The Landscape of Bounds for Binary Search Trees

Binary search trees (BSTs) with rotations can adapt to various kinds of structure in search sequences, achieving amortized access times substantially better than the Theta(log n) worst-case guarantee. Classical examples of structural properties include static optimality, sequential access, working set, key-independent optimality, and dynamic finger, all of which are now known to be achieved by the two famous online BST algorithms (Splay and Greedy). (...) In this paper, we introduce novel properties that explain the efficiency of sequences not captured by any of the previously known properties, and which provide new barriers to the dynamic optimality conjecture. We also establish connections between various properties, old and new. For instance, we show the following. (i) A tight bound of O(n log d) on the cost of Greedy for d-decomposable sequences. The result builds on the recent lazy finger result of Iacono and Langerman (SODA 2016). On the other hand, we show that lazy finger alone cannot explain the efficiency of pattern avoiding sequences even in some of the simplest cases. (ii) A hierarchy of bounds using multiple lazy fingers, addressing a recent question of Iacono and Langerman. (iii) The optimality of the Move-to-root heuristic in the key-independent setting introduced by Iacono (Algorithmica 2005). (iv) A new tool that allows combining any finite number of sound structural properties. As an application, we show an upper bound on the cost of a class of sequences that all known properties fail to capture. (v) The equivalence between two families of BST properties. The observation on which this connection is based was known before - we make it explicit, and apply it to classical BST properties. (...

Partly melted DNA conformations obtained with a probability peak finding method

Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate the alternative conformations that coexist in equilibrium and the range of their fluctuations. This yields a representation of the conformational ensemble at a given temperature, which is illustrated in a single diagram called a stitch profile. This article describes the methodology and discusses stitch profiles vs. the ordinary probability profiles using the phage lambda genome as an example.Comment: 11 pages, 9 figures; v3: major changes; v4: applications sectio

An Overview of Schema Theory

The purpose of this paper is to give an introduction to the field of Schema Theory written by a mathematician and for mathematicians. In particular, we endeavor to to highlight areas of the field which might be of interest to a mathematician, to point out some related open problems, and to suggest some large-scale projects. Schema theory seeks to give a theoretical justification for the efficacy of the field of genetic algorithms, so readers who have studied genetic algorithms stand to gain the most from this paper. However, nothing beyond basic probability theory is assumed of the reader, and for this reason we write in a fairly informal style. Because the mathematics behind the theorems in schema theory is relatively elementary, we focus more on the motivation and philosophy. Many of these results have been proven elsewhere, so this paper is designed to serve a primarily expository role. We attempt to cast known results in a new light, which makes the suggested future directions natural. This involves devoting a substantial amount of time to the history of the field. We hope that this exposition will entice some mathematicians to do research in this area, that it will serve as a road map for researchers new to the field, and that it will help explain how schema theory developed. Furthermore, we hope that the results collected in this document will serve as a useful reference. Finally, as far as the author knows, the questions raised in the final section are new.Comment: 27 pages. Originally written in 2009 and hosted on my website, I've decided to put it on the arXiv as a more permanent home. The paper is primarily expository, so I don't really know where to submit it, but perhaps one day I will find an appropriate journa

Smooth heaps and a dual view of self-adjusting data structures

We present a new connection between self-adjusting binary search trees (BSTs) and heaps, two fundamental, extensively studied, and practically relevant families of data structures. Roughly speaking, we map an arbitrary heap algorithm within a natural model, to a corresponding BST algorithm with the same cost on a dual sequence of operations (i.e. the same sequence with the roles of time and key-space switched). This is the first general transformation between the two families of data structures. There is a rich theory of dynamic optimality for BSTs (i.e. the theory of competitiveness between BST algorithms). The lack of an analogous theory for heaps has been noted in the literature. Through our connection, we transfer all instance-specific lower bounds known for BSTs to a general model of heaps, initiating a theory of dynamic optimality for heaps. On the algorithmic side, we obtain a new, simple and efficient heap algorithm, which we call the smooth heap. We show the smooth heap to be the heap-counterpart of Greedy, the BST algorithm with the strongest proven and conjectured properties from the literature, widely believed to be instance-optimal. Assuming the optimality of Greedy, the smooth heap is also optimal within our model of heap algorithms. As corollaries of results known for Greedy, we obtain instance-specific upper bounds for the smooth heap, with applications in adaptive sorting. Intriguingly, the smooth heap, although derived from a non-practical BST algorithm, is simple and easy to implement (e.g. it stores no auxiliary data besides the keys and tree pointers). It can be seen as a variation on the popular pairing heap data structure, extending it with a "power-of-two-choices" type of heuristic.Comment: Presented at STOC 2018, light revision, additional figure