Data Science Commons^™

Multi-Modality Automatic Lung Tumor Segmentation Method Using Deep Learning And Radiomics, Siqiu Wang

Theses and Dissertations

Delineation of the tumor volume is the initial and fundamental step in the radiotherapy planning process. The current clinical practice of manual delineation is time-consuming and suffers from observer variability. This work seeks to develop an effective automatic framework to produce clinically usable lung tumor segmentations. First, to facilitate the development and validation of our methodology, an expansive database of planning CTs, diagnostic PETs, and manual tumor segmentations was curated, and an image registration and preprocessing pipeline was established. Then a deep learning neural network was constructed and optimized to utilize dual-modality PET and CT images for lung tumor segmentation. …

Incorporating Ontological Information In Biomedical Entity Linking Of Phrases In Clinical Text, Evan French

Theses and Dissertations

Biomedical Entity Linking (BEL) is the task of mapping spans of text within biomedical documents to normalized, unique identifiers within an ontology. Translational application of BEL on clinical notes has enormous potential for augmenting discretely captured data in electronic health records, but the existing paradigm for evaluating BEL systems developed in academia is not well aligned with real-world use cases. In this work, we demonstrate a proof of concept for incorporating ontological similarity into the training and evaluation of BEL systems to begin to rectify this misalignment. This thesis has two primary components: 1) a comprehensive literature review and 2) …

Computational Analysis Of Drug Targets And Prediction Of Protein-Compound Interactions, Sina Ghadermarzi

Theses and Dissertations

Computational prediction of compound-protein interactions generated a substantial amount of interest in the recent years owing to the importance of the knowledge of these interaction for drug discovery and drug repurposing efforts. Research suggests that the currently known drug targets constitute only a fraction of a complete set of drug targets, limiting our ability to identify suitable targets to develop new drugs or to repurpose current drugs for new diseases. These efforts are further thwarted by our limited knowledge of protein-drug (and more generally protein-compound) interactions, where only a subset of drug targets is typically known for the currently used …

Cooking Up A Data Literacy Course, Claire Nickerson Mlis

Library Faculty Publications

This asynchronous online course, Interdisciplinary Studies 815: Introduction to Data, was developed for graduate students in the information analysis and communication concentration of the Fort Hays State University master of liberal studies degree. The course is designed for professionals who need to make data-driven decisions such as educators, policy makers, and nonprofit employees. It is a survey course, so it does not go into great depth on any of the topics covered but rather provides a basic grounding for developing further data literacy skills. It exclusively uses zero-cost resources, including openly licensed content, library-licensed e-books and articles, and free online …

Scholarly Big Data Quality Assessment: A Case Study Of Document Linking And Conflation With S2orc, Jian Wu, Ryan Hiltabrand, Dominik Soós, C. Lee Giles

Computer Science Faculty Publications

Recently, the Allen Institute for Artificial Intelligence released the Semantic Scholar Open Research Corpus (S2ORC), one of the largest open-access scholarly big datasets with more than 130 million scholarly paper records. S2ORC contains a significant portion of automatically generated metadata. The metadata quality could impact downstream tasks such as citation analysis, citation prediction, and link analysis. In this project, we assess the document linking quality and estimate the document conflation rate for the S2ORC dataset. Using semi-automatically curated ground truth corpora, we estimated that the overall document linking quality is high, with 92.6% of documents correctly linking to six major …

Air Quality: Assessment Of Pollutant Levels And Chemistry In Kitchener, On Using Multisensor Pods, Wisam Mohammed

Theses and Dissertations (Comprehensive)

Air quality is a growing concern amongst governmental bodies worldwide. A large number of scientific studies accumulated over the past 25 years suggest that poor ambient air quality is attributed to adverse health effects, especially in vulnerable communities that exhibit pre-existing conditions. The United Nations Children’s Fund (UNICEF) reported around 600 000 deaths globally in children under the age of 5 as a result of acute lower respiratory infections caused by poor air quality. With the current statistics on air quality impacts, it is clear that more needs to be done. This MSc work aims to put into perspective the …

On Performance Optimization And Prediction Of Parallel Computing Frameworks In Big Data Systems, Haifa Alquwaiee

Dissertations

A wide spectrum of big data applications in science, engineering, and industry generate large datasets, which must be managed and processed in a timely and reliable manner for knowledge discovery. These tasks are now commonly executed in big data computing systems exemplified by Hadoop based on parallel processing and distributed storage and management. For example, many companies and research institutions have developed and deployed big data systems on top of NoSQL databases such as HBase and MongoDB, and parallel computing frameworks such as MapReduce and Spark, to ensure timely data analyses and efficient result delivery for decision making and business …

Private And Federated Deep Learning: System, Theory, And Applications For Social Good, Han Hu

Dissertations

During the past decade, drug abuse continues to accelerate towards becoming the most severe public health problem in the United States. The ability to detect drug­abuse risk behavior at a population scale, such as among the population of Twitter users, can help to monitor the trend of drug­abuse incidents. However, traditional methods do not effectively detect drug­abuse risk behavior in tweets, mainly due to the sparsity of such tweets and the noisy nature of tweets. In the first part of this dissertation work, the task of classifying tweets as containing drug­abuse risk behavior or not, is studied. Millions of public …

A Comparison Of K-Means And Agglomerative Clustering For Users Segmentation Based On Question Answerer Reputation In Brainly Platform, Puji Winar Cahyo, Landung Sudarmana

Elinvo (Electronics, Informatics, and Vocational Education)

Brainly is a question and answer (Q&A) site that students can use as a media for questions and answers. Students can also use Brainly to find and share educational information that helps students solve their homework problems. In Brainly, users can answer questions according to their interests. However, it could be that the interest is not necessarily following the competencies possessed. It causes many answers to the questions given not to have a high rating because the answers given are of low quality to be prioritized as the main answer. This study aims to apply the K-Means and Agglomerative Clustering …

A Novel Arabic Corpus For Text Classification Using Deep Learning And Word Embedding, Roua A. Abou Khachfeh, Islam El Kabani, Ziad Osman

BAU Journal - Science and Technology

Over the last years, Natural Language Processing (NLP) for Arabic language has obtained increasing importance due to the massive textual information available online in an unstructured text format, and its capability in facilitating and making information retrieval easier. One of the widely used NLP task is “Text Classification”. Its goal is to employ machine learning technics to automatically classify the text documents into one or more predefined categories. An important step in machine learning is to find suitable and large data for training and testing an algorithm. Moreover, Deep Learning (DL), the trending machine learning research, requires a lot of …

Stress Classification Using Deep Learning With 1d Convolutional Neural Networks, Abdulrazak Yahya Saleh, Lau Khai Xian

Knowledge Engineering and Data Science

Stress has been a major problem impacting people in various ways, and it gets serious every day. Identifying whether someone is suffering from stress is crucial before it becomes a severe illness. Artificial Intelligence (AI) interprets external data, learns from such data, and uses the learning to achieve specific goals and tasks. Deep Learning (DL) has created an impact in the field of Artificial Intelligence as it can perform tasks with high accuracy. Therefore, the primary purpose of this paper is to evaluate the performance of 1D Convolutional Neural Networks (1D CNNs) for stress classification. A Psychophysiological stress (PS) dataset …

Prediction Of Body Fat Percentage Based On Anthropometric Measurements Using Data Mining Approach, Hamsa Amro, Prof. Mohammed Awad

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

In recent years, heart disease, diabetes, and some types of cancers have been reported as some main causes of death in most countries of the world, and obesity, which is often attributed to excess body fat, is one of the most common risk factors for these diseases. To make the vast amounts of data produced by health care information systems useful to the potential, the researchers applied knowledge discovery through predictive modeling. This study used anthropometric measurements as input data to different data mining techniques to predict body fat percentage. Fisher’s Method of Scoring was used to select the most …

Application Of Competitive Intelligence For Insular Territories: Automatic Analysis Of Scientific And Technology Trends To Fight The Negative Effects Of Climate Change, Henri Dou, Pierre Fournie

