Local interactions drive emergent collective behavior, which pervades biological and social complex systems. These behaviors are scalable and robust, motivating biomimicry: engineering nature-inspired distributed systems. But uncovering the interactions that produce a desired behavior remains a core challenge. In this thesis, I present EvoSOPS, an evolutionary framework that searches landscapes of stochastic distributed algorithms for those that achieve a mathematically specified target behavior. These algorithms govern self-organizing particle systems (SOPS) comprising individuals with strictly local sensing and movement and no persistent memory. For aggregation, phototaxing, and separation behaviors, EvoSOPS discovers algorithms that achieve 4.2–15.3% higher fitness than those from the existing “stochastic approach to SOPS” based on mathematical theory from statistical physics. EvoSOPS is also flexibly applied to new behaviors such as object coating where the stochastic approach would require bespoke, extensive analysis. Across repeated runs, EvoSOPS explores distinct regions of genome space to produce genetically diverse solutions. Finally, I provide insights into the best-fitness genomes for object coating, demonstrating how EvoSOPS can bootstrap future theoretical investigations into SOPS algorithms for challenging new behaviors.

This thesis details a Python-based software designed to calculate the Jones polynomial, a vital mathematical tool from Knot Theory used for characterizing the topological and geometrical complexity of curves in 3-space, which is essential in understanding physical systems of filaments, including the behavior of polymers and biopolymers. The Jones polynomial serves as a topological invariant capable of distinguishing between different knot structures. This capability is fundamental to characterizing the architecture of molecular chains, such as proteins and DNA. Traditional computational methods for deriving the Jones polynomial have been limited by closure-schemes and high execu- tion costs, which can be impractical for complex structures like those that appear in real life. This software implements methods that significantly reduce calculation times, allowing for more efficient and practical applications in the study of biological poly- mers. It utilizes a divide-and-conquer approach combined with parallel computing and applies recursive Reidemeister moves to optimize the computation, transitioning from an exponential to a near-linear runtime for specific configurations. This thesis provides an overview of the software’s functions, detailed performance evaluations using protein structures as test cases, and a discussion of the implications for future research and potential algorithmic improvements.

A storage system requiring file redundancy and on-line repairability can be represented as a Steiner system, a combinatorial design with the property that every $t$-subset of its points occurs in exactly one of its blocks. Under this representation, files are the points and storage units are the blocks of the Steiner system, or vice-versa. Often, the popularities of the files of such storage systems run the gamut, with some files receiving hardly any attention, and others receiving most of it. For such systems, minimizing the difference in the collective popularity between any two storage units is nontrivial; this is the access balancing problem. With regard to the representative Steiner system, the access balancing problem in its simplest form amounts to constructing either a point or block labelling: an assignment of a set of integer labels (popularity ranks) to the Steiner system's point set or block set, respectively, requiring of the former assignment that the sums of the labelled points of any two blocks differ as little as possible and of the latter that the sums of the labels assigned to the containing blocks of any two distinct points differ as little as possible. The central aim of this dissertation is to supply point and block labellings for Steiner systems of block size greater than three, for which up to this point no attempt has been made. Four major results are given in this connection. First, motivated by the close connection between the size of the independent sets of a Steiner system and the quality of its labellings, a Steiner triple system of any admissible order is constructed with a pair of disjoint independent sets of maximum cardinality. Second, the spectrum of resolvable Bose triple systems is determined in order to label some Steiner 2-designs with block size four. Third, several kinds of independent sets are used to point-label Steiner 2-designs with block size four. Finally, optimal and close to optimal block labellings are given for an infinite class of 1-rotational resolvable Steiner 2-designs with arbitrarily large block size by exploiting their underlying group-theoretic properties.

In combinatorial mathematics, a Steiner system is a type of block design. A Steiner triple system is a special case of Steiner system where all blocks contain 3 elements and each pair of points occurs in exactly one block. Independent sets in Steiner triple systems is the topic which is discussed in this thesis. Some properties related to independent sets in Steiner triple system are provided. The distribution of sizes of maximum independent sets of Steiner triple systems of specific order is also discussed in this thesis. An algorithm for constructing a Steiner triple system with maximum independent set whose size is restricted with a lower bound is provided. An alternative way to construct a Steiner triple system using an affine plane is also presented. A modified greedy algorithm for finding a maximal independent set in a Steiner triple system and a post-optimization method for improving the results yielded by this algorithm are established.

Secure Scuttlebutt is a digital social network in which the network data is distributed among the users.<br/>This is done to secure several benefits, like offline browsing, censorship resistance, and to imitate natural social networks, but it comes with downsides, like the lack of an obvious implementation of a recommendation algorithm.<br/>This paper proposes Whuffie, an algorithm that tracks each user's reputation for having information that is interesting to a user using conditional probabilities.<br/>Some errors in the main Secure Scuttlebutt network prevent current large-scale testing of the usefulness of the algorithm, but testing on my own personal account led me to believe it a success.

