Seminars

2012-03-24T12:00:06Z

Llins:

== Feb 1, 2012. Eli Cortez ==

http://www.dcc.ufam.edu.br/~eccv/

Title: Information Extraction over Textual Sources

Abstract: The growing use of text files for information exchange, such as HTML pages, XML documents, e-mail, blogs posts, tweets, RSS and SMS messages, brings numerous problems related to how to properly exploit the information contained therein. In particular, problems related to Information Extraction (IE) from text have motivated several works in various scientific communities in areas such as Databases, Data Mining, Information Retrieval and Artificial Intelligence. In this talk, it will be presented an overview of the IE problem and methods that have been proposed in recent literature to deal with it. The IE problem consists in extracting values of interest arranged in unstructured texts, such as postal addresses, bibliographic citations, classified ads, that are implicitly present in textual sources from a variety of different domains. It will be discussed the main and most recent approaches proposed in the literature, with particular emphasis on probabilistic methods.

== Feb 8, 2012. Chris Bregler ==

http://mrl.nyu.edu/~bregler/

Title: Overview of Chris Bregler's Research

== Feb 15, 2012. Jonathan Viventi ==

http://www.tneuro.com/jviventi

Title: High-Resolution Brain Machine Interfaces using Flexible SiliconElectronics: Research and Clinical Applications

Current implantable brain devices for clinical and research
applications require that each electrode is individually wired to a
separate electronic system. Establishing a high-resolution interface
over broad regions of the brain is infeasible under this constraint,
as an electrode array with thousands of passive contacts would require
thousands of wires to be individually connected. To overcome this
limitation, we have developed new implantable electrode array
technology that incorporates active, flexible electronics. This
technology has enabled extremely flexible arrays of 720 and soon,
thousands of multiplexed and amplified sensors spaced as closely as
250 µm apart, which are connected using just a few wires. These
devices yield an unprecedented level of spatial and temporal
micro-electrocorticographic (µECoG) resolution for recording and
stimulating distributed neural networks. µECoG is one of the many
possible applications of this technology, which also include cardiac,
peripheral nerve and retinal prosthetic devices. I will present the
development of this technology and examples of retinotopic and
tonotopic maps produced from in vivo recordings. I will also present
examples of finely detailed spatial and temporal patterns from feline
neocortex that give rise to seizures and suggest new stimulation
paradigms to treat epilepsy.

== Feb 22, 2012. Marcel Hlawatsch ==

http://www.vis.uni-stuttgart.de/~hlawatml

== Mar 14, 2012. Richard Bonneau ==

http://biology.as.nyu.edu/object/RichardBonneau

Title: Overview of Richard Bonneau's Research

Our lab is focused on a number of computational biology problems that,
if solved, would remove key bottlenecks in biology and systems
biology. We focus on two main categories of computational biology:
learning networks from functional genomics data and predicting and
modeling protein structure. In the area of structure prediction we
were early contributors to the Rosetta code; a platform for structure
prediction, design and docking. In the area of network inference we
worked on two computational methods that were used to demonstrate the
first predictive genome-wide model of regulatory dynamics (i.e. the
first case where a genome-wide model could predict the whole
transcriptional state of cells at future time points not part of the
training set). Both network inference and protein structure prediction
remain grand challenges and in spite of our progress much exciting
work remains to be done in the coming years as we continue to improve,
scale and apply these methods.

== Mar 21, 2012. Thomas J. Peters ==

http://www.engr.uconn.edu/~tpeters/

Title: Topological Biomolecular Steering

DataVis2012/Schedule

2012-03-19T15:27:11Z

Llins: /* 3/5 2D Visualization Techniques */

== 1/23: Introduction to visualization ==

Lecturer: Claudio

Topics: Scientific Visualization

Notes: [http://www.cs.utah.edu/~csilva/courses/cs5630/lec01-notes.pdf lec01-notes.pdf]

Slides: TBA

Animations: [http://www.cs.utah.edu/~csilva/courses/cs5630/fall2007/SevereTstorm.mov NCSA storm animation]

Further reading:

[http://www.cs.ubc.ca/labs/imager/tr/2009/VisChapter Visualization by Tamara Munzner] (see PDF on her page)

(Optional reading) [http://www.sci.utah.edu/~csilva/papers/cise2008a.pdf Provenance for Computational Tasks: A Survey]

(Optional reading) [http://www.cs.utah.edu/~csilva/courses/cs5630/reproducible_vis.pdf Provenance for Visualizations: Reproducibility and Beyond], C. Silva, J. Freire, and S. Callahan, IEEE Computing in Science and Engineering, 2008.

== 1/30: The visualization pipeline ==

Lecturer: Huy Vo

Topics: Procedural vs. Dataflow programming; Using Dataflow for the Vis Pipeline; Dataflow programming with VTK; Dataflow programming with VisTrails; python.

