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Full-Text Articles in Physical Sciences and Mathematics

Deciphering Complex Mechanisms Of Resistance And Loss Of Potency Through Coupled Molecular Dynamics And Machine Learning, Florian Leidner, Nese Kurt Yilmaz, Celia A. Schiffer Jun 2020

Deciphering Complex Mechanisms Of Resistance And Loss Of Potency Through Coupled Molecular Dynamics And Machine Learning, Florian Leidner, Nese Kurt Yilmaz, Celia A. Schiffer

University of Massachusetts Medical School Faculty Publications

Drug resistance threatens many critical therapeutics through mutations in the drug target. The molecular mechanisms by which combinations of mutations, especially involving those distal from the active site, alter drug binding to confer resistance are poorly understood and thus difficult to counteract. A strategy coupling parallel molecular dynamics simulations and machine learning to identify conserved mechanisms underlying resistance was developed. A series of 28 HIV-1 protease variants with up to 24 varied substitutions were used as a rigorous model of this strategy. Many of the mutations were distal from the active site and the potency to darunavir varied from low ...


Emerging Technologies In Healthcare: Analysis Of Unos Data Through Machine Learning, Reyhan Merekar May 2020

Emerging Technologies In Healthcare: Analysis Of Unos Data Through Machine Learning, Reyhan Merekar

Student Theses

The healthcare industry is primed for a massive transformation in the coming decades due to emerging technologies such as Artificial Intelligence (AI) and Machine Learning. With a practical application to the UNOS (United Network of Organ Sharing) database, this Thesis seeks to investigate how Machine Learning and analytic methods may be used to predict one-year heart transplantation outcomes. This study also sought to improve on predictive performances from prior studies by analyzing both Donor and Recipient data. Models built with algorithms such as Stacking and Tree Boosting gave the highest performance, with AUC’s of 0.6810 and 0.6804 ...


Ml-Medic: A Preliminary Study Of An Interactive Visual Analysis Tool Facilitating Clinical Applications Of Machine Learning For Precision Medicine, Laura Stevens, David Kao, Jennifer Hall, Carsten Görg, Kaitlyn Abdo, Erik Linstead May 2020

Ml-Medic: A Preliminary Study Of An Interactive Visual Analysis Tool Facilitating Clinical Applications Of Machine Learning For Precision Medicine, Laura Stevens, David Kao, Jennifer Hall, Carsten Görg, Kaitlyn Abdo, Erik Linstead

Engineering Faculty Articles and Research

Accessible interactive tools that integrate machine learning methods with clinical research and reduce the programming experience required are needed to move science forward. Here, we present Machine Learning for Medical Exploration and Data-Inspired Care (ML-MEDIC), a point-and-click, interactive tool with a visual interface for facilitating machine learning and statistical analyses in clinical research. We deployed ML-MEDIC in the American Heart Association (AHA) Precision Medicine Platform to provide secure internet access and facilitate collaboration. ML-MEDIC’s efficacy for facilitating the adoption of machine learning was evaluated through two case studies in collaboration with clinical domain experts. A domain expert review was ...


Comparison Of A Collective Intelligence Tailored Messaging System On Smoking Cessation Between African American And White People Who Smoke: Quasi-Experimental Design, Jamie Faro, Catherine S. Nagawa, Jeroan J. Allison, Stephenie C. Lemon, Kathleen M. Mazor, Thomas K. Houston, Rajani S. Sadasivam Apr 2020

Comparison Of A Collective Intelligence Tailored Messaging System On Smoking Cessation Between African American And White People Who Smoke: Quasi-Experimental Design, Jamie Faro, Catherine S. Nagawa, Jeroan J. Allison, Stephenie C. Lemon, Kathleen M. Mazor, Thomas K. Houston, Rajani S. Sadasivam

Open Access Articles

BACKGROUND: The Patient Experience Recommender System for Persuasive Communication Tailoring (PERSPeCT) is a machine learning recommender system with a database of messages to motivate smoking cessation. PERSPeCT uses the collective intelligence of users (ie, preferences and feedback) and demographic and smoking profiles to select motivating messages. PERSPeCT may be more beneficial for tailoring content to minority groups influenced by complex, personally relevant factors.

