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Full-Text Articles in Engineering

A Cathode Support Structure For Use In A Magnetron Oscillator Experiment, Daylon Black, Ryan Harper, Patrick Ward, Jacob Davlin, Omar Bentancourt, Donald Plumlee, Jim Browning Sep 2020

A Cathode Support Structure For Use In A Magnetron Oscillator Experiment, Daylon Black, Ryan Harper, Patrick Ward, Jacob Davlin, Omar Bentancourt, Donald Plumlee, Jim Browning

Electrical and Computer Engineering Faculty Publications and Presentations

A Low Temperature Cofired Ceramic (LTCC) material system has been used to develop a protype field emission cathode structure for use in an experimental magnetron oscillator. The structure is designed for used with 30 Gated Field Emission Array (GFEA) die electrically connected through silver metal traces and electrical vias. To approximate a cylinder, the cathode structure (48 mm long and 13.7 mm in diameter) is comprised of 10 faceted plates which cover the GFEA dies. Slits in the facet plates allow electron injection. The GFEA die (3 mm x 8 mm) are placed in axial columns of 3 and spaced …


Simulation Of A Time-Varying Distributed Cathode In A Linear Format Crossed-Field Amplifier, Marcus Pearlman, Jim Browning Aug 2019

Simulation Of A Time-Varying Distributed Cathode In A Linear Format Crossed-Field Amplifier, Marcus Pearlman, Jim Browning

Electrical and Computer Engineering Faculty Publications and Presentations

The effects of a temporally modulated, distributed cathode in a linear format crossed-field amplifier (CFA) are simulated in VSim and analyzed. A linear format, 150 MHz, low power (100 W), moderate gain (7 dB), meander line CFA is used as the basis for the simulation model. This paper describes simulations with different time-varying distributed cathodes in which electron injection is modulated at the RF frequency both in and out of phase with the RF input. At low RF input power the modulated electron injection dominates the operation. Injecting in phase with the RF input shows gain increases from 23 dB …


Work In Progress: Mastery-Based Grading In An Introduction To Circuits Class, Noah Salzman, Kurtis D. Cantley, Gary L. Hunt Jun 2019

Work In Progress: Mastery-Based Grading In An Introduction To Circuits Class, Noah Salzman, Kurtis D. Cantley, Gary L. Hunt

Electrical and Computer Engineering Faculty Publications and Presentations

Circuits is often the first required course in an electrical engineering curriculum that demands application of multiple concepts from prerequisite math and physics courses. This integration of knowledge can be a challenge for many students. Effective teaching methods can enhance the overall learning experience, increase program retention, and improve student understanding of foundational topics in electrical engineering. This paper outlines a mastery-based grading structure implemented in a sophomore-level circuits class. The focus is placed at this level because the course is a critical prerequisite for many other courses in the electrical and computer engineering (ECE) curriculum. The knowledge that students …


A Spatiotemporal Pattern Detector, Robert Ivans, Kurtis D. Cantley Jan 2019

A Spatiotemporal Pattern Detector, Robert Ivans, Kurtis D. Cantley

Electrical and Computer Engineering Faculty Publications and Presentations

A spatiotemporal pattern detector design is presented which can identify three fundamental spatiotemporal patterns consisting of two spikes (from different neurons or from the same neuron). These fundamental cases provide the building blocks for construction of more complicated arbitrary spatiotemporal patterns. The overall design consists of three primary subcircuits, and the operation of each is described. The detection of the three cases of spatiotemporal patterns, and the detection of a more complicated pattern by a network of Spatiotemporal Pattern Detectors, is then demonstrated through simulation using the Cadence Virtuoso platform.


Learning Behavior Of Memristor-Based Neuromorphic Circuits In The Presence Of Radiation, Sumedha Gandharava Dahl, Robert C. Ivans, Kurtis D. Cantley Jan 2019

Learning Behavior Of Memristor-Based Neuromorphic Circuits In The Presence Of Radiation, Sumedha Gandharava Dahl, Robert C. Ivans, Kurtis D. Cantley

Electrical and Computer Engineering Faculty Publications and Presentations

In this paper, a feed-forward spiking neural network with memristive synapses is designed to learn a spatio-temporal pattern representing the 25-pixel character ‘B’ by separating correlated and uncorrelated afferents. The network uses spike-timing-dependent plasticity (STDP) learning behavior, which is implemented using biphasic neuron spikes. A TiO2 memristor non-linear drift model is used to simulate synaptic behavior in the neuromorphic circuit. The network uses a many-to-one topology with 25 pre-synaptic neurons (afferent) each connected to a memristive synapse and one post-synaptic neuron. The memristor model is modified to include the experimentally observed effect of state-altering radiation. During the learning process, …


