Ramsey theorem for trees with successor operation

We prove a general Ramsey theorem for trees with a successor operation. This theorem is a common generalization of the Carlson-Simpson Theorem and the Milliken Tree Theorem for regularly branching trees. Our theorem has a number of applications both in finite and infinite combinatorics. For example, we give a short proof of the unrestricted Ne\v{s}et\v{r}il-R\"odl theorem, and we recover the Graham-Rothschild theorem. Our original motivation came from the study of big Ramsey degrees - various trees used in the study can be viewed as trees with a successor operation. To illustrate this, we give a non-forcing proof of a theorem of Zucker on big Ramsey degrees.Comment: 37 pages, 9 figure

Infinite Jordan Permutation Groups

Abstract If G is a transitive permutation group on a set X, then G is a Jordan group if there is a partition of X into non-empty subsets Y and Z with |Z| > 1, such that the pointwise stabilizer in G of Y acts transitively on Z (plus other non-degeneracy conditions). There is a classification theorem by Adeleke and Macpherson for the infinite primitive Jordan permutation groups: such group preserves linear-like structures, or tree-like structures, or Steiner systems or a ‘limit’ of Steiner systems, or a ‘limit’ of betweenness relations or D-relations. In this thesis we build a structure M whose automorphism group is an infinite oligomorphic primitive Jordan permutation group preserving a limit of D-relations. In Chapter 2 we build a class of finite structures, each of which is essentially a finite lower semilinear order with vertices labelled by finite D-sets, with coherence conditions. These are viewed as structures in a relational language with relations L,L',S,S',Q,R. We describe possible one point extensions, and prove an amalgamation theorem. We obtain by Fra¨ıss´e’s Theorem a Fra¨ıss´e limit M. In Chapter 3, we describe in detail the structure M and its automorphism group. We show that there is an associated dense lower semilinear order, again with vertices labelled by (dense) D-sets, again with coherence conditions. By a method of building an iterated wreath product described by Cameron which is based on Hall’s wreath power, we build in Chapter 4 a group K < Aut(M) which is a Jordan group with a pre-direction as its Jordan set. Then we find, by properties of Jordan sets, that a pre-D-set is a Jordan set for Aut(M). Finally we prove that the Jordan group G = Aut(M) preserves a limit of D-relations as a main result of this thesis

Applications of finite geometries to designs and codes

This dissertation concerns the intersection of three areas of discrete mathematics: finite geometries, design theory, and coding theory. The central theme is the power of finite geometry designs, which are constructed from the points and t-dimensional subspaces of a projective or affine geometry. We use these designs to construct and analyze combinatorial objects which inherit their best properties from these geometric structures. A central question in the study of finite geometry designs is Hamada’s conjecture, which proposes that finite geometry designs are the unique designs with minimum p-rank among all designs with the same parameters. In this dissertation, we will examine several questions related to Hamada’s conjecture, including the existence of counterexamples. We will also study the applicability of certain decoding methods to known counterexamples. We begin by constructing an infinite family of counterexamples to Hamada’s conjecture. These designs are the first infinite class of counterexamples for the affine case of Hamada’s conjecture. We further demonstrate how these designs, along with the projective polarity designs of Jungnickel and Tonchev, admit majority-logic decoding schemes. The codes obtained from these polarity designs attain error-correcting performance which is, in certain cases, equal to that of the finite geometry designs from which they are derived. This further demonstrates the highly geometric structure maintained by these designs. Finite geometries also help us construct several types of quantum error-correcting codes. We use relatives of finite geometry designs to construct infinite families of q-ary quantum stabilizer codes. We also construct entanglement-assisted quantum error-correcting codes (EAQECCs) which admit a particularly efficient and effective error-correcting scheme, while also providing the first general method for constructing these quantum codes with known parameters and desirable properties. Finite geometry designs are used to give exceptional examples of these codes

Studying Evolutionary Change: Transdisciplinary Advances in Understanding and Measuring Evolution