OBJECTIVE: The objective of this study was to describe and evaluate the use of PERSPeCT in African American people who smoke compared with white people who smoke.

METHODS: Using a quasi-experimental design, we compared African American people ...


Machine Learning Prediction Of Glioblastoma Patient One-Year Survival, Andrew Du '20, Warren Mcgee, Jane Y. Wu Jan 2020

Machine Learning Prediction Of Glioblastoma Patient One-Year Survival, Andrew Du '20, Warren Mcgee, Jane Y. Wu

Student Publications & Research

Glioblastoma (GBM) is a grade IV astrocytoma formed primarily from cancerous astrocytes and sustained by intense angiogenesis. GBM often causes non-specific symptoms, creating difficulty for diagnosis. This study aimed to utilize machine learning techniques to provide an accurate one-year survival prognosis for GBM patients using clinical and genomic data from the Chinese Glioma Genome Atlas. Logistic regression (LR), support vector machines (SVM), random forest (RF), and ensemble models were used to identify and select predictors for GBM survival and to classify patients into those with an overall survival (OS) of less than one year and one year or greater. With ...


Model-Based Machine Learning To Identify Clinical Relevance In A High-Resolution Simulation Of Sepsis And Trauma, Zachary H. Silberman Md, Robert Chase Cockrell Phd, Gary An Md Jan 2020

Model-Based Machine Learning To Identify Clinical Relevance In A High-Resolution Simulation Of Sepsis And Trauma, Zachary H. Silberman Md, Robert Chase Cockrell Phd, Gary An Md

Larner College of Medicine Fourth Year Advanced Integration Teaching/Scholarly Projects

Introduction: Sepsis is a devastating, costly, and complicated disease. It represents the summation of varied host immune responses in a clinical and physiological diagnosis. Despite extensive research, there is no current mediator-directed therapy, nor a biomarker panel able to categorize disease severity or reliably predict outcome. Although still distant from direct clinical translation, dynamic computational and mathematical models of acute systemic inflammation and sepsis are being developed. Although computationally intensive to run and calibrate, agent-based models (ABMs) are one type of model well suited for this. New analytical methods to efficiently extract knowledge from ABMs are needed. Specifically, machine-learning techniques ...


Orbit Image Analysis Machine Learning Software Can Be Used For The Histological Quantification Of Acute Ischemic Stroke Blood Clots, Sean Fitzgerald, Shunli Wang, Daying Dai, Dennis H. Murphree Jr., Abhay Pandit, Andrew Douglas, Asim Rizvi, Ramanathan Kadirvel, Michael Gilvarry, Ray Mccarthy, Manuel Stritt, Matthew J. Gounis, Waleed Brinjikji, David F. Kallmes, Karen M. Doyle Dec 2019

Orbit Image Analysis Machine Learning Software Can Be Used For The Histological Quantification Of Acute Ischemic Stroke Blood Clots, Sean Fitzgerald, Shunli Wang, Daying Dai, Dennis H. Murphree Jr., Abhay Pandit, Andrew Douglas, Asim Rizvi, Ramanathan Kadirvel, Michael Gilvarry, Ray Mccarthy, Manuel Stritt, Matthew J. Gounis, Waleed Brinjikji, David F. Kallmes, Karen M. Doyle

Open Access Articles

Our aim was to assess the utility of a novel machine learning software (Orbit Image Analysis) in the histological quantification of acute ischemic stroke (AIS) clots. We analyzed 50 AIS blood clots retrieved using mechanical thrombectomy procedures. Following HandE staining, quantification of clot components was performed by two different methods: a pathologist using a reference standard method (Adobe Photoshop CC) and an experienced researcher using Orbit Image Analysis. Following quantification, the clots were categorized into 3 types: RBC dominant (>/=60% RBCs), Mixed and Fibrin dominant ( > /=60% Fibrin). Correlations between clot composition and Hounsfield Units density on Computed Tomography (CT) were ...


