Matching Items (112)
Description
In shotgun proteomics, liquid chromatography coupled to tandem mass spectrometry
(LC-MS/MS) is used to identify and quantify peptides and proteins. LC-MS/MS produces mass spectra, which must be searched by one or more engines, which employ
algorithms to match spectra to theoretical spectra derived from a reference database.
These engines identify and characterize proteins and their component peptides. By
training a convolutional neural network on a dataset of over 6 million MS/MS spectra
derived from human proteins, we aim to create a tool that can quickly and effectively
identify spectra as peptides prior to database searching. This can significantly reduce search space and thus run time for database searches, thereby accelerating LCMS/MS-based proteomics data acquisition. Additionally, by training neural networks
on labels derived from the search results of three different database search engines, we
aim to examine and compare which features are best identified by individual search
engines, a neural network, or a combination of these.
(LC-MS/MS) is used to identify and quantify peptides and proteins. LC-MS/MS produces mass spectra, which must be searched by one or more engines, which employ
algorithms to match spectra to theoretical spectra derived from a reference database.
These engines identify and characterize proteins and their component peptides. By
training a convolutional neural network on a dataset of over 6 million MS/MS spectra
derived from human proteins, we aim to create a tool that can quickly and effectively
identify spectra as peptides prior to database searching. This can significantly reduce search space and thus run time for database searches, thereby accelerating LCMS/MS-based proteomics data acquisition. Additionally, by training neural networks
on labels derived from the search results of three different database search engines, we
aim to examine and compare which features are best identified by individual search
engines, a neural network, or a combination of these.
ContributorsWhyte, Cameron Stafford (Author) / Suren, Jayasuriya (Thesis director) / Gil, Speyer (Committee member) / Patrick, Pirrotte (Committee member) / School of Mathematical and Statistical Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
In recent years, the development of new Machine Learning models has allowed for new technological advancements to be introduced for practical use across the world. Multiple studies and experiments have been conducted to create new variations of Machine Learning models with different algorithms to determine if potential systems would prove to be successful. Even today, there are still many research initiatives that are continuing to develop new models in the hopes to discover potential solutions for problems such as autonomous driving or determining the emotional value from a single sentence. One of the current popular research topics for Machine Learning is the development of Facial Expression Recognition systems. These Machine Learning models focus on classifying images of human faces that are expressing different emotions through facial expressions. In order to develop effective models to perform Facial Expression Recognition, researchers have gone on to utilize Deep Learning models, which are a more advanced implementation of Machine Learning models, known as Neural Networks. More specifically, the use of Convolutional Neural Networks has proven to be the most effective models for achieving highly accurate results at classifying images of various facial expressions. Convolutional Neural Networks are Deep Learning models that are capable of processing visual data, such as images and videos, and can be used to identify various facial expressions. The purpose of this project, I focused on learning about the important concepts of Machine Learning, Deep Learning, and Convolutional Neural Networks to implement a Convolutional Neural Network that was previously developed by a recommended research paper.
ContributorsFrace, Douglas R (Author) / Demakethepalli Venkateswara, Hemanth Kumar (Thesis director) / McDaniel, Troy (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Deep learning and AI have grabbed tremendous attention in the last decade. The substantial accuracy improvement by neural networks in common tasks such as image classification and speech recognition has made deep learning as a replacement for many conventional machine learning techniques. Training Deep Neural networks require a lot of data, and therefore vast of amounts of computing resources to process the data and train the model for the neural network. The most obvious solution to solving this problem is to speed up the time it takes to train Deep Neural networks.
AI and deep learning workloads are different from the conventional cloud and mobile workloads, with respect to: (1) Computational Intensity, (2) I/O characteristics, and (3) communication pattern. While there is a considerable amount of research activity on the theoretical aspects of AI and Deep Learning algorithms that run with greater efficiency, there are only a few studies on the infrastructural impact of Deep Learning workloads on computing and storage resources in distributed systems.
It is typical to utilize a heterogeneous mixture of CPU and GPU devices to perform training on a neural network. Google Brain has a developed a reinforcement model that can place training operations across a heterogeneous cluster. Though it has only been tested with local devices in a single cluster. This study will explore the method’s capabilities and attempt to apply this method on a cluster with nodes across a network.
AI and deep learning workloads are different from the conventional cloud and mobile workloads, with respect to: (1) Computational Intensity, (2) I/O characteristics, and (3) communication pattern. While there is a considerable amount of research activity on the theoretical aspects of AI and Deep Learning algorithms that run with greater efficiency, there are only a few studies on the infrastructural impact of Deep Learning workloads on computing and storage resources in distributed systems.
It is typical to utilize a heterogeneous mixture of CPU and GPU devices to perform training on a neural network. Google Brain has a developed a reinforcement model that can place training operations across a heterogeneous cluster. Though it has only been tested with local devices in a single cluster. This study will explore the method’s capabilities and attempt to apply this method on a cluster with nodes across a network.
