Theory and Algorithms Commons^™

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

New Fast Polynomial Root-Finders, Soo Go

Dissertations, Theses, and Capstone Projects

Univariate polynomial root-finding has been studied for four millennia and very intensively in the last decades. Our {\em black box root-finder} involves no coefficients and works for a black box polynomial, defined by an oracle (that is, black box subroutine) for its evaluation. Such root-finders have various benefits, e.g., are particularly efficient where a polynomial can be evaluated fast, say, is a sum of a small number of shifted monomials (x-c)^a.

Our root-finder approximates all d complex zeros of a dth degree polynomial p(x) (aka roots of equation p(x)=0) by using Las Vegas expected number of bit-operations within a factor …

Online Visual Query System For Real-Time Large-Scale Spatio-Temporal Data Explorations With Error Bounds, Xueqi Huang

Dissertations, Theses, and Capstone Projects

Modern datasets continue to grow in size, dimensionality, and heterogeneity, creating increasing tension between the need for responsive, interactive analysis and the computational cost of accessing, aggregating, and visualizing large volumes of data. Traditional database engines and visualization tools often assume that full data retrieval is feasible or that exact computation is necessary for meaningful insight. In practice, however, analysts frequently benefit from timely, uncertainty-aware approximations than from delayed and exact results. This thesis investigates how data summarization techniques, specifically mergeable sketches can be combined with progressive, out-of-core visualization methods to support interactive exploration of datasets that exceed main memory. …

An Empirical Framework For Evaluating Semantic Preservation Using Hugging Face, Nan Jia, Anita Raja, Raffi Khatchadourian

Publications and Research

As machine learning (ML) becomes an integral part of high-autonomy systems, it is critical to ensure the trustworthiness of learning-enabled software systems (LESS). Yet, the nondeterministic and run-time-defined semantics of ML complicate traditional software refactoring. We define semantic preservation in LESS as the property that optimizations of intelligent components do not alter the system's overall functional behavior. This paper introduces an empirical framework to evaluate semantic preservation in LESS by mining model evolution data from HuggingFace. We extract commit histories, $\textit{Model Cards}$, and performance metrics from a large number of models. To establish baselines, we conducted case studies in three …

Csc36000 - Modern Distributed Computing Assignment, Saptarashmi Bandyopadhyay

Open Educational Resources

This assignment covers standard performance metrics for Distributed Systems and the basics of Multiprocessing for CSC36000 - Modern Distributed Computing at the City College of New York CUNY. It is an interactive coding assignment intended to be executed in a Python notebook.

Intuiting Interaction: Meta-Reasoning And Meta-Learning As Foundations For Intelligent User Interfaces, Jeffrey Hsu

Theses and Dissertations

This research presents MARCO—a cognitive framework for Intelligent User Interfaces that uses meta-reasoning for context-aware adaptation across diverse tasks. It integrates multiple reasoning modules coordinated by a Meta-Cognitive Unit that selects strategies based on evolving demands. Evaluations show MARCO outperforms baselines in reasoning accuracy and computational efficiency.

Machine Learning: Face Recognition, Mohammed E. Amin

Publications and Research

This project explores the cutting-edge intersection of machine learning (ML) and face recognition (FR) technology, utilizing the OpenCV library to pioneer innovative applications in real-time security and user interface enhancement. By processing live video feeds, our system encodes visual inputs and employs advanced face recognition algorithms to accurately identify individuals from a database of photos. This integration of machine learning with OpenCV not only showcases the potential for bolstering security systems but also enriches user experiences across various technological platforms. Through a meticulous examination of unique facial features and the application of sophisticated ML algorithms and neural networks, our project …

Evaluation Of Symmetric Functions And Boolean Functions Over Stochastic Input, Naifeng Liu

Dissertations, Theses, and Capstone Projects

In our daily life, we often face situations where we need to make precise judgments based on initially unknown information, while gathering all the evidence to make informed conclusions can be very costly. In this dissertation, we explore the problem of optimizing the decision-making process under uncertainty, and we focus on problems that can be found in both theoretical computer science and discrete mathematics. The primary goal is to develop approximation algorithms with guaranteed worst-case performance. These algorithms aim to minimize the expected cost of acquiring information necessary for evaluating fundamental functions, such as Boolean and symmetric functions. Furthermore, we …

Balanced Blended Space: Foundational Human–Ai Dialogues In A Symmetry-Based Mediation Framework, David Smith

Publications and Research

This working paper documents the early development of the Balanced Blended Space (BBS) framework through a series of iterative interactions between a cognitive agent (human researcher) and a computational agent (AI system) conducted in 2023. The work is motivated by the need for a universal theoretical model capable of describing the integration of physical, virtual, and conceptual spaces, particularly in response to increasing fragmentation across contemporary communication systems.

