Optimization for Radiology and Social Media Ken Goldberg IEOR (EECS, School of Information, BCNM) UC...
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Transcript of Optimization for Radiology and Social Media Ken Goldberg IEOR (EECS, School of Information, BCNM) UC...
Optimization for Radiology and Social Media
Ken GoldbergIEOR (EECS, School of Information, BCNM)
UC Berkeley College of Engineering Research Council, May 2010
Outline
• IEOR Dept, BCNM• Radiology• Social Media
UC Berkeley IEOR Department• The only IEOR department in the UC system
• Ranked #3 in USA
• 55 BS, 10 BA, 30 MS, 5-8 PhD degrees per year
IEOR Faculty:Ilan AdlerAlper AtamturkJon BurgstoneYing-Ju ChenLaurent El Ghaoui Ken GoldbergXin GuoDorit S. HochbaumRichard Karp Philip M. KaminskyRobert C. LeachmanAndrew LimShmuel S. OrenChristos PapadimitriouRhonda L. Righter (Chair)Lee W. SchrubenZuo-Jun "Max" ShenIkhlaq SidhuCandace Yano
Mission
To critically analyze and shape developments in new media from trans-disciplinary and global perspectives that emphasize humanities and the public interest.
bcnm.berkeley.edu
New Media Initiative
Art/Design
Humanities
Technology
Rhetoric
Philosophy
BAMPFA
Art History
Film Studies
EECS
IEOR
Public Health
Journalism
Architecture
Music
Art Practice
iSchool
ME
BioE
Theater
Education
CITRIS
Radiology
Ken Goldberg, Alper Atamturk, Laurent El Ghaoui (IEOR) James O’Brien, Jonathan Shewchuck (EECS)
I.-C. Hsu, MD, J. Pouliot, PhD (UCSF)
8
Prostate Cancer
1 in 6 men will be diagnosed with prostate cancer
over 230,000 cases each year in the USone death every 16 minutes
High Dose Rate Brachytherapy
http://www.prostatebrachytherapyinfo.net/PCT21.html
http://automation.berkeley.edu/projects/needlesteering/
Robot Motion Planning
• Theorem (Completeness): A sensorless plan exists for any polygonal part.• Theorem (Complexity): For a polygon of n sides, the algorithm runs in time
O(n2) and finds plans of length O(n).
• Extensions:• Stochastically Optimal Plans• Extension to Non-Zero Friction • Geometric Eccentricity / constant time complexity• Part Fixturing and Holding
Dosimetry: Inverse Planning
Color Dose
Blue < 75%
Cyan 75% - 100%
Green 100% - 120%
Yellow 120% - 150%
Orange 150% - 200%
Red > 200%
Index Requirement
VP100 > 90%
HI > 60%
VU120 < 0.1 cc
VR75 < 1.0 cc
VB75 < 1.0 ccDosimetric Criteria
Dose Distribution
Inverse Planning with Simulated Annealing (IPSA)
• Inverse planning software developed at UCSF by Pouliot group • FDA-approved: used clinically worldwide• Simulated annealing dose point penalty method
Inverse Planning with Linear Programming (IPLP)
• LP formulation (UC Berkeley)• Guarantees global optima• Optimization of HDR Brachytherapy Dose Distributions using Linear Programming with Penalty Costs.
Ron Alterovitz, Etienne Lessard, Jean Pouliot, I-Chow Joe Hsu, James F. O'Brien, and Ken Goldberg. Medical Physics, vol. 33, no. 11, pp. 4012-4019, Nov. 2006.
