Welcome Seminar 

Date/Time: Monday, August 26 4:10 p.m - 5:00 p.m.

Location: Barnard Hall 108

Speaker: John Paxton

Abstract: This seminar will provide new and continuing graduate students with (1) useful information, (2) an opportunity to meet other students, staff and faculty, and (3) an opportunity to ask questions.


Title: Award Seminar

Date/Time: Monday, April 22 4:10 p.m - 5:00 p.m.
Location: Barnard 108

Facilitator: John Paxton

Abstract: At the end of every academic year, we celebrate the accomplishments of members of the Gianforte School of Computing.   Join us for this year's celebration where we will reflect on our accomplishments and present awards.  Light refreshments will be served.

Title: Parameter Inference and Parameter Advising in Computational Biology

Date/Time: Monday, April 15 4:10 p.m - 5:00 p.m.
Location: Barnard 108
Speaker: John Kececioglu

Abstract: Many scenarios in computational biology involve an optimization model that is solved to find the best reconstruction of an unobserved phenomenon, such as when assembling a genome sequence, inferring an evolutionary tree, predicting the folded state of a protein or RNA molecule, or computing a multiple sequence alignment. Key to such models is the objective function being optimized, which often has many free parameters that must be tuned. Setting these parameter values is crucial, as they can radically affect the accuracy of the reconstructions output by tools that optimize such models. We discuss two forms of the problem of automatically finding good parameter settings for such models: (1) parameter inference, which finds the best default parameter setting that yields reconstructions of highest average accuracy over a collection of benchmark training examples; and (2) parameter advising, which selects a good parameter choice from a collection of possible settings to yield a reconstruction of highest estimated accuracy for a user's specific input data. We present general and efficient algorithms for parameter inference and parameter advising, and report concrete results for the context of protein multiple sequence alignment. This is joint work with Dan DeBlasio and Eagu Kim.

Title: A LeadDyno History

Date/Time: Monday, April 8 4:10p.m - 5:00 p.m.
Location: Barnard 108
Speaker:Carson Gross

Abstract: In this talk we will discuss the history of leaddyno, starting with the genesis of the idea and how the team came together, followed by a discussion of the general architecture of the system, then how intercooler.js emerged from our front end work. We will finish with some LeadDyno growth history and amusing support stories, followed by a Q&A session.

Bio: Carson Gross is a long time computer programmer and entrepreneur. He attended U.C. Berkeley for undergraduate and got his MS in Computer Science from Stanford University. He has worked for a variety of different companies, e.g. consulting firms, Bank of America, Google, Guidewire Software and LeadDyno. He has worked on many open source projects, the most significant of which are Gosu, a JVM programming langauge, and intercooler.js, a javascript front end library. He is currently the CTO of LeadDyno.

Title: Knowledge Construction in a Connected World

Date/Time: Friday, April4:10 p.m - 5:00 p.m.
Location: Barnard 108
Speaker:Heather Robinson

Abstract: I will speak about my current and future research. This includes the topics of care theory for online instructional design, open learning communities, and learning and thinking with things. I will share results from two publications and explain how this research has informed and improved my teaching. Lastly, I will briefly discuss my goal of mentoring and recruiting women and underrepresented populations to the field of computer science.

Biosketch: Heather Robinson has worked in the computer technology field for 20 years and is presently the Instructional Technology Information Specialist at Jackson Hole High School and teaches for the University of North Texas. She holds a Master’s in Information Science and a Ph.D. in Learning Technologies. Heather has presented and is published on her research on social-constructivist online learning, open learning spaces, and faculty experiences with technology adoption.  

