Plamenka Borovska

• DSc
• Professor at Technical University of Sofia

Genomic technologies in archaeology have been used to study migration patterns, origin of and genetic similarity between ancient populations. Researchers are, however, just beginning to employ these technologies to evaluate the genomic health of ancient communities. In this study we screen publicly available whole-genome sequencing data of pre-cont...

Publicly available genome-wide data, sequenced from 2730 ancient human samples were analyzed for genetic predisposition to malignancy. The temporal and spatial incidence of risk variants for cancer diseases in ancient genomes was recorded, allowing for estimates of their frequencies in ancient human communities. We identified 55 risk alleles associ...

Genetic disease burden in ancient communities has barely been evaluated despite an ever expanding body of ancient genomes becoming available. In this study, we inspect 2729 publicly available ancient genomes (100 BP—52000 BP) for the presence of pathogenic variants in 32643 disease-associated loci. We base our subsequent analyses on 19 variants in...

Ancient human genome data accumulated in recent years can be employed to establish the spatiotemporal trajectories of genetic variants associated with human diseases. Such knowledge might illuminate if and how past adaptations impact contemporary human health and medicine. Scarcely any studies have yet attempted to evaluate genetic susceptibility t...

In this paper we have proposed a conceptual model of differential analytical scientific workflow for imaging diagnostics of abnormal pneumonias. The model is based on the method of deep convolutional neural networks (CNN) and the approach of Gradient-weighted Class Activation Mapping (Grad-CAM), which uses specific for the class information from th...

In this paper we have revealed and analyzed the anatomy of the intersection of Internet of Things (IoT) ecosystem security and blockchain technology in the context of Industry 4.0. The design principles and related innovative technologies to Industry 4.0 such as Industrial Internet of Things (IIoT) and edge computing have been considered. IoT and e...

Due to their importance for computational biology, the methods and algorithms for multiple alignment of biological sequences have been the subject of continuous intensive research and innovation in the last 30 years. Within a PRACE research project we have designed and implemented metaheuristic algorithm for massively parallel MSA and based on it p...

In this paper we have analyzed the IoT security issues in the context of security intelligence and IoT analytics. Furthermore, the potential and benefits of applying Big data technologies have been revealed for building up intelligent security solutions for the IoT ecosystem. We have suggested design approach for building up parallel differentiated...

Presented for the acquisition of scientific degree Doctor of Science - Informatics and Computer Science

Resume of the thesis for the acquisition of scientific degree Doctor of Science

The paper presents intelligent integrated digital platform InSilicoKDD based on scientific workflows in support of precision medicine designed, implemented and deployed at the Faculty of Applied Mathematics and Informatics, Technical University of Sofia. The platform is built upon our method for adaptive in silico knowledge data discovery and intel...

Multiple biological sequences alignment is one of the fundamental tasks in computational biology. The problem is NP-hard and has been subjected to intense research during the last 10 years. Exact MSA algorithms such as Clustawl have considerable serial sections (for building up the guide tree) which limit the efficiency of code parallelization and...

The following paper presents an overview of medical imaging platforms and cloud solutions for the case study of cancer diagnostics. It introduces medical breast cancer imaging concept describing the medical apparatuses for breast cancer detection and monitoring, the features of the images they produce and the image processing needed for extracting...

The paper introduces the latest trends in interactive presentation of cultural and historical heritage based on the analyses of available electronic resources and their representation in European thematic networks for cultural and historical heritage. The idea of this paper is to present the summary of used digital technologies for interactive pres...

The paper introduces the latest trends in IT and the novel achievements of data science in breast cancer risk evaluation in support of personalized medicine. The idea of this publication is to present the summary and classification of breast cancer risk factors and available breast cancer risk evaluation models and tools. The goal is is to propose...

Breast cancer (BC) has the highest rate of cancer in women and causes the highest number of deaths, approximately 15% of all female cancer deaths. High incidence and mortality make it a leading socially significant disease. In practice, different specialists in different clinics carry out the different stages - screening, diagnosis, treatment and r...

In the past years, researchers and analysts worldwide determine big data as a revolution in scientific research and one of the most promising trends that has given impetus to the intensive development of methods and technologies for their investigation and has resulted in the emergence of a new paradigm for scientific research Data-Intensive Scient...

Multiple biological sequences alignment is one of the fundamental tasks in computational biology. The problem is NP-hard and has been subjected to intense research during the last 10 years. Exact MSA algorithms such as Clustawl have considerable serial sections (for building up the guide tree) which limit the efficiency of code parallelization and...

