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Big Data Network Analysis of Genetic Variation and Gene Expression in Individuals with Breast Cancer
Description
The advent of big data analytics tools and frameworks has allowed for a plethora of new approaches to research and analysis, making data sets that were previously too large or complex more accessible and providing methods to collect, store, and investigate non-traditional data. These tools are starting to be applied in more creative ways, and are being used to improve upon traditional computation methods through distributed computing. Statistical analysis of expression quantitative trait loci (eQTL) data has classically been performed using the open source tool PLINK - which runs on high performance computing (HPC) systems. However, progress has been made in running the statistical analysis in the ecosystem of the big data framework Hadoop, resulting in decreased run time, reduced storage footprint, reduced job micromanagement and increased data accessibility. Now that the data can be more readily manipulated, analyzed and accessed, there are opportunities to use the modularity and power of Hadoop to further process the data. This project focuses on adding a component to the data pipeline that will perform graph analysis on the data. This will provide more insight into the relation between various genetic differences in individuals with breast cancer, and the resulting variation - if any - in gene expression. Further, the investigation will look to see if there is anything to be garnered from a perspective shift; applying tools used in classical networking contexts (such as the Internet) to genetically derived networks.
ContributorsRandall, Jacob Christopher (Author) / Buetow, Kenneth (Thesis director) / Meuth, Ryan (Committee member) / Almalih, Sara (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Behavioral economics suggests that emotions can affect an individual’s decision making. Recent research on this idea’s application on large societies hints that there may exist some correlation or maybe even some causation relationship between public sentiment—at least what can be pulled from Twitter—and the movement of the stock market. One major result of consistent research on whether or not public sentiment can predict the movement of the stock market is that public sentiment, as a feature, is becoming more and more valid as a variable for stock-market-based machine learning models. While raw values typically serve as invaluable points of data, when training a model, many choose to “engineer” new features for their models—deriving rates of change or range values to improve model accuracy.
Since it doesn’t hurt to attempt to utilize feature extracted values to improve a model (if things don’t work out, one can always use their original features), the question may arise: how could the results of feature extraction on values such as sentiment affect a model’s ability to predict the movement of the stock market? This paper attempts to shine some light on to what the answer could be by deriving TextBlob sentiment values from Twitter data, and using Granger Causality Tests and logistic and linear regression to test if there exist a correlation or causation between the stock market and features extracted from public sentiment.
Since it doesn’t hurt to attempt to utilize feature extracted values to improve a model (if things don’t work out, one can always use their original features), the question may arise: how could the results of feature extraction on values such as sentiment affect a model’s ability to predict the movement of the stock market? This paper attempts to shine some light on to what the answer could be by deriving TextBlob sentiment values from Twitter data, and using Granger Causality Tests and logistic and linear regression to test if there exist a correlation or causation between the stock market and features extracted from public sentiment.
ContributorsYu, James (Author) / Meuth, Ryan (Thesis director) / Nakamura, Mutsumi (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Machine learning is the process of training a computer with algorithms to learn from data and make informed predictions. In a world where large amounts of data are constantly collected, machine learning is an important tool to analyze this data to find patterns and learn useful information from it. Machine learning applications expand to numerous fields; however, I chose to focus on machine learning with a business perspective for this thesis, specifically e-commerce.
The e-commerce market utilizes information to target customers and drive business. More and more online services have become available, allowing consumers to make purchases and interact with an online system. For example, Amazon is one of the largest Internet-based retail companies. As people shop through this website, Amazon gathers huge amounts of data on its customers from personal information to shopping history to viewing history. After purchasing a product, the customer may leave reviews and give a rating based on their experience. Performing analytics on all of this data can provide insights into making more informed business and marketing decisions that can lead to business growth and also improve the customer experience.
For this thesis, I have trained binary classification models on a publicly available product review dataset from Amazon to predict whether a review has a positive or negative sentiment. The sentiment analysis process includes analyzing and encoding the human language, then extracting the sentiment from the resulting values. In the business world, sentiment analysis provides value by revealing insights into customer opinions and their behaviors. In this thesis, I will explain how to perform a sentiment analysis and analyze several different machine learning models. The algorithms for which I compared the results are KNN, Logistic Regression, Decision Trees, Random Forest, Naïve Bayes, Linear Support Vector Machines, and Support Vector Machines with an RBF kernel.
The e-commerce market utilizes information to target customers and drive business. More and more online services have become available, allowing consumers to make purchases and interact with an online system. For example, Amazon is one of the largest Internet-based retail companies. As people shop through this website, Amazon gathers huge amounts of data on its customers from personal information to shopping history to viewing history. After purchasing a product, the customer may leave reviews and give a rating based on their experience. Performing analytics on all of this data can provide insights into making more informed business and marketing decisions that can lead to business growth and also improve the customer experience.
For this thesis, I have trained binary classification models on a publicly available product review dataset from Amazon to predict whether a review has a positive or negative sentiment. The sentiment analysis process includes analyzing and encoding the human language, then extracting the sentiment from the resulting values. In the business world, sentiment analysis provides value by revealing insights into customer opinions and their behaviors. In this thesis, I will explain how to perform a sentiment analysis and analyze several different machine learning models. The algorithms for which I compared the results are KNN, Logistic Regression, Decision Trees, Random Forest, Naïve Bayes, Linear Support Vector Machines, and Support Vector Machines with an RBF kernel.
ContributorsMadaan, Shreya (Author) / Meuth, Ryan (Thesis director) / Nakamura, Mutsumi (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Dean, W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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