Title: MOOSE: Multiphyiscs Object Oriented Simulation Environment Creating Extensible, Composable Algorithms and Software

Date/Time: Monday, April 1 4:10 p.m - 5:00 p.m.
Location: Barnard 108
Speaker: Andrew Slaughter

Abstract: Multiphysics, by its very nature, is best achieved through collaboration. Researchers usually have deep knowledge within a single discipline, thus attempting to tie multiple disciplines together within a single simulation requires reaching out to peers in a collaborative effort. To the contrary, researchers regularly maintain unique code bases and adhere to a variety of software development workflows making sharing code nearly impossible. The open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) is a platform designed by Idaho National Laboratory (INL) scientists for creating collaborative software, and more importantly creating cross-discipline, finite-element, multiphysics simulation tools. This is accomplished by allowing scientists to work independently within their specializations and then smoothly connect their efforts together to achieve high-fidelity, scalable, Multiphysics simulations. MOOSE has many features for enabling multiphysics collaboration including a unique object structure, execution of multiple simultaneous MOOSE-based calculations with data transfers, and a collaboratively created set of physics "modules". In addition, it includes tools for testing, visualization, and documentation. These aspects have helped define a workflow for scientific software at INL and beyond that has accelerated a multitude of multiphysics endeavors such as multiscale material science, full-core nuclear reactor simulation, and geophysical simulation. An overview of the design of MOOSE, the associated workflow, how it has accelerated collaboration, and associated examples will be presented with the goal of expanding our long list of collaborators to Montana State University.

Biosketch: Andrew began his academic studies focusing on structural engineering while studying at Michigan Technological University (B.S.) and Washington State University (M.S.). He shifted focus for a Ph.D. at Montana State University where he studied Applied Engineering Mechanics and researched snow and avalanche physics. This worked included extensive field, laboratory, and computational research and paved the way for him being awarded a National Science Foundation Postdoctoral Fellowship at Cornell University in 2011, where he focused on developing a phase-tracking snow microstructure model. In 2013, Andrew joined Idaho National Laboratory (INL) and the Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) team, adding to the wide spectrum of research expertise. Since joining INL, he has worked as a developer and has focused on simulation output, control structure, stochastic analysis, as well as the level set and shallow water physics modules. He also has contributed significantly to the MOOSE-based seismic analysis tool MASTODON and a variety of other projects including enhancing software quality practices and visualization.

Title: What We Have Learned About Using Software Engineering Practices in Research Software

Date/Time: Monday, March 25 4:10 p.m - 5:00 p.m.
Location: Barnard 108
Speaker: Jeffrey Carver

Abstract: The increase in the importance of Research Software (i.e. software developed to support research) motivates the need to identify and understand which software engineering (SE) practices are appropriate. Because of the uniqueness of the research software domain, existing SE tools and techniques developed for the business/IT community are often not efficient or effective. Appropriate SE solutions must account for the salient characteristics of the research software development environment. To identify these solutions, members of the SE community must interact with members of the research software community. This presentation will discuss the findings from a series of case studies of research software projects, an ongoing workshop series, and the results of interactions between my research group and research software projects. 

Biosketch: Jeffrey C. Carver is professor in the Department of Computer Science, University of Alabama. He received the PhD degree in computer science from the University of Maryland in 2003, under supervision of Prof. Victor Basili. His main research interests include empirical software engineering, peer code review, human factors in software engineering, software engineering for research software, human errors, software quality, and software process improvement. Prof. Carver is editor of the Practitioner's Corner column in IEEE Software, the Special Content Editor for Information and Software Technology, an Associate Editor-In-Chief for Computing in Science & Engineering, and on the editorial board for IEEE Transactions on Software Engineering, Empirical Software Engineering (Springer), and the Software Quality Journal (Springer). Contact him at carver@cs.ua.edu.

Title: Ecological Forecasting on the Cloud:  Future Habitat Succession in Yellowstone

Date/Time: Monday, March 11 4:10 p.m - 5:00 p.m.
Location: Barnard 108
Speaker: Roby Roberts

Abstract: What is cloud computing and why do I care? Using a real-world example of a monolithic ecological predictive forecasting model written in Fortran, the presentation will cover some of the strategies and benefits of utilizing cloud computing.