Introducing The Boise State Bangla Handwriting Dataset And An Efficient Offline Recognizer Of Isolated Bangla Characters, Nishatul Majid, Elisa H. Barney Smith Aug 2018

Introducing The Boise State Bangla Handwriting Dataset And An Efficient Offline Recognizer Of Isolated Bangla Characters, Nishatul Majid, Elisa H. Barney Smith

Electrical and Computer Engineering Faculty Publications and Presentations

This introduces the Boise State Bangla Handwriting Dataset, a publicly accessible offline handwriting dataset of Bangla script. This can be found at https://scholarworks.boisestate.edu/saipl/1/

A basic character recognition method is presented where the features are extracted based on zonal pixel counts, structural strokes and grid points with U-SURF descriptors modeled with bag of features.

Benchmarking with this approach on 3 other publicly available Bangla datasets is reported. The highest classification accuracy obtained with an SVM classifier based on a cubic kernel is 96.8%.


Introducing The Xxx Bangla Handwriting Dataset And An Efficient Offline Recognizer Of Isolated Bangla Characters, Nishatul Majid, Elisa H. Barney Smith Jan 2018

Introducing The Xxx Bangla Handwriting Dataset And An Efficient Offline Recognizer Of Isolated Bangla Characters, Nishatul Majid, Elisa H. Barney Smith

Electrical and Computer Engineering Faculty Publications and Presentations

This paper presents a publicly accessible Bangla offline handwriting dataset, as well as benchmarking with a simple and robust isolated handwritten character recognition scheme. The dataset is named XXX Bangla Handwriting Dataset. The dataset contains 2 pages. The first has a 104 word/364 character essay. The essay uses 49 basic characters, all 11 vowel diacritics and 32 high frequency consonant conjuncts. The second page contains 84 isolated units containing all basic characters, numbers, vowel diacritics and several high frequency conjuncts. The initial release is based on the voluntary contribution of 100 different writers. One of the highlights and unique features …


Spatio-Temporal Pattern Recognition In Neural Circuits With Memory-Transistor-Driven Memristive Synapses, Kurtis D. Cantley, Robert C. Ivans, Anand Subramaniam, Eric M. Vogel Jan 2017

Spatio-Temporal Pattern Recognition In Neural Circuits With Memory-Transistor-Driven Memristive Synapses, Kurtis D. Cantley, Robert C. Ivans, Anand Subramaniam, Eric M. Vogel

Electrical and Computer Engineering Faculty Publications and Presentations

Spiking neural circuits have been designed in which the memristive synapses exhibit spike timing-dependent plasticity (STDP). STDP is a learning mechanism where synaptic weight (the strength of the connection between two neurons) depends on the timing of pre-and post-synaptic action potentials. A known capability of networks with STDP is detection of simultaneously recurring patterns within the population of afferent neurons. This work uses SPICE (simulation program with integrated circuit emphasis) to demonstrate the spatio-temporal pattern recognition (STPR) effect in networks with 25 afferent neurons. The neuron circuits are the leaky integrate-and-fire (I&F) type and implemented using extensively validated ambipolar nano-crystalline …


A Cmos Synapse Design Implementing Tunable Asymmetric Spike Timing-Dependent Plasticity, Robert C. Ivans, Kurtis D. Cantley, Justin L. Shumaker Jan 2017

A Cmos Synapse Design Implementing Tunable Asymmetric Spike Timing-Dependent Plasticity, Robert C. Ivans, Kurtis D. Cantley, Justin L. Shumaker

Electrical and Computer Engineering Faculty Publications and Presentations

A CMOS synapse design is presented which can perform tunable asymmetric spike timing-dependent learning in asynchronous spiking neural networks. The overall design consists of three primary subcircuit blocks, and the operation of each is described. Pair-based Spike Timing-Dependent Plasticity (STDP) of the entire synapse is then demonstrated through simulation using the Cadence Virtuoso platform. Tuning of the STDP curve learning window and rate of synaptic weight change is possible using various control parameters. With appropriate settings, it is shown the resulting learning rule closely matches that observed in biological systems.