Exploring Emotion Recognition For Vr-Ebt Using Deep Learning On A Multimodal Physiological Framework, Nicholas Dass Dec 2019

Exploring Emotion Recognition For Vr-Ebt Using Deep Learning On A Multimodal Physiological Framework, Nicholas Dass

Faculty of Applied Science and Technology - Exceptional Student Work, Applied Computing Theses

Post-Traumatic Stress Disorder is a mental health condition that affects a growing number of people. A variety of PTSD treatment methods exist, however current research indicates that virtual reality exposure-based treatment has become more prominent in its use.Yet the treatment method can be costly and time consuming for clinicians and ultimately for the healthcare system. PTSD can be delivered in a more sustainable way using virtual reality. This is accomplished by using machine learning to autonomously adapt virtual reality scene changes. The use of machine learning will also support a more efficient way of inserting positive stimuli in virtual ...


A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman, William Stafford Noble Aug 2019

A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman, William Stafford Noble

Open Access Articles

Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the target cell type. Here we present annotations of 164 human cell types using 1615 data sets. To produce these annotations, we automated the label interpretation step to produce a fully automated annotation strategy. Using these annotations, we developed a measure of the importance of each genomic position called the "conservation-associated activity score." We further combined all annotations into a single, cell type-agnostic encyclopedia that catalogs all human regulatory ...


Identifying Depression In The National Health And Nutrition Examination Survey Data Using A Deep Learning Algorithm, Jihoon Oh, Kyongsik Yun, Uri Maoz, Tae-Suk Kim, Jeong-Ho Chae Jul 2019

Identifying Depression In The National Health And Nutrition Examination Survey Data Using A Deep Learning Algorithm, Jihoon Oh, Kyongsik Yun, Uri Maoz, Tae-Suk Kim, Jeong-Ho Chae

Psychology Faculty Articles and Research

Background

As depression is the leading cause of disability worldwide, large-scale surveys have been conducted to establish the occurrence and risk factors of depression. However, accurately estimating epidemiological factors leading up to depression has remained challenging. Deep-learning algorithms can be applied to assess the factors leading up to prevalence and clinical manifestations of depression.

Methods

Customized deep-neural-network and machine-learning classifiers were assessed using survey data from 19,725 participants from the NHANES database (from 1999 through 2014) and 4949 from the South Korea NHANES (K-NHANES) database in 2014.

Results

A deep-learning algorithm showed area under the receiver operating characteristic curve ...


Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre May 2019

Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre

Honors Scholar Theses

Abnormal ocular motility is a common manifestation of many underlying pathologies particularly those that are neurological. Dynamics of saccades, when the eye rapidly changes its point of fixation, have been characterized for many neurological disorders including concussions, traumatic brain injuries (TBI), and Parkinson’s disease. However, widespread saccade analysis for diagnostic and research purposes requires the recognition of certain eye movement parameters. Key information such as velocity and duration must be determined from data based on a wide set of patients’ characteristics that may range in eye shapes and iris, hair and skin pigmentation [36]. Previous work on saccade analysis ...


Eeg-Based Processing And Classification Methodologies For Autism Spectrum Disorder: A Review, Gunavaran Brihadiswaran, Dilantha Haputhanthri, Sahan Gunathilaka, Dulani Meedeniya, Sampath Jayarathna Jan 2019

Eeg-Based Processing And Classification Methodologies For Autism Spectrum Disorder: A Review, Gunavaran Brihadiswaran, Dilantha Haputhanthri, Sahan Gunathilaka, Dulani Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

Autism Spectrum Disorder is a lifelong neurodevelopmental condition which affects social interaction, communication and behaviour of an individual. The symptoms are diverse with different levels of severity. Recent studies have revealed that early intervention is highly effective for improving the condition. However, current ASD diagnostic criteria are subjective which makes early diagnosis challenging, due to the unavailability of well-defined medical tests to diagnose ASD. Over the years, several objective measures utilizing abnormalities found in EEG signals and statistical analysis have been proposed. Machine learning based approaches provide more flexibility and have produced better results in ASD classification. This paper presents ...