Notes: [http://www.cs.utah.edu/~csilva/courses/cs5630/lec02-notes.pdf lec02-notes.pdf]

Slides: [http://www.vistrails.org/download/download.php?type=PUB&id=dataflow.pdf dataflow.pdf]

Further reading:

[http://www.cmake.org/cmake/help/cmake_tutorial.html CMake Tutorial]

[http://www.vtk.org/Wiki/VTK/Tutorials/New_Pipeline VTK Pipeline]

[http://www.vtk.org/Wiki/VTK/Tutorials VTK Tutorial]

[http://www.paraview.org/Wiki/The_ParaView_Tutorial ParaView Tutorial]

== 2/6: Modeling Data for Visualization ==

Lecturer: Claudio Silva

Topics: Discrete vs continous data; Sampling and interpolation; Point vs triangulated data; Meshing data types; Regular vs irregular data; Tabular data; Vector and tensor fields; Geometry Processing: Reconstruction and meshing; Simplification; Smoothing; Other Filtering algorithms

Topics (here???): Basic linear algebra; vectors; basic differential geometry (space curves, tangents, normals, surfaces); basic vector calculus (gradient, divergence, curl, gauss' theorem, green's theorem)

Notes: [http://www.vistrails.org/download/download.php?type=PUB&id=week2.pdf modeling data]

Slides: [http://www.vistrails.org/download/download.php?type=PUB&id=processing.ppt processing.ppt]

Further reading:

[http://www.cs.wisc.edu/graphics/Courses/559-s2001/notes/hanrahan.pdf Basic Signal Processing]

[http://graphics.cs.uiuc.edu/~garland/papers/quadrics.pdf Surface Simplification Using Quadric Error Metrics]

(Optional Reading) [http://www.sci.utah.edu/~csilva/papers/vis2001b.pdf A Memory Insensitive Technique for Large Model Simplification]

(Optional Reading) [http://graphics.cs.uiuc.edu/~garland/papers/TR-2004-2450.pdf Quadric-based Simplification in any Dimension]

http://en.wikipedia.org/wiki/Least_squares

(Optional Reading) [http://www.sci.utah.edu/~csilva/papers/sig2005.pdf Robust Moving Least-squares Fitting with Sharp Features]

(Optional Reading) [http://www.sci.utah.edu/~cscheid/pubs/band_mls.pdf Optimal Bandwidth Selection for MLS Surfaces]

== 2/13: Plotting ==

Lecturer: Claudio

Topics: Simple Plotting Methods: Dot Plots, Connected Symbol Plots, Scatter Plots, Histograms, Others. Advanced Plotting Methods: Multimodal, Higher Dimensional, Correlation, Uncertainty and Variation.

Notes: [http://www.sci.utah.edu/~stevec/classes/cs5630/PlottingNotes.pdf PlottingNotes.pdf]

Slides: [http://www.sci.utah.edu/~stevec/slides/SciVis/Plotting1.pdf Plotting1.pdf] and [http://www.vistrails.org/download/download.php?type=PUB&id=Plotting2.pdf Plotting2.pdf]

Vistrails: [http://www.sci.utah.edu/~stevec/classes/cs5630/PlottingVistrails.zip PlottingVistrails.zip] - Unzip this file in the examples directory of your VisTrails installation and it will add the vistrails along with their data sets (in the data directory).

Further Reading:

* The Elements of Graphing Data. William S. Cleveland, Hobart Press, 2nd Edition, 1994.

* Visualizing Data. William S. Cleveland, Hobart Press, 1993.

* The Visual Display of Quantitative Information. Edward R. Tufte, Graphics Press, 2001.

* Visual Explanations: Images and Quantities, Evidence and Narrative. Edward R. Tufte, Graphics Press, 2997.

* [http://www.fmrib.ox.ac.uk/analysis/techrep/tr00mj2/tr00mj2/node24.html Histogram Bin Size]

* [http://en.wikipedia.org/wiki/Correlation Correlation]

* [http://en.wikipedia.org/wiki/Linear_regression Linear Regression]

* [http://en.wikipedia.org/wiki/Box_plot Box Plots]

== 2/20: NO CLASS (President's Day) ==

== 2/27: Color and Human Perception ==

Lecturer: Huy Vo

Topics: Human vision system; Optical illusions; Color Science; Color spaces; Color Blindness; Color maps;

Notes:

Slides: [http://www.cs.utah.edu/~csilva/courses/cs5630/human-vision.pdf human-vision.pdf] [http://www.cs.utah.edu/~csilva/courses/cs5630/colorvision-jens.pdf colorvision-jens.pdf]

Links:

* http://en.wikipedia.org/wiki/Eye

* http://www.handprint.com/HP/WCL/color2.html

* [http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm How NOT to Lie with Visualization], Bernice E. Rogowitz, Lloyd A. Treinish, IBM Research.

* [http://www-graphics.stanford.edu/courses/cs248-08/color/color1.html Color Theory, ColorSpaces], Marc Levoy, Stanford Graphics Lab.

* http://en.wikipedia.org/wiki/Opponent_process

* http://en.wikipedia.org/wiki/Color_models

* http://en.wikipedia.org/wiki/Absolute_color_space

* http://en.wikipedia.org/wiki/Additive_color

* http://en.wikipedia.org/wiki/Subtractive_color

* http://en.wikipedia.org/wiki/RGB_color_model

* http://en.wikipedia.org/wiki/SRGB_color_space

* http://en.wikipedia.org/wiki/CIE_XYZ_color_space

== 3/5 2D Visualization Techniques ==

Lecturer: Lauro

Topics: 2-D scalar fields: Color mapping; height fields; 2-D contours, marching tris, marching quads; 2-D vector fields: div, grad, curl in 2D; Glyphs; Steady vs Unsteady flows; 2-D streamlines, streaklines, pathlines

Slides: [http://www.vistrails.org/download/download.php?type=PUB&id=2d_scalar_vis.pdf 2D Scalar Fields (pdf file)]; [http://www.vistrails.org/download/download.php?type=PUB&id=2d_vector_vis.pdf 2d Vector Fields (pdf file)]

Notes: [http://www.vistrails.org/download/download.php?type=PUB&id=2d_scalar_vis_notes.pdf 2d Scalar Fields (pdf file)]

Vistrails: [http://www.vistrails.org/download/download.php?type=DATA&id=ozone_and_data.zip zip file with ozone.vt and data] [http://www.vistrails.org/download/download.php?type=DATA&id=asymptotic_decider.vt asymptotic decider in 2d] [http://www.vistrails.org/download/download.php?type=DATA&id=elevation.zip heightfields]

Note: These vistrails use relative file paths so you don't need to change each of them individually to match your directory structure. Simply unzip the file to whichever location is more convenient. Then, inside VisTrails, open the VisTrails shell, type:

import os
os.chdir("c:/directory/where/you/unzipped/it")

This will change the directory so you should be able to just run the pipelines.