Evolutionary processes can be found in almost any historical, i.e. evolving, system that erroneously copies from the past. Well studied examples do not only originate in evolutionary biology but also in historical linguistics. Yet an approach that would bind together studies of such evolving systems is still elusive. This thesis is an attempt to narrowing down this gap to some extend. An evolving system can be described using characters that identify their changing features. While the problem of a proper choice of characters is beyond the scope of this thesis and remains in the hands of experts we concern ourselves with some theoretical as well data driven approaches. Having a well chosen set of characters describing a system of different entities such as homologous genes, i.e. genes of same origin in different species, we can build a phylogenetic tree. Consider the special case of gene clusters containing paralogous genes, i.e. genes of same origin within a species usually located closely, such as the well known HOX cluster. These are formed by step- wise duplication of its members, often involving unequal crossing over forming hybrid genes. Gene conversion and possibly other mechanisms of concerted evolution further obfuscate phylogenetic relationships. Hence, it is very difficult or even impossible to disentangle the detailed history of gene duplications in gene clusters. Expanding gene clusters that use unequal crossing over as proposed by Walter Gehring leads to distinctive patterns of genetic distances. We show that this special class of distances helps in extracting phylogenetic information from the data still. Disregarding genome rearrangements, we find that the shortest Hamiltonian path then coincides with the ordering of paralogous genes in a cluster. This observation can be used to detect ancient genomic rearrangements of gene clus- ters and to distinguish gene clusters whose evolution was dominated by unequal crossing over within genes from those that expanded through other mechanisms. While the evolution of DNA or protein sequences is well studied and can be formally described, we find that this does not hold for other systems such as language evolution. This is due to a lack of detectable mechanisms that drive the evolutionary processes in other fields. Hence, it is hard to quantify distances between entities, e.g. languages, and therefore the characters describing them. Starting out with distortions of distances, we first see that poor choices of the distance measure can lead to incorrect phylogenies. Given that phylogenetic inference requires additive metrics we can infer the correct phylogeny from a distance matrix D if there is a monotonic, subadditive function ζ such that ζ^−1(D) is additive. We compute the metric-preserving transformation ζ as the solution of an optimization problem. This result shows that the problem of phylogeny reconstruction is well defined even if a detailed mechanistic model of the evolutionary process is missing. Yet, this does not hinder studies of language evolution using automated tools. As the amount of available and large digital corpora increased so did the possibilities to study them automatically. The obvious parallels between historical linguistics and phylogenetics lead to many studies adapting bioinformatics tools to fit linguistics means. Here, we use jAlign to calculate bigram alignments, i.e. an alignment algorithm that operates with regard to adjacency of letters. Its performance is tested in different cognate recognition tasks. Using pairwise alignments one major obstacle is the systematic errors they make such as underestimation of gaps and their misplacement. Applying multiple sequence alignments instead of a pairwise algorithm implicitly includes more evolutionary information and thus can overcome the problem of correct gap placement. They can be seen as a generalization of the string-to-string edit problem to more than two strings. With the steady increase in computational power, exact, dynamic programming solutions have become feasible in practice also for 3- and 4-way alignments. For the pairwise (2-way) case, there is a clear distinction between local and global alignments. As more sequences are consid- ered, this distinction, which can in fact be made independently for both ends of each sequence, gives rise to a rich set of partially local alignment problems. So far these have remained largely unexplored. Thus, a general formal frame- work that gives raise to a classification of partially local alignment problems is introduced. It leads to a generic scheme that guides the principled design of exact dynamic programming solutions for particular partially local alignment problems

Classical Algebraic Geometry

Algebraic geometry studies properties of specific algebraic varieties, on the one hand, and moduli spaces of all varieties of fixed topological type on the other hand. Of special importance is the moduli space of curves, whose properties are subject of ongoing research. The rationality versus general type question of these and related spaces is of classical and also very modern interest with recent progress presented in the conference. Certain different birational models of the moduli space of curves and maps have an interpretation as moduli spaces of singular curves and maps. For specific varieties a wide range of questions was addressed, including extrinsic questions (syzygies, the k-secant lemma) and intrinsic ones (generalization of notions of positivity of line bundles, closure operations on ideals and sheaves)

