University of Montana: Computer Science
COMPUTER SCIENCE
Special Issue: Faculty Research
Spring 2011
As the Spring semester is
now in full-swing, we find
ourselves as busy as ever. We
wished Alden Wright Bon
Voyage as he headed to New
Zealand to do a semester of
research at the University of
Otago, we ushered in a brand
new department website
(http://www.cs.umt.edu) and
blog that we hope is more
user friendly and up-to-date,
we are meeting new
classmates from MSU as we
host our graduate level
Cryptography course through
distance learning
technologies, we welcome
two new adjunct instructors
to teach Networking and
Computer Graphics, and
1
we are planning for
upcoming events like the
Montana State Science Fair.
We hope to get more
involved this semester with
both the Undergraduate
Research Conference and the
Graduate Faculty Research
Conference and are actively
encouraging our students to
participate. We continue to
share information about a
number of promising
internship opportunities, and
are pleased to report that our
computer club remains
vibrant. The remainder of this
special issue is devoted to
faculty research.
Newsletter
Inside this Issue
Research Projects:
Taking Blackfoot speeches as
input, the system generates a list
of audio clips containing a
sequence of sounds or certain
accent patterns …
2
In cloud computing, heavy
computations on data are
outsourced to "the cloud" over
the Internet.
2
… randomly generated RNA
sequences and their affinity for a
particular protein (nucleocapsid
protein (N) from River Valley
Fever Virus (RVFV)).
3
The unstructured mesh (black
triangles) delivers resolution
where it is needed, but reduces
computational overhead in
regions of slower change.
3
Results of this study indicate that
participants have a strong
preference for software that
reduces the need for excess
program window …
4
Genetic algorithms are
computational methods based on
the biological concepts of
genetics and evolution.
4
Plus Achievements and
Recent Publications
University of Montana: Computer Science Spring 2011

Dr Min Chen: Blackfoot Linguistic Preservation

An example speech transcription

and audio analysis
Supported by an NEH grant, we are in the process of developing a multimedia database system to automatically
capture and manage interesting sound clips in Blackfoot (an endangered language spoken in Alberta, Canada,
and Montana) for language preservation. Taking Blackfoot speeches as input, the system generates a list of
audio clips containing a sequence of sounds or certain accent patterns based on research interests. Existing
computational linguistic techniques such as information processing and artificial intelligence are extended to
tackle issues specific to Blackfoot linguistics, and database techniques are adopted to support better data
management and linguistic queries.

Cryptographic Objects: Dr. Mike Rosulek

In cloud computing, heavy computations Dr. Mike Rosulek's recent cloud to perform only the
on data are outsourced to "the cloud" research has developed new desired computation. Future
over the Internet. One important encryption techniques that allow work in this area involves
cryptographic challenge for cloud very simple computations to be expanding the feature-set of
computing is providing data privacy, the blindly carried out on encrypted these robust computations on
ability for the cloud to carry out the data, but in a way that forces the encrypted data.
computation, and an assurance to the
user that the cloud indeed performed the
desired computation. One approach to
cloud computing is for users to
encrypt their data, and for the cloud
to perform blind computations on
that encrypted data. However,
existing encryption techniques have
not easily allowed blind
computations as well as enforced
data integrity.

2
University of Montana: Computer Science Spring 2011

In collaboration with partners in the Biochemistry Department, Identification of

several of the graduate students and Dr. Douglas Raiford
will begin investigating methods of identifying common Ribonucleac Acid
secondary (and possibly tertiary) structures of functionally similar
RNA sequences. Functional Structure
This work will involve the analysis of experimentally derived data
on randomly generated RNA sequences and their affinity for a
particular protein (nucleocapsid protein (N) from River Valley
Fever Virus (RVFV)). All of the resulting RNA sequences will
have a known affinity for this protein (aptamer status) and it will
be our job to identify their secondary structures as well as
common structural features, the implication being that these
secondary structures (and their resultant tertiary structures) are
responsible for the sequence's high affinity for the target protein.

Algorithmic approaches will include calculation of tree edit

distances, dynamic programming techniques for identifying
minimum energy states, as well as clustering and classifier
algorithms.

Ice Sheet Modeling

DR. Jesse Johnson is working with colleagues in UM Geoscience
to develop an ice sheet model capable of combining the best
available observations with detailed physical descriptions of the ice.
Once the data has been 'assimilated', the model can be used to assess
the impact of climate change on the ice sheet's stability. Model output
in this figure of Greenland shows the results of a recent assimilation
of satellite derived surface velocity data into the model. The
unstructured mesh (black triangles) delivers resolution where it is
needed, but reduces computational overhead in regions of slower
change. Ultimately, the purpose of models like Johnson's is to
determine the amount of sea level change that ice sheets produce.

