI
  • 91. Summary User-Centric Design Considerations Data Format Human Knowledge Solutions Graph Biological Mechanisms Increased speed, accuracy, and confidence in validating predictions High- dimensional Vectors Classes Improved user satisfaction level & annotation accuracy Concepts Reveal and fix concept mismatches that are hidden in previous methods Steer !"#$%&'()"& $*()+%$(&$ #,%'( #*%-(! .(%$/-(# Interpret Anchor 0''(,$ 1(2('$ 0!! 1(3&( $-%"&"&4 !%$% $(#$"&4) !%$% ! " # $ $ Model Fine-tuning Update Partial Compression See-Through Item Label Group Label label 1 label2 1D grouping 2D grouping Representative Average label1 22 Path Explanation E s c i t a l o p r a m D e s v e n l a f a x i n e F l u o x e t i n e M i r t a z a p i n e C l o z a p i n e C l o m i p r a m i n e I s o c a r d b o x a z i d 11 2 5 13 2 13 disease gene/protein molecular_function drug 1 1 1 2 1 2 disease gene/protein drug unipolar depres... HTR7 Clozapine associated targets 〃 HTR2C 〃 associated targets 〃 〃 Clomipramine associated targets 1 disease gene/protein pathway drug 20 17 20 20 15 14 11 disease gene/protein anatomy drug Users can compare the explanations of different selected drugs Users can hide ( ), unhide ( ), collapse ( ), or expand ( ) a group of explanation paths based on the meta-path gene/protein gene/protein gene/protein 2 3 1 Ditto mark (〃) indicates this node is the same as the node in the above path Interpreting and Steering AI Explanations 91 Usable and Useful AI Applications through interactive visual explanations that imitate the communication process between humans
  • 92. Summary User-Centric Design Considerations Data Format Human Knowledge Solutions Graph Biological Mechanisms Increased speed, accuracy, and confidence in validating predictions High- dimensional Vectors Classes Improved user satisfaction level & annotation accuracy Concepts Reveal and fix concept mismatches that are hidden in previous methods Steer !"#$%&'()"& $*()+%$(&$ #,%'( #*%-(! .(%$/-(# Interpret Anchor 0''(,$ 1(2('$ 0!! 1(3&( $-%"&"&4 !%$% $(#$"&4) !%$% ! " # $ $ Model Fine-tuning Update Partial Compression See-Through Item Label Group Label label 1 label2 1D grouping 2D grouping Representative Average label1 22 Path Explanation E s c i t a l o p r a m D e s v e n l a f a x i n e F l u o x e t i n e M i r t a z a p i n e C l o z a p i n e C l o m i p r a m i n e I s o c a r d b o x a z i d 11 2 5 13 2 13 disease gene/protein molecular_function drug 1 1 1 2 1 2 disease gene/protein drug unipolar depres... HTR7 Clozapine associated targets 〃 HTR2C 〃 associated targets 〃 〃 Clomipramine associated targets 1 disease gene/protein pathway drug 20 17 20 20 15 14 11 disease gene/protein anatomy drug Users can compare the explanations of different selected drugs Users can hide ( ), unhide ( ), collapse ( ), or expand ( ) a group of explanation paths based on the meta-path gene/protein gene/protein gene/protein 2 3 1 Ditto mark (〃) indicates this node is the same as the node in the above path 92 Interpreting and Steering AI Explanations Usable and Useful AI Applications through interactive visual explanations that imitate the communication process between humans
  • 93. Beyond Publications Open-Source Real-World Users Media Coverage 93 Users of ML4VIS Over 3,000 visits across 40+ countries Users of Gosling Over 15,000 NPM downloads across 120+ countries
  • 94. Research Agenda Previous Studies 94 Design Frameworks and Guidelines Narvis (VIS 18) ML4VIS (TVCG 2021) User-Centric XAI🏅(VIS 22) SineStream (VIS 20) Visualization Techniques/Tools for Human-AI Collaboration HypoML (VIS 20) DiscriLens (VIS 20) ATMSeer (CHI 19) GNNLens (TVCG 21) DNN Genealogy (TVCG 19) ThreadStates (VIS 21) DrugExplorer🏅(VIS 22) Polyphony🏅(VIS 22, Biovis ISMB 22) PapARVis (CHI 20) Biomedical Applications OncoThreads (Bioinformatics 21) Polyphony🏅(VIS 22, Biovis ISMB 22) Gosling🏅(VIS 21, Biovis ISMB 21) GenoRec (VIS 22) ThreadStates (VIS 21) DrugExplorer🏅(VIS 22, Biovis ISMB 21) Future Research Agenda Towards Multimodality https://storyset.com/illustration/data-points/rafiki 8 txt Safeguards for Interaction https://storyset.com/illustration/warning/rafiki Hypothesis for New Biological Knowledge https://storyset.com/illustration/stem-cell-research/rafiki
  • 95. Research Agenda 95 Human-AI Teaming: Safeguards for Interaction https://storyset.com/illustration/warning/ AI is imperfect, so are humans • When and Why do users give biased/inconsistent feedback for AI explanations? • How to help users provide informed and accurate feedback? • How to detect biased/inconsistent user feedback in Human-AI collaboration?