Algorithmic embeddings

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (p. 233-242).We present several computationally efficient algorithms, and complexity results on low distortion mappings between metric spaces. An embedding between two metric spaces is a mapping between the two metric spaces and the distortion of the embedding is the factor by which the distances change. We have pioneered theoretical work on relative (or approximation) version of this problem. In this setting, the question is the following: for the class of metrics C, and a host metric M', what is the smallest approximation factor a > 1 of an efficient algorithm minimizing the distortion of an embedding of a given input metric M E C into M'? This formulation enables the algorithm to adapt to a given input metric. In particular, if the host metric is "expressive enough" to accurately model the input distances, the minimum achievable distortion is low, and the algorithm will produce an embedding with low distortion as well. This problem has been a subject of extensive applied research during the last few decades. However, almost all known algorithms for this problem are heuristic. As such, they can get stuck in local minima, and do not provide any global guarantees on solution quality. We investigate several variants of the above problem, varying different host and target metrics, and definitions of distortion.(cont.) We present results for different types of distortion: multiplicative versus additive, worst-case versus average-case and several types of target metrics, such as the line, the plane, d-dimensional Euclidean space, ultrametrics, and trees. We also present algorithms for ordinal embeddings and embedding with extra information.by Mihai Bădoiu.Ph.D

Vertex sparsification and universal rounding algorithms

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 125-129).Suppose we are given a gigantic communication network, but are only interested in a small number of nodes (clients). There are many routing problems we could be asked to solve for our clients. Is there a much smaller network - that we could write down on a sheet of paper and put in our pocket - that approximately preserves all the relevant communication properties of the original network? As we will demonstrate, the answer to this question is YES, and we call this smaller network a vertex sparsifier. In fact, if we are asked to solve a sequence of optimization problems characterized by cuts or flows, we can compute a good vertex sparsifier ONCE and discard the original network. We can run our algorithms (or approximation algorithms) on the vertex sparsifier as a proxy - and still recover approximately optimal solutions in the original network. This novel pattern saves both space (because the network we store is much smaller) and time (because our algorithms run on a much smaller graph). Additionally, we apply these ideas to obtain a master theorem for graph partitioning problems - as long as the integrality gap of a standard linear programming relaxation is bounded on trees, then the integrality gap is at most a logarithmic factor larger for general networks. This result implies optimal bounds for many well studied graph partitioning problems as a special case, and even yields optimal bounds for more challenging problems that had not been studied before. Morally, these results are all based on the idea that even though the structure of optimal solutions can be quite complicated, these solution values can be approximated by crude (even linear) functions.by Ankur Moitra.Ph.D

Vertex sparsification and universal rounding algorithms

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 125-129).Suppose we are given a gigantic communication network, but are only interested in a small number of nodes (clients). There are many routing problems we could be asked to solve for our clients. Is there a much smaller network - that we could write down on a sheet of paper and put in our pocket - that approximately preserves all the relevant communication properties of the original network? As we will demonstrate, the answer to this question is YES, and we call this smaller network a vertex sparsifier. In fact, if we are asked to solve a sequence of optimization problems characterized by cuts or flows, we can compute a good vertex sparsifier ONCE and discard the original network. We can run our algorithms (or approximation algorithms) on the vertex sparsifier as a proxy - and still recover approximately optimal solutions in the original network. This novel pattern saves both space (because the network we store is much smaller) and time (because our algorithms run on a much smaller graph). Additionally, we apply these ideas to obtain a master theorem for graph partitioning problems - as long as the integrality gap of a standard linear programming relaxation is bounded on trees, then the integrality gap is at most a logarithmic factor larger for general networks. This result implies optimal bounds for many well studied graph partitioning problems as a special case, and even yields optimal bounds for more challenging problems that had not been studied before. Morally, these results are all based on the idea that even though the structure of optimal solutions can be quite complicated, these solution values can be approximated by crude (even linear) functions.by Ankur Moitra.Ph.D