Biosketch: Roby Roberts is the Director of Cloud Services at the Yellowstone Ecological Research Center. He is a cloud computing professional with 30+ years experience in the information technology industry. At the Yellowstone Ecological Research Center (YERC), Roby is responsible for implementation of cloud related services.  Previously, Roby was a IaaS Cloud Engineer and Architect at Oracle America where he was responsible for the research, evaluation and engineering of IaaS cloud solutions focusing on Openstack environments. Developed automation for CI/CD workflows and processes for the creation and deployment of Openstack environments

Title: Opening Doors Through Working in the Dark - An Introduction to the ARL

Date/Time: Monday, February 25 4:10 p.m - 5:00 p.m.
Location: Barnard Hall 108
Speaker: Kendra Cook and Griffin Rowell

Abstract: This presentation provides an overview of US Government classifications and a history of classified programs.  It also introduces the Applied Research Laboratory, a new facility that will allow PIs and students at MSU to conduct classified research.  The benefits of working on classified programs at MSU will be discussed, and information on employment opportunities will be provided.

Biosketch: Kendra Cook is the Director of Special Programs at Montana State University. She has worked on classified government programs for more than 20 years.  Kendra served seven years as an Officer in the United States Air Force as an Aerospace Engineer specializing in UAVs and air-launched weapons systems. Kendra is a certified Project Management Professional (PMP) and a Certified U.S. Export Compliance Officer (CUSECO). Kendra is also proficient in Mandarin Chinese. Kendra has a B.S. in Aerospace Engineering from Boston University and M.S. degrees in both Astronautical Engineering and Computer Engineering from the Air Force Institute of Technology.

Griffin Rowell is the Deputy Director of Special Programs at Montana State University.  He served eight years as an Officer in the United States Air Force as a crew member aboard the E-3 Sentry with three combat deployments and nearly 2,000 flight hours. Griffin served as the chief of requirements E-3 Mission Systems and chief of E-3 testing at Tinker Air Force Base heading the operational testing of a $300 million modernization effort.  Griffin is also a qualified Air Force acquisitions officer.  Griffin holds a B.S.in Physics from the University of California Santa Barbara and a M.S. in Aeronautical and Astronautical Engineering from Purdue University.

Title: Free Software and Your Freedom

Date/Time: Monday, February 11 4:15 p.m - 6:15 p.m.
Location: Inspiration Hall, Norm Asbjornson Hall
Speaker: Richard Stallman

Abstract: The Free Software Movement campaigns for computer users' freedom to cooperate and control their own computing. The Free Software Movement developed the GNU operating system, typically used together with the kernel Linux, specifically to make these freedoms possible.

Biosketch: Dr. Richard Stallman launched the free software movement in 1983 and started the development of the GNU operating system (seewww.gnu.org) in 1984. GNU is free software: every- one has the freedom to copy it and redistribute it, with or without changes. The GNU/Linux system, basically the GNU operating system with Linux added, is used on tens of millions of computers today. Stallman has received the ACM Grace Hopper Award and the ACM Software and Systems Award, a MacArthur Foundation fellowship, the Electronic Frontier Foundation's Pioneer Award, and the the Takeda Award for Social/Economic Betterment, as well as several doctorates honoris causa, and has been inducted into the Internet Hall of Fame.

Title: The Development and Efficacy of Immersive Technologies in Healthcare

Date/Time: Friday, February 8 4:10 p.m - 5:00 p.m.
Location: Barnard Hall 108
Speaker: Laura Stanley

Abstract: Research demonstrates that ten percent of the population becomes addicted to opioids from exposure to narcotics in the operative setting. The abuse and addiction from these drugs have now placed the US in the center of an “opioid epidemic”. As a result, a variety of programs and interventions are being explored to treat the pain and anxiety associated with surgery and the addiction resulting from opioid use disorder while minimizing or eliminating the need for pharmaceutical intervention. One such “alternative” treatment for pain, anxiety, and addiction involves the use of immersive technologies (e.g. virtual, augmented, and mixed reality) as a primary or adjunct technique. Dr. Stanley will present her team’s on-going clinical research trials at Prisma Health involving the development and efficacy of immersive technologies to address pain and anxiety in operative and cancer treatment environments, and addiction for those suffering from opioid use disorder.  She will discuss her cyber-human systems approach to addressing mental health challenges utilizing knowledge from a variety of computing domains such as affective computing, human computer interaction, and computational psychophysiology.