Further reading:

[http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5290706 BubbleSets (technique that uses 2d countours)] [http://www.youtube.com/watch?v=Ju2hSThmPWA (video)]

http://ieeexplore.ieee.org/iel5/4271943/4271944/04272091.pdf

http://www.jstor.org/stable/pdfplus/2683294.pdf

[http://www.inf.ufrgs.br/%7Eoliveira/pubs_files/Kuhn_Oliveira_Fernandes_Vis2008.pdf An Efﬁcient Naturalness-Preserving Image-Recoloring Method for Dichromats]

== 3/12 NO CLASS (Spring Break) ==

== 3/19 Volume Visualization ==

Lecturer:

Topics: Slicing; Contours; Marching algorithms; Accelerating structures; High-quality contours

Slides:

References:

== 3/26 Volume Visualization ==

Lecturer:

Topics: Structured grid techniques: ray-casting, splatting, texture slicing, shear-warp; Unstructured grid techniques; Transfer function specification

Slides:

Notes:

Vistrails:

References:

== 4/2 Midterm ==

== 4/9 Vector & Tensor Visualization ==

Lecturer:

Topics: DT/MRI intro, glyphs, colormapping, volume rendering; 3D techniques, critical points

Slides:

References:

== 4/16: Information Visualization ==

Lecturer:

Topics: Parallel coordinates; Graph visualization; Trees and Graphs; InfoVis Examples

Slides:

Links:

== 4/23: Information Visualization ==

Lecturer:

Topics: Parallel coordinates; Graph visualization; Trees and Graphs; InfoVis Examples

Slides:

Links:

== 5/7: Information Visualization ==

Lecturer:

Topics: Parallel coordinates; Graph visualization; Trees and Graphs; InfoVis Examples

Slides:

Links:

Seminars

2012-03-15T13:27:47Z

Llins: /* Feb 8, 2012. Chris Bregler */

== Feb 1, 2012. Eli Cortez ==

http://www.dcc.ufam.edu.br/~eccv/

Title: Information Extraction over Textual Sources

Abstract: The growing use of text files for information exchange, such as HTML pages, XML documents, e-mail, blogs posts, tweets, RSS and SMS messages, brings numerous problems related to how to properly exploit the information contained therein. In particular, problems related to Information Extraction (IE) from text have motivated several works in various scientific communities in areas such as Databases, Data Mining, Information Retrieval and Artificial Intelligence. In this talk, it will be presented an overview of the IE problem and methods that have been proposed in recent literature to deal with it. The IE problem consists in extracting values of interest arranged in unstructured texts, such as postal addresses, bibliographic citations, classified ads, that are implicitly present in textual sources from a variety of different domains. It will be discussed the main and most recent approaches proposed in the literature, with particular emphasis on probabilistic methods.

== Feb 8, 2012. Chris Bregler ==

http://mrl.nyu.edu/~bregler/

Title: Overview of Chris Bregler's Research

== Feb 15, 2012. Jonathan Viventi ==

http://www.tneuro.com/jviventi

Title: High-Resolution Brain Machine Interfaces using Flexible SiliconElectronics: Research and Clinical Applications

Current implantable brain devices for clinical and research
applications require that each electrode is individually wired to a
separate electronic system. Establishing a high-resolution interface
over broad regions of the brain is infeasible under this constraint,
as an electrode array with thousands of passive contacts would require
thousands of wires to be individually connected. To overcome this
limitation, we have developed new implantable electrode array
technology that incorporates active, flexible electronics. This
technology has enabled extremely flexible arrays of 720 and soon,
thousands of multiplexed and amplified sensors spaced as closely as
250 µm apart, which are connected using just a few wires. These
devices yield an unprecedented level of spatial and temporal
micro-electrocorticographic (µECoG) resolution for recording and
stimulating distributed neural networks. µECoG is one of the many
possible applications of this technology, which also include cardiac,
peripheral nerve and retinal prosthetic devices. I will present the
development of this technology and examples of retinotopic and
tonotopic maps produced from in vivo recordings. I will also present
examples of finely detailed spatial and temporal patterns from feline
neocortex that give rise to seizures and suggest new stimulation
paradigms to treat epilepsy.

== Feb 22, 2012. Marcel Hlawatsch ==

http://www.vis.uni-stuttgart.de/~hlawatml

== Mar 14, 2012. Richard Bonneau ==

http://biology.as.nyu.edu/object/RichardBonneau

Title: Overview of Richard Bonneau's Research

Our lab is focused on a number of computational biology problems that,
if solved, would remove key bottlenecks in biology and systems
biology. We focus on two main categories of computational biology:
learning networks from functional genomics data and predicting and
modeling protein structure. In the area of structure prediction we
were early contributors to the Rosetta code; a platform for structure
prediction, design and docking. In the area of network inference we
worked on two computational methods that were used to demonstrate the
first predictive genome-wide model of regulatory dynamics (i.e. the
first case where a genome-wide model could predict the whole
transcriptional state of cells at future time points not part of the
training set). Both network inference and protein structure prediction
remain grand challenges and in spite of our progress much exciting
work remains to be done in the coming years as we continue to improve,
scale and apply these methods.