Electroencephalogram (Eeg) For Delineating Objective Measure Of Autism Spectrum Disorder, Sampath Jayarathna, Yasith Jayawardana, Mark Jaime, Sashi Thapaliya Jan 2019

Electroencephalogram (Eeg) For Delineating Objective Measure Of Autism Spectrum Disorder, Sampath Jayarathna, Yasith Jayawardana, Mark Jaime, Sashi Thapaliya

Computer Science Faculty Publications

Autism spectrum disorder (ASD) is a developmental disorder that often impairs a child's normal development of the brain. According to CDC, it is estimated that 1 in 6 children in the US suffer from development disorders, and 1 in 68 children in the US suffer from ASD. This condition has a negative impact on a person's ability to hear, socialize, and communicate. Subjective measures often take more time, resources, and have false positives or false negatives. There is a need for efficient objective measures that can help in diagnosing this disease early as possible with less effort. EEG ...


Data Patterns Discovery Using Unsupervised Learning, Rachel A. Lewis Jan 2019

Data Patterns Discovery Using Unsupervised Learning, Rachel A. Lewis

Electronic Theses and Dissertations

Self-care activities classification poses significant challenges in identifying children’s unique functional abilities and needs within the exceptional children healthcare system. The accuracy of diagnosing a child's self-care problem, such as toileting or dressing, is highly influenced by an occupational therapists’ experience and time constraints. Thus, there is a need for objective means to detect and predict in advance the self-care problems of children with physical and motor disabilities. We use clustering to discover interesting information from self-care problems, perform automatic classification of binary data, and discover outliers. The advantages are twofold: the advancement of knowledge on identifying self-care ...


Doppler Radar-Based Non-Contact Health Monitoring For Obstructive Sleep Apnea Diagnosis: A Comprehensive Review, Vinh Phuc Tran, Adel Ali Al-Jumaily, Syed Mohammed Shamsul Islam Jan 2019

Doppler Radar-Based Non-Contact Health Monitoring For Obstructive Sleep Apnea Diagnosis: A Comprehensive Review, Vinh Phuc Tran, Adel Ali Al-Jumaily, Syed Mohammed Shamsul Islam

ECU Publications Post 2013

Today’s rapid growth of elderly populations and aging problems coupled with the prevalence of obstructive sleep apnea (OSA) and other health related issues have affected many aspects of society. This has led to high demands for a more robust healthcare monitoring, diagnosing and treatments facilities. In particular to Sleep Medicine, sleep has a key role to play in both physical and mental health. The quality and duration of sleep have a direct and significant impact on people’s learning, memory, metabolism, weight, safety, mood, cardio-vascular health, diseases, and immune system function. The gold-standard for OSA diagnosis is the overnight ...


Cleaver: Classification Of Everyday Activities Via Ensemble Recognizers, Samantha Hsu Dec 2018

Cleaver: Classification Of Everyday Activities Via Ensemble Recognizers, Samantha Hsu

Master's Theses and Project Reports

Physical activity can have immediate and long-term benefits on health and reduce the risk for chronic diseases. Valid measures of physical activity are needed in order to improve our understanding of the exact relationship between physical activity and health. Activity monitors have become a standard for measuring physical activity; accelerometers in particular are widely used in research and consumer products because they are objective, inexpensive, and practical. Previous studies have experimented with different monitor placements and classification methods. However, the majority of these methods were developed using data collected in controlled, laboratory-based settings, which is not reliably representative of real ...


Assessing The Readability Of Medical Documents: A Ranking Approach, Jiaping Zheng, Hong Yu Mar 2018

Assessing The Readability Of Medical Documents: A Ranking Approach, Jiaping Zheng, Hong Yu

Open Access Articles

BACKGROUND: The use of electronic health record (EHR) systems with patient engagement capabilities, including viewing, downloading, and transmitting health information, has recently grown tremendously. However, using these resources to engage patients in managing their own health remains challenging due to the complex and technical nature of the EHR narratives.