In silico biological sequence processing is a key task in molecular biology. This scientific area requires powerful computing resources for exploring large sets of biological data. Parallel in silico simulations based on methods and algorithms for analysis of biological data using high-performance distributed computing is essential for accelerating...

The huge amount of biological sequences accumulated in the world nucleotide and protein databases leads to the necessity of efficient tools for structural genomic and functional analysis. This scientific area requires powerful computing resources for exploring large sets of biological data. Multiple sequence alignment is an important method in the...

The focus of this paper is on advanced IT and the fourth scientific research paradigm Data Intensive Scientific Discovery (DISD) in support of precision medicine, specifically, for the case study of fighting breast cancer. We suggest intelligent method for adaptive in silico knowledge data discovery based on Big genomic data analytics which is adap...

This paper presents the concept and the modern advances in architecture, models and services in cloud. The goal of the paper is the development of cloud architecture and to show how an absolutely secure, fast and powerful cloud computing environment can be built in an easy and economical way to serve as an end product. For this purpose, it will be...

This paper presents the concept and the modern advances of big data analytics and its influence in the area of genomics for adaptive in-silico knowledge discovery and decision-making with respect to precision and personalized medicine. The goal of the paper is to build up the scalable framework, providing a set of software tools for applying the me...

In this paper we investigate the efficiency of parallel metaheuristics for optimizing the combinatorial problem of resource scheduling in virtualized heterogeneous computer clusters. We propose a parallel computational model based on Swarm metaheuristics Artificial Bee Colony to perform resource scheduling of heterogeneous multicore superserver of...

In this paper the role of advanced IT technologies such as Internet of medical imaging Things and analytics in support and promotion of precision medicine has been revealed considering the case study of early thyroid cancer diagnostics. The concept of precision medicine has been presented and analyzed from the point of view of computational science...

The paper introduces the new technological revolution in digital world, the Internet of Things (IoT) and the opportunities for its application medicine and healthcare. Futhermore, the paper reviews and analyzes the machine learning approaches and methods for big data analytics in IoMIT ecosystem. The main goal of the paper is to present the experim...

Parallel metaheuristics provides innovative and powerful alternative for combinatorial optimization providing the opportunity to find out near-optimal solutions in reasonable time. The goal of this paper is to reveal the experience of utilizing the experimental parallel metaheuristics framework ParMetaOpt, developed at Computer Systems Dept., Techn...

bstrаct: This pаpеr rеviеws thе еxisting mеthods for dеtеction of еnhаncеr-promotеr intеrаctions. It prеsеnts thе еxpеrimеntаl invеstigаtion for dеtеction of еnhаncеr-promotеr intеrаctions from gеnomic big dаtа bаsеd on mаchinе lеаrning. Thе аuthors аrе spеnt timе to еxplаin thе importаncе of promotеrs аnd еnhаncеrs аnd thеir impаcts on gеnе еxprеs...

This pаpеr rеviеws thе еxisting mеthods for dеtеction of еnhаncеr-promotеr intеrаctions. It prеsеnts thе еxpеrimеntаl invеstigаtion for dеtеction of еnhаncеr-promotеr intеrаctions from gеnomic big dаtа bаsеd on mаchinе lеаrning. Thе аuthors аrе spеnt timе to еxplаin thе importаncе of promotеrs аnd еnhаncеrs аnd thеir impаcts on gеnе еxprеssion. Thе...

This work is aimed to investigate and to improve the performance of multiple sequence alignment software ClustalW on the test platform EURORA at CINECA, for the case study of the influenza virus sequences. The objective is code optimization, porting, scaling and performance evaluation of parallel multiple sequence alignment software ClustalW for In...

This paper focuses on the potential of the innovative Big data technologies to facilitate genetic research for the case study of gene mapping. The problem of gene mapping has been formulated on the basis of the computer model of DNA and from the point of view of computer based technologies. Conceptual model of the Big genomic data ecosystem has bee...

The paper focuses on performance investigation and improvement of multiple biological sequence alignment software MSA_BG on the BlueGene/Q supercomputer JUQUEEN. For this purpose, scientific experiments in the area of bioinformatics have been carried out, using as case study influenza virus sequences. The objectives of the investigation are code op...

in silico технологиите и четвъртата парадигма за научни изследвания в аспекта на откриване на знания от данни. Анализиран е спектърът на in silico технологиите с акцент върху персонализираната и прецизната медицина. Представен е концептуален модел на екосистемата на големите данни и свързаните технологии като Internet of Things и облачните изчислен...

Accelerating the development and deployment of advanced communication technologies and complex databases will require a comprehensive strategy integrating efforts from invention to deployment. The concurrent high-performance computing systems are composed of hundreds of thousands of computational nodes, as well as deep memory hierarchies and comple...