Pulse Shape And Timing Dependence On The Spike-Timing Dependent Plasticity Response Of Ion-Conducting Memristors As Synapses, Kris A. Campbell, Kolton T. Drake, Elisa H. Barney Smith Dec 2016

Pulse Shape And Timing Dependence On The Spike-Timing Dependent Plasticity Response Of Ion-Conducting Memristors As Synapses, Kris A. Campbell, Kolton T. Drake, Elisa H. Barney Smith

Electrical and Computer Engineering Faculty Publications and Presentations

Ion-conducting memristors comprised of the layered materials Ge2Se3/SnSe/Ag are promising candidates for neuromorphic computing applications. Here, the spike-timing dependent plasticity (STDP) application is demonstrated for the first time with a single memristor type operating as a synapse over a timescale of 10 orders of magnitude, from nanoseconds through seconds. This large dynamic range allows the memristors to be useful in applications that require slow biological times, as well as fast times such as needed in neuromorphic computing, thus allowing multiple functions in one design for one memristor type—a “one size fits all” approach. This work also …


Thermodynamics And Kinetics Of Dna Nanotube Polymerization From Single-Filament Measurements, Rizal F. Hariadi, Bernard Yurke, Erik Winfree Apr 2015

Thermodynamics And Kinetics Of Dna Nanotube Polymerization From Single-Filament Measurements, Rizal F. Hariadi, Bernard Yurke, Erik Winfree

Electrical and Computer Engineering Faculty Publications and Presentations

DNA nanotubes provide a programmable architecture for molecular self-assembly and can serve as model systems for one-dimensional biomolecular assemblies. While a variety of DNA nanotubes have been synthesized and employed as models for natural biopolymers, an extensive investigation of DNA nanotube kinetics and thermodynamics has been lacking. Using total internal reflection microscopy, DNA nanotube polymerization was monitored in real time at the single filament level over a wide range of free monomer concentrations and temperatures. The measured polymerization rates were subjected to a global nonlinear fit based on polymerization theory in order to simultaneously extract kinetic and thermodynamic parameters. For …


Template Generation From Postmarks Using Cascaded Unsupervised Learning, Elisa H. Barney Smith, Gernot Fink Jan 2015

Template Generation From Postmarks Using Cascaded Unsupervised Learning, Elisa H. Barney Smith, Gernot Fink

Electrical and Computer Engineering Faculty Publications and Presentations

Information in historical datasets comes in many forms. We are working with a set of World War I era postcards that contain hand written text, some preprinted text, postage stamps and postmark/cancellation stamps. The postmarks are of considerable interest to collectors looking for images of samples they had not previously seen. The postmarks also provide information on the originating location of the card that complements the information in the address block.

The postmarks vary considerably with towns and dates, but also styles. The styles can be grouped into categories. A method for automatically extracting templates for each category of these …


Chiral Plasmonic Dna Nanostructures With Switchable Circular Dichroism, Ngoc Luong, Bernard Yurke, Wan Kuang Dec 2013

Chiral Plasmonic Dna Nanostructures With Switchable Circular Dichroism, Ngoc Luong, Bernard Yurke, Wan Kuang

Electrical and Computer Engineering Faculty Publications and Presentations

Circular dichroism spectra of naturally occurring molecules and also of synthetic chiral arrangements of plasmonic particles often exhibit characteristic bisignate shapes. Such spectra consist of peaks next to dips (or vice versa) and result from the superposition of signals originating from many individual chiral objects oriented randomly in solution. Here we show that by first aligning and then toggling the orientation of DNA-origami-scaffolded nanoparticle helices attached to a substrate, we are able to reversibly switch the optical response between two distinct circular dichroism spectra corresponding to either perpendicular or parallel helix orientation with respect to the light beam. The observed …


On The Biophysics And Kinetics Of Toehold-Mediated Dna Strand Displacement, Bernard Yurke Dec 2013

On The Biophysics And Kinetics Of Toehold-Mediated Dna Strand Displacement, Bernard Yurke

Electrical and Computer Engineering Faculty Publications and Presentations

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold …


Multiscaffold Dna Origami Nanoparticle Waveguides, William P. Klein, Charles N. Schmidt, Blake Rapp, Sadao Takabayashi, William B. Knowlton, Jeunghoon Lee, Bernard Yurke, William L. Hughes, Elton Graugnard, Wan Kuang Aug 2013