Biosketch: Dr. Stanley holds a B.S. in Industrial & Systems Engineering from Virginia Tech, M.S. and Ph.D. in Engineering (Option: Industrial Engineering) from Montana State University.  She served as Program Director in the Directorate for Computer & Information Science & Engineering at the NSF.  In this capacity, she contributed to ~ $75 million in research funding decisions for Cyber-Human Systems, Cyber-Physical Systems, Smart & Connected Communities, and Smart & Autonomous Systems.  During her time at the NSF, she was appointed to serve on NSF’s Working Group on The Future of Graduate Education.  Dr. Stanley serves as a Guest Editor for IEEE Transactions on Multi-Faceted Driver-Vehicle systems and is an Associate Editor for IEEE Transactions on Human-Machine Systems and Human Factors and Ergonomics in Manufacturing & Service Industries Journal.  Dr. Stanley has authored 71 peer-reviewed publications and has assisted in garnering nearly $13M in research funding at Virginia Tech, Montana State University, and now Clemson University.  Her research interests focus primarily on human factors, human-computer interaction, and human-centered design in technology development.  She has applied those interests across a variety of domains, with the greatest emphasis on applications within the transportation and health care domains.

Title: Securing Our Most Personal Devices and Networks in the Internet of Things

Date/Time: Friday, February 1 4:10 p.m - 5:00 p.m.
Location: Barnard Hall 108
Speaker: Travis Peters

Abstract: In the Internet of Things (IoT) , everyday objects are equipped with the ability to compute and communicate. These smart things  have invaded the lives of everyday people, entering into our homes, our oces, our cars, and are even being constantly carried or worn on our bodies; they have intimate and daily access to our most personal data as well as all of the other devices that we own and encounter throughout our day. Without a doubt, the devices and networks of today are more personal than ever. It should, therefore, come as no surprise that our personal devices and data are frequent targets of ever-present threats. Securing these devices and networks, however, is challenging.

In this talk, I present my work on developing designs, techniques, and tools to harden software and systems in a way that aims to prevent  and detect  prominent threats to our most personal devices and networks. First, I present our Trusted I/O solution for protecting sensitive user data transferred between wirelessly connected (Bluetooth) devices. Specically, I will discuss our BASTION-SGX project, which shows how in-transit data can be protected from privileged threats (e.g., compromised OS) on commodity systems. I present insights into the Bluetooth architecture, Intel's Software Guard Extensions (SGX), and how a Trusted I/O solution can be engineered on commodity devices equipped with SGX. Second, I discuss how we can both improve the utility and security of microcontroller-based devices. Specically, I will discuss our Amulet project and how we successfully built a wearable health hub that can run multiple health applications, provide strong security properties, and operate on a single charge for weeks or even months at a time. I will present the mobile health scenario that Amulet addresses, dig into the software and hardware architectures of the Amulet platform, and present some of the interesting results that Amulet achieves. This talk will conclude with a discussion on some of my planned future work towards improving the state of security within personal devices and networks, as well as a glimpse into some of my ongoing work on the active detection of threats within this context.

Biosketch: Travis Peters is a doctoral candidate in computer science at Dartmouth College, working in the Mobile Health (mHealth) Security & Privacy Lab, led by Professor David Kotz. He received his B.S. in computer science and
mathematics from Western Washington University prior to his arrival at Dartmouth College. While at Dartmouth,
he has worked on two large, multi-university NSF projects, completed two internships at Intel’s Security & Privacy
Research Labs, and published in top systems and security venues such as SenSys, HASP, and MobiCom. His primary
research interests are in computer and network security and privacy, particularly as it applies to mobile and wearable
health systems.