Seminars

2012-03-15T13:27:09Z

Llins: /* Mar 14, 2012. Richard Bonneau */

== Feb 1, 2012. Eli Cortez ==

http://www.dcc.ufam.edu.br/~eccv/

Title: Information Extraction over Textual Sources

Abstract: The growing use of text files for information exchange, such as HTML pages, XML documents, e-mail, blogs posts, tweets, RSS and SMS messages, brings numerous problems related to how to properly exploit the information contained therein. In particular, problems related to Information Extraction (IE) from text have motivated several works in various scientific communities in areas such as Databases, Data Mining, Information Retrieval and Artificial Intelligence. In this talk, it will be presented an overview of the IE problem and methods that have been proposed in recent literature to deal with it. The IE problem consists in extracting values of interest arranged in unstructured texts, such as postal addresses, bibliographic citations, classified ads, that are implicitly present in textual sources from a variety of different domains. It will be discussed the main and most recent approaches proposed in the literature, with particular emphasis on probabilistic methods.

== Feb 8, 2012. Chris Bregler ==

http://mrl.nyu.edu/~bregler/

== Feb 15, 2012. Jonathan Viventi ==

http://www.tneuro.com/jviventi

Title: High-Resolution Brain Machine Interfaces using Flexible SiliconElectronics: Research and Clinical Applications

Current implantable brain devices for clinical and research
applications require that each electrode is individually wired to a
separate electronic system. Establishing a high-resolution interface
over broad regions of the brain is infeasible under this constraint,
as an electrode array with thousands of passive contacts would require
thousands of wires to be individually connected. To overcome this
limitation, we have developed new implantable electrode array
technology that incorporates active, flexible electronics. This
technology has enabled extremely flexible arrays of 720 and soon,
thousands of multiplexed and amplified sensors spaced as closely as
250 µm apart, which are connected using just a few wires. These
devices yield an unprecedented level of spatial and temporal
micro-electrocorticographic (µECoG) resolution for recording and
stimulating distributed neural networks. µECoG is one of the many
possible applications of this technology, which also include cardiac,
peripheral nerve and retinal prosthetic devices. I will present the
development of this technology and examples of retinotopic and
tonotopic maps produced from in vivo recordings. I will also present
examples of finely detailed spatial and temporal patterns from feline
neocortex that give rise to seizures and suggest new stimulation
paradigms to treat epilepsy.

== Feb 22, 2012. Marcel Hlawatsch ==

http://www.vis.uni-stuttgart.de/~hlawatml

== Mar 14, 2012. Richard Bonneau ==

http://biology.as.nyu.edu/object/RichardBonneau

Title: Overview of Richard Bonneau's Research

Our lab is focused on a number of computational biology problems that,
if solved, would remove key bottlenecks in biology and systems
biology. We focus on two main categories of computational biology:
learning networks from functional genomics data and predicting and
modeling protein structure. In the area of structure prediction we
were early contributors to the Rosetta code; a platform for structure
prediction, design and docking. In the area of network inference we
worked on two computational methods that were used to demonstrate the
first predictive genome-wide model of regulatory dynamics (i.e. the
first case where a genome-wide model could predict the whole
transcriptional state of cells at future time points not part of the
training set). Both network inference and protein structure prediction
remain grand challenges and in spite of our progress much exciting
work remains to be done in the coming years as we continue to improve,
scale and apply these methods.

Seminars

2012-03-15T13:19:24Z

Llins: /* Feb 15, 2012. Jonathan Viventi */

Seminars

2012-03-15T13:19:11Z

Llins: /* Feb 15, 2012. Jonathan Viventi */

2009-04-02T19:27:44Z

Llins: /* VIS 2009 SCI Submission List */

VisLunch/Spring2009/

2009-04-02T19:27:23Z

Llins: /* VIS 2009 SCI Submission List */

VisLunch/Spring2009/

2009-04-02T19:26:35Z

2009-01-30T20:53:23Z

Llins:

VisLunch/Spring2009/

2009-01-30T20:50:23Z

Llins: New page: Vislunch Spring 2009 *** VACET Emanuele - Scidat Hao - Topology *** Vislunch Schedule 02-06 Hao & Carlos - uncertainty 02-13 Carson 02-20 Hao - detection of critical points 02-27 E...

Vislunch Spring 2009

*** VACET
Emanuele - Scidat
Hao - Topology

*** Vislunch Schedule

02-06 Hao & Carlos - uncertainty
02-13 Carson
02-20 Hao - detection of critical points
02-27 Erik - timeseries
03-06 Erik
03-13 Mathias
03-20 Lin & Tiago
03-27 Tiago
04-03 Emanuele
04-10 Julian
04-17 Luiz & Alex
04-24 Huy
05-01
05-08
05-15
05-22
05-29
06-05
06-12
06-19
06-26
07-03

VisLunch/Fall2008

2008-11-20T00:22:59Z

Llins:

__NOTOC__

== Coming up next Friday (11/21) ==

=== Towards Gigapixel displays : What?, How? and Why? (Chris Goodyer) ===

Chris Goodyer from the University of Leeds in the UK will be
talking about his recent work on multi-monitor displays:

http://www.comp.leeds.ac.uk/ceg/IB3dviewer.htm

Here is his web page:

http://www.comp.leeds.ac.uk/ceg/

Towards Gigapixel displays : What?, How? and Why?