Multiscaffold Dna Origami Nanoparticle Waveguides, William P. Klein, Charles N. Schmidt, Blake Rapp, Sadao Takabayashi, William B. Knowlton, Jeunghoon Lee, Bernard Yurke, William L. Hughes, Elton Graugnard, Wan Kuang

Electrical and Computer Engineering Faculty Publications and Presentations

DNA origami templated self-assembly has shown its potential in creating rationally designed nanophotonic devices in a parallel and repeatable manner. In this investigation, we employ a multiscaffold DNA origami approach to fabricate linear waveguides of 10 nm diameter gold nanoparticles. This approach provides independent control over nanoparticle separation and spatial arrangement. The waveguides were characterized using atomic force microscopy and far-field polarization spectroscopy. This work provides a path toward large-scale plasmonic circuitry.


Reconfigurable Threshold Logic Gates Using Memristive Devices, Adrian Rothenbuhler, Thanh Tran, Elisa H. Barney Smith, Vishal Saxena, Kristy A. Campbell Jun 2013

Reconfigurable Threshold Logic Gates Using Memristive Devices, Adrian Rothenbuhler, Thanh Tran, Elisa H. Barney Smith, Vishal Saxena, Kristy A. Campbell

Electrical and Computer Engineering Faculty Publications and Presentations

We present our design exploration of reconfigurable Threshold Logic Gates (TLG) implemented using silver–chalcogenide memristive devices combined with CMOS circuits. Results from simulations and physical circuits are shown. A variety of linearly separable logic functions including AND, OR, NAND, NOR have been realized in discrete hardware using a single-layer TLG. The functionality can be changed between these operations by reprogramming the resistance of the memristive devices.


Robust Self-Replication Of Combinatorial Information Via Crystal Growth And Scission, Rebecca Schulman, Bernard Yurke, Erik Winfree Apr 2012

Robust Self-Replication Of Combinatorial Information Via Crystal Growth And Scission, Rebecca Schulman, Bernard Yurke, Erik Winfree

Electrical and Computer Engineering Faculty Publications and Presentations

Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different …


Effect Of “Ground Truth” On Image Binarization, Elisa H. Barney Smith, Chang An Mar 2012

Effect Of “Ground Truth” On Image Binarization, Elisa H. Barney Smith, Chang An

Electrical and Computer Engineering Faculty Publications and Presentations

Image binarization has a large effect on the rest of the document image analysis processes in character recognition. Algorithm development is still a major focus of research. Evaluation of image binarization has been done by comparison of the result of OCR systems on images binarized by different methods. That has been criticized in that the binarization alone is not evaluated, but rather how it interacts with the downstream processes. Recently pixel accurate "ground truth" images have been introduced for use in binarization algorithm evaluation. This has been shown to be open to interpretation. The choice of binarization ground truth affects …


Application Of Image Processing To Track Twin Boundary Motion In Magnetic Shape Memory Alloys, Adrian Rothenbuhler, Elisa Barney Smith, Peter Müllner Jan 2012

Application Of Image Processing To Track Twin Boundary Motion In Magnetic Shape Memory Alloys, Adrian Rothenbuhler, Elisa Barney Smith, Peter Müllner

Electrical and Computer Engineering Faculty Publications and Presentations

Materials scientists make use of image processing tools more and more as technology advances and the data volume that needs to be analyzed increases. We propose a method to optically measure magnetic eld induced strain (MFIS) as well as twin boundary movement in Ni2MnGa single crystal shape memory alloys to facilitate spatially resolved tracking of deformation. Current magneto-mechanical experiments used to measure MFIS can measure strain only in one direction and do not provide information about the movement of individual twin boundaries. A sequence of images captured from a high resolution camera is analyzed by a boundary detection …


Towards Improved Paper-Based Election Technology, Elisa H. Barney Smith, Daniel Lopresti, George Nagy, Ziyan Wu Sep 2011

Towards Improved Paper-Based Election Technology, Elisa H. Barney Smith, Daniel Lopresti, George Nagy, Ziyan Wu

Electrical and Computer Engineering Faculty Publications and Presentations

Resources are presented for fostering paper-based election technology. They comprise a diverse collection of real and simulated ballot and survey images, and software tools for ballot synthesis, registration, segmentation, and ground-truthing. The grids underlying the designated location of voter marks are extracted from 13,315 degraded ballot images. The actual skew angles of sample ballots, recorded as part of complete ballot descriptions compiled with the interactive ground-truthing tool, are compared with their automatically extracted parameters. The average error is 0.1 degrees. These results provide a baseline for the application of digital image analysis to the scrutiny of electoral ballots.


