Generation, Ranking and Unranking of Ordered Trees with Degree Bounds

We study the problem of generating, ranking and unranking of unlabeled ordered trees whose nodes have maximum degree of $\Delta$. This class of trees represents a generalization of chemical trees. A chemical tree is an unlabeled tree in which no node has degree greater than 4. By allowing up to $\Delta$ children for each node of chemical tree instead of 4, we will have a generalization of chemical trees. Here, we introduce a new encoding over an alphabet of size 4 for representing unlabeled ordered trees with maximum degree of $\Delta$. We use this encoding for generating these trees in A-order with constant average time and O(n) worst case time. Due to the given encoding, with a precomputation of size and time O(n^2) (assuming $\Delta$ is constant), both ranking and unranking algorithms are also designed taking O(n) and O(nlogn) time complexities.Comment: In Proceedings DCM 2015, arXiv:1603.0053

Generation of Neuronal Trees by a New Three Letters Encoding

A neuronal tree is a rooted tree with n leaves whose each internal node has at least two children; this class not only is defined based on the structure of dendrites in neurons, but also refers to phylogenetic trees or evolutionary trees. More precisely, neuronal trees are rooted-multistate phylogenetic trees whose size is defined as the number of leaves. In this paper, a new encoding over an alphabet of size 3 (minimal cardinality) is introduced for representing the neuronal trees with a given number of leaves. This encoding is used for generating neuronal trees with n leaves in A-order with constant average time and O(n) time complexity in the worst case. Also, new ranking and unranking algorithms are presented in time complexity of O(n) and O(n log n), respectively

A parallel dynamic programming algorithm for unranking set partitions

In this paper, an O(n) parallel algorithm is presented for unranking set partitions in Hutchinson’s representation. A simple sequential algorithm is derived on the basis of a dynamic programming paradigm. In the parallel algorithm, processing is performed in a dedicated parallel architecture combining certain systolic and associative features. The algorithm consists of two phases. In the first phase, a coefficient table is created by systolic computations. Then, n subsequent elements of a partition codeword are computed, in O(1) time each, through associative search operations

New Combinatorial Properties and Algorithms for AVL Trees

In this thesis, new properties of AVL trees and a new partitioning of binary search trees named core partitioning scheme are discussed, this scheme is applied to three binary search trees namely AVL trees, weight-balanced trees, and plain binary search trees. We introduce the core partitioning scheme, which maintains a balanced search tree as a dynamic collection of complete balanced binary trees called cores. Using this technique we achieve the same theoretical efficiency of modern cache-oblivious data structures by using classic data structures such as weight-balanced trees or height balanced trees (e.g. AVL trees). We preserve the original topology and algorithms of the given balanced search tree using a simple post-processing with guaranteed performance to completely rebuild the changed cores (possibly all of them) after each update. Using our core partitioning scheme, we simultaneously achieve good memory allocation, space-efficient representation, and cache-obliviousness. We also apply this scheme to arbitrary binary search trees which can be unbalanced and we produce a new data structure, called Cache-Oblivious General Balanced Tree (COG-tree). Using our scheme, searching a key requires O(log_B n) block transfers and O(log n) comparisons in the external-memory and in the cache-oblivious model. These complexities are theoretically efficient. Interestingly, the core partition for weight-balanced trees and COG-tree can be maintained with amortized O(log_B n) block transfers per update, whereas maintaining the core partition for AVL trees requires more than a poly-logarithmic amortized cost. Studying the properties of these trees also lead us to some other new properties of AVL trees and trees with bounded degree, namely, we present and study gaps in AVL trees and we prove Tarjan et al.'s conjecture on the number of rotations in a sequence of deletions and insertions

Random generation of RNA secondary structures according to native distributions

Nebel M, Scheid A, Weinberg F. Random generation of RNA secondary structures according to native distributions. Algorithms for Molecular Biology. 2011;6(1): 24

Advances and Novel Approaches in Discrete Optimization

Discrete optimization is an important area of Applied Mathematics with a broad spectrum of applications in many fields. This book results from a Special Issue in the journal Mathematics entitled ‘Advances and Novel Approaches in Discrete Optimization’. It contains 17 articles covering a broad spectrum of subjects which have been selected from 43 submitted papers after a thorough refereeing process. Among other topics, it includes seven articles dealing with scheduling problems, e.g., online scheduling, batching, dual and inverse scheduling problems, or uncertain scheduling problems. Other subjects are graphs and applications, evacuation planning, the max-cut problem, capacitated lot-sizing, and packing algorithms