Over the past couple of years there has been a growing trend for high
resolution display walls, intriguingly named "gigapixel displays" or
"powerwalls". These are tiled multile projectors or multiple screens
connected to a cluster. Besides looking visually impressive there are
important research questions concerning what advantages there would be to
using them over conventional large displays. In addition, the methods used
for interacting with applications running across such large numbers of
displays needs to be carefully considered.

In this talk I shall summarize some of the work we have been doing at the
University of Leeds on our 53-megapixel wall. I will discuss several of
the software environments available for deploying applications along with
their shortcomings. I shall also pose the important questions of "How big
is big enough?" and conversely "How big is too big?"

== Sessions ==

=== 08/29: Open Discussion and Semester Planning===

Lauro's suggestion:

Seeing in Four Dimensions

The article
http://www.sciencenews.org/view/generic/id/35740/title/Seeing_in_four_dimensions

The site
http://www.dimensions-math.org/

Valerio Pascucci talked about his work of computing
Reeb graphs.

The original plan for the session:

Our plan to this Friday's session is to have an open 
discussion of any interesting ideas that you want to 
bring in and to plan/schedule presentations for the 
following Fridays.

A common practice for VisLunch is to use some of its 
sessions as a mean to let people know about the work 
of the new people around: new faculties, new post docs, 
new PhD. students . As there are lots of new faces 
around, we hope to schedule some of these presentations 
in this session.

This semester Lauro Lins will be responsible for 
organizing the VisLunch sessions. Here is his contact 
informations:

Lauro Lins
Room: 4887
Phone: 581-8061
vislunch@sci.utah.edu

And here is the wikipage where we want to keep 
all the information related to this semesters' 
VisLunch:

http://www.vistrails.org/index.php/VisLunch/Fall2008

=== 09/05 - Summer Internships One ===
In this Vislunch session we are going to see what some 
PhD. Students did in their summer internships. 
This week we will have Carson Brownlee, 
Erik Anderson, Mark Kim and David Koop 
talking about... 
 

'''Carson Brownlee''' (15 min) 
Worked at LANL for the summer with Patrick McCormick 
on an analytic visualization tool called SCOUT writing 
volume renderers and animation systems. 
He did do some work on visualizing cosmological 
datasets (dark halos) and worked on simulating 
Sclieren visualization which is an old optical 
technique used to look at invisible differences 
in inhomogeneous data (such as shockwaves or 
heat dissipation). 
 

'''Erik Anderson''' (15 min) 
Worked at Los Alamos National Lab (LANL) with 
Jim Ahrens and Patrick McCormick. Iplemented a 
method for discovering correlations in extremely 
high dimensional datasets such as Oceanographic 
data (3200 x 2400 x 42 x 114 x 52 (x,y,z,d,time)). 
Additionally researched and implemented various 
metrics to assist in distance visualization 
prioritization and transmission. 
 

'''Mark Kim''' (15 min) 
Worked at LANL under Pat McCormick on a vis tool 
called Scout (just like Carson). He did some mundane 
stuff like a volume renderer and spent some time 
visualizing lyman alpha lines. He also wrote a 
particle-mesh n-body simulator for Scout and in CUDA. 
 

'''David Koop''' (15 min.) 
Worked at Microsoft Research on a workflow tool called 
Trident (http://www.microsoft.com/mscorp/tc/trident.mspx). 
Specifically, he worked on linking workflows with their 
data inputs, and supporting general computational commands 
like "process this data" or "re-run this workflow with 
the latest data" using provenance, metadata, and semantics. 
This involved digging into Windows Workflow Foundation 
(http://msdn.microsoft.com/en-us/netframework/aa663328.aspx) 
which Trident is based on, and figuring out how to extract 
necessary metadata, inject input data, and capture 
provenance information. 

=== 09/12 - Summer Internships Two===
In this Vislunch session we are going to see what some 
PhD. Students did in their summer internships. 
This week we will have Emanuele Santos, 
Kristi Potter and Abe Stephens 
talking about... 
 

'''Emanuele Santos''' (15 min) 
"I worked on manipulating collections of workflows. We 
(joint work with Lauro, Claudio, Juliana and Jim Ahrens) 
wrote a paper in which we propose different similarity 
measures for comparing workflows. I also worked on 
"Workflow Medleys", which is a framework to manipulate and 
interact with collections of workflows that can be used to 
generate user-driven visualizations. I also helped on 
extending VisTrails and other tools to facilitate the creation 
of documents (papers, presentations and web pages) containing 
visualizations." 
 

'''Kristi Potter''' (15 min) 
"My internship this summer was at Sandia national Labs in 
Albuquerque, NM working with Andy Wilson. Our work focused 
on the visualization of ensemble data in VTK. This type of data 
consists of a collection of models run using various input 
perturbations with the goal of getting a more accurate estimate 
of the modeled phenomenon. Over the summer, we worked with 
short-term weather forecast data. We have created a prototype 
system to investigate methods for displaying this data, and 
understanding the uncertainty and confidence levels associated 
with the data." 
 