Evaluation Of Voting With Form Dropout Techniques For Ballot Vote Counting, Elisa H. Barney Smith, Shatakshi Goyal, Robbie Scott, Daniel Lopresti Sep 2011

Evaluation Of Voting With Form Dropout Techniques For Ballot Vote Counting, Elisa H. Barney Smith, Shatakshi Goyal, Robbie Scott, Daniel Lopresti

Electrical and Computer Engineering Faculty Publications and Presentations

Vote counting accuracy has become a well-known issue in the vote collection process. Digital image processing techniques can be incorporated in the analysis of printed election ballots. Current image processing techniques in the vote collection process are heavily dependent on the anticipated, geometric positioning of the vote. These techniques don’t account for markings made outside of the requested field of input. Using various form dropout techniques, however, every mark on the form can be extracted and used by the machine to make an intelligent decision. Most methods will still miss a few marks and result in a few false alarms. …


Enhancement Of Historical Printed Document Images By Combining Total Variation Regularization And Non-Local Means Filtering, Laurence Likforman-Sulem, Jérôme Darbon, Elisa H. Barney Smith Apr 2011

Enhancement Of Historical Printed Document Images By Combining Total Variation Regularization And Non-Local Means Filtering, Laurence Likforman-Sulem, Jérôme Darbon, Elisa H. Barney Smith

Electrical and Computer Engineering Faculty Publications and Presentations

This paper proposes a novel method for document enhancement which combines two recent powerful noise-reduction steps. The first step is based on the total variation framework. It flattens background grey-levels and produces an intermediate image where background noise is considerably reduced. This image is used as a mask to produce an image with a cleaner background while keeping character details. The second step is applied to the cleaner image and consists of a filter based on non-local means: character edges are smoothed by searching for similar patch images in pixel neighborhoods. The document images to be enhanced are real historical …


Characterizing Challenged Minnesota Ballots, George Nagy, Daniel Lopresti, Elisa H. Barney Smith, Ziyan Wu Jan 2011

Characterizing Challenged Minnesota Ballots, George Nagy, Daniel Lopresti, Elisa H. Barney Smith, Ziyan Wu

Electrical and Computer Engineering Faculty Publications and Presentations

Photocopies of the ballots challenged in the 2008 Minnesota elections, which constitute a public record, were scanned on a high-speed scanner and made available on a public radio website. The PDF files were downloaded, converted to TIF images, and posted on the PERFECT website. Based on a review of relevant image-processing aspects of paper-based election machinery and on additional statistics and observations on the posted sample data, robust tools were developed for determining the underlying grid of the targets on these ballots regardless of skew, clipping, and other degradations caused by high-speed copying and digitization. The accuracy and robustness of …


A Mask-Based Enhancement Method For Historical Documents, Elisa H. Barney Smith, Jerôme Darbon, Laurence Likforman-Sulem Jan 2011

A Mask-Based Enhancement Method For Historical Documents, Elisa H. Barney Smith, Jerôme Darbon, Laurence Likforman-Sulem

Electrical and Computer Engineering Faculty Publications and Presentations

This paper proposes a novel method for document enhancement. The method is based on the combination of two state-of-the-art filters through the construction of a mask. The mask is applied to a TV (Total Variation) -regularized image where background noise has been reduced. The masked image is then filtered by NLmeans (Non-Local Means) which reduces the noise in the text areas located by the mask. The document images to be enhanced are real historical documents from several periods which include several defects in their background. These defects result from scanning, paper aging and bleed-through. We observe the improvement of this …


Descreening Of Color Halftone Images In The Frequency Domain, C. J. Stanger, Thanh Tran, Elisa H. Barney Smith Jan 2011

Descreening Of Color Halftone Images In The Frequency Domain, C. J. Stanger, Thanh Tran, Elisa H. Barney Smith

Electrical and Computer Engineering Faculty Publications and Presentations

Scanning a halftone image introduces halftone artifacts, known as Moiré patterns, which significantly degrade the image quality. Printers that use amplitude modulation (AM) screening for halftone printing position dots in a periodic pattern. Therefore, frequencies relating halftoning are easily identifiable in the frequency domain. This paper proposes a method for descreening scanned color halftone images using a custom band reject filter designed to isolate and remove only the frequencies related to halftoning while leaving image edges sharp without image segmentation or edge detection. To enable hardware acceleration, the image is processed in small overlapped windows. The windows are filtered individually …