BBS is proposed as a symmetry-based mediation framework in which relationships between domains—such as physical and virtual space, cognition and computation, and multiple sensory modalities—are treated as structurally equivalent and mappable. Central …

Performance Modeling For Network Anomaly Detection And Sensor Networks, Jie Chu

Dissertations, Theses, and Capstone Projects

Computer networks have become one of the fundamental communication infrastructures of the modern world. Data collection and data analysis over computer networks is a broad area of research and is getting more and more complicated as the ever-increasing complexity of the computer networks. In this dissertation, I will conduct performance modeling work for a few network scenarios and applications. In the first part of this dissertation, I will focus on two vital perspectives of the Internet, one from network administrators and the other from network users. Network administrators are key to manage and protect a computer network. I will study …

Structural Anomaly Detection, Shoufu Luo

Dissertations, Theses, and Capstone Projects

As computer systems become more complex and powerful, the threat of sophisticated and persistent computer attacks increases dramatically. Traditional intrusion detection systems that rely on log analysis struggle to keep pace with these evolving threats, as the attacking trails are often buried in high-volume and high-velocity legitimate activities in the system. Despite tremendous progress in applying machine learning techniques to anomaly-based intrusion detection, such methods continue to suffer from a high false positive rate due to the diversity and variability of individual behavior.To address this problem, this thesis proposes a new framework for detecting structural anomalies in computer systems. The …

Combinatorics Syllabus, Tugce Ozdemir

Open Educational Resources

No abstract provided.

Artificial Intelligence And The Situational Rationality Of Diagnosis: Human Problem-Solving And The Artifacts Of Health And Medicine, Michael W. Raphael

Publications and Research

What is the problem-solving capacity of artificial intelligence (AI) for health and medicine? This paper draws out the cognitive sociological context of diagnostic problem-solving for medical sociology regarding the limits of automation for decision-based medical tasks. Specifically, it presents a practical way of evaluating the artificiality of symptoms and signs in medical encounters, with an emphasis on the visualization of the problem-solving process in doctor-patient relationships. In doing so, the paper details the logical differences underlying diagnostic task performance between man and machine problem-solving: its principle of rationality, the priorities of its means of adaptation to abstraction, and the effects …

An Analysis Of The Friendship Paradox And Derived Sampling Methods, Yitzchak Novick

Dissertations, Theses, and Capstone Projects

The friendship paradox (FP) is the famous sampling-bias phenomenon that leads to the seemingly paradoxical truth that, on average, people’s friends have more friends than they do. Among the many far-reaching research findings the FP inspired is a sampling method that samples neighbors of vertices in a graph in order to acquire random vertices that are of higher expected degree than average.

Our research examines the friendship paradox on a local level. We seek to quantify the impact of the FP on an individual vertex by defining the vertex’s “friendship index”, a measure of the extent to which the phenomenon …

On The Cryptographic Deniability Of The Signal Protocol, Nihal Vatandas

Dissertations, Theses, and Capstone Projects

Offline deniability is the ability to a posteriori deny having participated in a particular communication session. This property has been widely assumed for the Signal messaging application, yet no formal proof has appeared in the literature. In this work, we present the first formal study of the offline deniability of the Signal protocol. Our analysis shows that building a deniability proof for Signal is non-trivial and requires strong assumptions on the underlying mathematical groups where the protocol is run.

To do so, we study various implicitly authenticated key exchange protocols, including MQV, HMQV, and 3DH/X3DH, the latter being the core …

Coded Distributed Function Computation, Pedro J. Soto

Dissertations, Theses, and Capstone Projects

A ubiquitous problem in computer science research is the optimization of computation on large data sets. Such computations are usually too large to be performed on one machine and therefore the task needs to be distributed amongst a network of machines. However, a common problem within distributed computing is the mitigation of delays caused by faulty machines. This can be performed by the use of coding theory to optimize the amount of redundancy needed to handle such faults. This problem differs from classical coding theory since it is concerned with the dynamic coded computation on data rather than just statically …

The Significance Of Sonic Branding To Strategically Stimulate Consumer Behavior: Content Analysis Of Four Interviews From Jeanna Isham’S “Sound In Marketing” Podcast, Ina Beilina

Student Theses and Dissertations

Purpose:
Sonic branding is not just about composing jingles like McDonald’s “I’m Lovin’ It.” Sonic branding is an industry that strategically designs a cohesive auditory component of a brand’s corporate identity. This paper examines the psychological impact of music and sound on consumer behavior reviewing studies from the past 40 years and investigates the significance of stimulating auditory perception by infusing sound in consumer experience in the modern 2020s.

