Physical Sciences and Mathematics Commons^™

The International Conference On Intelligent Biology And Medicine (Icibm) 2018: Bioinformatics Towards Translational Applications, Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhuan Ruan, Degui Zhi

Publications and Research

The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks, which covered a wild range of aspects of bioinformatics, medical informatics, systems biology and intelligent computing. Here, we summarize nine research articles selected for publishing in BMC Bioinformatics.

Open Source Foundations For Spatial Decision Support Systems, Jochen Albrecht

Publications and Research

Spatial Decision Support Systems (SDSS) were a hot topic in the 1990s, when researchers tried to imbue GIS with additional decision support features. Successful practical developments such as HAZUS or CommunityViz have since been built, based on commercial desktop software and without much heed for theory other than what underlies their process models. Others, like UrbanSim, have been completely overhauled twice but without much external scrutiny. Both the practical and the theoretical foundations of decision support systems have developed considerably over the past 20 years. This article presents an overview of these developments and then looks at what corresponding tools …

Historical Effects Of Electronic Interfaces, G James Mitchell

Publications and Research

Electronic interfaces are a primary tool for most professional and personal communication currently happening. Electronics, like the human mind, are limited by the understanding of executing will, or commands. This can be characterized as “interface limitations” of digital technology. Identifying this bottleneck in technological development has been critical in historical changes to both hardware and software technology. Recent medical research examines a novel user interface to reduce task load. I hypothesize, interface developments that take cues from nonverbal human communication enhance and sustain the significance of those technologies in society. By examining pivotal moments of historical technology we can identify …

A Dexterous, Glove-Based Teleoperable Low-Power Soft Robotic Arm For Delicate Deep-Sea Biological Exploration, Brennan T. Phillips, Kaitlyn P. Becker, Shunichi Kurumaya, Kevin C. Galloway, Griffin Whittredge, Daniel M. Vogt, Clark B. Teeple, Michelle H. Rosen, Vincent A. Pieribone, David F. Gruber, Robert J. Wood

Publications and Research

Modern marine biologists seeking to study or interact with deep-sea organisms are confronted with few options beyond industrial robotic arms, claws, and suction samplers. This limits biological interactions to a subset of “rugged” and mostly immotile fauna. As the deep sea is one of the most biologically diverse and least studied ecosystems on the planet, there is much room for innovation in facilitating delicate interactions with a multitude of organisms. The biodiversity and physiology of shallow marine systems, such as coral reefs, are common study targets due to the easier nature of access; SCUBA diving allows for in situ delicate …

A Tool For Optimizing Java 8 Stream Software Via Automated Refactoring, Raffi T. Khatchadourian, Yiming Tang, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

Streaming APIs are pervasive in mainstream Object-Oriented languages. For example, the Java 8 Stream API allows for functional-like, MapReduce-style operations in processing both finite and infinite data structures. However, using this API efficiently involves subtle considerations like determining when it is best for stream operations to run in parallel, when running operations in parallel can be less efficient, and when it is safe to run in parallel due to possible lambda expression side-effects. In this paper, we describe the engineering aspects of an open source automated refactoring tool called Optimize Streams that assists developers in writing optimal stream software in …

An Application Of Game Theory In Distributed Collaborative Decision Making, Angran Xiao

Publications and Research

In a distributed product realization environment, new paradigms and accompanying software systems are necessary to support the collaborative work of geographically dispersed engineering teams from different disciplines who have different knowledge, experience, tools and resources. To verify the concept of collaboration by separation, we propose a generic information communication medium to enable knowledge representation and exchange between engineering teams, a digital interface. Across digital interfaces, each engineering team maintains its own perspective towards the product realization problem, and each controls a subset of design variables and seeks to maximize its own payoff function subject to individual constraints. Hence, we postulate …

Poster: Towards Safe Refactoring For Intelligent Parallelization Of Java 8 Streams, Yiming Tang, Raffi T. Khatchadourian, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

The Java 8 Stream API sets forth a promising new programming model that incorporates functional-like, MapReduce-style features into a mainstream programming language. However, using streams correctly and efficiently may involve subtle considerations. In this poster, we present our ongoing work and preliminary results towards an automated refactoring approach that assists developers in writing optimal stream code. The approach, based on ordering and typestate analysis, determines when it is safe and advantageous to convert streams to parallel and optimize a parallel streams.