ContributorsNguyen, Andrew Hoang (Author) / Zhao, Ming (Thesis director) / Biookaghazadeh, Saman (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Convolutional neural networks boast a myriad of applications in artificial intelligence, but one of the most common uses for such networks is image extraction. The ability of convolutional layers to extract and combine data features for the purpose of image analysis can be leveraged for pose estimation on an object - detecting the presence and attitude of corners and edges allows a convolutional neural network to identify how an object is positioned. This task can assist in working to grasp an object correctly in robotics applications, or to track an object more accurately in 3D space. However, the effectiveness of pose estimation may change based on properties of the object; the pose of a complex object, complexity being determined by internal occlusions, similar faces, etcetera, can be difficult to resolve.
This thesis is part of a collaboration between ASU’s Interactive Robotics Laboratory and NASA’s Jet Propulsion Laboratory. In this thesis, the training pipeline from Sharma’s paper “Pose Estimation for Non-Cooperative Spacecraft Rendezvous Using Convolutional Neural Networks” was modified to perform pose estimation on a complex object - specifically, a segment of a hollow truss. After initial attempts to replicate the architecture used in the paper and train solely on synthetic images, a combination of synthetic dataset generation and transfer learning on an ImageNet-pretrained AlexNet model was implemented to mitigate the difficulty of gathering large amounts of real-world data. Experimentation with pose estimation accuracy and hyperparameters of the model resulted in gradual test accuracy improvement, and future work is suggested to improve pose estimation for complex objects with some form of rotational symmetry.
This thesis is part of a collaboration between ASU’s Interactive Robotics Laboratory and NASA’s Jet Propulsion Laboratory. In this thesis, the training pipeline from Sharma’s paper “Pose Estimation for Non-Cooperative Spacecraft Rendezvous Using Convolutional Neural Networks” was modified to perform pose estimation on a complex object - specifically, a segment of a hollow truss. After initial attempts to replicate the architecture used in the paper and train solely on synthetic images, a combination of synthetic dataset generation and transfer learning on an ImageNet-pretrained AlexNet model was implemented to mitigate the difficulty of gathering large amounts of real-world data. Experimentation with pose estimation accuracy and hyperparameters of the model resulted in gradual test accuracy improvement, and future work is suggested to improve pose estimation for complex objects with some form of rotational symmetry.
ContributorsDsouza, Susanna Roshini (Author) / Ben Amor, Hani (Thesis director) / Maneparambil, Kailasnath (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The use of Artificial Intelligence in assistive systems is growing in application and efficiency. From self-driving cars, to medical and surgical robots and industrial tasked unsupervised co-robots; the use of AI and robotics to eliminate human error in high-stress environments and perform automated tasks is something that is advancing society’s status quo. Not only has the understanding of co-robotics exploded in the industrial world, but in research as well. The National Science Foundation (NSF) defines co-robots as the following: “...a robot whose main purpose is to work with people or other robots to accomplish a goal” (NSF, 1). The latest iteration of their National Robotics Initiative, NRI-2.0, focuses on efforts of creating co-robots optimized for ‘scalability, customizability, lowering barriers to entry, and societal impact’(NSF, 1). While many avenues have been explored for the implementation of co-robotics to create more efficient processes and sustainable lifestyles, this project’s focus was on societal impact co-robotics in the field of human safety and well-being. Introducing a co-robotics and computer vision AI solution for first responder assistance would help bring awareness and efficiency to public safety. The use of real-time identification techniques would create a greater range of awareness for first responders in high-stress situations. A combination of environmental features collected through sensors (camera and radar) could be used to identify people and objects within certain environments where visual impairments and obstructions are high (eg. burning buildings, smoke-filled rooms, ect.). Information about situational conditions (environmental readings, locations of other occupants, etc.) could be transmitted to first responders in emergency situations, maximizing situational awareness. This would not only aid first responders in the evaluation of emergency situations, but it would provide useful data for the first responder that would help materialize the most effective course of action for said situation.
ContributorsScott, Kylel D (Author) / Benjamin, Victor (Thesis director) / Liu, Xiao (Committee member) / Engineering Programs (Contributor) / College of Integrative Sciences and Arts (Contributor) / Department of Information Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
Immunotherapy is an effective treatment for cancer which enables the patient's immune system to recognize tumor cells as pathogens. In order to design an individualized treatment, the t cell receptors (TCR) which bind to a tumor's unique antigens need to be determined. We created a convolutional neural network to predict the binding affinity between a given TCR and antigen to enable this.
