Evolving Graphs by Graph Programming

Graphs are a ubiquitous data structure in computer science and can be used to represent solutions to difficult problems in many distinct domains. This motivates the use of Evolutionary Algorithms to search over graphs and efficiently find approximate solutions. However, existing techniques often represent and manipulate graphs in an ad-hoc manner. In contrast, rule-based graph programming offers a formal mechanism for describing relations over graphs. This thesis proposes the use of rule-based graph programming for representing and implementing genetic operators over graphs. We present the Evolutionary Algorithm Evolving Graphs by Graph Programming and a number of its extensions which are capable of learning stateful and stateless digital circuits, symbolic expressions and Artificial Neural Networks. We demonstrate that rule-based graph programming may be used to implement new and effective constraint-respecting mutation operators and show that these operators may strictly generalise others found in the literature. Through our proposal of Semantic Neutral Drift, we accelerate the search process by building plateaus into the fitness landscape using domain knowledge of equivalence. We also present Horizontal Gene Transfer, a mechanism whereby graphs may be passively recombined without disrupting their fitness. Through rigorous evaluation and analysis of over 20,000 independent executions of Evolutionary Algorithms, we establish numerous benefits of our approach. We find that on many problems, Evolving Graphs by Graph Programming and its variants may significantly outperform other approaches from the literature. Additionally, our empirical results provide further evidence that neutral drift aids the efficiency of evolutionary search

Complement factor H and the hemolytic uremic syndrome

Immune recognition is coupled to powerful proinflammatory effector pathways that must be tightly regulated. The ancient alternative pathway of complement activation is one such proinflammatory pathway. Genetic susceptibility factors have been identified in both regulators and activating components of the alternative pathway that are associated with thrombotic microangiopathies, glomerulonephritides, and chronic conditions featuring debris deposition. These observations indicate that excessive alternative pathway activation promotes thrombosis in the microvasculature and tissue damage during debris accumulation. Intriguingly, distinct genetic changes in factor H (FH), a key regulator of the alternative pathway, are associated with hemolytic uremic syndrome (HUS), membranoproliferative glomerulonephritis (dense deposit disease), or age-related macular degeneration (AMD). A mouse model of HUS designed to mirror human mutations in FH has now been developed, providing new understanding of the molecular pathogenesis of complement-related endothelial disorders

Evolving Graphs with Semantic Neutral Drift

We introduce the concept of Semantic Neutral Drift (SND) for genetic programming (GP), where we exploit equivalence laws to design semantics preserving mutations guaranteed to preserve individuals' fitness scores. A number of digital circuit benchmark problems have been implemented with rule-based graph programs and empirically evaluated, demonstrating quantitative improvements in evolutionary performance. Analysis reveals that the benefits of the designed SND reside in more complex processes than simple growth of individuals, and that there are circumstances where it is beneficial to choose otherwise detrimental parameters for a GP system if that facilitates the inclusion of SND

Thematic Process and Motivic-Developmental Approaches to Composition in three works for Jazz Orchestra

This exegesis examines key structural processes found in selected large-scale, extended compositions for jazz orchestra, with a particular focus on composers Maria Schneider, Darcy James Argue, Jim McNeely. These composers are archetypal jazz orchestral composers and are currently active. I will discuss their approaches to structure and the formal function of musical materials within selected compositions. The aim of this exegesis is to uncover the way in which jazz orchestral composition invokes concepts related to theme and development identified in classical analytical literature. As such, I will argue that the works analysed here suggest a move more toward forms associated with the classical period, such as sonata form

Bayesian Flow Networks

This paper introduces Bayesian Flow Networks (BFNs), a new class of generative model in which the parameters of a set of independent distributions are modified with Bayesian inference in the light of noisy data samples, then passed as input to a neural network that outputs a second, interdependent distribution. Starting from a simple prior and iteratively updating the two distributions yields a generative procedure similar to the reverse process of diffusion models; however it is conceptually simpler in that no forward process is required. Discrete and continuous-time loss functions are derived for continuous, discretised and discrete data, along with sample generation procedures. Notably, the network inputs for discrete data lie on the probability simplex, and are therefore natively differentiable, paving the way for gradient-based sample guidance and few-step generation in discrete domains such as language modelling. The loss function directly optimises data compression and places no restrictions on the network architecture. In our experiments BFNs achieve competitive log-likelihoods for image modelling on dynamically binarized MNIST and CIFAR-10, and outperform all known discrete diffusion models on the text8 character-level language modelling task

The Road to General Intelligence

Humans have always dreamed of automating laborious physical and intellectual tasks, but the latter has proved more elusive than naively suspected. Seven decades of systematic study of Artificial Intelligence have witnessed cycles of hubris and despair. The successful realization of General Intelligence (evidenced by the kind of cross-domain flexibility enjoyed by humans) will spawn an industry worth billions and transform the range of viable automation tasks.The recent notable successes of Machine Learning has lead to conjecture that it might be the appropriate technology for delivering General Intelligence. In this book, we argue that the framework of machine learning is fundamentally at odds with any reasonable notion of intelligence and that essential insights from previous decades of AI research are being forgotten. We claim that a fundamental change in perspective is required, mirroring that which took place in the philosophy of science in the mid 20th century. We propose a framework for General Intelligence, together with a reference architecture that emphasizes the need for anytime bounded rationality and a situated denotational semantics. We given necessary emphasis to compositional reasoning, with the required compositionality being provided via principled symbolic-numeric inference mechanisms based on universal constructions from category theory. • Details the pragmatic requirements for real-world General Intelligence. • Describes how machine learning fails to meet these requirements. • Provides a philosophical basis for the proposed approach. • Provides mathematical detail for a reference architecture. • Describes a research program intended to address issues of concern in contemporary AI. The book includes an extensive bibliography, with ~400 entries covering the history of AI and many related areas of computer science and mathematics.The target audience is the entire gamut of Artificial Intelligence/Machine Learning researchers and industrial practitioners. There are a mixture of descriptive and rigorous sections, according to the nature of the topic. Undergraduate mathematics is in general sufficient. Familiarity with category theory is advantageous for a complete understanding of the more advanced sections, but these may be skipped by the reader who desires an overall picture of the essential concepts This is an open access book