'''Abe Stephens''' (30 min) 
This year at SIGGRAPH NVIDIA demonstrated an interactive 
ray tracer running on the GPU at HD resolution. The example 
has practical implications for both the graphics and the 
GPU computing communities. This talk will offer some 
observations about these implications, the state of parallel 
programming in CUDA, and discuss hybrid tracing and 
rasterization. Abe Stephens is graduate student finishing 
his PhD at SCI with Steven Parker. He spent part of the 
spring and summer collaborating with NVIDIA Research in 
Santa Clara and Salt Lake City. 
 

=== 09/19 - Poisson Editing: Past, Present, and Future ===

Friday 09/19, 12pm, in our VisLunch session 
we are going to see Michael Bellem and Brian Summa 
presenting: 

''"Poisson Editing: Past, Present, and Future'' 

''Operating in the gradient-domain has become a standard 
''method in image processing with applications in areas 
''such as image compositing and tone-mapping. 

''Tomorrow we will cover the general Poisson method for 
''editing images in the gradient domain. Also, we will 
''discuss the problems with this method when dealing 
''with gigapixel sized images. We will look at how to 
''extend and accelerate this method using quadtrees, 
''and the most recent work in Poisson editing: streaming 
''multigrid." 

=== 09/26 - Robust analysis of Vector Field Topology ===

Tomorrow (Friday 09/26, 12pm) in our VisLunch session 
we are going to see Harsh Bhatia and Shreeraj Jadhav 
presenting: 

"Robust analysis of Vector Field Topology, 

We will be speaking about the combinatorial ways of analyzing topology 
of vector fields. More specifically, we will study the topology in terms of 
directed graphs called Morse Connection Graphs (MCG), & 
Entity Connection Graphs (ECG). We will do their comparative study, 
and discuss their robustness. We will also discuss efficient algorithms to 
generate the graphs. 

The algorithms are suggested by Guoning Chen, Konstantin Mischaikow, 
Robert S. Laramee, and Eugene Zhang in 'Efficient Morse Decompositions of Vector Fields', 
published at IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 
VOL. 14, NO. 4, JULY/AUGUST 2008." 

=== 10/03 VIS 2008 papers: Session I ===

Tomorrow (Friday 10/03, 12pm) in our VisLunch session 
we are going to see Carlos Scheidegger and David Koop 
presenting their VIS 2008 papers: 

'''Revisiting Histograms and Isosurface Statistics''' 
Carlos Scheidegger, John Schreiner, Brian Duffy, Hamish Carr, Claudio Silva 
http://www.sci.utah.edu/~cscheid/vis2008/histograms 

''Abstract'' 
Recent results have shown a link between geometric properties of isosurfaces and statistical properties of the underlying sampled data. However, this has two defects: not all of the properties described converge to the same solution, and the statistics computed are not always invariant under isosurface-preserving transformations. We apply Federer's Coarea Formula from geometric measure theory to explain these discrepancies. We describe an improved substitute for histograms based on weighting with the inverse gradient magnitude, develop a statistical model that is invariant under isosurface-preserving transformations, and argue that this provides a consistent method for algorithm evaluation across multiple datasets based on histogram equalization. We use our corrected formulation to reevaluate recent results on average isosurface complexity, and show evidence that noise is one cause of the discrepancy between the expected figure and the observed one.

'''VisComplete: Automating Suggestions for Visualization Pipelines''' 
David Koop, Carlos E. Scheidegger, Steven P. Callahan, Juliana Freire, Claudio T. Silva 

''Abstract'' 
Building visualization and analysis pipelines is a large hurdle in the adoption of visualization and workflow systems by domain scientists. In this paper, we propose techniques to help users construct pipelines by consensus—automatically suggesting completions based on a database of previously created pipelines. In particular, we compute correspondences between existing pipeline subgraphs from the database, and use these to predict sets of likely pipeline additions to a given partial pipeline. By presenting these predictions in a carefully designed interface, users can create visualizations and other data products more efficiently because they can augment their normal work patterns with the suggested completions. We present an implementation of our technique in a publicly-available, open-source scientific workflow system and demonstrate efficiency gains in real-world situations.

=== 10/10 - Vis Conference: Jens, Geoff ===

=== 10/17 - Fall Break (no lunch) ===

=== 10/24 - VisWeek (no lunch) ===

=== 10/31 - Vis Highlights ===

=== 11/21 - Towards Gigapixel displays : What?, How? and Why? (Chris Goodyer) ===

Chris Goodyer from the University of Leeds in the UK will be visiting on Nov 21.
He is talking about his recent work on multi-monitor displays:

http://www.comp.leeds.ac.uk/ceg/IB3dviewer.htm

Here is his web page:

http://www.comp.leeds.ac.uk/ceg/

Towards Gigapixel displays : What?, How? and Why?

Over the past couple of years there has been a growing trend for high
resolution display walls, intriguingly named "gigapixel displays" or
"powerwalls". These are tiled multile projectors or multiple screens
connected to a cluster. Besides looking visually impressive there are
important research questions concerning what advantages there would be to
using them over conventional large displays. In addition, the methods used
for interacting with applications running across such large numbers of
displays needs to be carefully considered.

In this talk I shall summarize some of the work we have been doing at the
University of Leeds on our 53-megapixel wall. I will discuss several of
the software environments available for deploying applications along with
their shortcomings. I shall also pose the important questions of "How big
is big enough?" and conversely "How big is too big?"