This activity with the project is aimed to investigate and to improve the performance of multiple sequence alignment software ClustalW on the computer system Eurora, for the case study of the influenza virus sequences. The objective is code optimization, porting, scaling and performance evaluation of parallel multiple sequence alignment software Cl...

High performance routers are fundamental building blocks of the system wide interconnection networks for high performance computing systems. Through collective interaction they provide reliable communication between the computing nodes and manage the communicational dataflow. The development process of specialized router architecture has high compl...

The early warning disaster system aims to detect and prevent natural disasters (fires, flooding, deforestation and water pollution) by remote sensing of the earth’s surface by processing multispectral data from remote sensing of Earth.

The whitepaper reports our investigation into the porting, optimization and subsequent performance of the astrophysics software package GADGET, on the Intel Xeon Phi. The GADGET code is intended for cosmological N-body/SPH simulations to solve a wide range of astrophysical tasks. The test cases within the project were simulations of galaxy systems....

This work is aimed to investigate and to improve the performance of multiple sequence alignment software ClustalW on the test platform EURORA at CINECA, for the case study of the influenza virus sequences. The objective is code optimization, porting, scaling and performance evaluation of parallel multiple sequence alignment software ClustalW for In...

This activity with the project is aimed to investigate and to improve the performance of the multiple sequence alignment software MSA_BG on the computer system EURORA at CINECA, for the case study of the influenza virus sequences. The objective is code optimization, porting, scaling and performance evaluation of the parallel multiple sequence align...

This paper investigates the efficiency of a model of parallel genetic computation of the traveling salesman problem with circular periodic chromosomes migration. The parallel model is verified by MPI-based program implementation on a multicomputer platform. The correlation of the application and architectural spaces has been investigated by explori...

The paper focuses on the latest trends in supercomputer and high-performance computer architectures with emphasis of the important parameters for parallel computer performance. The main objective is to propose the high-speed network architecture for collective communications in supercomputers "Silicon Galaxy" that provides high-bandwidth, low laten...

This paper explores the efficiency of various strategies for parallel genetic computation of optimization problems on multicomputer platforms. The strategies for designing parallel genetic algorithms on multicomputer platforms are investigated considering the correlations of the algorithmic and the architectural spaces. Two parallel genetic computa...

The project focuses on performance investigation and improvement of multiple biological sequence alignment software MSA_BG on the BlueGene/Q supercomputer JUQUEEN. For this purpose, scientific experiments in the area of bioinformatics have been carried out, using as case study influenza virus sequences. The objectives of the project are code optimi...

In this paper is proposed optimization, scaling, performance evaluation and profiling of parallel multiple sequence alignment based on ClustalW algorithm on the supercomputer BlueGene/Q, so-called JUQUEEN, for the case study of the influenza virus sequences. For this purpose a parallel I/O interface for simultaneous and independent access to single...

In silico biological sequence processing is a key task in molecular biology. This scientific area requires powerful computing resources for exploring large sets of biological data. Parallel in silico simulations based on methods and algorithms for analysis of biological data using high-performance distributed computing is essential for accelerating...

Biocomputing and molecular biology are areas, demanding knowledge and skills for acquisition, storing, management, analysis, interpretation and dissemination of biological information. This requires the utilization of high performance computers and innovative software tools for the management of the vast information, as well as the deployment of in...

The parallel in silico simulations based on methods and algorithms for analysis of biological data using high-performance distributed computing is essential for accelerating the research and reduce the investment. This paper presents a high-performance Grid environment integrating various services and middleware to facilitate access to distributed...

As modern research and engineering computing methodologies, the demands for high-speed computational resources are growing at a rapid rate. The communication performance of collective network is a crucial factor influencing the communication performance of supercomputers which form the prevailing parallel architecture of modern high-performance com...

As modern research and engineering computing methodologies, the demands for high-speed computational resources are growing at a rapid rate. The communication performance of collective network is a crucial factor influencing the communication performance of supercomputers which form the prevailing parallel architecture of modern high-performance com...

In silico biological sequence processing is a key for molecular biology. This scientific area requires powerful computing resources for exploring large sets of biological data. Multiple sequence alignment is widely used method for biological sequence processing. The goal of this method is DNA and protein sequences alignment. This paper presents an...

The flow-control mechanism determinates the manner in which the communicational resources are allocated. Well-designed flow-control mechanism should provide efficient allocation of the communicational resources in wide variety of interconnection networks. The goal of this paper is to suggest a highly effective “Step-Back-on-Blocking” buffered flow...

