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Coupling Informatics Algorithm Development and Visual Analysis

Coupling Informatics Algorithm Development and Visual Analysis. Danny Dunlavy , Pat Crossno, Tim Shead Sandia National Laboratories SIAM Annual Meeting July 7, 2008 SAND2008-4470P.

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Coupling Informatics Algorithm Development and Visual Analysis

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  1. Coupling Informatics Algorithm Development and Visual Analysis Danny Dunlavy, Pat Crossno, Tim Shead Sandia National Laboratories SIAM Annual Meeting July 7, 2008 SAND2008-4470P Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company,for the United States Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

  2. <DOC><DOCNO><s docid="APW19990519.0113" num="1" stype="-1">APW19990519.0113</s></DOCNO><DATE_TIME><P> <s docid="APW19990519.0113" num="2" stype="-1"> 1999-05-19 21:11:17</s> </P></DATE_TIME><BODY><CATEGORY><s docid="APW19990519.0113" num="3"stype="-1"> usa</s></CATEGORY><HEADLINE><P> <s docid="APW19990519.0113" num="4" stype="0"> Pulses May Ease SchizophrenicVoices</s> </P></HEADLINE><TEXT><P> <s docid="APW19990519.0113" num="5" stype="1"> WASHINGTON (AP)Schizophrenia patients whose medication couldn't stop the imaginary voices in theirheads gained some relief after researchers repeatedly sent a magnetic field into asmall area of their brains.</s> </P><P><s docid="APW19990519.0113" num="6"stype="1"> About half of 12 patients studied said their hallucinations becamemuch less severe after the treatment, which feels like ``having a woodpeckerknock on your head'' once a second for up to 16 minutes, said researcherDr.Ralph Hoffman.</s> <s docid="APW19990519.0113" num="7" stype="1">The voices stopped completely in three of these patients.</s> </P><P><sdocid="APW19990519.0113" num="8" stype="1"> The effect lasted for up toa few days for most participants, and one man reported that it lasted seven weeksafterbeing treated daily for four days.</s> </P><P><sdocid="APW19990519.0113" num="9" stype="1"> Hoffman stressed that thestudy is only preliminary and can't prove that the treatment would be useful.</s> <sdocid="APW19990519.0113" num="10" stype="1"> ``We need to do much moreresearch on this,'' he said in an interview.</s> </P><P><sdocid="APW19990519.0113" num="11" stype="1"> Hoffman, deputy medicaldirector of the Yale Psychiatric Institute, is scheduled to present the workThursday at the annual meeting of the American Psychiatric Association.</s> </P><P><s docid="APW19990519.0113" num="12" stype="1"> Not all people withschizophrenia hear voices, and of those who do, Hoffman estimated that maybe 25percent can't control them with medications even when other disease symptomsabate.</s> <s docid="APW19990519.0113" num="13" stype="1"> So the workcould pay off for ``a small but very ill group of patients,'' he said.</s> </P><P><sdocid="APW19990519.0113" num="14" stype="1"> The treatment is calledtranscranial magnetic stimulation, or TMS.</s> <s docid="APW19990519.0113"num="15" stype="1"> While past research indicates it mightbe helpful in lifting depression, it hasn't been studied much in schizophrenia.</s> </P><P><s docid="APW19990519.0113" num="16" stype="1"> In TMS, anelectromagnetic coil is placed on the scalp and current is turned on and off to create apulsing magnetic field that reaches into a small area of the brain.</s> <sdocid="APW19990519.0113" num="17" stype="1"> The goal is to make brain cellsunderneath the coil fire messages to adjoining cells.</s> </P><P><sdocid="APW19990519.0113" num="18" stype="1"> The procedure is muchdifferent from electroconvulsive therapy, called ECT, which applies pulses ofelectricity rather than a magnetic field to the brain.</s> <sdocid="APW19990519.0113"num="19" stype="1"> Unlike TMS, ECT creates a briefseizure and is performed under general anesthesia.</s> <sdocid="APW19990519.0113" num="20" stype="1"> ECT is used most often fortreatingsevere depression.</s> </P><P><s docid="APW19990519.0113" num="21"stype="1"> In TMS, the magnetic pulses are thought to calm the affected partof the brain if they're given as slowly as once per second, Hoffman said.</s> <s docid="APW19990519.0113" num="22" stype="1"> He and colleagues targeted an area involved in understanding speech, above and behind the left ear, on the theory that hallucinated voices come from overactivity there.</s> </P><P><s docid="APW19990519.0113" num="23" stype="1"> The treatment can make scalp muscles muscle contract, leading tothe woodpecker feeling, he said, but patients could tolerate it.</s> <s docid="APW19990519.0113" num="24" stype="1">Headachewas the most common side effect, and there was no sign that the treatment affected the ability to understandspeech, he said.</s> </P><P><s docid="APW19990519.0113" num="25" stype="1"> To make sure the study resultsdidn'treflect just the psychological boost of getting a treatment, researchers gave sham and real treatments to each studyparticipant and studied the difference in how patients responded.</s> <s docid="APW19990519.0113" num="26" starting with