Designing Smart Applications Using Ar (Augmented Reality), Kimberly A. De La Santa

Publications and Research

Augmented Reality is rapidly developing in popularity because it brings elements of the virtual world, into our real world. Augmented Reality (AR) is a variation of Virtual Reality (VR). VR technologies immerses a user inside an imaginary environment. While immersed, the user cannot see the real world around them. In contrast, AR allows the user to see the real world, with virtual objects and information intertwined. Therefore, AR supplements reality and enhances the things we see, hear, and feel. This research project will implement a Web page that gives the user the opportunity to experiment with AR.

Proactive Empirical Assessment Of New Language Feature Adoption Via Automated Refactoring: The Case Of Java 8 Default Methods, Raffi T. Khatchadourian, Hidehiko Masuhara

Publications and Research

Programming languages and platforms improve over time, sometimes resulting in new language features that offer many benefits. However, despite these benefits, developers may not always be willing to adopt them in their projects for various reasons. In this paper, we describe an empirical study where we assess the adoption of a particular new language feature. Studying how developers use (or do not use) new language features is important in programming language research and engineering because it gives designers insight into the usability of the language to create meaning programs in that language. This knowledge, in turn, can drive future innovations …

Proactive Empirical Assessment Of New Language Feature Adoption Via Automated Refactoring: The Case Of Java 8 Default Methods, Raffi T. Khatchadourian, Hidehiko Masuhara

Publications and Research

Programming languages and platforms improve over time, sometimes resulting in new language features that offer many benefits. However, despite these benefits, developers may not always be willing to adopt them in their projects for various reasons. In this paper, we describe an empirical study where we assess the adoption of a particular new language feature. Studying how developers use (or do not use) new language features is important in programming language research and engineering because it gives designers insight into the usability of the language to create meaning programs in that language. This knowledge, in turn, can drive future innovations …

Multiple Sclerosis Identification Based On Fractional Fourier Entropy And A Modified Jaya Algorithm, Shui-Hua Wang, Hong Cheng, Preetha Phillips, Yu-Dong Zhang

Publications and Research

Aim: Currently, identifying multiple sclerosis (MS) by human experts may come across the problem of “normal-appearing white matter”, which causes a low sensitivity. Methods: In this study, we presented a computer vision based approached to identify MS in an automatic way. This proposed method first extracted the fractional Fourier entropy map from a specified brain image. Afterwards, it sent the features to a multilayer perceptron trained by a proposed improved parameter-free Jaya algorithm. We used cost-sensitivity learning to handle the imbalanced data problem. Results: The 10 × 10-fold cross validation showed our method yielded a sensitivity of 97.40 ± 0.60%, …

Poster: Towards Safe Refactoring For Intelligent Parallelization Of Java 8 Streams, Yiming Tang, Raffi T. Khatchadourian, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

The Java 8 Stream API sets forth a promising new programming model that incorporates functional-like, MapReduce-style features into a mainstream programming language. However, using streams correctly and efficiently may involve subtle considerations. In this poster, we present our ongoing work and preliminary results to- wards an automated refactoring approach that assists developers in writing optimal stream code. The approach, based on ordering and typestate analysis, determines when it is safe and advantageous to convert streams to parallel and optimize a parallel streams.

Cryptosystems Using Subgroup Distortion, Indira Chatterji, Delaram Kahrobaei, Ni Yen Lu

Publications and Research

In this paper we propose cryptosystems based on subgroup distortion in hyperbolic groups. We also include concrete examples of hyperbolic groups as possible platforms.

On The Use Of Semantic-Based Aig To Automatically Generate Programming Exercises, Laura Zavala, Benito Mendoza

Publications and Research

In introductory programming courses, proficiency is typically achieved through substantial practice in the form of relatively small assignments and quizzes. Unfortunately, creating programming assignments and quizzes is both, time-consuming and error-prone. We use Automatic Item Generation (AIG) in order to address the problem of creating numerous programming exercises that can be used for assignments or quizzes in introductory programming courses. AIG is based on the use of test-item templates with embedded variables and formulas which are resolved by a computer program with actual values to generate test-items. Thus, hundreds or even thousands of test-items can be generated with a single …

Predicting The Next Us President By Simulating The Electoral College, Boyan Kostadinov

Publications and Research

We develop a simulation model for predicting the outcome of the US Presidential election based on simulating the distribution of the Electoral College. The simulation model has two parts: (a) estimating the probabilities for a given candidate to win each state and DC, based on state polls, and (b) estimating the probability that a given candidate will win at least 270 electoral votes, and thus win the White House. All simulations are coded using the high-level, open-source programming language R. One of the goals of this paper is to promote computational thinking in any STEM field by illustrating how probabilistic …

An Information Theory Approach To Hypothesis Testing In Criminological Research, Gohar A. Petrossian, Mike Maxfield

Publications and Research

Background: This research demonstrates how the Akaike information criterion (AIC) can be an alternative to null hypothesis significance testing in selecting best fitting models. It presents an example to illustrate how AIC can be used in this way.

