Target Code Selection by Tilling AST with the Use of Tree Pattern Pushdown Automaton

A new and simple method for target code selection by tilling an abstract syntax tree is presented. As it is usual, tree patterns corresponding to target machine instructions are matched in the abstract syntax tree. Matching tree patterns is performed with the use of tree pattern pushdown automaton, which accepts all tree patterns matching the abstract syntax tree in the linear postfix bar notation and represents a full index of the abstract syntax tree for tree patterns. The use of the index allows to match patterns quickly, in time depending on the size of patterns and not depending on the size of the tree. The selection of a particular target instruction corresponds to a modification of the abstract syntax tree and also a corresponding incremental modification of the index is performed. A reference to a fully functional prototype is provided

Algorithmic patterns for H\mathcal{H}-matrices on many-core processors

In this work, we consider the reformulation of hierarchical ($\mathcal{H}$) matrix algorithms for many-core processors with a model implementation on graphics processing units (GPUs). $\mathcal{H}$ matrices approximate specific dense matrices, e.g., from discretized integral equations or kernel ridge regression, leading to log-linear time complexity in dense matrix-vector products. The parallelization of $\mathcal{H}$ matrix operations on many-core processors is difficult due to the complex nature of the underlying algorithms. While previous algorithmic advances for many-core hardware focused on accelerating existing $\mathcal{H}$ matrix CPU implementations by many-core processors, we here aim at totally relying on that processor type. As main contribution, we introduce the necessary parallel algorithmic patterns allowing to map the full $\mathcal{H}$ matrix construction and the fast matrix-vector product to many-core hardware. Here, crucial ingredients are space filling curves, parallel tree traversal and batching of linear algebra operations. The resulting model GPU implementation hmglib is the, to the best of the authors knowledge, first entirely GPU-based Open Source $\mathcal{H}$ matrix library of this kind. We conclude this work by an in-depth performance analysis and a comparative performance study against a standard $\mathcal{H}$ matrix library, highlighting profound speedups of our many-core parallel approach

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Pattern Formation on Trees

Networks having the geometry and the connectivity of trees are considered as the spatial support of spatiotemporal dynamical processes. A tree is characterized by two parameters: its ramification and its depth. The local dynamics at the nodes of a tree is described by a nonlinear map, given rise to a coupled map lattice system. The coupling is expressed by a matrix whose eigenvectors constitute a basis on which spatial patterns on trees can be expressed by linear combination. The spectrum of eigenvalues of the coupling matrix exhibit a nonuniform distribution which manifest itself in the bifurcation structure of the spatially synchronized modes. These models may describe reaction-diffusion processes and several other phenomena occurring on heterogeneous media with hierarchical structure.Comment: Submitted to Phys. Rev. E, 15 pages, 9 fig

Compressed Representations of Conjunctive Query Results

Relational queries, and in particular join queries, often generate large output results when executed over a huge dataset. In such cases, it is often infeasible to store the whole materialized output if we plan to reuse it further down a data processing pipeline. Motivated by this problem, we study the construction of space-efficient compressed representations of the output of conjunctive queries, with the goal of supporting the efficient access of the intermediate compressed result for a given access pattern. In particular, we initiate the study of an important tradeoff: minimizing the space necessary to store the compressed result, versus minimizing the answer time and delay for an access request over the result. Our main contribution is a novel parameterized data structure, which can be tuned to trade off space for answer time. The tradeoff allows us to control the space requirement of the data structure precisely, and depends both on the structure of the query and the access pattern. We show how we can use the data structure in conjunction with query decomposition techniques, in order to efficiently represent the outputs for several classes of conjunctive queries.Comment: To appear in PODS'18; 35 pages; comments welcom