Teaching Computational Science (WTCS) Session 1

Time and Date: 13:15 - 14:55 on 12th June 2018

Room: M5

Chair: Angela B. Shiflet

61 Revealing Hidden Markov Models in Educational Modules and the Classroom [abstract]
Abstract: Prof. Angela Shiflet in computer science and mathematics and Prof. George Shiflet in biology are Fulbright Specialists. In January, 2015, they participated in a three-week collaborative project at University “Magna Græcia” of Catanzaro in Italy, in the Department of Medical and Surgical Sciences, hosted by Prof. Mario Cannataro. While there, the three along with Prof. Pietro Hiram Guzzi started a project to develop educational modules on high-performance-computing bioinformatics algorithms. Drs. Cannataro and Guzzi have written a book, Data Management of Protein Interaction Networks (Wiley, 2011), and regularly teach bioinformatics and HPC. Upon returning to the United States, the Drs. Shiflet applied to have undergraduates Daniel Couch and Dmitriy Kaplun be Blue Waters Interns in subsequent years, working on the project. The NSF-funded Blue Waters Project, which provides a stipend for the intern, supports “experiences involving the application of high-performance computing to problems in the sciences, engineering, or mathematics” (http://computationalscience.org/bwsip/). Each student participated in a two-week workshop at the National Center for Supercomputing Applications (NCSA) facilities on the University of Illinois Urbana-Champaign campus. In the 2016-2017 year of the project, Kaplun wrote sequential and HPC programs and performed timings to accompany a pair of educational modules, “What Are the Chances?--Hidden Markov Models” and “Viterbi Hidden Markov Models,” available at http://www.wofford.edu/ecs/. Hidden Markov Models (HMM) are used in numerous applications that involve recognition, such as image tracking in sports, speech or facial recognition, handwriting analysis, language translation, cryptanalysis, predicting protein structure, aligning multiple nucleotide sequences, and discovering locations of genes. After an introductory vignette, the first module explains the mathematics behind HMM, particularly probability, and develops a sequential HMM forward algorithm to determine the likelihood of a hidden sequence of states. After motivating the need for HPC, the module also discusses a parallel forward algorithm, its implementation, and timings with speedups, as developed by the intern. To aid students, the module contains sixteen Quick Review Questions, many with multiple parts; three exercises; and five projects. Using similar pedagogical features, the second module discusses the Viterbi algorithm to solve another type of HMM problem, decoding. Completed sequential and parallel C with OpenMP programs are available upon request by instructors. Students and faculty members in a bioinformatics course at University “Magna Græcia” of Catanzaro used the materials, which Ph.D. student Chiara Zucco assisted in incorporating and evaluating.
Angela Shiflet, George Shiflet, Dmitriy Kaplun, Chiara Zucco, Pietro Guzzi and Mario Cannataro
168 Design and Analysis of an Undergraduate Computational Engineering Degree at Federal University of Juiz de Fora [abstract]
Abstract: The undergraduate course in Computational Engineering at Federal University of Juiz de Fora, Brazil, was created in 2008 as a joint initiative of two distinct departments in the University, Computer Science, located in the Exact Science Institute, and Applied and Computational Mechanics, located in the School of Engineering. First freshmen began in 2009 and graduated in 2014. This work presents the curriculum structure of this pioneering full bachelor's degree in Computational Engineering in Brazil.
Marcelo Lobosco, Flávia de Souza Bastos, Bernardo Martins Rocha and Rodrigo Santos
166 Extended Cognition Hypothesis View on Computational Thinking in Computer Science Education [abstract]
Abstract: Computational thinking is a much-used concept in the computer science education. Here we examine the concept from the viewpoint of the extended cognition hypothesis. The analysis reveals that the extent of the concept is limited by its strong historical roots in computer science and software engineering. According to the extended cognition hypothesis, there is no meaningful distinction between human cognitive functions and the technology. This standpoint promotes a broader interpretation of the human-technology interaction. Human cognitive processes spontaneously adapt available technology enhanced skills when technology is used in cognitively relevant levels and modalities. A new concept technology synchronized thinking is presented to denote this conclusion. More diverse and practical approach is suggested for the computer science education.
Mika Letonsaari