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University of Montana: Computer Science Spring 2011

FACULTY
ACHIEVEMENTS
GIG:
Global Dr. Joel Henry
Information was recently recertified as an IEEE
Software Development
Gatherer Professional. There are only about
450 people worldwide with this
certification, and Joel is the only
one in Montana. Dr. Henry also had
Dr. Yolanda Reimer continues work on her Career grant research a paper entitled entitled
involving information management, assimilation, and notetaking in the “MATTLAB Automated Test Tool
digital age. With the GIG software prototype implemented and fully (MATT)” accepted for publication
functional, her research group recently completed a longitudinal and in the NASA Tech Briefs magazine.
unrestricted evaluation of its utility with two large sections of a This magazine highlights those
Management Information Systems class. Results of this study indicate products and processes proven
that participants have a strong preference for software that reduces the effective in critical NASA missions.
need for excess program window manipulation, that provides citation Additionally, MATT has been
support and integrated web browsing, and that incorporates a progressive nominated for an Excellence in
user interface design. On the third and final survey of our evaluation, we Technology award within NASA
learned that a majority (over 70%) of participants thought that GIG is based on five years of integration
helpful for managing and making sense of the large volume of into NASA projects.
information they are exposed to everyday. A manuscript describing this
evaluation is currently under review with JASIST, Journal of the
American Society for Information Science and Technology.

Dr. Alden Wright is currently doing

final revisions on the paper “On the
Movement of Vertex Fixed Points in the
Simple GA” which will be published in the
proceedings of the FOGA 2011 workshop.
This paper concerns a dynamical system
model of the simple genetic algorithm.
Genetic algorithms are computational
methods based on the biological concepts
of genetics and evolution.

Dr. Wright is also working with Dr. Raiford (of the CS department) and Dr.
Holben (of the Division of Biological Sciences) on metagenomics, which is the
exciting field of analyzing DNA sequence information taken from
Dr. Douglas Raiford's
environmental samples.
research was featured as the cover
Dr. Wright is currently visiting the University of Otago in Dunedin, New art for IEEE/ACM Transactions on
Zealand. He has a blog about his personal activities at http:// Computational Biology and
oldmtnbiker.wordpress.com Bioinformatics, June 2008 issue.

4
University of Montana: Computer Science Newsletter

Select Faculty Publications

* Indicates Computer Science student
Chen, M. (in press) Temporal-based video event detection and retrieval. In C.-H. Wei (Ed.), Machine learning techniques for adaptive multimedia
retrieval: technologies applications and perspectives, IGI Global.

Chen, M., Chen, S.-C., & Shyu, M.-L. (in press) Content-based retrieval of video. P. Sheu, H. Yu, C.V. Ramamoorthy, A. Joshi, & L. Zadeh (Eds.),
Semantic computing, IEEE Press/Wiley.

*D.J. Brinkerhoff, T.W. Meierbachtol, J.V. Johnson, J.T. Harper, (2011) “Sensitivity of the frozen-melted basal boundary to perturbations of basal
traction and geothermal heat flux: Isunnguata Sermia, western Greenland”, Annals of Glaciology, vol. 59 pp. XX XX (in press).

R. Calov, R. Greve, A. Abe-Ouchi, E. Bueler, P. Huybrechts, J.V. Johnson, F. Pattyn, D. Pollard, C. Ritz, F. Saito, L. Tarasov (2010) Results from
the Ice- Sheet Model Intercomparison ProjectHeinrich Event INtercOmparison (ISMIP HEINO). Journal of Glaciology vol. 56 (197) pp. 371-383.

Raiford, Douglas W., Doom, Travis E., Krane, Dan E., & Raymer, Michael E. 2010. A genetic optimization approach for isolating translational
efficiency bias. Accepted for publication in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11 February, 2010. IEEE
computer Society Digital Library, IEEE Computer Society.

Raiford, Douglas W., Krane, Dan E., Doom, Travis E., Raymer, Michael L. Automated Isolation of Translational Efficiency Bias that Resists the
Confounding Effect of GC(AT)-Content, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19 June 2008. IEEE Computer
Society Digital Library. IEEE Computer Society, 30 June 2008.

Reimer, Y.J., *Hagedal, M., & *Wolf, P. (2010). Evaluating a Global Information Gathering Tool for Students. Proceedings of E-LEARN 2010 -
World Conference on E-Learning in Corporate, Government, Healthcare & Higher Education, Orlando, Florida, October 2010, pp. 2688-2695.
Chesapeake, VA:AACE.

Reimer, Y.J., *Brimhall, E., *Cao, C., & *O’Reilly, K. (May 2009). Empirical User Studies Inform the Design of an E-Notetaking and Information
Assimilation System for Students in Higher Education, Computers & Education Journal 52, pp. 898-913. DOI information: 10.1016/j.compedu.
2008.12.013

H.K. Maji, M. Prabhakaran, M. Rosulek. Attribute-Based Signatures. To appear, CT-RSA: RSA Conference, Cryptographers' Track 2011.

H.K. Maji, M. Prabhakaran, M. Rosulek. Exploring the Limits of Common Coins using Frontier Analysis of Protocols. To appear, Theory of
Cryptography Conference (TCC) 2011.

Jonathan E. Rowe, Michael D. Vose, Alden H. Wright. Representation Invariant Genetic Operators Evolutionary Computation Winter 2010, Vol.
18, No. 4: 635–660.

Alden H. Wright, Tomas Gedeon, J. Neal Richter. On the Movement of Vertex Fixed Points in the Simple GA Proceedings of the eleventh ACM
SIGEVO workshop on Foundations of Genetic Algorithms, Hans-Georg Beyer and William Langdon (editors), ACM, 2011.

[more complete list found at: http://www-test.cs.umt.edu/faculty_and_research/publications.php]

Department of Computer Science

[Social Science Building Room 401]
[The University of Montana]
[Missoula], [MT][59812]
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[Phone: 406-243-2883] the UM Foundation at The University of Montana
[FAX: 406-243-5139] Foundation, P.O. Box 7159, Missoula, MT
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