Computer Sciences Commons^™

(2021 Revision) Chapter 6: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

Open Educational Resources

No abstract provided.

Appendix: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

Open Educational Resources

No abstract provided.

Unit 2 - Customizing The Ubuntu Desktop And Updating App Software, George A. Nossa

Open Educational Resources

This document demonstrates the steps to customize the Linux-Ubuntu 20.04 desktop and the steps to add a Media Player and a Video Editor to the desktop.

This is a course lab in the CIS 440 UNIX course.

Unit 4 - Installing Packages And Shared Libraries On Ubuntu 20.04, George A. Nossa, Ahmet Kok

Open Educational Resources

This document details the steps necessary for Installing Packages and Shared Libraries on the Ubuntu 20.04 Operating System. This is a course lab of the CIS 440 UNIX course and this lab runs on a virtual machine installed on the student's home computer. The creation and configuration of this virtual machine is described in the Unit 1 document previously posted.

(2021 Revision) Chapter 2: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

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No abstract provided.

(2021 Revision) Chapter 1: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

Open Educational Resources

No abstract provided.

(2021 Revision) Chapter 3: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

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No abstract provided.

(2021 Revision) Chapter 5: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

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No abstract provided.

Unit 3 - Displaying Hardware And Data Files, George A. Nossa, Ahmet Kok

Open Educational Resources

This document is a lab assignment of the CIS 440 UNIX Course. This course is mostly based on lab assignments that are performed by students using their home computers (desktops or laptops). The home computers are configured as virtual machines by installing the Oracle Virtual Box Version 6.12 The Ubuntu Desktop Operating System (version 20.04) is then installed on these virtual machines, which are then used to run the course labs.

This lab assignment titled “Unit 3 - Displaying Hardware and Data Files” was originally developed by the National Information Security and Geospatial Technologies Consortium (NISGTC)and is licensed under …

Logics Of Resource And Justification, Hirohiko Kushida

Dissertations, Theses, and Capstone Projects

It is a well-known result by G ̈odel in 1933 that the Intuitionistic Logic can be embedded into a system which is essentially equivalent to the modal logic S4. This can be considered to be an attempt to provide a provability semantics to the Intuitionistic Logic. This work had caused some problems: the exact arithmetical meaning of the Intuitionistic Logic and S4, the exact axiomatization of formal provability in formal arithmetic and the standard model of arithmetic. These days the arithmetical interpretation has been extended and generalized to epistemological interpretation for various modal logics, which resulted in various systems of …

Adversarial Training For Skill Learning In A Mobile Robot, Todd W. Flyr

Dissertations, Theses, and Capstone Projects

Machine Learning in mobile robotics is sometimes hampered by the difficulties associated with the creation of a large corpus of labeled data that most neural network based learning algorithms demand. In recent years, advances in the field of machine learning have been facilitated via the creation of large collaboratively-created labeled training datasets that researchers can use as the basis for experiments to validate and improve their candidate neural network architectures. For the field of robotics, however, tasks are so disparate and the physical devices so varied that in most cases the creation of collaborative benchmark datasets are impractical. Obtaining data …

Piecewise Linear Manifold Clustering, Artyom Diky

Dissertations, Theses, and Capstone Projects

This work studies the application of topological analysis to non-linear manifold clustering. A novel method, that exploits the data clustering structure, allows to generate a topological representation of the point dataset. An analysis of topological construction under different simulated conditions is performed to explore the capabilities and limitations of the method, and demonstrated statistically significant improvements in performance. Furthermore, we introduce a new information-theoretical validation measure for clustering, that exploits geometrical properties of clusters to estimate clustering compressibility, for evaluation of the clustering goodness-of-fit without any prior information about true class assignments. We show how the new validation measure, when …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Solving Multiple Inference In Graphical Models, Cong Chen

Dissertations, Theses, and Capstone Projects

For inference problems in graphical models, much effort has been directed at algorithms for obtaining one single optimal prediction. In practice, the data is often noisy or incomplete, which makes one single optimal solution unreliable. To address this problem, multiple Inference is proposed to find several best solutions, M-Best, where multiple hypotheses are preferred for advanced reasoning. People use oracle accuracy as an evaluation criterion expecting one of the solutions has high accuracy with the ground truth. It has been shown that it is beneficial for the top solutions to be diverse. Approaches for solving diverse multiple inference are proposed …

Novel Hybrid Resampling Algorithms For Parallel/Distributed Particle Filters, Xudong Zhang

Dissertations, Theses, and Capstone Projects

Particle filters, also known as sequential Monte Carlo (SMC) methods, use the Bayesian inference and the stochastic sampling technique to estimate the states of dynamic systems from given observations. Parallel/Distributed particle filters were introduced to improve the performance of sequential particle filters by using multiple processing units (PUs). The classical resampling algorithm used in parallel/distributed particle filters is a centralized scheme, called centralized resampling, which needs a central unit (CU) to serve as a hub for data transfers. As a result, the centralized resampling procedures produce extra communication costs, which lowers the speedup factors in parallel computing. Even though some …

Unit 1 - Virtual Machine Creation And Configuration, George A. Nossa

Open Educational Resources

The COVID pandemic has challenged us in continuing our instructional mission and provide high quality learning activities remotely. A key requirement for advanced technology courses is to duplicate the BMCC Computer Lab environment on the student's home computers.