This activity with the project PRACE-2IP is aimed to investigate and improve the performance of multiple sequence alignment software ClustalW on the supercomputer BlueGene/Q, so-called JUQUEEN, for the case study of the influenza virus sequences. Porting, tuning, profiling, and scaling of this code has been accomplished in this aspect. A parallel I...

An effective resource utilization of the modern high performance computing (HPC) systems is a subject for many scientific research investigations. In this paper a new generation programming languages and models for high performance computing systems have been systematized and presented. The motives for development of modern methods for multithreadi...

The interconnection network is a crucial part of high-performance computer systems. It significantly determines parallel system performance as well as the development and the operating cost. In this paper we suggest efficient and scalable hierarchical multi-ring interconnection network architecture. For building up the interconnection network we ha...

the flow control mechanism is crucial element for achieving low communicational latency and high utilization of the interconnection network resources. A well-designed flow control should balance the communicational load in respect to both uniform and non-uniform traffic patterns. It significantly determines the communication performance of the inte...

Concurrent high performance computing systems are based on highly parallel architectures. As the complexity of the parallel systems increases, it becomes more difficult to predict the interaction between the computational nodes. Failing to foresee the basic dependencies can result in parallel performance degradation and inefficient use of the hardw...

The present study provides a brief overview of the differential methods for contour image segmentation. The starting criteria are the precision in defining the contour of an object in the image and the noise resistance, determined by the ratio between the number of the wrongly detected contours and the number and size of the contour discontinuit...

The flow control mechanism is crucial element for attaining optimal allocation of the communicational resources and achieving high communicational performance. In this paper the current flow control mechanisms have been examined in more details and new highly effective flow control mechanism has been proposed. The behavior and the effectiveness of...

NEMO (Nucleus for European Modeling of the Ocean) is a software package, which allows execution of complex computations related to oceanology. This scientific area requires powerful computing resources for investigation of large data sets, giving numerical solutions of the ocean dynamics, sea-ice model and ocean biogeochemistry. The paper presents...

Nowadays the study of the variability of influenza virus is a problem of very great importance. Influenza type A viruses cause epidemics and pandemics. The problem of restricting the spreading of pandemics and the treatment of the people infected by the influenza virus is widely based on the latest achievements of molecular biology, bioinformatics...

The parallel implementation of methods and algorithms for analysis of biological data using high-performance computing is essential for accelerating the research and reduce the investment. The paper presents a high-performance framework for carrying out scientific experiments in the area of bioinformatics, on the basis of parallel computer simulati...

The study of the variability of influenza virus is very of great importance problem nowadays. Influenza type A viruses cause epidemics and pandemics. The problem of restricting the spreading of pandemics and the treatment of the infected by the influenza virus people is widely based on the latest achievements of molecular biology, bioinformatics an...

Traditionally batch process control is one of the most difficult and complex control domain for implementation since it includes feedback controllers as well as logic control operating under supervisory recipe-based sequential control. Because of the focus on dynamic cross-organizational integration, Web Services technologies complement rather than...

Many-cores processor era havebeen reached already, because the power wall was hit and Moore's Law leads to direction of using these increasing numbers of gates not only for larger caches, complicated branch-prediction logic and larger pipelines – they are used also for clustering a large number of cores, wired by sophisticated on-chip routers.

Modeling of new network topologies requires analytical motivation, followed by simulation confirmation of the expected results. This paper describes the motivation and the development process of a generalized simulation model of a switch. The switch will be implemented in the newly proposed topologies in order to test and explore their performance....

The performance of an interconnection network is highly dependable on both-topology and switch design. There is one more key feature which can make the difference between these network-routing algorithms have the power to make a perfect network completely useless, and on the other hand, it can make it a masterpiece. In this paper we have traced the...

Biological sequence processing is a key of information technology for molecular biology. This scientific area requires powerful computing resources for exploring large sets of biological data. The huge amount of biological sequences accumulated in the world nucleotide and protein databases requires efficient parallel tools for structural genomic an...

The goal of this paper is to propose the performance evaluation of the scaling of parallel software for biological sequence alignment and homology searching based on blast algorithm for sequence searching and clustalw algorithm for multiple sequence alignment on the supercomputer BlueGene/P for the case study of influenza virus sequences variabilit...

The paper presents architectural and programming aspects of modern GPUs in terms of their use for non-graphical calculations. The concept of GPGPU is presented as well as the platform and the programming models of the two common GPGPU standard OpenCL and CUDA. Parallel programming models for image processing on CPU and GPU are suggested. The experi...

Biological sequence processing is a key of information technology for molecular biology. This scientific area requires powerful computing resources for exploring large sets of biological data. Multiple sequence alignment is an important method in the DNA and protein analysis. ClustalW has become the most popular tool and implements a progressive me...

