Tomasz Kowalski | Technical University of Lodz (original) (raw)

Papers by Tomasz Kowalski

Chaos: An Interdisciplinary Journal of Nonlinear Science

Sample-based methods are a useful tool in analyzing the global behavior of multi-stable systems o... more Sample-based methods are a useful tool in analyzing the global behavior of multi-stable systems originating from various branches of science. Classical methods, such as bifurcation diagrams, Lyapunov exponents, and basins of attraction, often fail to analyze complex systems with many coexisting attractors. Thus, we have to apply a different strategy to understand the dynamics of such systems. We can distinguish basin stability, extended basin stability, constrained basin stability, basin entropy, time dependent stability margin, and survivability among sample-based methods. Each method has specific properties and gives us important data about the behavior of the analyzed system. However, none of the methods provides complete information. Hence, to have a full overview of the dynamics, one has to collect data from two or more approaches. This study describes the sample-based methods and presents their advantages and disadvantages for the archetypal nonlinear oscillator with multiple ...

SummaryGenomes within the same species reveal large similarity, exploited by specialized multiple... more SummaryGenomes within the same species reveal large similarity, exploited by specialized multiple genome compressors. The existing algorithms and tools are however targeted at large, e.g., mammalian, genomes, and their performance on bacteria strains is mediocre. In this work, we propose MBGC, a specialized genome compressor making use of specific redundancy of bacterial genomes. Our tool is not only compression efficient, but also fast. On a collection of 168,311 bacterial genomes, totalling 587 GB, we achieve the compression ratio around the factor of 730, and the compression (resp. decompression) speed around 1070 MB/s (resp. 740 MB/s) using 8 hardware threads, on a computer with a 6-core / 12-thread CPU and a fast SSD, being about 4 times more succinct and more than an order of magnitude faster in the compression than our main competitors.Availability and implementationMBGC is freely available at github.com/kowallus/mbgc.

Proceedings of the 2019 Federated Conference on Computer Science and Information Systems, Sep 26, 2019

This paper presents an overview of what Big Data can bring to the modern industry. Through follow... more This paper presents an overview of what Big Data can bring to the modern industry. Through following the history of contemporary Big Data frameworks the authors observe that the tools available have reached sufficient maturity so as to be usable in an industrial setting. The authors propose the concept of a system for collecting, organising, processing and analysing experimental data obtained from measurements with process tomography. Process tomography is used for noninvasive flow monitoring and data acquisition. The measurement data is collected, stored and processed to identify process regimes and process threats. Further general examples of solutions that aim to take advantage of the existence of such tools are presented as proof of viability of such approach. As the first step in the process of creating the proposed system, a scalable, distributed, containerisation-based cluster has been constructed, with consumer-grade hardware.

The paper presents an analysis of the influence of the mechanical properties' heterogeneity of kn... more The paper presents an analysis of the influence of the mechanical properties' heterogeneity of knitted fabrics and the method of determining their characteristics of stress and relaxation (deformation) on the value of unit pressure of compression garments. Changes in the value of force as a function of relative elongation were described by experimental dependencies for stress and relaxation phases for the 6 th hysteresis loop, taking into account the confidence intervals. Model calculations were performed for a wide range of body circumferences G 1 = 5-110 cm and for two values of unit pressure: 20 and 30 hPa using Laplace's law and experimental functions determined which describe the relationship between force and relative elongation of a knitted fabric. The research indicates one of the reasons for changes in the unit pressure in the compression garments designed.

GigaScience, 2022

Background Genomes within the same species reveal large similarity, exploited by specialized mult... more Background Genomes within the same species reveal large similarity, exploited by specialized multiple genome compressors. The existing algorithms and tools are however targeted at large, e.g., mammalian, genomes, and their performance on bacteria strains is rather moderate. Results In this work, we propose MBGC, a specialized genome compressor making use of specific redundancy of bacterial genomes. Its characteristic features are finding both direct and reverse-complemented LZ-matches, as well as a careful management of a reference buffer in a multi-threaded implementation. Our tool is not only compression efficient but also fast. On a collection of 168,311 bacterial genomes, totalling 587 GB, we achieve a compression ratio of approximately a factor of 1,265 and compression (respectively decompression) speed of ∼1,580 MB/s (respectively 780 MB/s) using 8 hardware threads, on a computer with a 14-core/28-thread CPU and a fast SSD, being almost 3 times more succinct and >6 times fa...

