Data Science Commons^™

Fusionai, A Dna-Sequence-Based Deep Learning Protocol Reduces The False Positives Of Human Fusion Gene Prediction, Pora Kim, Hua Tan, Jiajia Liu, Himansu Kumar, Xiaobo Zhou

Faculty, Staff and Student Publications

Even though there were many tool developments of fusion gene prediction from NGS data, too many false positives are still an issue. Wise use of the genomic features around the fusion gene breakpoints will be helpful to identify reliable fusion genes efficiently. For this aim, we developed FusionAI, a deep learning pipeline predicting human fusion gene breakpoints from DNA sequence. FusionAI is freely available via https://compbio.uth.edu/FusionGDB2/FusionAI. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021b).

Use Of The Deep Learning Approach To Measure Alveolar Bone Level, Chun-Teh Lee, Tanjida Kabir, Jiman Nelson, Sally Sheng, Hsiu-Wan Meng, Thomas E Van Dyke, Muhammad F Walji, Xiaoqian Jiang, Shayan Shams

Faculty, Staff and Student Publications

AIM: The goal was to use a deep convolutional neural network to measure the radiographic alveolar bone level to aid periodontal diagnosis.

MATERIALS AND METHODS: A deep learning (DL) model was developed by integrating three segmentation networks (bone area, tooth, cemento-enamel junction) and image analysis to measure the radiographic bone level and assign radiographic bone loss (RBL) stages. The percentage of RBL was calculated to determine the stage of RBL for each tooth. A provisional periodontal diagnosis was assigned using the 2018 periodontitis classification. RBL percentage, staging, and presumptive diagnosis were compared with the measurements and diagnoses made by the …

Fusiongdb 20: Fusion Gene Annotation Updates Aided By Deep Learning, Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou

Faculty, Staff and Student Publications

A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies. FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims. In this study, we report fusion gene annotation updates aided by deep learning (FusionGDB 2.0) available at https://compbio.uth.edu/FusionGDB2/. FusionGDB 2.0 has substantial updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with 44 human …

Integrated Gradients Is A Nonlinear Generalization Of The Industry Standard Approach To Variable Attribution For Credit Risk Models, Jonathan Boardman, Md Shafiul Alam, Xiao Huang, Ying Xie

Published and Grey Literature from PhD Candidates

In modern society, epistemic uncertainty limits trust in financial relationships, necessitating transparency and accountability mechanisms for both consumers and lenders. One upshot is that credit risk assessments must be explainable to the consumer. In the United States regulatory milieu, this entails both the identification of key factors in a decision and the provision of consistent actions that would improve standing. The traditionally accepted approach to explainable credit risk modeling involves generating scores with Generalized Linear Models (GLMs) - usually logistic regression, calculating the contribution of each predictor to the total points lost from the theoretical maximum, and generating reason codes …

Fashion Compatibility Prediction Using Ensemble Learning, Nathan Utzman

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fashion is important both financially and for self-expression. There are many tasks in the fashion domain which can be addressed with artificial intelligence. The task of fashion compatibility prediction is to determine how well a set of items work together to form an outfit. Two main tasks are typically used to evaluate the performance of a fashion compatibility prediction model – Outfit Compatibility Prediction and Fill in the Blank.

In this work, a compatibility prediction model, which is based on the graph autoencoder, is evaluated. This same model is then used in a homogeneous ensemble learning approach, proposed to improve …

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 …

Emotion Integrated Music Recommendation System Using Generative Adversarial Networks, Mrinmoy Bhaumik, Patrica U. Attah, Faizan Javed

SMU Data Science Review

Music can stimulate emotions within us; hence is often called the “language of emotion.” This study explores emotion as an additional feature in generating a playlist with a deep learning model to improve the current music recommendation system. This study will sample emotions from certain subjects for each song in a sample of the data. Since the effect of music on emotion is subjective and is different person to person, this study would need a considerable number of subjects to reduce subjectivity. Due to the limited resources, a portion of the data will be labeled with emotion from subjects and …

Analyzing And Detecting Android Malware And Deepfake, Md Shohel Rana

Dissertations

Rapid advances in artificial intelligence (AI), machine learning (ML), and deep learning (DL) over the past several decades have produced a variety of technologies and tools that, among numerous cybersecurity issues, have enticed cybercriminals and hackers to design malware for the Android operating systems and/or manipulate multimedia. For example, high-quality and realistic fake videos, images, or audios have been created to spread misinformation and propaganda, foment political discord and hate, or even harass and blackmail people; these manipulated, high-quality and realistic videos became known recently as Deepfake. There has been much work done in recent years on malware analysis and …

Visualizing Features From Deep Neural Networks Trained On Alzheimer’S Disease And Few-Shot Learning Models For Alzheimer’S Disease, John Reeder

All Theses

Alzheimer’s disease is an incurable neural disease, usually affecting the elderly. The afflicted suffer from cognitive impairments that get dramatically worse at each stage. Previous research on Alzheimer’s disease analysis in terms of classification leveraged statistical models such as support vector machines. However, statistical models such as support vector machines train the from numerical data instead of medical images. Today, convolutional neural networks (CNN) are widely considered as the one which can achieve the state-of-the- art image classification performance. However, due to their black box nature, there can be reluctance amongst medical professionals for their use. On the other hand, …

Analysis Of Deep Learning Methods For Wired Ethernet Physical Layer Security Of Operational Technology, Lucas Torlay

All Theses

The cybersecurity of power systems is jeopardized by the threat of spoofing and man-in-the-middle style attacks due to a lack of physical layer device authentication techniques for operational technology (OT) communication networks. OT networks cannot support the active probing cybersecurity methods that are popular in information technology (IT) networks. Furthermore, both active and passive scanning techniques are susceptible to medium access control (MAC) address spoofing when operating at Layer 2 of the Open Systems Interconnection (OSI) model. This thesis aims to analyze the role of deep learning in passively authenticating Ethernet devices by their communication signals. This method operates at …

Multi-Modal Self-Supervised Representation Learning For Earth Observation, Pallavi Jain, Bianca Schoen Phelan, Robert J. Ross

Conference papers

Self-Supervised learning (SSL) has reduced the performance gap between supervised and unsupervised learning, due to its ability to learn invariant representations. This is a boon to the domains like Earth Observation (EO), where labelled data availability is scarce but unlabelled data is freely available. While Transfer Learning from generic RGB pre-trained models is still common-place in EO, we argue that, it is essential to have good EO domain specific pre-trained model in order to use with downstream tasks with limited labelled data. Hence, we explored the applicability of SSL with multi-modal satellite imagery for downstream tasks. For this we utilised …

Learn Biologically Meaningful Representation With Transfer Learning, Di He

Dissertations, Theses, and Capstone Projects

Machine learning has made significant contributions to bioinformatics and computational biol­ogy. In particular, supervised learning approaches have been widely used in solving problems such as bio­marker identification, drug response prediction, and so on. However, because of the limited availability of comprehensively labeled and clean data, constructing predictive models in super­ vised settings is not always desirable or possible, especially when using data­hunger, red­hot learning paradigms such as deep learning methods. Hence, there are urgent needs to develop new approaches that could leverage more readily available unlabeled data in driving successful machine learning ap­ plications in this area.

In my dissertation, …

Soarnet, Deep Learning Thermal Detection For Free Flight, Jake T. Tallman

Master's Theses

Thermals are regions of rising hot air formed on the ground through the warming of the surface by the sun. Thermals are commonly used by birds and glider pilots to extend flight duration, increase cross-country distance, and conserve energy. This kind of powerless flight using natural sources of lift is called soaring. Once a thermal is encountered, the pilot flies in circles to keep within the thermal, so gaining altitude before flying off to the next thermal and towards the destination. A single thermal can net a pilot thousands of feet of elevation gain, however estimating thermal locations is not …

Convolutional Neural Networks For Deflate Data Encoding Classification Of High Entropy File Fragments, Nehal Ameen

LSU New Orleans Theses and Dissertations

Data reconstruction is significantly improved in terms of speed and accuracy by reliable data encoding fragment classification. To date, work on this problem has been successful with file structures of low entropy that contain sparse data, such as large tables or logs. Classifying compressed, encrypted, and random data that exhibit high entropy is an inherently difficult problem that requires more advanced classification approaches. We explore the ability of convolutional neural networks and word embeddings to classify deflate data encoding of high entropy file fragments after establishing ground truth using controlled datasets. Our model is designed to either successfully classify file …

Analyzing Empirical Quality Metrics Of Deep Learning Models For Antimicrobial Resistance, Huy H. Nguyen, Sanjay Pillay, Allison Roderick, Hao Wang, John Santerre

SMU Data Science Review

Antimicrobial Resistance (AMR) is a growing concern in the medical field. Over-prescription of antibiotics as well as bacterial mutations have caused some once lifesaving drugs to become ineffective against bacteria. However, the problem of AMR might be addressed using Machine Learning (ML) thanks to increased availability of genomic data and large computing resources. The Pathosystems Resource Integration Center (PATRIC) has genomic data of various bacterial genera with sample isolates that are either resistant or susceptible to certain antibiotics. Past research has used this database to use ML algorithms to model AMR with successful results, including accuracies over 80%. To better …

Generating And Smoothing Handwriting With Long Short-Term Memory Networks, Muchigi Kimari, Edward Fry, Ikenna Nwaogu, Yumei Bennett, John Santerre

SMU Data Science Review

This project explores the different neural network methods to generate synthetic handwriting text. The goal is to offer an AI tool that generates handwriting, while maintaining an individual’s style, to people suffering with Dysgraphia. As part of this project, an application development framework is setup on GitHub, in such a way that others can continue to explore and improve the AI tool.

Profile Modeling In Hierarchical Deep Architecture By Mutual Support, Honglai Peng, Meng Han, Jing (Selena) He

Master of Science in Computer Science Theses

Despite significant advances in the field of face analysis over last decade, the current studies are still limited to specific face computation tasks using deep learning approaches. In this paper, we propose an end-to-end hierarchical deep learning structure, called Multi-Features Convolutional Neural Networks (MFCNN), which can comprehensively implement face analysis including age, gender, race and emotion. Moreover, we take the advantages of the mutual support among different facial features from individual tasks to improve the performance of our model. We also contribute one all-labeling dataset called Multiple Facial Features Computation (MFFC) based on Apparent-age-V2 dataset. Firstly, we train four different …

Assessing The Re-Identification Risk In Ecg Datasets And An Application Of Privacy Preserving Techniques In Ecg Analysis, Arin Ghazarian

Computational and Data Sciences (PhD) Dissertations

In this work, first we investigate the use of ECG signal as a biometric in human identification systems using deep learning models. We train convolutional neural network models on ECG samples from approximately 81k patients. Our models achieved an over-all accuracy of 95.69%. Further, we assess the accuracy of our ECG identification model for distinct groups of patients with particular heart conditions and combinations of such conditions. For example, we observed that the identification accuracy was the highest (99.7%) for patients with both ST changes and supraventricular tachycardia. On the other hand, we also found that the identification rate was …

Machine Learning Approaches To Dribble Hand-Off Action Classification With Sportvu Nba Player Coordinate Data, Dembe Stephanos

Electronic Theses and Dissertations

Recently, strategies of National Basketball Association teams have evolved with the skillsets of players and the emergence of advanced analytics. One of the most effective actions in dynamic offensive strategies in basketball is the dribble hand-off (DHO). This thesis proposes an architecture for a classification pipeline for detecting DHOs in an accurate and automated manner. This pipeline consists of a combination of player tracking data and event labels, a rule set to identify candidate actions, manually reviewing game recordings to label the candidates, and embedding player trajectories into hexbin cell paths before passing the completed training set to the classification …

Using Deep Learning To Automate The Diagnosis Of Skin Melanoma, Akhil Reddy Alasandagutti

Honors Theses

Machine learning and image processing techniques have been widely implemented in the field of medicine to help accurately diagnose a multitude of medical conditions. The automated diagnosis of skin melanoma is one such instance. However, a majority of the successful machine learning models that have been implemented in the past have used deep learning approaches where only raw image data has been utilized to train machine learning models, such as neural networks. While they have been quite effective at predicting the condition of these lesions, they lack key information about the images, such as clinical data, and features that medical …

Node Classification On Relational Graphs Using Deep-Rgcns, Nagasai Chandra

Master's Theses

Knowledge Graphs are fascinating concepts in machine learning as they can hold usefully structured information in the form of entities and their relations. Despite the valuable applications of such graphs, most knowledge bases remain incomplete. This missing information harms downstream applications such as information retrieval and opens a window for research in statistical relational learning tasks such as node classification and link prediction. This work proposes a deep learning framework based on existing relational convolutional (R-GCN) layers to learn on highly multi-relational data characteristic of realistic knowledge graphs for node property classification tasks. We propose a deep and improved variant, …

Multi-Stream Longitudinal Data Analysis Using Deep Learning, Sajjad Fouladvand

Theses and Dissertations--Computer Science

Longitudinal healthcare data encompasses all tasks where patients information are collected at multiple follow-up times. Analyzing this data is critical in addressing many real world problems in healthcare such as disease prediction and prevention. In this thesis, technical challenges in analyzing longitudinal administrative claims data are addressed and novel deep learning based models are proposed for multi-stream data analysis and disease prediction tasks. These algorithms and frameworks are assessed mainly on substance use disorders prediction tasks and specifically designed to tackled these disorders. Substance use disorder is a public health crisis costing the US an estimated $740 billion annually in …

Improving Space Efficiency Of Deep Neural Networks, Aliakbar Panahi

Theses and Dissertations

Language models employ a very large number of trainable parameters. Despite being highly overparameterized, these networks often achieve good out-of-sample test performance on the original task and easily fine-tune to related tasks. Recent observations involving, for example, intrinsic dimension of the objective landscape and the lottery ticket hypothesis, indicate that often training actively involves only a small fraction of the parameter space. Thus, a question remains how large a parameter space needs to be in the first place — the evidence from recent work on model compression, parameter sharing, factorized representations, and knowledge distillation increasingly shows that models can be …

Data: The Good, The Bad And The Ethical, John D. Kelleher, Filipe Cabral Pinto, Luis M. Cortesao

Articles

It is often the case with new technologies that it is very hard to predict their long-term impacts and as a result, although new technology may be beneficial in the short term, it can still cause problems in the longer term. This is what happened with oil by-products in different areas: the use of plastic as a disposable material did not take into account the hundreds of years necessary for its decomposition and its related long-term environmental damage. Data is said to be the new oil. The message to be conveyed is associated with its intrinsic value. But as in …

Segmentation Method For Face Modelling In Thermal Images, Albar Albar, Hendrick Hendrick, Rahmat Hidayat

Knowledge Engineering and Data Science

Face detection is mostly applied in RGB images. The object detection usually applied the Deep Learning method for model creation. One method face spoofing is by using a thermal camera. The famous object detection methods are Yolo, Fast Region Based Convolutional Neural Networks (RCNN), Faster RCNN, SSD, and Mask RCNN. We proposed a segmentation Mask RCNN method to create a face model from thermal images. This model was able to locate the face area in images. The dataset was established using 1600 images. The images were created from direct capturing and collecting from the online dataset. The Mask RCNN was …

Convolutional Neural Network On Tanned And Synthetic Leather Textures, Faadihilah Ahnaf Faiz, Ahmad Azhari

Knowledge Engineering and Data Science

Tanned leather is an output from complex processes called tanning. Leather tanning is an important step that used to protect the fiber or protein structure of animal’s skin. Another reason of tanning process is to prevent the animal’s skin from any defect or rot. After the tanning is complete, the leather can be applied to produce a wide variety of leather products. Thus, the leather prices usually more expensive because it takes longer time in process. Another way to get cheaper price is make non-animal leather that usually known as synthetic or imitation leather. The purpose of this paper is …

Meta-Rcnn: Meta Learning For Few-Shot Object Detection, Xiongwei Wu, Doyen Sahoo, Steven Hoi

Research Collection School Of Computing and Information Systems

Despite significant advances in deep learning based object detection in recent years, training effective detectors in a small data regime remains an open challenge. This is very important since labelling training data for object detection is often very expensive and time-consuming. In this paper, we investigate the problem of few-shot object detection, where a detector has access to only limited amounts of annotated data. Based on the meta-learning principle, we propose a new meta-learning framework for object detection named "Meta-RCNN", which learns the ability to perform few-shot detection via meta-learning. Specifically, Meta-RCNN learns an object detector in an episodic learning …

A Study Of Information Bots And Knowledge Bots, Amartya Hatua

Dissertations

In this dissertation, a study of different aspects of information bots and knowledge bots is done. The research contributes to a better understanding of the various characteristics of information bots as well as the different patterns and factors responsible for the information diffusion in a social network. This research also shows how these factors can be used to predict information diffusion for a particular topic in a social network. The second part of the research is focused on strategies for improving the knowledge base of knowledge bots, where two different approaches are studied. In the first approach, knowledge is transferred …

Machine Learning Approaches For Improving Prediction Performance Of Structure-Activity Relationship Models, Gabriel Idakwo

Dissertations

In silico bioactivity prediction studies are designed to complement in vivo and in vitro efforts to assess the activity and properties of small molecules. In silico methods such as Quantitative Structure-Activity/Property Relationship (QSAR) are used to correlate the structure of a molecule to its biological property in drug design and toxicological studies. In this body of work, I started with two in-depth reviews into the application of machine learning based approaches and feature reduction methods to QSAR, and then investigated solutions to three common challenges faced in machine learning based QSAR studies.

First, to improve the prediction accuracy of learning …

Understanding Spatial Language In Radiology: Representation Framework, Annotation, And Spatial Relation Extraction From Chest X-Ray Reports Using Deep Learning, Surabhi Datta, Yuqi Si, Laritza Rodriguez, Sonya E Shooshan, Dina Demner-Fushman, Kirk Roberts

Faculty, Staff and Student Publications

Radiology reports contain a radiologist's interpretations of images, and these images frequently describe spatial relations. Important radiographic findings are mostly described in reference to an anatomical location through spatial prepositions. Such spatial relationships are also linked to various differential diagnoses and often described through uncertainty phrases. Structured representation of this clinically significant spatial information has the potential to be used in a variety of downstream clinical informatics applications. Our focus is to extract these spatial representations from the reports. For this, we first define a representation framework based on the Spatial Role Labeling (SpRL) scheme, which we refer to as …