The paper presents a software package BlueVision for parallel processing of multispectral data from remote sensing of the Earth. The purpose is to provide a software framework for high-performance analysis aimed at detection and monitoring of different natural hazards. The package consists of five modules that implement parallel computational modul...

Rennet coagulation of milk is the basic structure forming process for the manufacture of cheese. During this process, the milk passes from a sol to a gel. The process is irreversible, which suggests the use of non destructive methods of control. This control is implemented with a computer system that allows non-contact study of the process in dynam...

A comparative analysis of the two wavelet transforms – the two-dimensional discrete stationary transform and the repagulary one is provided in this paper. The experiment is produced on recognition of 3D medical images.

As grid computing becomes a de facto standard for host- ing calcul-intensive applications, current grid middleware technologies do not deal with interactive (i.e. non-batch) applications. From a Telco (or any service-provider) perspective, such class of applications is highly sensitive. We propose a grid service platform that dynamically provisions...

As modern scientific and engineering computing matures, the demands for high-speed computational resources are growing at a rapid rate. The communication performance of system area network is a crucial factor influencing the parallel performance of computer clusters which form the prevailing architecture of modern high-performance computer systems....

The paper presents parallel computational models of Smith-Waterman algorithm for CPU and GPU. An investigation is made of the performance parameters of computing similarity indexes between query sequences and a reference sequence using the suggested parallel programming models. Implementations for GPU based sequence alignment using nVIDIA CUDA and...

The GRID infrastructure provides an aggregation of a wide variety of distributed resources for solving large-scale data intensive problems in various fields. The aim of this paper is to propose a method for grid resource management based on lottery scheduling. The lottery scheduling algorithm is implemented as an extension of GridSim simulator that...

Bioniformatics is area, demanding knowledge and skills for acquisition, storing, management, analysis, interpretation and dissemination of biological information. This scientific area requires powerful computing resources for exploring large sets of biological data. Biological sequence processing is a key for molecular biology. Smith-Waterman algor...

This paper suggest a model of parallel computation based on Bacteria Foraging metaheuristics for Job Shop Scheduling optimization problem. The parallel model is verified experimentally by Hybrid (MPI + OpenMP) programming implementations, run on heterogeneous computer cluster. The experimental study comprises parallel performance evaluation, parall...

The huge sequences of biological data, being accumulated in databases, require the development of efficient tools for genome sequences comparative analysis and using powerful clusters. The main challenge for data analysis in life sciences is to propose to the molecular biologists an integrated access to progressively increasing amounts of data in m...

Switch and system area network architectural designs are significantly influenced by next generation high-performance computer systems and supercomputer technology. As technology evolves, this impact on interconnection network needs to be considered and reevaluated. In this paper we evaluate a communication performance of a high-speed switch and TO...

Bioinformatics is a scientific area requiring powerful computing resources for exploring large sets of biological data. Sequence alignment is an important method in DNA and protein analysis. BLAST has become the most popular tool and implements a fast heuristic method for sequence alignment and searching. The goal of this paper is to estimate the s...

Switch and system area network architectural designs are significantly influenced by next generation high-performance computer systems and supercomputer technology. As technology evolves, this impact on interconnection network needs to be considered and reevaluated. In this paper we evaluate a communication performance of a high-speed switch and TO...

The aim of this paper is to investigate the efficiency of sequence alignment. The parallel computational model is based on mpiBlast algorithm, data decomposition and manager-worker algorithmic paradigm utilizing massage passing based on MPI and is verified on the basis of flat parallel program implementation on a supercomputer BlueGene/P.

The purpose of this paper is to propose a classifiers design by means of a fast parallel algorithm for training and classification of samples for material recognition. The investigated classifiers are based on spectral analysis of input signals through discrete wavelet transform (DWT). The research line is accelerating the performance of the classi...

Traditionally batch process control is one of the most difficult and complex control system for implementation since it includes basic regulatory as well as logic control operating under supervisory recipe-based sequential control. The focus of this paper should be to present the benefits of web-driven technologies for batch control domain and to p...

The paper treats parallelisms, the utilization of which results in performance improvement of computing platforms that execute multiple processes concurrently. A new method for processes parallelization on second level is suggested which utilizes the standard Process Pool. The queues are served in a round-robin fashion and processes of the various...

The problem of restraining the spreading of pandemics and the treatment of the infected by the influenza virus people is widely based on the latest achievements of molecular biology, cellular biology, biocomputing, as well as many other advanced areas of modern science. In this paper we have performed comparative analyses of viral nucleotide sequen...