Methods: Using data from Milwaukee, Wisconsin, we test models of place-based predictor variables on street robbery and commercial robbery. We build models to balance explanatory power and parsimony. Measures include the presence of different kinds of businesses, together with selected age groups and social disadvantage.

Results: Models including place-based measures of land use emerged as the best models among the set of …

Component Tree Analysis Of Cystovirus Φ6 Nucleocapsid Cryo-Em Single Particle Reconstructions, Lucas Oliveira, Ze Ye, Al Katz, Alexandra Alimova, Hui Wei, Gabor T. Herman, Paul Gottlieb

Publications and Research

The 3-dimensional structure of the nucleocapsid (NC) of bacteriophage φ6 is described utilizing component tree analysis, a topological and geometric image descriptor. The component trees are derived from density maps of cryo-electron microscopy single particle reconstructions. Analysis determines position and occupancy of structure elements responsible for RNA packaging and transcription. Occupancy of the hexameric nucleotide triphosphorylase (P4) and RNA polymerase (P2) are found to be essentially complete in the NC. The P8 protein lattice likely fixes P4 and P2 in place during maturation. We propose that the viral procapsid (PC) is a dynamic structural intermediate where the P4 and P2 …

The Legacy Of Multics And Secure Operating Systems Today, John Schriner

Publications and Research

This paper looks to the legacy of Multics from 1963 and its influence on computer security. It discusses kernel-based and virtualization-based containment in projects like SELinux and Qubes, respectively. The paper notes the importance of collaborative and research-driven projects like Qubes and Tor Project.

Two-Dimensional Maximal Repetitions, Amihood Amir, Gad M. Landau, Shoshana Marcus, Dina Sokol

Publications and Research

Maximal repetitions or runs in strings have a wide array of applications and thus have been extensively studied. In this paper, we extend this notion to 2-dimensions, precisely defining a maximal 2D repetition. We provide initial bounds on the number of maximal 2D repetitions that can occur in a matrix. The main contribution of this paper is the presentation of the first algorithm for locating all maximal 2D repetitions in a matrix. The algorithm is efficient and straightforward, with runtime O(n^2 log n log log n+ rho log n), where n^2 is the size of the input, and rho is …

Proceedings Of The Cuny Games Conference 4.0: The Interactive Course, Robert O. Duncan, Joe Bisz, Julie Cassidy, Kathleen Offenholley, Maura A. Smale, Carolyn Stallard, Deborah Sturm, Anders A. Wallace, Cuny Games Network

Publications and Research

Proceedings of the CUNY Games Conference, held from January 22-23, 2018, at the CUNY Graduate Center and Borough of Manhattan Community College.

Critical Play with History (Panel) - Composition & Storytelling - Health & Cognitive Sciences - Gaming Anthropology: Teaching Culture and Power Through Games and Design (Panel) - Twine & Writing Games - Easy Ideas II - STEM Games - Global Games for Change Catalog (Panel) - Comics & Active Learning - Fact Checking & Research - Computer Science & Game Design - SimGlobal: Building a Serious Roleplay Course for the Social Sciences (Panel) - Role Playing Games, Narrative, …

Design Of Cloud Based Robots Using Big Data Analytics And Neuromorphic Computing, Ashwin Satyanarayana, Janusz Kusyk, Yu-Wen Chen

Publications and Research

Understanding the brain is perhaps one of the greatest challenges facing twenty-first century science. While a traditional computer excels in precision and unbiased logic, its abilities to interact socially lags behind those of biological neural systems. Recent technologies, such as neuromorphic engineering, cloud infrastructure, and big data analytics, have emerged that can narrow the gap between traditional robots and human intelligence. Neuromorphic robotics mimicking brain functions can contribute in developing intelligent machines capable of learning and making autonomous decisions. Cloud-based robotics take advantage of remote resources for parallel computation and sharing large amounts of information while benefiting from analysis of …