This document provides detailed instructions for creating a "virtual machine" on the student's home computer. This document assumes the home computer is a PC desktop or laptop but this document will also work on computers running MacOS with an Intel X86 compatible chip,

Once the virtual machine is created, this document details the steps to install and configure an Ubuntu 20.04 Operating …

Teaching Machine Learning For The Physical Sciences: A Summary Of Lessons Learned And Challenges, Viviana Acquaviva

Publications and Research

This paper summarizes some challenges encountered and best practices established in several years of teaching Machine Learning for the Physical Sciences at the undergraduate and graduate level. I discuss motivations for teaching ML to physicists, desirable properties of pedagogical materials, such as accessibility, relevance, and likeness to real-world research problems, and give examples of components of teaching units.

An Adaptive Cryptosystem On A Finite Field, Awnon Bhowmik, Unnikrishnan Menon

Publications and Research

Owing to mathematical theory and computational power evolution, modern cryptosystems demand ingenious trapdoor functions as their foundation to extend the gap between an enthusiastic interceptor and sensitive information. This paper introduces an adaptive block encryption scheme. This system is based on product, exponent, and modulo operation on a finite field. At the heart of this algorithm lies an innovative and robust trapdoor function that operates in the Galois Field and is responsible for the superior speed and security offered by it. Prime number theorem plays a fundamental role in this system, to keep unwelcome adversaries at bay. This is a …

On Communication For Distributed Babai Point Computation, Maiara F. Bollauf, Vinay A. Vaishampayan, Sueli I.R. Costa

Publications and Research

We present a communication-efficient distributed protocol for computing the Babai point, an approximate nearest point for a random vector X∈Rn in a given lattice. We show that the protocol is optimal in the sense that it minimizes the sum rate when the components of X are mutually independent. We then investigate the error probability, i.e. the probability that the Babai point does not coincide with the nearest lattice point, motivated by the fact that for some cases, a distributed algorithm for finding the Babai point is sufficient for finding the nearest lattice point itself. Two different probability models for X …

Graph-Theoretic Partitioning Of Rnas And Classification Of Pseudoknots-Ii, Louis Petingi

Publications and Research

Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called blocks and determine whether each block contains a pseudoknot or not. As pseudoknots can not be contained into two different blocks, this characterization allow us to efficiently isolate smaller RNA fragments and classify them as pseudoknotted or pseudoknot-free regions, while keeping these sub-structures intact. Moreover we have extended the partitioning algorithm by classifying a pseudoknot as either recursive or non-recursive in order to continue with our research …

Decoding Clinical Biomarker Space Of Covid-19: Exploring Matrix Factorization-Based Feature Selection Methods, Farshad Saberi-Movahed, Mahyar Mohammadifard, Adel Mehrpooya, Mohammad Rezaei-Ravari, Kamal Berahmand, Mehrdad Rostami, Saeed Karami, Mohammad Najafzadeh, Davood Hajinezhad, Mina Jamshidi, Farshid Abedi, Mahtab Mohammadifard, Elnaz Farbod, Farinaz Safavi, Mohammadreza Dorvash, Shahrzad Vahedi, Mahdi Eftekhari, Farid Saberi-Movahed, Iman Tavassoly

Publications and Research

One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ characteristics are usually utilized to identify those patients who need more critical care. However, the clinical evidence shows an unmet need to determine more accurate and optimal clinical biomarkers to triage patients under a condition like the COVID-19 crisis. Here we have presented a machine learning approach to find a group of clinical indicators from the blood tests of a set of COVID-19 …

Covid-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning, Yang Liu, You Wu, Xiaoke Shen, Lei Xie

Publications and Research

The life-threatening disease COVID-19 has inspired significant efforts to discover novel therapeutic agents through repurposing of existing drugs. Although multi-targeted (polypharmacological) therapies are recognized as the most efficient approach to system diseases such as COVID-19, computational multi-targeted compound screening has been limited by the scarcity of high-quality experimental data and difficulties in extracting information from molecules. This study introduces MolGNN , a new deep learning model for molecular property prediction. MolGNN applies a graph neural network to computational learning of chemical molecule embedding. Comparing to state-of-the-art approaches heavily relying on labeled experimental data, our method achieves equivalent or superior prediction …

The “Knapsack Problem” Workbook: An Exploration Of Topics In Computer Science, Steven Cosares

Open Educational Resources

This workbook provides discussions, programming assignments, projects, and class exercises revolving around the “Knapsack Problem” (KP), which is widely a recognized model that is taught within a typical Computer Science curriculum. Throughout these discussions, we use KP to introduce or review topics found in courses covering topics in Discrete Mathematics, Mathematical Programming, Data Structures, Algorithms, Computational Complexity, etc. Because of the broad range of subjects discussed, this workbook and the accompanying spreadsheet files might be used as part of some CS capstone experience. Otherwise, we recommend that individual sections be used, as needed, for exercises relevant to a course in …