== Mail List: vislunch@sci.utah.edu ==

People that are currently in the vislunch mail list (29 total):

Aaron Knoll Emanuele Santos Linh Ha
Adam Bargteil Erik Anderson Mark Kim
Berger Geoff Draper Mathias Schott
Carlos Scheidegger Hao Wang Siddarth Shankar
Carson Browlee Huy Vo Steve Callahan
Charles Hansen Jens Kruger Tiago Etiene
Chems Toutai
Chris Johnson Jianrong Shu Valerio Pascucci
Claudio Silva John Schreiner Wan Yong
Claurissa Tuttle Josh Stratton
David Koop Lauro Lins

VisLunch/Fall2008

2008-10-27T16:27:08Z

Llins: /* 11/21 - Chris Goodyer */

__NOTOC__

== Coming up next Friday (10/03) ==
=== VIS 2008 papers: Session I ===

Tomorrow (Friday 10/03, 12pm) in our VisLunch session 
we are going to see Carlos Scheidegger and David Koop 
presenting their VIS 2008 papers: 

'''Revisiting Histograms and Isosurface Statistics''' 
Carlos Scheidegger, John Schreiner, Brian Duffy, Hamish Carr, Claudio Silva 
http://www.sci.utah.edu/~cscheid/vis2008/histograms 

''Abstract'' 
Recent results have shown a link between geometric properties of isosurfaces and statistical properties of the underlying sampled data. However, this has two defects: not all of the properties described converge to the same solution, and the statistics computed are not always invariant under isosurface-preserving transformations. We apply Federer's Coarea Formula from geometric measure theory to explain these discrepancies. We describe an improved substitute for histograms based on weighting with the inverse gradient magnitude, develop a statistical model that is invariant under isosurface-preserving transformations, and argue that this provides a consistent method for algorithm evaluation across multiple datasets based on histogram equalization. We use our corrected formulation to reevaluate recent results on average isosurface complexity, and show evidence that noise is one cause of the discrepancy between the expected figure and the observed one.

'''VisComplete: Automating Suggestions for Visualization Pipelines''' 
David Koop, Carlos E. Scheidegger, Steven P. Callahan, Juliana Freire, Claudio T. Silva 

''Abstract'' 
Building visualization and analysis pipelines is a large hurdle in the adoption of visualization and workflow systems by domain scientists. In this paper, we propose techniques to help users construct pipelines by consensus—automatically suggesting completions based on a database of previously created pipelines. In particular, we compute correspondences between existing pipeline subgraphs from the database, and use these to predict sets of likely pipeline additions to a given partial pipeline. By presenting these predictions in a carefully designed interface, users can create visualizations and other data products more efficiently because they can augment their normal work patterns with the suggested completions. We present an implementation of our technique in a publicly-available, open-source scientific workflow system and demonstrate efficiency gains in real-world situations.

== Sessions ==

=== 08/29: Open Discussion and Semester Planning===

Lauro's suggestion:

Seeing in Four Dimensions

The article
http://www.sciencenews.org/view/generic/id/35740/title/Seeing_in_four_dimensions

The site
http://www.dimensions-math.org/

Valerio Pascucci talked about his work of computing
Reeb graphs.

The original plan for the session:

Our plan to this Friday's session is to have an open 
discussion of any interesting ideas that you want to 
bring in and to plan/schedule presentations for the 
following Fridays.

A common practice for VisLunch is to use some of its 
sessions as a mean to let people know about the work 
of the new people around: new faculties, new post docs, 
new PhD. students . As there are lots of new faces 
around, we hope to schedule some of these presentations 
in this session.

This semester Lauro Lins will be responsible for 
organizing the VisLunch sessions. Here is his contact 
informations:

Lauro Lins
Room: 4887
Phone: 581-8061
vislunch@sci.utah.edu

And here is the wikipage where we want to keep 
all the information related to this semesters' 
VisLunch:

http://www.vistrails.org/index.php/VisLunch/Fall2008

=== 09/05 - Summer Internships One ===
In this Vislunch session we are going to see what some 
PhD. Students did in their summer internships. 
This week we will have Carson Brownlee, 
Erik Anderson, Mark Kim and David Koop 
talking about... 
 

'''Carson Brownlee''' (15 min) 
Worked at LANL for the summer with Patrick McCormick 
on an analytic visualization tool called SCOUT writing 
volume renderers and animation systems. 
He did do some work on visualizing cosmological 
datasets (dark halos) and worked on simulating 
Sclieren visualization which is an old optical 
technique used to look at invisible differences 
in inhomogeneous data (such as shockwaves or 
heat dissipation). 
 

'''Erik Anderson''' (15 min) 
Worked at Los Alamos National Lab (LANL) with 
Jim Ahrens and Patrick McCormick. Iplemented a 
method for discovering correlations in extremely 
high dimensional datasets such as Oceanographic 
data (3200 x 2400 x 42 x 114 x 52 (x,y,z,d,time)). 
Additionally researched and implemented various 
metrics to assist in distance visualization 
prioritization and transmission. 
 

'''Mark Kim''' (15 min) 
Worked at LANL under Pat McCormick on a vis tool 
called Scout (just like Carson). He did some mundane 
stuff like a volume renderer and spent some time 
visualizing lyman alpha lines. He also wrote a 
particle-mesh n-body simulator for Scout and in CUDA. 
 

'''David Koop''' (15 min.) 
Worked at Microsoft Research on a workflow tool called 
Trident (http://www.microsoft.com/mscorp/tc/trident.mspx). 
Specifically, he worked on linking workflows with their 
data inputs, and supporting general computational commands 
like "process this data" or "re-run this workflow with 
the latest data" using provenance, metadata, and semantics. 
This involved digging into Windows Workflow Foundation 
(http://msdn.microsoft.com/en-us/netframework/aa663328.aspx) 
which Trident is based on, and figuring out how to extract 
necessary metadata, inject input data, and capture 
provenance information. 