Development Of Dna Based Active Macro-Materials For Biology And Medicine: A Review, Frank Xue Jiang, Bernard Yurke, Devendra Verma, Michelle Previtera, Rene Schloss, Noshir A. Langrana Jan 2011

Development Of Dna Based Active Macro-Materials For Biology And Medicine: A Review, Frank Xue Jiang, Bernard Yurke, Devendra Verma, Michelle Previtera, Rene Schloss, Noshir A. Langrana

Electrical and Computer Engineering Faculty Publications and Presentations

DNA was first discovered as the carrier of genetic information for the majority of the known living organisms, encoding the secret of life. Its delicate design based upon double helical structure and base pairing offers a stable and reliable media for storing hereditary codes, laying the foundation for the central dogma (Watson et al. 2003). The impact of this molecule is far reaching into scientific community and our society, as manifested in many fields, for instance, forensics (Budowle et al. 2003), besides medicine. To date, a great deal of research effort has been directed towards understanding


Cavity Resonant Mode In A Metal Film Perforated With Two-Dimensional Triangular Lattice Hole Arrays, Wan Kuang, Alex English, William B. Knowlton, Jeunghoon Lee, William L. Hughes, Bernard Yurke Oct 2010

Cavity Resonant Mode In A Metal Film Perforated With Two-Dimensional Triangular Lattice Hole Arrays, Wan Kuang, Alex English, William B. Knowlton, Jeunghoon Lee, William L. Hughes, Bernard Yurke

Electrical and Computer Engineering Faculty Publications and Presentations

The transmission property of metallic films with two-dimensional hole arrays is studied experimentally and numerically. For a triangular lattice subwavelength hole array in a 150 nm thick Ag film, both cavity resonance and planar surface modes are identified as the sources of enhanced optical transmissions. Semi-analytical models are developed for calculating the dispersion relation of the cavity resonant mode. They agree well with the experimental results and full-wave numerical calculations. Strong interaction between the cavity resonant mode and surface modes is also observed.


Joint Loop End Modeling Improves Covariance Model Based Non-Coding Rna Gene Search, Jennifer Smith Sep 2010

Joint Loop End Modeling Improves Covariance Model Based Non-Coding Rna Gene Search, Jennifer Smith

Electrical and Computer Engineering Faculty Publications and Presentations

The effect of more detailed modeling of the interface between stem and loop in non-coding RNA hairpin structures on efficacy of covariance-model-based non-coding RNA gene search is examined. Currently, the prior probabilities of the two stem nucleotides and two loop-end nucleotides at the interface are treated the same as any other stem and loop nucleotides respectively. Laboratory thermodynamic studies show that hairpin stability is dependent on the identities of these four nucleotides, but this is not taken into account in current covariance models. It is shown that separate estimation of emission priors for these nucleotides and joint treatment of substitution …


An Analysis Of Binarization Ground Truthing, Elisa H. Barney Smith Jun 2010

An Analysis Of Binarization Ground Truthing, Elisa H. Barney Smith

Electrical and Computer Engineering Faculty Publications and Presentations

The accuracy of a binarization algorithm is often calculated relative to a ground truth image. Except for synthetically generated images, no ground truth image exists. Evaluating binarization on real images is preferred. The ground truthing between and among different operators is compared. Four direct metrics were used. The variability of the results of five different automatic binarization algorithms were compared to that of manual ground truth results. Significant variability in the ground truth results was found.


Computation Intelligence Method To Find Generic Non-Coding Rna Search Models, Jennifer A. Smith May 2010

Computation Intelligence Method To Find Generic Non-Coding Rna Search Models, Jennifer A. Smith

Electrical and Computer Engineering Faculty Publications and Presentations

Fairly effective methods exist for finding new noncoding RNA genes using search models based on known families of ncRNA genes (for example covariance models). However, these models only find new members of the existing families and are not useful in finding potential members of novel ncRNA families. Other problems with family-specific search include large processing requirements, ambiguity in defining which sequences form a family and lack of sufficient numbers of known sequences to properly estimate model parameters. An ncRNA search model is proposed which includes a collection of non-overlapping RNA hairpin structure covariance models. The hairpin models are chosen from …