  • 96. Research Agenda 96 Human-AI Teaming: Safeguards for Interaction https://storyset.com/illustration/warning/ AI is imperfect, so are humans • When and Why do users give biased/ inconsistent feedback for AI explanations? • How to help users provide informed and accurate feedback? • How to detect biased/inconsistent user feedback in Human-AI collaboration? My previous study: Framework of designing interactive visual explanations Testbeds Drava, Polyphony, DrugExplorer, TheadStates, etc Partial Compression See-Through Item Label Group Label label 1 label2 1D grouping 2D grouping Representative Average label1 22 Path Explanation E s c i t a l o p r a m D e s v e n l a f a x i n e F l u o x e t i n e M i r t a z a p i n e C l o z a p i n e C l o m i p r a m i n e I s o c a r d b o x a z i d 11 2 5 13 2 13 disease gene/protein molecular_function drug 1 1 1 2 1 2 disease gene/protein drug unipolar depres... HTR7 Clozapine associated targets 〃 HTR2C 〃 associated targets 〃 〃 Clomipramine associated targets 1 disease gene/protein pathway drug 20 17 20 20 15 14 11 disease gene/protein anatomy drug Users can compare the explanations of different selected drugs Users can hide ( ), unhide ( ), collapse ( ), or expand ( ) a group of explanation paths based on the meta-path gene/protein gene/protein gene/protein 2 3 1 Ditto mark (〃) indicates this node is the same as the node in the above path
  • 97. Towards Relatable Explainable AI with the Perceptual Process, Zhang et al. 2022 Research Agenda 97 Human-AI Communication: Towards Multimodality https://storyset.com/illustration/data-points/rafiki 8 txt Multimodality enables • Comprehensive Analysis: highlight patterns that might be missed by using a single modality. • Effective Communication: improve visual representations through the integration of other modalities (e.g., text).
  • 98. Research Agenda 98 Human-AI Communication: Towards Multimodality https://storyset.com/illustration/data-points/rafiki 8 txt Multimodality enables • Comprehensive Analysis: highlight patterns that might be missed by using a single modality. • Effective Communication: improve visual representations through the integration of other modalities (e.g., text). Pathology Radiology Genomic Data Electronic Medical Record Diagnosis and Treatment
  • 99. Research Agenda 99 AI for Science: Hypothesis Generation and Validation https://storyset.com/illustration/stem-cell-research/rafiki Learning new knowledge from AI • How to evaluate AI explanations when there is no ground truth? • How to systematically generate hypotheses from AI explanations? Consistent with the off-label prescription decisions made by clinicians in a large healthcare system (1,272,085 patients, 480 diseases, and 1,290 drugs)
  • 101. Thanks! Data Format Human Knowledge Solutions Graph Biological Mechanisms Increased speed, accuracy, and confidence in validating AI predictions DrugExplorer🏅 (VIS 22, IMLH@ICML 21) High- dimensional Vectors Classes Improved user satisfaction level & annotation accuracy Polyphony🏅 (VIS 22, Biovis ISMB 22) Concepts Reveal and fix concept mismatches that are hidden in previous methods Drava (ACM CHI 23) Steer !"#$%&'()"& $*()+%$(&$ #,%'( #*%-(! .(%$/-(# Interpret Anchor 0''(,$ 1(2('$ 0!! 1(3&( $-%"&"&4 !%$% $(#$"&4) !%$% ! " # $ $ Model Fine-tuning Update Partial Compression See-Through Item Label Group Label label 1 label2 1D grouping 2D grouping Representative Average label1 22 Path Explanation E s c i t a l o p r a m D e s v e n l a f a x i n e F l u o x e t i n e M i r t a z a p i n e C l o z a p i n e C l o m i p r a m i n e I s o c a r d b o x a z i d 11 2 5 13 2 13 disease gene/protein molecular_function drug 1 1 1 2 1 2 disease gene/protein drug unipolar depres... HTR7 Clozapine associated targets 〃 HTR2C 〃 associated targets 〃 〃 Clomipramine associated targets 1 disease gene/protein pathway drug 20 17 20 20 15 14 11 disease gene/protein anatomy drug Users can compare the explanations of different selected drugs Users can hide ( ), unhide ( ), collapse ( ), or expand ( ) a group of explanation paths based on the meta-path gene/protein gene/protein gene/protein 2 3 1 Ditto mark (〃) indicates this node is the same as the node in the above path Present users explanations Help users generate insights Enable users to steer AI Usable and Useful AI Applications through interactive visual explanations that imitate the communication process between humans https://qianwen.info qianwen@umn.edu