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Description
Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell. As a result, various genomic and proteomic sequence processing methods have been proposed from diverse disciplines, including biology, chemistry,

Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell. As a result, various genomic and proteomic sequence processing methods have been proposed from diverse disciplines, including biology, chemistry, physics, computer science and electrical engineering. In particular, signal processing techniques were applied to the problems of sequence querying and alignment, that compare and classify regions of similarity in the sequences based on their composition. However, although current approaches obtain results that can be attributed to key biological properties, they require pre-processing and lack robustness to sequence repetitions. In addition, these approaches do not provide much support for efficiently querying sub-sequences, a process that is essential for tracking localized database matches. In this work, a query-based alignment method for biological sequences that maps sequences to time-domain waveforms before processing the waveforms for alignment in the time-frequency plane is first proposed. The mapping uses waveforms, such as time-domain Gaussian functions, with unique sequence representations in the time-frequency plane. The proposed alignment method employs a robust querying algorithm that utilizes a time-frequency signal expansion whose basis function is matched to the basic waveform in the mapped sequences. The resulting WAVEQuery approach is demonstrated for both DNA and protein sequences using the matching pursuit decomposition as the signal basis expansion. The alignment localization of WAVEQuery is specifically evaluated over repetitive database segments, and operable in real-time without pre-processing. It is demonstrated that WAVEQuery significantly outperforms the biological sequence alignment method BLAST for queries with repetitive segments for DNA sequences. A generalized version of the WAVEQuery approach with the metaplectic transform is also described for protein sequence structure prediction. For protein alignment, it is often necessary to not only compare the one-dimensional (1-D) primary sequence structure but also the secondary and tertiary three-dimensional (3-D) space structures. This is done after considering the conformations in the 3-D space due to the degrees of freedom of these structures. As a result, a novel directionality based 3-D waveform mapping for the 3-D protein structures is also proposed and it is used to compare protein structures using a matched filter approach. By incorporating a 3-D time axis, a highly-localized Gaussian-windowed chirp waveform is defined, and the amino acid information is mapped to the chirp parameters that are then directly used to obtain directionality in the 3-D space. This mapping is unique in that additional characteristic protein information such as hydrophobicity, that relates the sequence with the structure, can be added as another representation parameter. The additional parameter helps tracking similarities over local segments of the structure, this enabling classification of distantly related proteins which have partial structural similarities. This approach is successfully tested for pairwise alignments over full length structures, alignments over multiple structures to form a phylogenetic trees, and also alignments over local segments. Also, basic classification over protein structural classes using directional descriptors for the protein structure is performed.
ContributorsRavichandran, Lakshminarayan (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Spanias, Andreas S (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Lacroix, Zoé (Committee member) / Arizona State University (Publisher)
Created2011
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Description
The study of acoustic ecology is concerned with the manner in which life interacts with its environment as mediated through sound. As such, a central focus is that of the soundscape: the acoustic environment as perceived by a listener. This dissertation examines the application of several computational tools in the

The study of acoustic ecology is concerned with the manner in which life interacts with its environment as mediated through sound. As such, a central focus is that of the soundscape: the acoustic environment as perceived by a listener. This dissertation examines the application of several computational tools in the realms of digital signal processing, multimedia information retrieval, and computer music synthesis to the analysis of the soundscape. Namely, these tools include a) an open source software library, Sirens, which can be used for the segmentation of long environmental field recordings into individual sonic events and compare these events in terms of acoustic content, b) a graph-based retrieval system that can use these measures of acoustic similarity and measures of semantic similarity using the lexical database WordNet to perform both text-based retrieval and automatic annotation of environmental sounds, and c) new techniques for the dynamic, realtime parametric morphing of multiple field recordings, informed by the geographic paths along which they were recorded.
ContributorsMechtley, Brandon Michael (Author) / Spanias, Andreas S (Thesis advisor) / Sundaram, Hari (Thesis advisor) / Cook, Perry R. (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Digital sound synthesis allows the creation of a great variety of sounds. Focusing on interesting or ecologically valid sounds for music, simulation, aesthetics, or other purposes limits the otherwise vast digital audio palette. Tools for creating such sounds vary from arbitrary methods of altering recordings to precise simulations of vibrating