  3. singular values documents concepts Doc & term relationships Information retrieval terms concepts Text corpus Concept space Clustering Latent Semantic Analysis low rank approximation documents … d1 d2 d3 d4 dn t1 t2 . . . terms Truncated SVD tm

  4. Concept Space • policy • planning • politics • tomlinson • 1986 • Sport in Society: policy, Politics and Culture, ed A. Tomlinson (1990) • Policy and Politics in Sport, PE and Leisure eds S. Fleming, M. Talbot and A. Tomlinson (1995) • Policy and Planning (II), ed J. Wilkinson (1986) • Policy and Planning (I), ed J. Wilkinson (1986) • Leisure: Politics, Planning and People, ed A. Tomlinson (1985) • parker • lifestyles • 1989 • part • Work, Leisure and Lifestyles (Part 2), ed S. R. Parker (1989) • Work, Leisure and Lifestyles (Part 1), ed S. R. Parker (1989) [Leisure Studies of America Data]

  5. singular values documents concepts term concepts DT  T ParaText™ Operations • Document parsing, matrix creation and weighting • SVD: • Truncated SVD: • Query scores (query as new “doc”): • LSA Ranking: • Document similarities: • Term Similarities: • Similarity statistics • Mean, standard deviation (thresholded → sparse)

  6. Document Similarity Graphs Document similarity matrix Document similarity graph • Each document (or term, entity, etc.) is a vertex • Each row defines an edge singular values documents concepts sparse coordinate format concepts documents threshold

  7. Similarity Statistics Statistics on edges • One graph: one-sample t statistic • Two graphs: two-sample t statistic Graph 1 Graph 2

  8. Doc Sim Graph Comparison k = 40 k = 10 [DUC 2003, Task 2 Data: 297 documents, 30 manual clusters]

  9. Layout Comparison Force directed Simple 2D [DUC 2003, Task 2 Data: 297 documents, 30 manual clusters]

  10. Sparse Matrix View

  11. Rank Comparison k = 10 k = 40 [DUC 2003, Task 2 Data: 297 documents, 30 manual clusters]

  12. Matrix Differences k = 10 k = 40 [DUC 2003, Task 2 Data: 297 documents, 30 manual clusters]

  13. Small Multiples k = 20 k = 30 k = 40 k = 50 k = 10 k = 20 k = 30 k = 40 [DUC 2003, Task 2 Data: 297 documents, 30 manual clusters]

  14. LSAView

  15. LSAView Impact • Document similarities: • Inner product view: • Scaled inner product view: • What is the best scaling for document similarity graph generation? original scaling no scaling inverse sqrt inverse [Leisure Studies of America Data]

  16. Conclusions • LSAView • Analysis and exploration of impact of informatics algorithms on end-user visual analysis of data • Aids in discovery process of optimal algorithm parameters for given data and tasks • Impact • Used in developing and understanding ParaText™ and LSALIB algorithms • Future Work • Other graph-based metrics • Diameter, cycles, vertex degree distribution, shortest cycle length, etc. • Other Decompositions and algorithms • Incremental SVD, SDD, CUR, Clustering • Other statistics/inference tests and visualization • New problem domains

  17. Coupling Informatics Algorithm Development and Visual Analysis Danny Dunlavy Email:dmdunla@sandia.gov URL:http://www.cs.sandia.gov/~dmdunla

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