Title: Data-oriented and Trustworthy IoT Services for a Cyber-Physical World

Date/Time: Friday, January 25 4:10 p.m - 5:00 p.m.
Location: Barnard Hall 108
Speaker: Ruozhou Yu

Abstract: The Internet-of-Things (IoT) has the potential to revolutionize our daily lives. Yet, we are facing major challenges in deploying IoT to solve real-world problems. On one hand, the huge volume of data generated by IoT devices must be transmissible and comprehensible by our existing infrastructures. On the other hand, the complexity, heterogeneity and scale of IoT-based systems have led to new security risks in our digital or even physical lives. Resolving these challenges require sophisticated computing and analytical mechanisms in data science, machine learning, cybersecurity, and/or social sciences, but the applicability of these mechanisms in IoT is largely restricted by the limited computing, networking and energy resources in many real-world IoT scenarios.

In this talk, I will focus on my efforts in addressing the above challenges in resource-constrained IoT. To solve the big data challenge, I design algorithmic solutions for cross-layer networking and computing design, providing guaranteed performance for IoT services and applications, while increasing resource utilization, reducing congestion, and improving system robustness. To solve the security challenge, I propose using the blockchain as a basic building block for establishing a secure IoT platform, and introduce how it can be extended to enable a global scale on-demand IoT marketplace. While the proposed solutions can largely address the above challenges in IoT, many of them also have applications and extensions beyond this specific context.

Biosketch: Ruozhou is a PhD candidate in the School of Computing, Informatics, and Decision System Engineering at Arizona State University. His research expertise lies at the intersection of cybersecurity, networking, and distributed systems. His current research interests include blockchain-based IoT, blockchain payment channels, IoT security, big data computing and analytics, etc. His work has been published on top-tier conferences and journals such as IEEE INFOCOM, IEEE JSAC and IEEE/ACM ToN. He has served as reviewers for top journals such as IEEE JSAC, TMC, TPDS, TWC, etc.

Title: Phylofactorization: evolution + a graph-partitioning algorithm = machine learning + human understanding of biological data

Date/Time: Monday, January 14 4:10 p.m - 5:00 p.m.
Location: Barnard Hall 108
Speaker: Alex Washburne

Abstract:  Biologists are obtaining massive datasets of hundreds of thousands of species and their abundances, traits, and other features. From microbes living in our gut to birds found in tropical rainforests, there is a universal need to make sense of which organisms are sensitive to climate change, which are associated with disease, and more. The theory of evolution defines a history of organisms in the form of a tree going back to common ancestors over 3.6 billion years ago. In this talk, I will discuss how that tree - an acyclic graph - can be used to define a graph-partitioning algorithm for interpretable dimensionality reduction of biological data. So far, this algorithm has yielded insights on the evolution of mammals over the past 65 million years, the microbes who thrive in the intestines of patients with Crohn's Disease or Inflammatory Bowel Disease, the microbes differentiating our intestinal communities over America, how mammalian viruses are more or less likely to jump from animals to people, how mammalian reservoirs are more or less likely to have pathogens capable of infecting people, and more. This algorithm connecting the theory of evolution to reduced rank regression, artificial neural networks, and virtually every tool used for data analysis is accelerating the machine learning and human understanding of biological systems.

Biosketch: Dr. Alex Washburne received undergraduate degrees in Biology and Applied Mathematics from the University of New Mexico. He received his Ph.D. from Princeton University in Quantitative and Computational Biology, where he discovered a mathematical commonality between the dynamics of microbes in humans, trees in tropical rainforests, stocks in the stock market and other entities in competitive systems. The underlying symmetry of competition was used to create statistical tests of competitive intensity which landed Dr. Washburne a job in a hedge fund. While working at a hedge fund, he did a post-doc at Duke University with Diana Nemergut who passed away within 3 months of the start date but secured funding for Alex to continue his research for two years. In this time, he conceived phylofactorization and began work on statistical models of pathogen spillover. He is now a research scientist at MSU working with Raina Plowright on Defense Advanced Research Projects Agency (DARPA) funded projects predicting and preempting the spillover of pathogens like Ebola from wildlife to people. He is the founder and head of Selva Analytics LLC, a consulting firm developing statistical tools to facilitate the accumulation of domain expertise for clients in sectors ranging from biotech and energy to finance and resource management.

 Seminars from 2018.