Design/methodology/approach:
Qualitative content analysis of audio media was used to test two hypotheses. Four archival oral interview recordings from Jeanna Isham’s podcast “Sound in Marketing” featuring the sonic branding experts …

Introduction To Discrete Mathematics: An Oer For Ma-471, Mathieu Sassolas

Open Educational Resources

The first objective of this book is to define and discuss the meaning of truth in mathematics. We explore logics, both propositional and first-order , and the construction of proofs, both formally and human-targeted. Using the proof tools, this book then explores some very fundamental definitions of mathematics through set theory. This theory is then put in practice in several applications. The particular (but quite widespread) case of equivalence and order relations is studied with detail. Then we introduces sequences and proofs by induction, followed by number theory. Finally, a small introduction to combinatorics is …

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 …

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 …

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 …

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 …

Modeling And Analysis Of Affiliation Networks With Subsumption, Alexey Nikolaev

Dissertations, Theses, and Capstone Projects

An affiliation (or two-mode) network is an abstraction commonly used for representing systems with group interactions. It consists of a set of nodes and a set of their groupings called affiliations. We introduce the notion of affiliation network with subsumption, in which no affiliation can be a subset of another. A network with this property can be modeled by an abstract simplicial complex whose facets are the affiliations of the network.

We introduce a new model for generating affiliation networks with and without subsumption (represented as simplicial complexes and hypergraphs, respectively). In this model, at each iteration, a constant number …

Extending Import Detection Algorithms For Concept Import From Two To Three Biomedical Terminologies, Vipina K. Keloth, James Geller, Yan Chen, Julia Xu

Publications and Research

Background: While enrichment of terminologies can be achieved in different ways, filling gaps in the IS-A hierarchy backbone of a terminology appears especially promising. To avoid difficult manual inspection, we started a research program in 2014, investigating terminology densities, where the comparison of terminologies leads to the algorithmic discovery of potentially missing concepts in a target terminology. While candidate concepts have to be approved for import by an expert, the human effort is greatly reduced by algorithmic generation of candidates. In previous studies, a single source terminology was used with one target terminology.

Methods: In this paper, we are extending …

Unclonable Secret Keys, Marios Georgiou

Dissertations, Theses, and Capstone Projects

We propose a novel concept of securing cryptographic keys which we call “Unclonable Secret Keys,” where any cryptographic object is modified so that its secret key is an unclonable quantum bit-string whereas all other parameters such as messages, public keys, ciphertexts, signatures, etc., remain classical. We study this model in the authentication and encryption setting giving a plethora of definitions and positive results as well as several applications that are impossible in a purely classical setting.

In the authentication setting, we define the notion of one-shot signatures, a fundamental element in building unclonable keys, where the signing key not only …

Set Operators, Xiaojin Ye

Dissertations, Theses, and Capstone Projects

My research is centered on set operators. These are universally applicable regardless of the internal structure (numeric or non-numeric) of each individual observed datum. In our research, we have developed the theory of set operators to fill holes and gaps in observed data and eliminate paper shred garbage, thereby changing the observed symbolic data set into one whose pattern is closer to the pattern in the underlying population from which the observed data set was sampled with perturbations.

We describe different set operators including increasing operators, decreasing operators, ex- pansive operators, contractive operators, union preserving operators, intersection preserving op- erators, …

Novel Fast Algorithms For Low Rank Matrix Approximation, John T. Svadlenka

Dissertations, Theses, and Capstone Projects

Recent advances in matrix approximation have seen an emphasis on randomization techniques in which the goal was to create a sketch of an input matrix. This sketch, a random submatrix of an input matrix, having much fewer rows or columns, still preserves its relevant features. In one of such techniques random projections approximate the range of an input matrix. Dimension reduction transforms are obtained by means of multiplication of an input matrix by one or more matrices which can be orthogonal, random, and allowing fast multiplication by a vector. The Subsampled Randomized Hadamard Transform (SRHT) is the most popular among …

Philosophical Perspectives, Jochen Albrecht

Publications and Research

This entry follows in the footsteps of Anselin’s famous 1989 NCGIA working paper entitled “What is special about spatial?” (a report that is very timely again in an age when non-spatial data scientists are ignorant of the special characteristics of spatial data), where he outlines three unrelated but fundamental characteristics of spatial data. In a similar vein, I am going to discuss some philosophical perspectives that are internally unrelated to each other and could warrant individual entries in this Body of Knowledge. The first one is the notions of space and time and how they have evolved in …