OBJECTIVE: Our objective was to develop a machine learning-based system to assess readability levels of complex documents such as EHR notes.

METHODS: We collected difficulty ratings of EHR notes and Wikipedia articles using crowdsourcing from 90 readers. We built a supervised model to assess readability based on relative orders of text ...


Motion-Induced Artifact Mitigation And Image Enhancement Strategies For Four-Dimensional Fan-Beam And Cone-Beam Computed Tomography, Matthew J. Riblett Jan 2018

Motion-Induced Artifact Mitigation And Image Enhancement Strategies For Four-Dimensional Fan-Beam And Cone-Beam Computed Tomography, Matthew J. Riblett

Theses and Dissertations

Four dimensional imaging has become part of the standard of care for diagnosing and treating non-small cell lung cancer. In radiotherapy applications 4D fan-beam computed tomography (4D-CT) and 4D cone-beam computed tomography (4D-CBCT) are two advanced imaging modalities that afford clinical practitioners knowledge of the underlying kinematics and structural dynamics of diseased tissues and provide insight into the effects of regular organ motion and the nature of tissue deformation over time. While these imaging techniques can facilitate the use of more targeted radiotherapies, issues surrounding image quality and accuracy currently limit the utility of these images clinically.

The purpose of ...


Speech Processing Approach For Diagnosing Dementia In An Early Stage, Roozbeh Sadeghian, J. David Schaffer, Stephen A. Zahorian Aug 2017

Speech Processing Approach For Diagnosing Dementia In An Early Stage, Roozbeh Sadeghian, J. David Schaffer, Stephen A. Zahorian

Faculty Works

The clinical diagnosis of Alzheimer’s disease and other dementias is very challenging, especially in the early stages. Our hypothesis is that any disease that affects particular brain regions involved in speech production and processing will also leave detectable finger prints in the speech. Computerized analysis of speech signals and computational linguistics have progressed to the point where an automatic speech analysis system is a promising approach for a low-cost non-invasive diagnostic tool for early detection of Alzheimer’s disease.

We present empirical evidence that strong discrimination between subjects with a diagnosis of probable Alzheimer’s versus matched normal controls ...


Cancer Diagnosis Using Libs And Machine Learning Tools: Progress And Challenges, Noureddine Melikechi, Rosalba Gaudiuso, Ebo Ewusi-Annan May 2017

Cancer Diagnosis Using Libs And Machine Learning Tools: Progress And Challenges, Noureddine Melikechi, Rosalba Gaudiuso, Ebo Ewusi-Annan

UMass Center for Clinical and Translational Science Research Retreat

Despite numerous research and development efforts that provide important tools to fight cancer, this disease still poses great challenges to diagnosis and treatment, and it remains one of the leading causes of death worldwide. Early diagnosis is crucial to increase the survival rate and quality of life of cancer patients. Thus, developing non-invasive screening methods would represent a key step towards point-of-care large scale screening and prevention of asymptomatic tumors such as Epithelian Ovarian Cancer (EOC) and others. Our group has developed two experimental strategies to pursue early cancer diagnosis through Laser-Induced Breakdown Spectroscopy (LIBS), a versatile atomic spectroscopy technique ...


Identification Of Prognostic Genes And Gene Sets For Early-Stage Non-Small Cell Lung Cancer Using Bi-Level Selection Methods, Suyan Tian, Chi Wang, Howard H. Chang, Jianguo Sun Apr 2017

Identification Of Prognostic Genes And Gene Sets For Early-Stage Non-Small Cell Lung Cancer Using Bi-Level Selection Methods, Suyan Tian, Chi Wang, Howard H. Chang, Jianguo Sun

Biostatistics Faculty Publications

In contrast to feature selection and gene set analysis, bi-level selection is a process of selecting not only important gene sets but also important genes within those gene sets. Depending on the order of selections, a bi-level selection method can be classified into three categories – forward selection, which first selects relevant gene sets followed by the selection of relevant individual genes; backward selection which takes the reversed order; and simultaneous selection, which performs the two tasks simultaneously usually with the aids of a penalized regression model. To test the existence of subtype-specific prognostic genes for non-small cell lung cancer (NSCLC ...