Proceedings of the 2015 Federated Conference on Computer Science and Information Systems, 2015

Native functional-style querying extensions for programming languages (e.g., LINQ or Java 8 strea... more Native functional-style querying extensions for programming languages (e.g., LINQ or Java 8 streams) are widely considered as declarative. However, their very limited degree of optimisation when dealing with local collection processing contradicts this statement. We show that developers constructing complex LINQ queries or combining queries expose themselves to the risk of severe performance deterioration. For an inexperienced programmer, a way of getting an appropriate query form can be too complicated. Also, a manual query transformation is justified by the need of improving performance, but achieved at the expense of reflecting an actual business goal. As a result, benefits from a declarative form and an increased level of abstraction are lost. In this paper, we claim that moving of selected methods for automated optimisation elaborated for declarative query languages to the level of imperative programming languages is possible and desired. We propose an optimisation method for collection-processing constructs based on higher-order functions through factoring out of free expressions in order to avoid unnecessary multiple calculations. We have implemented and verified this idea as a simple proof-of-concept LINQ optimiser library.

In this paper, we claim that moving of selected methods for automated optimisation elaborated for declarative query languages to the level of imperative programming languages is possible and desired. Our approach is based on the assumption that programmer is able distinguish whether a language-integrated query is intentionally used to introduce some side-effects or its sole purpose is to only query the data. We propose two optimisation procedures through query unnesting designed to avoid unnecessary multiple calculations in collection-processing constructs based on higher-order functions. We have implemented and verified this idea as a simple proof-of-concept LINQ optimiser library.

The Experience of Designing and Application of CAD Systems in Microelectronics, 2003. CADSM 2003. Proceedings of the 7th International Conference., 2003

ABSTRACT In this paper, a reduced component tree structure that allows the building of efficient ... more ABSTRACT In this paper, a reduced component tree structure that allows the building of efficient algorithms for greyscale image comparison is proposed. The reduced component tree represents the "meaningful" information about the image and plays a central role in the development of a new approach to search problems. The examples of such a component tree and its features for different types of image are given.

In this paper, we describe a robust approach to the problem of the automatic index updating, i.e.... more In this paper, we describe a robust approach to the problem of the automatic index updating, i.e. maintaining cohesion between data and indices. Introducing object-oriented notions (classes, inheritance, polymorphism, class methods, etc.) in databases allows defining more complex selection predicates; nevertheless, in order to facilitate selection process through indices, index updating requires substantial revising. Inadequate index maintenance can lead to serious errors in query processing what has been shown on the example of Oracle 11g ORDBMS. The authors work is based on the Stack-Based Architecture (SBA) and has been implemented and tested in the ODRA (Object Database for Rapid Applications development) OODBMS prototype.

Modern Problems of Radio Engineering, Telecommunications and Computer Science (IEEE Cat. No.02EX542), 2002

... such a characteristic and transformations which are based on representation of digital image ... more ... such a characteristic and transformations which are based on representation of digital image as the graph G and which allow Volodymyr Mosorov Tomasz Marek Kowalski - Computer ... [4] D. Sankowski, A. Plaskowski, V. Mosorov, K. Strzecha, S. Jezewski, Image segmentation ...

Lecture Notes in Computer Science, 2009

The paper contains a short introduction to robust approach (including architecture) for realisati... more The paper contains a short introduction to robust approach (including architecture) for realisation of auto-updatable indexing of data in OODBMS, i.e. maintaining cohesion between data and indices. The authors work is based on the Stack-Based Query Language (SBQL) and has been implemented and verified in the ODRA (Object Database for Rapid Applications development) OODBMS prototype.

ODRA (Object Database for Rapid Application development) is an objectoriented database management... more ODRA (Object Database for Rapid Application development) is an objectoriented database management system provided as an integrated programming tool for building various business and administration applications, including centralized and distributed systems, Web applications, service buses, virtual repositories, P2P networks, and so on. The paper presents general architecture of ODRA, its object model, back-end interoperability facilities, front-end programming interfaces and integrated development environment. ODRA is based on the database query and programming language SBQL (Stack-Based Query Language) and virtual updateable views defined and used in SBQL. ODRA is the basis for two European projects: eGov Bus, aiming at the development of interoperability service bus for public administration, and VIDE, aiming at the development of a visual and textual programming language based on the OMG MDA and OMG specifications of Executable UML and a query language OCL.

The paper presents an analysis of the influence of the mechanical properties’ heterogeneity of kn... more The paper presents an analysis of the influence of the mechanical properties’ heterogeneity
of knitted fabrics and the method of determining their characteristics of stress and
relaxation (deformation) on the value of unit pressure of compression garments. Changes
in the value of force as a function of relative elongation were described by experimental
dependencies for stress and relaxation phases for the 6th hysteresis loop, taking into account
the confidence intervals. Model calculations were performed for a wide range of
body circumferences G1 = 5 - 110 cm and for two values of unit pressure: 20 and 30 hPa
using Laplace’s law and experimental functions determined which describe the relationship
between force and relative elongation of a knitted fabric. The research indicates one of the
reasons for changes in the unit pressure in the compression garments designed.

PloS one, 2015

We propose a lightweight data structure for indexing and querying collections of NGS reads data i... more We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating k-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments.