Tomasz Marek Kowalski

Indexing Arbitrary-Length k-Mers in Sequencing Reads

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.

Influence of a compression garment on average and local changes in unit pressure

On the basis of models developed and experimental studies, the impact of a compression garment on average and local changes in unit pressure was analysed. The study was based on the analysis of the results of 3D scans of selected parts of female and male bodies. It was found out that surface pressure exerted by the compression garment leads to some changes in the geometry of body circumferences and in their lengths and, consequently, to a change in the average pressure value, as well as local changes along the circumference. The main purpose of this work was to estimate the size of these changes in the example of selected parts of female and male bodies.

A step towards genuine declarative language-integrated queries

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.

Using a 3D Body Scanner in Designing Compression Products Supporting External Treatment

The work comprises a statistical tolerance analysis of human body dimensions using a 3D body scanner and its impact on the value of unit pressure exerted by a compression product on the subject’s body. Model calculations of changes in unit pressure due to the susceptibility of the human body were carried out on the basis of the Laplace law using experimentally determined values of circumferences of particular parts of a female subject, with and without a compression product. Experimentally documented changes in the body circumferences under the influence of a compression garment are one of the reasons for the differences between the intended and actual pressure value exerted by the product.

Issues Regarding the Design of Textile Compression Products for Small Body Circumferences

On the basis of models developed, an analysis was made of the impact of the seam and adopted manufacturing tolerances of a compression product on the value of unit pressure depending on the longitudinal rigidity of a compression fabric for relatively small body circumferences. Algorithms were developed using Laplaces law and can be applied for designing textile compression products connected by seams, with an intended value of unit pressure. The research results allowed to formulate some general guidelines for designing compression products for relatively small body circumferences.

Designing Seamless Compression Products Supporting the Process of External Treatment on Numerically Controlled Flat Knitting Machines

The paper presents a procedure for the design of seamless compression products with an intended value of unit pressure on numerically controlled flat knitting machines. Based on the algorithms developed, some important stages of product design are discussed, i.e. dimensioning of body parts by 3D scanning, selection of proper longitudinal rigidity of the fabric, and manufacturing the tolerance of the product in the form of five-finger gloves with covered and exposed fingers. An important stage in the design procedure is the selection of a knitted fabric with appropriate longitudinal rigidity in dependence on the anatomy of the hand.

Optimisation of language-integrated queries by query unnesting

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. 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.