Predicting Malignant Nodules From Screening Ct Scans, Samuel Hawkins, Hua Wang, Ying Liu, Alberto Garcia, Olya Stringfield, Henry Krewer, Qiang Li, Dmitry Cherezov, Matthew Schabath, Lawrence O. Hall, Robert J. Gillies Dec 2016

Predicting Malignant Nodules From Screening Ct Scans, Samuel Hawkins, Hua Wang, Ying Liu, Alberto Garcia, Olya Stringfield, Henry Krewer, Qiang Li, Dmitry Cherezov, Matthew Schabath, Lawrence O. Hall, Robert J. Gillies

Computer Science and Engineering Faculty Publications

Objectives

The aim of this study was to determine whether quantitative analyses (“radiomics”) of low-dose computed tomography lung cancer screening images at baseline can predict subsequent emergence of cancer.

Methods

Public data from the National Lung Screening Trial (ACRIN 6684) were assembled into two cohorts of 104 and 92 patients with screen-detected lung cancer and then matched with cohorts of 208 and 196 screening subjects with benign pulmonary nodules. Image features were extracted from each nodule and used to predict the subsequent emergence of cancer.

Results

The best models used 23 stable features in a random forests classifier and could ...


Multimodal Learning And Intelligent Prediction Of Symptom Development In Individual Parkinson's Patients, Andrzej W. Przybyszewski, Mark Kon, Stanislaw Szlufik, Artur Szymanski, Piotr Habela, Dariusz M. Koziorowski Sep 2016

Multimodal Learning And Intelligent Prediction Of Symptom Development In Individual Parkinson's Patients, Andrzej W. Przybyszewski, Mark Kon, Stanislaw Szlufik, Artur Szymanski, Piotr Habela, Dariusz M. Koziorowski

Open Access Articles

We still do not know how the brain and its computations are affected by nerve cell deaths and their compensatory learning processes, as these develop in neurodegenerative diseases (ND). Compensatory learning processes are ND symptoms usually observed at a point when the disease has already affected large parts of the brain. We can register symptoms of ND such as motor and/or mental disorders (dementias) and even provide symptomatic relief, though the structural effects of these are in most cases not yet understood. It is very important to obtain early diagnosis, which can provide several years in which we can ...


Eeg Interictal Spike Detection Using Artificial Neural Networks, Howard J. Carey Iii Jan 2016

Eeg Interictal Spike Detection Using Artificial Neural Networks, Howard J. Carey Iii

Theses and Dissertations

Epilepsy is a neurological disease causing seizures in its victims and affects approximately 50 million people worldwide. Successful treatment is dependent upon correct identification of the origin of the seizures within the brain. To achieve this, electroencephalograms (EEGs) are used to measure a patient’s brainwaves. This EEG data must be manually analyzed to identify interictal spikes that emanate from the afflicted region of the brain. This process can take a neurologist more than a week and a half per patient. This thesis presents a method to extract and process the interictal spikes in a patient, and use them to ...


Privacy And Accountability In Black-Box Medicine, Roger Allan Ford, W. Nicholson Price Ii Jan 2016

Privacy And Accountability In Black-Box Medicine, Roger Allan Ford, W. Nicholson Price Ii

Law Faculty Scholarship

Black-box medicine—the use of big data and sophisticated machine learning techniques for health-care applications—could be the future of personalized medicine. Black-box medicine promises to make it easier to diagnose rare diseases and conditions, identify the most promising treatments, and allocate scarce resources among different patients. But to succeed, it must overcome two separate, but related, problems: patient privacy and algorithmic accountability. Privacy is a problem because researchers need access to huge amounts of patient health information to generate useful medical predictions. And accountability is a problem because black-box algorithms must be verified by outsiders to ensure they are ...