Digital sound synthesis allows the creation of a great variety of sounds. Focusing on interesting or ecologically valid sounds for music, simulation, aesthetics, or other purposes limits the otherwise vast digital audio palette. Tools for creating such sounds vary from arbitrary methods of altering recordings to precise simulations of vibrating objects. In this work, methods of sound synthesis by re-sonification are considered. Re-sonification, herein, refers to the general process of analyzing, possibly transforming, and resynthesizing or reusing recorded sounds in meaningful ways, to convey information. Applied to soundscapes, re-sonification is presented as a means of conveying activity within an environment. Applied to the sounds of objects, this work examines modeling the perception of objects as well as their physical properties and the ability to simulate interactive events with such objects. To create soundscapes to re-sonify geographic environments, a method of automated soundscape design is presented. Using recorded sounds that are classified based on acoustic, social, semantic, and geographic information, this method produces stochastically generated soundscapes to re-sonify selected geographic areas. Drawing on prior knowledge, local sounds and those deemed similar comprise a locale's soundscape. In the context of re-sonifying events, this work examines processes for modeling and estimating the excitations of sounding objects. These include plucking, striking, rubbing, and any interaction that imparts energy into a system, affecting the resultant sound. A method of estimating a linear system's input, constrained to a signal-subspace, is presented and applied toward improving the estimation of percussive excitations for re-sonification. To work toward robust recording-based modeling and re-sonification of objects, new implementations of banded waveguide (BWG) models are proposed for object modeling and sound synthesis. Previous implementations of BWGs use arbitrary model parameters and may produce a range of simulations that do not match digital waveguide or modal models of the same design. Subject to linear excitations, some models proposed here behave identically to other equivalently designed physical models. Under nonlinear interactions, such as bowing, many of the proposed implementations exhibit improvements in the attack characteristics of synthesized sounds.
ContributorsFink, Alex M (Author) / Spanias, Andreas S (Thesis advisor) / Cook, Perry R. (Committee member) / Turaga, Pavan (Committee member) / Tsakalis, Konstantinos (Committee member) / Arizona State University (Publisher)
Created2013
Description
"EP \u2014 Kyan Palmer" is a compilation of three songs, "Hit List," "Queen Cobra," and "Burn Mona Lisa" all written and recorded by Barrett student, Kyan Palmer. The project explores the process involved in creating recorded music and exposes the vulnerability and self-reflection in writing a song. The following depicts

"EP \u2014 Kyan Palmer" is a compilation of three songs, "Hit List," "Queen Cobra," and "Burn Mona Lisa" all written and recorded by Barrett student, Kyan Palmer. The project explores the process involved in creating recorded music and exposes the vulnerability and self-reflection in writing a song. The following depicts the thought process that came about in the creation of each song from the lyrics, to the vocals, to the production. This paper depicts a journal-like writing style outlining the various events that took place while creating EP \u2014 Kyan Palmer. The bulk of this Thesis/Creative Project was the written, produced, and recorded music attached in the appendix. With that said, the following document is intended to be reflective rather than scholarly and acts as an accompaniment to the audio recordings and video entries.
ContributorsPalmer, Kyan (Author) / Swoboda, Deanna (Thesis director) / Tobias, Evan (Committee member) / W. P. Carey School of Business (Contributor) / School of Music (Contributor) / Department of Marketing (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The music business has constantly evolved since its inception. Sheet music was the first physical form of music sold and was influenced by innovations in printing technology. Recorded music came about in the late 1800s and early 1900s, with Thomas Edison pioneering the phonograph record. Technology shifted from records to