ContributorsCai, Michael Ray (Author) / Lee, Heewook (Thesis director) / Meuth, Ryan (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
Molecular pathology makes use of estimates of tumor content (tumor percentage) for pre-analytic and analytic purposes, such as molecular oncology testing, massive parallel sequencing, or next-generation sequencing (NGS), assessment of sample acceptability, accurate quantitation of variants, assessment of copy number changes (among other applications), determination of specimen viability for testing (since many assays require a minimum tumor content to report variants at the limit of detection) may all be improved with more accurate and reproducible estimates of tumor content. Currently, tumor percentages of samples submitted for molecular testing are estimated by visual examination of Hematoxylin and Eosin (H&E) stained tissue slides under the microscope by pathologists. These estimations can be automated, expedited, and rendered more accurate by applying machine learning methods on digital whole slide images (WSI).
ContributorsCirelli, Claire (Author) / Yang, Yezhou (Thesis director) / Yalim, Jason (Committee member) / Velu, Priya (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2022-05
Description
Hydrologic modeling in snowfed karst watersheds is important for many communities relying on their water for municipal and agricultural use, but the complexities of karst hydrology have made this task historically difficult. Here, two Long Short-Term Memory (LSTM) models are compared to investigate this problem from a deep-learning perspective within the context of the Logan River Canyon watershed, which supplies water to Logan City, UT. One is spatially lumped and the other spatially distributed, the latter with a potential to reveal underlying spatial watershed dynamics. Both use snowmelt and rainfall to predict daily streamflow downstream. I find distributed LSTMs consistently outperform lumped LSTMs in this task. Additionally, I find that a spatial sensitivity analysis of distributed LSTMs is unpromising in revealing spatial watershed dynamics but warrants further investigation.
ContributorsShaver, Ryan (Author) / Xu, Tianfang (Thesis director) / Jones, Don (Committee member) / Barrett, The Honors College (Contributor) / School of Earth and Space Exploration (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2022-05
Description
It is not merely an aggregation of static entities that a video clip carries, but alsoa variety of interactions and relations among these entities. Challenges still remain
for a video captioning system to generate natural language descriptions focusing on
the prominent interest and aligning with the latent aspects beyond observations. This
work presents a Commonsense knowledge Anchored Video cAptioNing (dubbed as
CAVAN) approach. CAVAN exploits inferential commonsense knowledge to assist the
training of video captioning model with a novel paradigm for sentence-level semantic
alignment. Specifically, commonsense knowledge is queried to complement per training
caption by querying a generic knowledge atlas ATOMIC, and form the commonsense-
caption entailment corpus. A BERT based language entailment model trained from
this corpus then serves as a commonsense discriminator for the training of video
captioning model, and penalizes the model from generating semantically misaligned
captions. With extensive empirical evaluations on MSR-VTT, V2C and VATEX
datasets, CAVAN consistently improves the quality of generations and shows higher
keyword hit rate. Experimental results with ablations validate the effectiveness of
CAVAN and reveals that the use of commonsense knowledge contributes to the video
caption generation.
ContributorsShao, Huiliang (Author) / Yang, Yezhou (Thesis advisor) / Jayasuriya, Suren (Committee member) / Xiao, Chaowei (Committee member) / Arizona State University (Publisher)
Created2022
Description
Speech analysis for clinical applications has emerged as a burgeoning field, providing valuable insights into an individual's physical and physiological state. Researchers have explored speech features for clinical applications, such as diagnosing, predicting, and monitoring various pathologies. Before presenting the new deep learning frameworks, this thesis introduces a study on conventional acoustic feature changes in subjects with post-traumatic headache (PTH) attributed to mild traumatic brain injury (mTBI). This work demonstrates the effectiveness of using speech signals to assess the pathological status of individuals. At the same time, it highlights some of the limitations of conventional acoustic and linguistic features, such as low repeatability and generalizability. Two critical characteristics of speech features are (1) good robustness, as speech features need to generalize across different corpora, and (2) high repeatability, as speech features need to be invariant to all confounding factors except the pathological state of targets. This thesis presents two research thrusts in the context of speech signals in clinical applications that focus on improving the robustness and repeatability of speech features, respectively. The first thrust introduces a deep learning framework to generate acoustic feature embeddings sensitive to vocal quality and robust across different corpora. A contrastive loss combined with a classification loss is used to train the model jointly, and data-warping techniques are employed to improve the robustness of embeddings. Empirical results demonstrate that the proposed method achieves high in-corpus and cross-corpus classification accuracy and generates good embeddings sensitive to voice quality and robust across different corpora. The second thrust introduces using the intra-class correlation coefficient (ICC) to evaluate the repeatability of embeddings. A novel regularizer, the ICC regularizer, is proposed to regularize deep neural networks to produce embeddings with higher repeatability. This ICC regularizer is implemented and applied to three speech applications: a clinical application, speaker verification, and voice style conversion. The experimental results reveal that the ICC regularizer improves the repeatability of learned embeddings compared to the contrastive loss, leading to enhanced performance in downstream tasks.
ContributorsZhang, Jianwei (Author) / Jayasuriya, Suren (Thesis advisor) / Berisha, Visar (Thesis advisor) / Liss, Julie (Committee member) / Spanias, Andreas (Committee member) / Arizona State University (Publisher)
Created2023