Limitations of Penalty Model
• Only specifies dosimetry at dose points, not to organs• Not equivalent to dosimetric indices
– Not intuitive for Physicians– Results not always clinically viable. – Results difficult to customize for special cases
• Dosimetric index: if dose at x > R, then x = 1, x = 0 otherwise• Discrete Variables
Inverse Planning with Integer Programming (IP2)
• Parameters:– Dsij: dose rate from j to s,i
– Rs: Dose threshold for s
– Ms: Max dose for points in s
– Ls: Lower bound for dosimetric s
– Us: Upper bound for dosimetric s
• Variables– tj: dwell time at j
– xsi: counting variable for s,i
• Model– Maximize Σ x0i
– Subject to:• Σ Dsij tj ≥ Rs xsi
• Σ Dsij tj ≤ Rs + (Ms – Rs) xsi
• Ls ≤ Σ xsi ≤ Us
• tj ≥ 0
• xsi є {0,1}
• Indices– s: organ– i: point in organ– j: dwell position
Initial Results: Comparing IPSA with IP2
• Average Runtime (sec):– IPSA: 5– IP2 (heuristic 1): 23– IP2 (heuristic 2): 900
• Compliance with all clinical criteria– IPSA: 0% of patients – IP2 (heuristic 1): 95% of patients– IP2 (heuristic 2): 100% of patients–
IP2 for Needle Reduction• Minimize number of needles
• Minimize trauma
• Speed Recovery
Possible Needles Optimal Needle Selection (example)
Future Work• Conic Optimization• Robust Optimization
Model uncertainties in:– Organ location, motion– Edema– Catheter displacement
19
Tissue Simulation
http://graphics.cs.berkeley.edu/papers/Chentanez-ISN-2009-08/
Nuttapong Chentanez, Ron Alterovitz, Daniel Ritchie, Lita Cho, Kris K. Hauser, Ken Goldberg, Jonathan R. Shewchuk, and James F. O'Brien. "Interactive Simulation of Surgical Needle Insertion and Steering". In Proceedings of
ACM SIGGRAPH 2009, pages 88:1–10, Aug 2009.
Superhuman Performance of Surgical Tasks by Robots using Iterative Learning
from Human-Guided Demonstrations
Jur van den Berg, Stephen Miller, Daniel Duckworth, Humphrey Hu, Andrew Wan, Xiao-Yu Fu, Ken Goldberg, Pieter Abbeel
University of California, Berkeley
Method:
• 1. Robot learns surgical task from human demonstrations– Knot tying– Suturing
• 2. Robot learns to execute tasks with superhuman performance– Increase smoothness– Increase speed
Social Media
Ken Goldberg, Gail de Kosnik, Kimiko RyokaiAlec Ross, Katie Dowd (US State Dept)
… …
……
Collaborative
collaborative robot control:
MultiTasking
Batch
Motivation
Goals of Organization• Engage community• Understand community
– Solicit input– Understand the distribution of
viewpoints– Discover insightful comments
Goals of Community• Understand relationships to other
community members• Consider a diversity of viewpoints• Express ideas, and be heard
Motivation
Classical approaches: surveys, polls
Drawbacks: limited samples, slow, doesn’t increase engagement
Current approaches: online forums, comment lists
Drawbacks: data deluge, cyberpolarization, hard to discover insights
Related Work: Visualization
Clockwise, starting from top left:
Morningside Analytics, MusicBox, Starry Night
Related Work: Info Filtering
• K. Goldberg et al, 2001: Eigentaste
• E. Bitton, 2009: spatial model• Polikar, 2006: ensemble
learning
Six 50-minute Learning Object Modules, preparation materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.
Canonical Correlation Analysis (CCA)
• Observed variables: x, y• Latent variable: z• Learn MLEs for low-rank
projections A and B• Equivalently, find inverse mapping
that maximizes correlation between A, B
zz
xx yyGraphical model for CCA
x = Az + εy = Bz + ε
z = A-1x = B-1y
zz
xx yy
Canonical Correlation Analysis (CCA)
zzxx
yy
CCA gives three posterior expectations E(z|x) E(z|y) E(z|x,y)
E(z|x,y) is used to visualize the opinion spaceTextual
Comment
Opinion Vector
Canonical Correlation Analysis (CCA)
Each point in the Canonical representation has an expected list of words associated to it.
A visualization of this list of words can be used to give users more information about their location
Opinion Space: Crowdsourcing InsightsScalability: n Participants, n Viewpointsn2 Peer to Peer ReviewsViewpoints are k-DimensionalDim. Reduction: 2D Map of Affinity/SimilarityInsight vs. Agreement: Nonlinear Scoring
Ken Goldberg, UC BerkeleyAlec Ross, U.S. State Dept
Optimization for Radiology and Social Media
Ken GoldbergIEOR (EECS, School of Information, BCNM)
UC Berkeley College of Engineering Research Council, May 2010
IP2 Heuristics• Capping
– Allocate dose budget to dose points that are likely to need it.
– :1. Solve LP relaxation
2. Analyze solution and impose new constraints on hottest dose points.
3. Resolve to feasible solution.
• Hard Cuts– Apply custom cuts so
that IP2 emphasizes dosimetric indices.
– :1. Solve LP relaxation.
