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. …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Rationality And Efficient Verifiable Computation, Matteo Campanelli

Dissertations, Theses, and Capstone Projects

In this thesis, we study protocols for delegating computation in a model where one of the parties is rational. In our model, a delegator outsources the computation of a function f on input x to a worker, who receives a (possibly monetary) reward. Our goal is to design very efficient delegation schemes where a worker is economically incentivized to provide the correct result f(x). In this work we strive for not relying on cryptographic assumptions, in particular our results do not require the existence of one-way functions.

We provide several results within the framework of rational proofs introduced by Azar …

List, Sample, And Count, Ali Assarpour

Dissertations, Theses, and Capstone Projects

Counting plays a fundamental role in many scientific fields including chemistry, physics, mathematics, and computer science. There are two approaches for counting, the first relies on analytical tools to drive closed form expression, while the second takes advantage of the combinatorial nature of the problem to construct an algorithm whose output is the number of structures. There are many algorithmic techniques for counting, they cover the explicit approach of counting by listing to the approximate approach of counting by sampling.

This thesis looks at counting three sets of objects. First, we consider a subclass of boolean functions that are monotone. …

Gradient Estimation For Attractor Networks, Thomas Flynn

Dissertations, Theses, and Capstone Projects

It has been hypothesized that neural network models with cyclic connectivity may be more powerful than their feed-forward counterparts. This thesis investigates this hypothesis in several ways. We study the gradient estimation and optimization procedures for several variants of these networks. We show how the convergence of the gradient estimation procedures are related to the properties of the networks. Then we consider how to tune the relative rates of gradient estimation and parameter adaptation to ensure successful optimization in these models. We also derive new gradient estimators for stochastic models. First, we port the forward sensitivity analysis method to the …

Relating Justification Logic Modality And Type Theory In Curry–Howard Fashion, Konstantinos Pouliasis

Dissertations, Theses, and Capstone Projects

This dissertation is a work in the intersection of Justification Logic and Curry--Howard Isomorphism. Justification logic is an umbrella of modal logics of knowledge with explicit evidence. Justification logics have been used to tackle traditional problems in proof theory (in relation to Godel's provability) and philosophy (Gettier examples, Russel's barn paradox). The Curry--Howard Isomorphism or proofs-as-programs is an understanding of logic that places logical studies in conjunction with type theory and -- in current developments -- category theory. The point being that understanding a system as a logic, a typed calculus and, a language of a class of categories constitutes …

Approximation Algorithms For Effective Team Formation, George Rabanca

Dissertations, Theses, and Capstone Projects

This dissertation investigates the problem of creating multiple disjoint teams of maximum efficacy from a fixed set of workers. We identify three parameters which directly correlate to the team effectiveness — team expertise, team cohesion and team size — and propose efficient algorithms for optimizing each in various settings. We show that under standard assumptions the problems we explore are not optimally solvable in polynomial time, and thus we focus on developing efficient algorithms with guaranteed worst case approximation bounds. First, we investigate maximizing team expertise in a setting where each worker has different expertise for each job and each …

A Combinatorial Framework For Multiple Rna Interaction Prediction, Syed Ali Ahmed

Dissertations, Theses, and Capstone Projects

The interaction of two RNA molecules involves a complex interplay between folding and binding that warranted recent developments in RNA-RNA interaction algorithms. However, biological mechanisms in which more than two RNAs take part in an interaction also exist.

A typical algorithmic approach to such problems is to find the minimum energy structure. Often the computationally optimal solution does not represent the biologically correct structure of the interaction. In addition, different biological structures may be observed, depending on several factors. Furthermore, scoring techniques often miss critical details about dependencies within different parts of the structure, which typically leads to lower scores …

Morphogenesis And Growth Driven By Selection Of Dynamical Properties, Yuri Cantor

Dissertations, Theses, and Capstone Projects

Organisms are understood to be complex adaptive systems that evolved to thrive in hostile environments. Though widely studied, the phenomena of organism development and growth, and their relationship to organism dynamics is not well understood. Indeed, the large number of components, their interconnectivity, and complex system interactions all obscure our ability to see, describe, and understand the functioning of biological organisms.

Here we take a synthetic and computational approach to the problem, abstracting the organism as a cellular automaton. Such systems are discrete digital models of real-world environments, making them more accessible and easier to study then their physical world …

Solving Algorithmic Problems In Finitely Presented Groups Via Machine Learning, Jonathan Gryak

Dissertations, Theses, and Capstone Projects

Machine learning and pattern recognition techniques have been successfully applied to algorithmic problems in free groups. In this dissertation, we seek to extend these techniques to finitely presented non-free groups, in particular to polycyclic and metabelian groups that are of interest to non-commutative cryptography.

As a prototypical example, we utilize supervised learning methods to construct classifiers that can solve the conjugacy decision problem, i.e., determine whether or not a pair of elements from a specified group are conjugate. The accuracies of classifiers created using decision trees, random forests, and N-tuple neural network models are evaluated for several non-free groups. …