Metabolic Network Alignments and their Applications

The accumulation of high-throughput genomic and proteomic data allows for the reconstruction of the increasingly large and complex metabolic networks. In order to analyze the accumulated data and reconstructed networks, it is critical to identify network patterns and evolutionary relations between metabolic networks. But even finding similar networks becomes computationally challenging. The dissertation addresses these challenges with discrete optimization and the corresponding algorithmic techniques. Based on the property of the gene duplication and function sharing in biological network,we have formulated the network alignment problem which asks the optimal vertex-to-vertex mapping allowing path contraction, vertex deletion, and vertex insertions. We have proposed the first polynomial time algorithm for aligning an acyclic metabolic pattern pathway with an arbitrary metabolic network. We also have proposed a polynomial-time algorithm for patterns with small treewidth and implemented it for series-parallel patterns which are commonly found among metabolic networks. We have developed the metabolic network alignment tool for free public use. We have performed pairwise mapping of all pathways among five organisms and found a set of statistically significant pathway similarities. We also have applied the network alignment to identifying inconsistency, inferring missing enzymes, and finding potential candidates

Hyperbolic Deep Neural Networks: A Survey

Recently, there has been a rising surge of momentum for deep representation learning in hyperbolic spaces due to theirhigh capacity of modeling data like knowledge graphs or synonym hierarchies, possessing hierarchical structure. We refer to the model as hyperbolic deep neural network in this paper. Such a hyperbolic neural architecture potentially leads to drastically compact model withmuch more physical interpretability than its counterpart in Euclidean space. To stimulate future research, this paper presents acoherent and comprehensive review of the literature around the neural components in the construction of hyperbolic deep neuralnetworks, as well as the generalization of the leading deep approaches to the Hyperbolic space. It also presents current applicationsaround various machine learning tasks on several publicly available datasets, together with insightful observations and identifying openquestions and promising future directions

Logic and Automata

Mathematical logic and automata theory are two scientific disciplines with a fundamentally close relationship. The authors of Logic and Automata take the occasion of the sixtieth birthday of Wolfgang Thomas to present a tour d'horizon of automata theory and logic. The twenty papers in this volume cover many different facets of logic and automata theory, emphasizing the connections to other disciplines such as games, algorithms, and semigroup theory, as well as discussing current challenges in the field