The music business has constantly evolved since its inception. Sheet music was the first physical form of music sold and was influenced by innovations in printing technology. Recorded music came about in the late 1800s and early 1900s, with Thomas Edison pioneering the phonograph record. Technology shifted from records to 8-tracks to cassettes, and finally, digital audio, which revolutionized the entire industry. Compact discs (CDs) skyrocketed in popularity during the 1990s and early 2000s, but so did file-sharing. To combat piracy, record labels began selling and streaming music online. Music sales have plummeted in all formats. Streaming reigns as the most popular form of music distribution, but it produces a mere fraction of the revenue traditional albums once did. The loss affects all those in the industry, especially the artists, who see an average of only $23.40 for every $1000 in music sold. But technology has allowed the independent artist to record and distribute their music to the world for little cost compared to their major label predecessors. Many wonder if the music industry is dead, but as with any other technological change in history, the adaptors and innovators will survive.
ContributorsDamiano, Alec (Author) / Swoboda, Deanna (Thesis director) / Whyte, Rutger (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor) / Walter Cronkite School of Journalism and Mass Communication (Contributor)
Created2015-05
Description
In its totality, “Love and Everything After” consists of five tracks. In musical circles, this is considered an EP (extended play), a collection of music longer than one song but generally more brief than a full album. Each track combines varying degrees of my own acoustic and piano instrumentation with

In its totality, “Love and Everything After” consists of five tracks. In musical circles, this is considered an EP (extended play), a collection of music longer than one song but generally more brief than a full album. Each track combines varying degrees of my own acoustic and piano instrumentation with modern production elements, all tied together with a corrected vocal and a quick mix and master by my producer who doubles as my sound engineer for this project. I will outline my experience with the creative process here as well as break down the development of each song. A fair bit of the lyrical composition is dedicated to background information that may seem to verge on oversharing, but alas, I am a writer. I consider verging on oversharing an inevitable cog in any successful songwriting operation. I’ve decided to tackle the songs in chronological order, prioritizing the time during which the bulk of the piece was first assembled.
ContributorsNelson, Christopher Michael (Author) / Wells, Cornelia (Thesis director) / Swoboda, Deanna (Committee member) / School of Politics and Global Studies (Contributor) / Hugh Downs School of Human Communication (Contributor) / Department of Marketing (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Composed by Adele Etheridge Woodson in 2018, Thrive is an original composition for live euphonium and prepared electronic backing track; it was commissioned by David Gonzalez and premiered at the International Women’s Brass Conference at Arizona State University. The musical piece incorporates multiple audio bytes from personal interviews and videos

Composed by Adele Etheridge Woodson in 2018, Thrive is an original composition for live euphonium and prepared electronic backing track; it was commissioned by David Gonzalez and premiered at the International Women’s Brass Conference at Arizona State University. The musical piece incorporates multiple audio bytes from personal interviews and videos found online, including words said by pop figure icons, Congressmen, and President Donald J. Trump. The goal of Thrive is to creatively highlight the fight for gender equality among a male-dominant, misogynist society. It also serves as a fresh piece of repertoire for the euphonium, which often lacks original compositions by living composers. This paper will discuss Etheridge Woodson’s creative writing process, creation of the backing track, its world premiere, audience reaction, and a personal reflection.
ContributorsEtheridge Woodson, Adele (Author) / Swoboda, Deanna (Thesis director) / Roumain, Daniel Bernard (Committee member) / School of Film, Dance and Theatre (Contributor) / School of Music (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
Due to increasing lack of resources and funding for budding student musicians, it is often not possible for this demographic to create, record, and produce their original music in the same high-budget studio environment in which music has been traditionally made. The objective of this project is to explore alternatives