2. Add cuts to incorrectly counted dose points.
3. Repeat until feasible for IP2
Hard Cutsx
dose
Hard cut
Constraints
Fractional Optimal Solution (cut off by Hard cut)
0
1
Dimensionality Reduction
Principal Component Analysis (PCA)• Assumes independence and linearity• Minimizes squared error• Scalable: compute position of new user in constant time
Approach: Visualization
Approach: Level the Playing Field
Approach: Wisdom of Crowds
“We’re moving from an Information Age to an Opinion Age.”- Warren Sack, UCSC
Berkeley Center for New Media (BCNM):
David Wong: EECS Undergraduate StudentTavi Nathanson: EECS Graduate StudentEphrat Bitton: IEOR Graduate StudentSiamak Faridani: IEOR Graduate StudentElizabeth Goodman: School of Information Graduate StudentAlex Sydell: EECS Undergraduate Student
Meghan Laslocky: Outside Consultant on ContentAri Wallach: Outside Consultant on Content and StrategySteve Weber: Outside Consultant on ContentPeter Feaver: Outside Consultant on Content
U.S. State Department:
Alec Ross: Senior Advisor for InnovationKatie Dowd: New Media DirectorDaniel Schaub: Director for Digital Communications
Multidimensional Scaling
• Goal: rearrange objects in low dim space so as to reproduce distances in higher dim
• Strategy: Rearrange & compare solns, maximizing goodness of fit:
• Can use any kind of similarity function• Pros
– Data need not be normal, relationships need not be linear
– Tends to yield fewer factors than FA• Con: slow, not scalable
dij f (ij ) 2i, j
δiji
j
diji
j
Kernel-based Nonlinear PCA
• Intuition: in general, can’t linearly separate n points in d < n dim, but can almost always do so in d ≥ n dim
• Method: compute covariance matrix after transforming data into higher dim space
• Kernel trick used to improve complexity• If Φ is the identity, Kernel PCA = PCA
C 1
m x j x j
T j1
m
Kernel-based Nonlinear PCA
• Pro: Good for finding clusters with arbitrary shape• Cons: Need to choose appropriate kernel (no unique
solution); does not preserve distance relationships
Input data KPCA output with Gaussian kernel
Stochastic Neighbor Embedding
• Converts Euclidean dists to conditional probabilities• pj|i = Pr(xi would pick xj as its neighbor | neighbors picked
according to their density under a Gaussian centered at xi)
• Compute similar prob qj|i in lower dim space
• Goal: minimize mismatch between pj|i and qj|i:
• Cons: tends to crowd points in center of map; difficult to optimize
C KL Pi Qi i
p j | i logp j | iq j | ij
i
Canonical Correlation Analysis (CCA)
CCA visualization with tag cloud for that location in the space. The tag cloud uses stemmed keywords.
Six 50-minute Learning Object Modules, preparation materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.
Opinion SpaceWisdom of Crowds: Insights are RareScalable, Self-Organizing, Spatial Interface Visualize Diversity of ViewpointsIncorporate Position into Scoring Metrics
Ken GoldbergUC Berkeley
Metavid
http://newscenter.lbl.gov/feature-stories/2010/04/26/wanda/
Optimization for Radiology Treatment and Visualizing Public Opinion
Ken GoldbergAlec Ross, Director of Innovation, U.S. State Dept
Opinion Space: Crowdsourcing InsightsScalability: N Participants, N ViewpointsEach Viewpoint is n-DimensionalDim. Reduction: 2D Map of Affinity/SimilarityInsight vs. Agreement: Nonlinear ScoringN2 Peer to Peer Reviews
Ken Goldberg, UC BerkeleyAlec Ross, U.S. State Dept
66
Objective Function Improvement over IPSA
Statistically significant improvement (P = 1.5410-7)
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
1 2 3 4 5 6 7 8 9 1011121314151617181920
Patient Case
Ob
ject
ive
Fu
nct
ion
% D
iffe
ren
ce
67
Standard Dosimetric Indices
No significant improvement in any dosimetric index (P > 0.01)
0
20
40
60
80
100
Pro
stat
eV
100
Pro
stat
eV
150
Ure
thra
V10
0
Ure
thra
V15
0
Rec
tum
V50
Rec
tum
V10
0
Bla
dder
V50
Bla
dder
V10
0
Do
sim
etr
ic In
de
x V
alu
e (
%)
IPSA solutions LP solutions
68
Prostate Dose Volume Histogram
0
20
40
60
80
100
0 500 1000 1500 2000 2500 3000 3500
Dose (cGy)
Volu
me (
%)
Desired
IPSA
LP
950 cGy
1425 cGy
69
Isodose Curves
IPSA LP