International Journal of Islands Research

Islands are fragile territories because of their geographical position. As a result, climate impacts can have serious consequences, of which some are irreversible. Therefore, it is necessary to allow insular territories to benefit from the latest scientific and technological advances in combating climate effects. The current article shows how to deal with automatic analysis of scientific information on the one hand, but also its applications via patents. We will analyse the latest scientific results as well as their possible applications using patent analysis. We will also focus on experts, laboratories, and leading companies, that are active on the field. The …

Physics-Informed Machine Learning To Predict Extreme Weather Events, Rthvik Raviprakash, Jonathan Buchanan, Mahdi Bu Ali

Discovery Undergraduate Interdisciplinary Research Internship

Extreme weather events refer to unexpected, severe, or unseasonal weather events, which are dynamically related to specific large-scale atmospheric patterns. These extreme weather events have a significant impact on human society and also natural ecosystems. For example, natural disasters due to extreme weather events caused more than $90 billion global direct losses in 2015. These extreme weather events are challenging to predict due to the chaotic nature of the atmosphere and are highly correlated with the occurrence of atmospheric blocking. A key aspect for preparedness and response to extreme climate events is accurate medium-range forecasting of atmospheric blocking events.

Unlike …

A Distance-Based Clustering Framework For Categorical Time Series: A Case Study In Episodes Of Care Healthcare Delivery System, Lauren Staples

Doctor of Data Science and Analytics Dissertations

Understanding how compensation structures influence overall healthcare costs is a central issue in health economics. Episodes of Care (EoC) is a compensation structure that bundles payments for healthcare interventions that belong to a well-defined health event. Since the variation of clinical pathways can drive the cost of healthcare, this research uses sequences of medical billing codes in Perinatal Episodes of Care claims data to study the extent of that variation by equating it to the number of reproducible clusters found. This research proposes a methodological framework to detect reproducible clusters in an unsupervised problem where the true number of clusters …

“Transitioning Organisations From A Data Quagmire To Knowledge Nirvana Through The Digital Thread”, David Twohig, Barry Heavey

Level 3

Historically, organisations have managed product data in a combination of Microsoft Office, Sharepoint and Document Management Systems. In this paper, we explore how different technologies can be leveraged to create digital product profiles, and in doing so structure data to enable effective knowledge management.

Introduction To Using Python In The Digital Humanities, Elisabeth Shook

Library Faculty Publications and Presentations

The materials here are from the Python for Digital Humanities Workshop taught on December 13, 2021 for the Boise State University Digital Humanities Group. This 3-hour workshop was created to provide both a very brief introduction to the various capabilities of Python and a small lesson in using Python to pull meaningful insight out of text files.

Processing Binding Data Using An Open-Source Workflow, Errol L G Samuel, Secondra L Holmes, Damian W Young

Faculty, Staff and Students Publications

The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There …

Aspect-Based Sentiment Analysis Of Movie Reviews, Samuel Onalaja, Eric Romero, Bosang Yun

SMU Data Science Review

This study investigates a comparison of classification models used to determine aspect based separated text sentiment and predict binary sentiments of movie reviews with genre and aspect specific driving factors. To gain a broader classification analysis, five machine and deep learning algorithms were compared: Logistic Regression (LR), Naive Bayes (NB), Support Vector Machine (SVM), and Recurrent Neural Network Long-Short-Term Memory (RNN LSTM). The various movie aspects that are utilized to separate the sentences are determined through aggregating aspect words from lexicon-base, supervised and unsupervised learning. The driving factors are randomly assigned to various movie aspects and their impact tied to …

Reading Level Identification Using Natural Language Processing Techniques, William Arnost, Ellen Lull, Joseph Schueder, Joseph Engler

SMU Data Science Review

This paper investigates using the Bidirectional Encoder Representations from Transformers (BERT) algorithm and lexical-syntactic features to measure readability. Readability is important in many disciplines, for functions such as selecting passages for school children, assessing the complexity of publications, and writing documentation. Text at an appropriate reading level will help make communication clear and effective. Readability is primarily measured using well-established statistical methods. Recent advances in Natural Language Processing (NLP) have had mixed success incorporating higher-level text features in a way that consistently beats established metrics. This paper contributes a readability method using a modern transformer technique and compares the results …