=== 09/12 - Summer Internships Two===
In this Vislunch session we are going to see what some 
PhD. Students did in their summer internships. 
This week we will have Emanuele Santos, 
Kristi Potter and Abe Stephens 
talking about... 
 

'''Emanuele Santos''' (15 min) 
"I worked on manipulating collections of workflows. We 
(joint work with Lauro, Claudio, Juliana and Jim Ahrens) 
wrote a paper in which we propose different similarity 
measures for comparing workflows. I also worked on 
"Workflow Medleys", which is a framework to manipulate and 
interact with collections of workflows that can be used to 
generate user-driven visualizations. I also helped on 
extending VisTrails and other tools to facilitate the creation 
of documents (papers, presentations and web pages) containing 
visualizations." 
 

'''Kristi Potter''' (15 min) 
"My internship this summer was at Sandia national Labs in 
Albuquerque, NM working with Andy Wilson. Our work focused 
on the visualization of ensemble data in VTK. This type of data 
consists of a collection of models run using various input 
perturbations with the goal of getting a more accurate estimate 
of the modeled phenomenon. Over the summer, we worked with 
short-term weather forecast data. We have created a prototype 
system to investigate methods for displaying this data, and 
understanding the uncertainty and confidence levels associated 
with the data." 
 

'''Abe Stephens''' (30 min) 
This year at SIGGRAPH NVIDIA demonstrated an interactive 
ray tracer running on the GPU at HD resolution. The example 
has practical implications for both the graphics and the 
GPU computing communities. This talk will offer some 
observations about these implications, the state of parallel 
programming in CUDA, and discuss hybrid tracing and 
rasterization. Abe Stephens is graduate student finishing 
his PhD at SCI with Steven Parker. He spent part of the 
spring and summer collaborating with NVIDIA Research in 
Santa Clara and Salt Lake City. 
 

=== 09/19 - Poisson Editing: Past, Present, and Future ===

Friday 09/19, 12pm, in our VisLunch session 
we are going to see Michael Bellem and Brian Summa 
presenting: 

''"Poisson Editing: Past, Present, and Future'' 

''Operating in the gradient-domain has become a standard 
''method in image processing with applications in areas 
''such as image compositing and tone-mapping. 

''Tomorrow we will cover the general Poisson method for 
''editing images in the gradient domain. Also, we will 
''discuss the problems with this method when dealing 
''with gigapixel sized images. We will look at how to 
''extend and accelerate this method using quadtrees, 
''and the most recent work in Poisson editing: streaming 
''multigrid." 

=== 09/26 - Robust analysis of Vector Field Topology ===

Tomorrow (Friday 09/26, 12pm) in our VisLunch session 
we are going to see Harsh Bhatia and Shreeraj Jadhav 
presenting: 

"Robust analysis of Vector Field Topology, 

We will be speaking about the combinatorial ways of analyzing topology 
of vector fields. More specifically, we will study the topology in terms of 
directed graphs called Morse Connection Graphs (MCG), & 
Entity Connection Graphs (ECG). We will do their comparative study, 
and discuss their robustness. We will also discuss efficient algorithms to 
generate the graphs. 

The algorithms are suggested by Guoning Chen, Konstantin Mischaikow, 
Robert S. Laramee, and Eugene Zhang in 'Efficient Morse Decompositions of Vector Fields', 
published at IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 
VOL. 14, NO. 4, JULY/AUGUST 2008." 

=== 10/03 - Vis Conference: Carlos, Dave ===

=== 10/10 - Vis Conference: Jens, Geoff ===

=== 10/17 - Fall Break (no lunch) ===

=== 10/24 - VisWeek (no lunch) ===

=== 10/31 - Vis Highlights ===

=== 11/21 - Towards Gigapixel displays : What?, How? and Why? (Chris Goodyer) ===

Chris Goodyer from the University of Leeds in the UK will be visiting on Nov 21.
He is talking about his recent work on multi-monitor displays:

http://www.comp.leeds.ac.uk/ceg/IB3dviewer.htm

Here is his web page:

http://www.comp.leeds.ac.uk/ceg/

Towards Gigapixel displays : What?, How? and Why?

Over the past couple of years there has been a growing trend for high
resolution display walls, intriguingly named "gigapixel displays" or
"powerwalls". These are tiled multile projectors or multiple screens
connected to a cluster. Besides looking visually impressive there are
important research questions concerning what advantages there would be to
using them over conventional large displays. In addition, the methods used
for interacting with applications running across such large numbers of
displays needs to be carefully considered.

In this talk I shall summarize some of the work we have been doing at the
University of Leeds on our 53-megapixel wall. I will discuss several of
the software environments available for deploying applications along with
their shortcomings. I shall also pose the important questions of "How big
is big enough?" and conversely "How big is too big?"

== Mail List: vislunch@sci.utah.edu ==

People that are currently in the vislunch mail list (29 total):

Aaron Knoll Emanuele Santos Linh Ha
Adam Bargteil Erik Anderson Mark Kim
Berger Geoff Draper Mathias Schott
Carlos Scheidegger Hao Wang Siddarth Shankar
Carson Browlee Huy Vo Steve Callahan
Charles Hansen Jens Kruger Tiago Etiene
Chems Toutai
Chris Johnson Jianrong Shu Valerio Pascucci
Claudio Silva John Schreiner Wan Yong
Claurissa Tuttle Josh Stratton
David Koop Lauro Lins