Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Predicting Pancreatic Cancer Using Support Vector Machine

This report presents an approach to predict pancreatic cancer using Support Vector Machine Classification algorithm. The research objective of this project it to predict pancreatic cancer on just genomic, just clinical and combination of genomic and clinical data. We have used real genomic data having 22,763 samples and 154 features per sample. We have also created Synthetic Clinical data having 400 samples and 7 features per sample in order to predict accuracy of just clinical data. To validate the hypothesis, we have combined synthetic clinical data with subset of features from real genomic data. In our results, we observed that prediction accuracy, precision, recall with just genomic data is 80.77%, 20%, 4%. Prediction accuracy, precision, recall with just synthetic clinical data is 93.33%, 95%, 30%. While prediction accuracy, precision, recall for combination of real genomic and synthetic clinical data is 90.83%, 10%, 5%. The combination of real genomic and synthetic clinical data decreased the accuracy since the genomic data is weakly correlated. Thus we conclude that the combination of genomic and clinical data does not improve pancreatic cancer prediction accuracy. A dataset with more significant genomic features might help to predict pancreatic cancer more accurately

Developing an HPV Infection Risk Prediction Model for Adult Females

According to the Centers for Disease Control and Prevention (CDC), nearly one in four people are currently infected with human papillomavirus (HPV) in the United States. Although most people with HPV never experience symptoms, there is a risk of developing different types of HPV-related cancers after infection. These cancers and other related diseases result in almost $8 billion spent annually for treatment. Currently, all boys and girls ages 11 or 12 years are recommended to receive HPV vaccination. Catch-up vaccines are recommended for males and females through the age of 21 and 26, respectively, if they did not get vaccinated previously. However, the uptake rates among young adult females remain low in the United States. This research seeks to create a risk prediction model with a focus on adult females that will assist these individuals to estimate the risk of HPV infection based on demographic, sexual behavior, and lifestyle factors. The focus of this thesis is on the impact diet and exercise have on risk of infection. A variety of predictive models were applied to the data collected to determine the best fit. These models include logistic regression, lasso regression, ridge regression, elastic net regression, and the random forest algorithm. Our results corroborate findings in other studies. Similar factors are recognized as significant such as sexual partners, age at first sexual activity, alcohol use, smoking habits, poverty level, and marital status. This study also found daily nutrition and sedentary activity has a significant role in HPV infection but was not able to show significance of daily exercise due to data constraints

Temporal Feature Selection with Symbolic Regression

Building and discovering useful features when constructing machine learning models is the central task for the machine learning practitioner. Good features are useful not only in increasing the predictive power of a model but also in illuminating the underlying drivers of a target variable. In this research we propose a novel feature learning technique in which Symbolic regression is endowed with a ``Range Terminal\u27\u27 that allows it to explore functions of the aggregate of variables over time. We test the Range Terminal on a synthetic data set and a real world data in which we predict seasonal greenness using satellite derived temperature and snow data over a portion of the Arctic. On the synthetic data set we find Symbolic regression with the Range Terminal outperforms standard Symbolic regression and Lasso regression. On the Arctic data set we find it outperforms standard Symbolic regression, fails to beat the Lasso regression, but finds useful features describing the interaction between Land Surface Temperature, Snow, and seasonal vegetative growth in the Arctic

Predicting time to graduation at a large enrollment American university

The time it takes a student to graduate with a university degree is mitigated by a variety of factors such as their background, the academic performance at university, and their integration into the social communities of the university they attend. Different universities have different populations, student services, instruction styles, and degree programs, however, they all collect institutional data. This study presents data for 160,933 students attending a large American research university. The data includes performance, enrollment, demographics, and preparation features. Discrete time hazard models for the time-to-graduation are presented in the context of Tinto's Theory of Drop Out. Additionally, a novel machine learning method: gradient boosted trees, is applied and compared to the typical maximum likelihood method. We demonstrate that enrollment factors (such as changing a major) lead to greater increases in model predictive performance of when a student graduates than performance factors (such as grades) or preparation (such as high school GPA).Comment: 28 pages, 11 figure