Jiri Dvorský

Word-Based Compression Methods and Indexing for Text Retrieval Systems

In this article we present a new compression method, called WLZW, which is a word-based modification of classic LZW. The modification is similar to the approach used in the HuffWord compression algorithm. The algorithm is two-phase, the compression ratio achieved is fairly good, on average 22%-20% (see [2],[3]). Moreover, the table of words, which is side product of compression, can be used to create full-text index, especially for dynamic text databases. Overhead of the index is good.

HyperLoom: A Platform for Defining and Executing Scientific Pipelines in Distributed Environments

Real-world scientific applications often encompass end-to-end data processing pipelines composed of a large number of interconnected computational tasks of various granularity. We introduce HyperLoom, an open source platform for defining and executing such pipelines in distributed environments and providing a Python interface for defining tasks. HyperLoom is a self-contained system that does not use an external scheduler for the actual execution of the task. We have successfully employed HyperLoom for executing chemogenomics pipelines used in pharmaceutic industry for novel drug discovery.

HyperLoom Possibilities for Executing Scientific Workflows on the Cloud

We have developed HyperLoom - a platform for defining and executing scientific workflows in large-scale HPC systems. The computational tasks in such workflows often have non-trivial dependency patterns, unknown execution time and unknown sizes of generated outputs. HyperLoom enables to efficiently execute the workflows respecting task requirements and cluster resources agnostically to the shape or size of the workflow. Although HPC infrastructures provide an unbeatable performance, they may be unavailable or too expensive especially for small to medium workloads. Moreover, for some workloads, due to HPCs not very flexible resource allocation policy, the system energy efficiency may not be optimal at some stages of the execution. In contrast, current public cloud providers such as Amazon, Google or Exoscale allow users a comfortable and elastic way of deploying, scaling and disposing a virtualized cluster of almost any size. In this paper, we describe HyperLoom virtualization and evaluate its performance in a virtualized environment using workflows of various shapes and sizes. Finally, we discuss the Hyperloom potential for its expansion to cloud environments.

Word Random Access Compression

Compression method (WRAC) based on finite automatons is presented in this paper. Simple algorithm for construction finite automaton for given regular expression is shown. The best advantage of this algorithm is the possibility of random access to a compressed text. The compression ratio achieved is fairly good. The method is independent on source alphabet i.e. algorithm can be character or word based.