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Optimization for Radiology and Social Media. Ken Goldberg IEOR (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

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Optimization for radiology and social media

Optimization for Radiology and Social Media

Ken Goldberg

IEOR (EECS, School of Information, BCNM)

UC Berkeley College of Engineering Research Council, May 2010


Outline
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


Humanities

Philosophy

Rhetoric

Journalism

Art History

Education

Architecture

iSchool

Public Health

Film Studies

Theater

IEOR

BAMPFA

CITRIS

Music

EECS

Art Practice

ME

Technology

Art/Design

BioE

New Media Initiative


Radiology
Radiology

Ken Goldberg, AlperAtamturk, Laurent El Ghaoui (IEOR)

James O’Brien, Jonathan Shewchuck (EECS)

I.-C. Hsu, MD, J. Pouliot, PhD (UCSF)


Prostate cancer
Prostate Cancer

1 in 6 men will be diagnosed with prostate cancer

over 230,000 cases each year in the US

one death every 16 minutes


High dose rate brachytherapy
High Dose Rate Brachytherapy

http://www.prostatebrachytherapyinfo.net/PCT21.html

http://automation.berkeley.edu/projects/needlesteering/


Robot motion planning
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
Dosimetry: Inverse Planning

Dose Distribution

Dosimetric Criteria


Inverse planning with simulated annealing ipsa
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
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
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)

  • Indices

    • s: organ

    • i: point in organ

    • j: dwell position

  • Variables

    • tj: dwell time at j

    • xsi: counting variable for s,i

  • 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

  • Model

    • Maximize Σ x0i

    • Subject to:

      • Σ Dsij tj ≥ Rs xsi

      • Σ Dsij tj ≤ Rs + (Ms – Rs) xsi

      • Ls ≤ Σ xsi ≤ Us

      • tj ≥ 0

      • xsiє {0,1}


Initial results comparing ipsa with ip 2
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


Ip 2 for needle reduction
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

Future Work


Tissue simulation
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
Method: Iterative Learning from Human-Guided Demonstrations

  • 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
Social Media Iterative Learning from Human-Guided Demonstrations

Ken Goldberg, Gail de Kosnik, Kimiko Ryokai

Alec Ross, Katie Dowd (US State Dept)


collaborative robot control: Iterative Learning from Human-Guided Demonstrations

Batch

MultiTasking

Collaborative


Motivation
Motivation Iterative Learning from Human-Guided Demonstrations

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


Motivation1
Motivation Iterative Learning from Human-Guided Demonstrations

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
Related Work: Visualization Iterative Learning from Human-Guided Demonstrations

Clockwise, starting from top left:

Morningside Analytics, MusicBox, Starry Night


Related work info filtering
Related Work: Info Filtering Iterative Learning from Human-Guided Demonstrations

  • 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
Canonical Correlation Analysis (CCA) materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

z

  • 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

x

y

Graphical model for CCA

x = Az + ε

y = Bz + ε

z = A-1x = B-1y


z materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

x

y


Canonical correlation analysis cca1
Canonical Correlation Analysis (CCA) materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

  • 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 space

Opinion Vector

x

z

y

Textual

Comment


Canonical correlation analysis cca2
Canonical Correlation Analysis (CCA) materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

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 Insights materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

Scalability: n Participants, n Viewpoints

n2 Peer to Peer Reviews

Viewpoints are k-Dimensional

Dim. Reduction: 2D Map of Affinity/Similarity

Insight vs. Agreement: Nonlinear Scoring

Ken Goldberg, UC Berkeley

Alec Ross, U.S. State Dept


Optimization for radiology and social media1

Optimization for materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.Radiology and Social Media

Ken Goldberg

IEOR (EECS, School of Information, BCNM)

UC Berkeley College of Engineering Research Council, May 2010


Ip 2 heuristics

Capping materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

Allocate dose budget to dose points that are likely to need it.

:

Solve LP relaxation

Analyze solution and impose new constraints on hottest dose points.

Resolve to feasible solution.

Hard Cuts

Apply custom cuts so that IP2 emphasizes dosimetric indices.

:

Solve LP relaxation.

Add cuts to incorrectly counted dose points.

Repeat until feasible for IP2

IP2 Heuristics


Hard cuts
Hard Cuts materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

x

Hard cut

1

Fractional Optimal Solution (cut off by Hard cut)

Constraints

0

dose


Dimensionality reduction
Dimensionality Reduction materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

Principal Component Analysis (PCA)

  • Assumes independence and linearity

  • Minimizes squared error

  • Scalable: compute position of new user in constant time


Approach visualization
Approach: Visualization materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.


Approach level the playing field
Approach: Level the Playing Field materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.


Approach wisdom of crowds
Approach: Wisdom of Crowds materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.



Berkeley Center for New Media (BCNM): Age.”

David Wong: EECS Undergraduate Student

Tavi Nathanson: EECS Graduate Student

Ephrat Bitton: IEOR Graduate Student

Siamak Faridani: IEOR Graduate Student

Elizabeth Goodman: School of Information Graduate Student

Alex Sydell: EECS Undergraduate Student

Meghan Laslocky: Outside Consultant on Content

Ari Wallach: Outside Consultant on Content and Strategy

Steve Weber: Outside Consultant on Content

Peter Feaver: Outside Consultant on Content

U.S. State Department:

Alec Ross: Senior Advisor for Innovation

Katie Dowd: New Media Director

Daniel Schaub: Director for Digital Communications


Multidimensional scaling
Multidimensional Scaling Age.”

  • 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

j

δij

i

j

dij

i


Kernel based nonlinear pca
Kernel-based Nonlinear PCA Age.”

  • 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


Kernel based nonlinear pca1
Kernel-based Nonlinear PCA Age.”

Input data

KPCA output with Gaussian kernel

  • Pro: Good for finding clusters with arbitrary shape

  • Cons: Need to choose appropriate kernel (no unique solution); does not preserve distance relationships


Stochastic neighbor embedding
Stochastic Neighbor Embedding Age.”

  • 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


Canonical correlation analysis cca3
Canonical Correlation Analysis (CCA) Age.”

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 Space materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

Wisdom of Crowds: Insights are Rare

Scalable, Self-Organizing, Spatial Interface Visualize Diversity of Viewpoints

Incorporate Position into Scoring Metrics

Ken Goldberg

UC Berkeley


Metavid
Metavid materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.


http://newscenter.lbl.gov/feature-stories/2010/04/26/wanda/ materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.


Optimization for radiology treatment and visualizing public opinion

Optimization for materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.Radiology Treatment and Visualizing Public Opinion

Ken Goldberg

Alec Ross, Director of Innovation, U.S. State Dept


Opinion Space: Crowdsourcing Insights materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

Scalability: N Participants, N Viewpoints

Each Viewpoint is n-Dimensional

Dim. Reduction: 2D Map of Affinity/Similarity

Insight vs. Agreement: Nonlinear Scoring

N2 Peer to Peer Reviews

Ken Goldberg, UC Berkeley

Alec Ross, U.S. State Dept


Objective function improvement over ipsa
Objective Function Improvement over IPSA materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

Statistically significant improvement (P = 1.5410-7)


Standard dosimetric indices
Standard Dosimetric Indices materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

No significant improvement in any dosimetric index (P > 0.01)


Prostate dose volume histogram
Prostate Dose Volume Histogram materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

950 cGy

1425 cGy


Isodose curves
Isodose Curves materials, slides for in-class lectures, discussion ideas, hand-on activities, and homework assignments.

LP

IPSA


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