Due to increasing lack of resources and funding for budding student musicians, it is often not possible for this demographic to create, record, and produce their original music in the same high-budget studio environment in which music has been traditionally made. The objective of this project is to explore alternatives which are more accessible to young independent musicians and reveal the most cost-efficient routes to obtain a high-quality result. To make this comparison, the group created budget recordings of their original music in a bedroom in true DIY fashion, and then recorded the same songs in a professional music studio using the best music and recording equipment available. The DIY recordings were mixed and mastered by the group members themselves, as well as separately by a professional audio engineer. The studio recordings were also mixed and mastered by a professional audio engineer, resulting in three final products with varying costs and quality. Ultimately, the group found that without mixing and mastering experience, it is very difficult to achieve high quality results. With the same budget recorded tracks, the group found that quality of the final product vastly increased when a professional audio engineer mixed and mastered the tracks. As far as the quality of the result, the studio recorded tracks were by far the best. Not only was the quality of the sounds from the high-end music and recording equipment much higher, the band had more freedom to be creative without the responsibility of simultaneously serving as recording engineers as was the case in the low budget recordings. The group concluded that this project was highly successful and demonstrated that high quality results could be obtained on a budget. The DIY recording techniques used in this project prove that independent musicians without access to expensive equipment and resources can still produce high quality music at the cost of more effort to serve as audio engineers in addition to musicians. However, recording in a studio with the help of a producer and professional audio engineers affords creative freedom and an increase in sound quality that is simply not possible to reproduce without the equipment and expertise that money can buy.
ContributorsBonk, Alan (Co-author) / Dhuyvetter, Nicholas Alan (Co-author) / Wickham, Kevin (Co-author) / Tobias, Evan (Thesis director) / Swoboda, Deanna (Committee member) / W.P. Carey School of Business (Contributor) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
This research aims to identify ways in which student live-in Musician-in-Residence programs help meet the social needs of older adults through university partnerships. Independent Living retirement communities face a gap in music programming. Student live-in Musician-in-Residence programs like the one at Mirabella at Arizona State University (Mirabella at ASU) were

This research aims to identify ways in which student live-in Musician-in-Residence programs help meet the social needs of older adults through university partnerships. Independent Living retirement communities face a gap in music programming. Student live-in Musician-in-Residence programs like the one at Mirabella at Arizona State University (Mirabella at ASU) were used to help determine how music impacted the quality of life of retirees and how it affected their relationships with a younger generation. Only residents in Independent Living were included in the study. Prior research has shown that when an older adult relocates to senior living, it can be viewed stereotypically as a sign that they are diminishing their capacity to live independently and are preparing to live the rest of their lives detached from society. Additionally, research shows that some retirement communities are unaware of how music programs can encourage the fostering of meaningful relationships for independent retired adults. As adults are retiring earlier, they are living healthier lives and require quality programming that reflects their active lifestyle. In this research, the questions asked provided qualitative responses and residents shared anecdotal reports of their experiences. Questions were divided into two categories, 1). Residential history and prior music experience, 2). Sense of belonging and retention. The results of this study suggest that intergenerational music programs contribute to maintaining older adults' social and emotional health by providing opportunities to engage in music through observation and participation. They also show that music programs serve as conduits for fostering relationships between seemingly disparate groups, in this case, the older and younger populations.
ContributorsCox, Tychiko Dustin (Author) / Swoboda, Deanna (Thesis advisor) / Hawkins, Gordon (Thesis advisor) / Wells, Christi Jay (Committee member) / Arizona State University (Publisher)
Created2023
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Description
This paper presents three new arrangements of works for solo tuba and piano, originally written by Black composers before 1950. The works presented here include Méphisto masqué by Edmond Dédé, Three Arabian Dances by Amanda Aldridge, and Warbling in the Moonlight by Alton Augustus Adams. Composer biographies, a formal analysis,

This paper presents three new arrangements of works for solo tuba and piano, originally written by Black composers before 1950. The works presented here include Méphisto masqué by Edmond Dédé, Three Arabian Dances by Amanda Aldridge, and Warbling in the Moonlight by Alton Augustus Adams. Composer biographies, a formal analysis, and form diagrams are included for each piece, along with the new transcriptions.
ContributorsMatejek, Matthew Ryan (Author) / Swoboda, Deanna (Thesis advisor) / Edwards, Bradley (Committee member) / Shea, Nicholas (Committee member) / Arizona State University (Publisher)
Created2023