Reverse Engineering The Human Brain: An Evolutionary Computation Approach To The Analysis Of Fmri, Nicholas Allgaier Jan 2015

Reverse Engineering The Human Brain: An Evolutionary Computation Approach To The Analysis Of Fmri, Nicholas Allgaier

Graduate College Dissertations and Theses

The field of neuroimaging has truly become data rich, and as such, novel analytical methods capable of gleaning meaningful information from large stores of imaging data are in high demand. Those methods that might also be applicable on the level of individual subjects, and thus potentially useful clinically, are of special interest. In this dissertation we introduce just such a method, called nonlinear functional mapping (NFM), and demonstrate its application in the analysis of resting state fMRI (functional Magnetic Resonance Imaging) from a 242-subject subset of the IMAGEN project, a European study of risk-taking behavior in adolescents that includes longitudinal ...


Variable Selection For Bart: An Application To Gene Regulation, Justin Bleich, Adam Kapelner, Edward I. George, Shane T. Jensen Oct 2014

Variable Selection For Bart: An Application To Gene Regulation, Justin Bleich, Adam Kapelner, Edward I. George, Shane T. Jensen

Statistics Papers

We consider the task of discovering gene regulatory networks, which are defined as sets of genes and the corresponding transcription factors which regulate their expression levels. This can be viewed as a variable selection problem, potentially with high dimensionality. Variable selection is especially challenging in high-dimensional settings, where it is difficult to detect subtle individual effects and interactions between predictors. Bayesian Additive Regression Trees [BART, Ann. Appl. Stat. 4 (2010) 266–298] provides a novel nonparametric alternative to parametric regression approaches, such as the lasso or stepwise regression, especially when the number of relevant predictors is sparse relative to the ...


Learning To Rank Figures Within A Biomedical Article, Feifan Liu, Hong Yu Mar 2014

Learning To Rank Figures Within A Biomedical Article, Feifan Liu, Hong Yu

University of Massachusetts Medical School Faculty Publications

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. This ever-increasing sheer volume has made it difficult for scientists to effectively and accurately access figures of their interest, the process of which is crucial for validating research facts and for formulating or testing novel research hypotheses. Current figure search applications can't fully meet this challenge as the "bag of figures" assumption doesn't take into account the relationship among figures. In our previous study, hundreds of biomedical researchers have annotated articles in which they serve as corresponding authors. They ranked each figure in ...


A Machine Learning Approach To Diagnosis Of Parkinson’S Disease, Sumaiya F. Hashmi Jan 2013

A Machine Learning Approach To Diagnosis Of Parkinson’S Disease, Sumaiya F. Hashmi

CMC Senior Theses

I will investigate applications of machine learning algorithms to medical data, adaptations of differences in data collection, and the use of ensemble techniques.

Focusing on the binary classification problem of Parkinson’s Disease (PD) diagnosis, I will apply machine learning algorithms to a primary dataset consisting of voice recordings from healthy and PD subjects. Specifically, I will use Artificial Neural Networks, Support Vector Machines, and an Ensemble Learning algorithm to reproduce results from [MS12] and [GM09].

Next, I will adapt a secondary regression dataset of PD recordings and combine it with the primary binary classification dataset, testing various techniques to ...


Improved Cardiovascular Risk Prediction Using Nonparametric Regression And Electronic Health Record Data, Edward Kennedy, Wyndy Wiitala, Rodney Hayward, Jeremy Sussman Dec 2012

Improved Cardiovascular Risk Prediction Using Nonparametric Regression And Electronic Health Record Data, Edward Kennedy, Wyndy Wiitala, Rodney Hayward, Jeremy Sussman

Edward H. Kennedy

Use of the electronic health record (EHR) is expected to increase rapidly in the near future, yet little research exists on whether analyzing internal EHR data using flexible, adaptive statistical methods could improve clinical risk prediction. Extensive implementation of EHR in the Veterans Health Administration provides an opportunity for exploration. Our objective was to compare the performance of various approaches for predicting risk of cerebrovascular and cardiovascular (CCV) death, using traditional risk predictors versus more comprehensive EHR data. Regression methods outperformed the Framingham risk score, even with the same predictors (AUC increased from 71% to 73% and calibration also improved ...