A complex social system, whether artificial or natural, can possess its macroscopic properties as a collective, which may change in real time as a result of local behavioral interactions among a number of agents in it. If a reliable indicator is available to abstract the macrolevel states, decision makers could use it to take a proactive action, whenever needed, in order for the entire system to avoid unacceptable states or con-verge to desired ones. In realistic scenarios, however, there can be many challenges in learning a model of dynamic global states from interactions of agents, such as 1) high complexity of the system itself, 2) absence of holistic perception, 3) variability of group size, 4) biased observations on state space, and 5) identification of salient behavioral cues. In this dissertation, I introduce useful applications of macrostate estimation in complex multi-agent systems and explore effective deep learning frameworks to ad-dress the inherited challenges. First of all, Remote Teammate Localization (ReTLo)is developed in multi-robot teams, in which an individual robot can use its local interactions with a nearby robot as an information channel to estimate the holistic view of the group. Within the problem, I will show (a) learning a model of a modular team can generalize to all others to gain the global awareness of the team of variable sizes, and (b) active interactions are necessary to diversify training data and speed up the overall learning process. The complexity of the next focal system escalates to a colony of over 50 individual ants undergoing 18-day social stabilization since a chaotic event. I will utilize this natural platform to demonstrate, in contrast to (b), (c)monotonic samples only from “before chaos” can be sufficient to model the panicked society, and (d) the model can also be used to discover salient behaviors to precisely predict macrostates.

The chromatic number $\chi(G)$ of a graph $G=(V,E)$ is the minimum

number of colors needed to color $V(G)$ such that no adjacent vertices

receive the same color. The coloring number $\col(G)$ of a graph

$G$ is the minimum number $k$ such that there exists a linear ordering

of $V(G)$ for which each vertex has at most $k-1$ backward neighbors.

It is well known that the coloring number is an upper bound for the

chromatic number. The weak $r$-coloring number $\wcol_{r}(G)$ is

a generalization of the coloring number, and it was first introduced

by Kierstead and Yang \cite{77}. The weak $r$-coloring number $\wcol_{r}(G)$

is the minimum integer $k$ such that for some linear ordering $L$

of $V(G)$ each vertex $v$ can reach at most $k-1$ other smaller

vertices $u$ (with respect to $L$) with a path of length at most

$r$ and $u$ is the smallest vertex in the path. This dissertation proves that $\wcol_{2}(G)\le23$ for every planar graph $G$.

The exact distance-$3$ graph $G^{[\natural3]}$ of a graph $G=(V,E)$

is a graph with $V$ as its set of vertices, and $xy\in E(G^{[\natural3]})$

if and only if the distance between $x$ and $y$ in $G$ is $3$.

This dissertation improves the best known upper bound of the

chromatic number of the exact distance-$3$ graphs $G^{[\natural3]}$

of planar graphs $G$, which is $105$, to $95$. It also improves

the best known lower bound, which is $7$, to $9$.

A class of graphs is nowhere dense if for every $r\ge 1$ there exists $t\ge 1$ such that no graph in the class contains a topological minor of the complete graph $K_t$ where every edge is subdivided at most $r$ times. This dissertation gives a new characterization of nowhere dense classes using generalized notions of the domination number.

The construction of many families of combinatorial objects remains a challenging problem. A t-restriction is an array where a predicate is satisfied for every t columns; an example is a perfect hash family (PHF). The composition of a PHF and any t-restriction satisfying predicate P yields another t-restriction also satisfying P with more columns than the original t-restriction had. This thesis concerns three approaches in determining the smallest size of PHFs.



Firstly, hash families in which the associated property is satisfied at least some number lambda times are considered, called higher-index, which guarantees redundancy when constructing t-restrictions. Some direct and optimal constructions of hash families of higher index are given. A new recursive construction is established that generalizes previous results and generates higher-index PHFs with more columns. Probabilistic methods are employed to obtain an upper bound on the optimal size of higher-index PHFs when the number of columns is large. A new deterministic algorithm is developed that generates such PHFs meeting this bound, and computational results are reported.



Secondly, a restriction on the structure of PHFs is introduced, called fractal, a method from Blackburn. His method is extended in several ways; from homogeneous hash families (every row has the same number of symbols) to heterogeneous ones; and to distributing hash families, a relaxation of the predicate for PHFs. Recursive constructions with fractal hash families as ingredients are given, and improve upon on the best-known sizes of many PHFs.



Thirdly, a method of Colbourn and Lanus is extended in which they horizontally copied a given hash family and greedily applied transformations to each copy. Transformations of existential t-restrictions are introduced, which allow for the method to be applicable to any t-restriction having structure like those of hash families. A genetic algorithm is employed for finding the "best" such transformations. Computational results of the GA are reported using PHFs, as the number of transformations permitted is large compared to the number of symbols. Finally, an analysis is given of what trade-offs exist between computation time and the number of t-sets left not satisfying the predicate.

Rapid growth of internet and connected devices ranging from cloud systems to internet of things have raised critical concerns for securing these systems. In the recent past, security attacks on different kinds of devices have evolved in terms of complexity and diversity. One of the challenges is establishing secure communication in the network among various devices and systems. Despite being protected with authentication and encryption, the network still needs to be protected against cyber-attacks. For this, the network traffic has to be closely monitored and should detect anomalies and intrusions. Intrusion detection can be categorized as a network traffic classification problem in machine learning. Existing network traffic classification methods require a lot of training and data preprocessing, and this problem is more serious if the dataset size is huge. In addition, the machine learning and deep learning methods that have been used so far were trained on datasets that contain obsolete attacks. In this thesis, these problems are addressed by using ensemble methods applied on an up to date network attacks dataset. Ensemble methods use multiple learning algorithms to get better classification accuracy that could be obtained when the corresponding learning algorithm is applied alone. This dataset for network traffic classification has recent attack scenarios and contains over fifteen attacks. This approach shows that ensemble methods can be used to classify network traffic and detect intrusions with less training times of the model, and lesser pre-processing without feature selection. In addition, this thesis also shows that only with less than ten percent of the total features of input dataset will lead to similar accuracy that is achieved on whole dataset. This can heavily reduce the training times and classification duration in real-time scenarios.