Towards Automated Software Evolution Of Data-Intensive Applications, Yiming Tang

Dissertations, Theses, and Capstone Projects

Recent years have witnessed an explosion of work on Big Data. Data-intensive applications analyze and produce large volumes of data typically terabyte and petabyte in size. Many techniques for facilitating data processing are integrated into data-intensive applications. API is a software interface that allows two applications to communicate with each other. Streaming APIs are widely used in today's Object-Oriented programming development that can support parallel processing. In this dissertation, an approach that automatically suggests stream code run in parallel or sequentially is proposed. However, using streams efficiently and properly needs many subtle considerations. The use and misuse patterns for stream …

Mechanism Design And Modeling To Analyze Complex Social Systems For Public Policy, Haripriya Chakraborty

Dissertations, Theses, and Capstone Projects

The study of complex systems is an important area of research. Many scenarios require the ability to simulate large multi-agent systems with minimal artificial assumptions. We are currently living in a world where the adoption of artificial intelligence (AI) in various areas is increasing rapidly. This, in turn, has serious consequences from a computational and policy perspective. The focus needs to be on designing systems that are not only computationally elegant and efficient but also ethical. The goal of this thesis is to examine some of the ways AI can be used to simulate complex social systems. In addition, we …

Learn Biologically Meaningful Representation With Transfer Learning, Di He

Dissertations, Theses, and Capstone Projects

Machine learning has made significant contributions to bioinformatics and computational biol­ogy. In particular, supervised learning approaches have been widely used in solving problems such as bio­marker identification, drug response prediction, and so on. However, because of the limited availability of comprehensively labeled and clean data, constructing predictive models in super­ vised settings is not always desirable or possible, especially when using data­hunger, red­hot learning paradigms such as deep learning methods. Hence, there are urgent needs to develop new approaches that could leverage more readily available unlabeled data in driving successful machine learning ap­ plications in this area.

In my dissertation, …

Metareasoning, Opportunistic Exploration, And Explanations For Autonomous Indoor Navigation, Raj Korpan

Dissertations, Theses, and Capstone Projects

Autonomous indoor navigation is an important task for mobile robots deployed without a map in real-world environments, such as museums or offices. While it travels, an autonomous robot navigator must contend with lack of prior knowledge, sensor noise, actuator error, and inquisitive people. This dissertation addresses these challenges with a cognitively-based hierarchical reasoning architecture that incorporates learning, exploration, reactivity, planning, heuristics, and explanations. Evaluation by simulation in large, complex, indoor environments shows that a robot controller can successfully navigate without a detailed map of every obstruction's location when it performs limited initial global exploration and plans in its learned spatial …

An Empirical Study Of Refactorings And Technical Debt In Machine Learning Systems, Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Rhia Singh, Ajani Stewart, Anita Raja

Publications and Research

Machine Learning (ML), including Deep Learning (DL), systems, i.e., those with ML capabilities, are pervasive in today’s data-driven society. Such systems are complex; they are comprised of ML models and many subsystems that support learning processes. As with other complex systems, ML systems are prone to classic technical debt issues, especially when such systems are long-lived, but they also exhibit debt specific to these systems. Unfortunately, there is a gap in knowledge of how ML systems evolve and are maintained. In this paper, we fill this gap by studying refactorings, i.e., source-to-source semantics-preserving program transformations, performed in real-world, open-source software, …

An Empirical Study Of Refactorings And Technical Debt In Machine Learning Systems, Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Rhia Singh, Ajani Stewart, Anita Raja

Publications and Research

Machine Learning (ML), including Deep Learning (DL), systems, i.e., those with ML capabilities, are pervasive in today’s data-driven society. Such systems are complex; they are comprised of ML models and many subsystems that support learning processes. As with other complex systems, ML systems are prone to classic technical debt issues, especially when such systems are long-lived, but they also exhibit debt specific to these systems. Unfortunately, there is a gap of knowledge in how ML systems actually evolve and are maintained. In this paper, we fill this gap by studying refactorings, i.e., source-to-source semantics-preserving program transformations, performed in real-world, open-source …

Deep Learning Predicts Chromosomal Instability From Histopathology Images, Zhuoran Xu, Akanksha Verma, Uska Naveed, Samuel F. Bakhoum, Pegah Khosravi, Olivier Elemento

Publications and Research

Chromosomal instability (CIN) is a hallmark of human cancer yet not readily testable for patients with cancer in routine clinical setting. In this study, we sought to explore whether CIN status can be predicted using ubiquitously available hematoxylin and eosin histology through a deep learning-based model. When applied to a cohort of 1,010 patients with breast cancer (Training set: n = 858, Test set: n = 152) from The Cancer Genome Atlas where 485 patients have high CIN status, our model accurately classified CIN status, achieving an area under the curve of 0.822 with 81.2% sensitivity and 68.7% specificity in …