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Catalog Publications
Year 2025
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Automatic Cleaning of Time Series Data in Rural Internet of Things Ecosystems That Use Nomadic Gateways
PublicationA serious limitation to the deployment of IoT solutions in rural areas may be the lack of available telecommunications infrastructure enabling the continuous collection of measurement data. A nomadic computing system, using a UAV carrying an on-board gateway, can handle this; it leads, however, to a number of technical challenges. One is the intermittent collection of data from ground sensors governed by weather conditions for...
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Collaborative Learning as a Service – a Blueprint for a Cloud Based Rural IoTs Deployment Facility.
PublicationVast spaces with inadequate telecommunications infrastructure pose a challenge to deploy IoT systems. A tech stack is proposed and implemented on TASKcloud at Gdansk Tech, based on widely available open-source technology components, making it possible to deploy various machine learning models developed on the cloud to constrained end devices, to make them capable of intelligently cleaning measurement data and optimizing their volume...
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Novel nonsteroidal steroid sulfatase inhibitors containing glutamic acid unit
PublicationIn the present work, we designed and successfully synthesized novel steroid sulfatase (STS) inhibitors based on coumarin, tyramine, triazole, and flavone cores with an additional glutamic acid residue in the structure. The molecular modeling studies revealed that designed derivatives have potential to bind to the molecular target active site, at least theoretically. The biological activity of synthesized compounds was evaluated...
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Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field
PublicationSecondary structure is a solid scaffold on which the three-dimensional structure of a protein is built. Therefore, care must be taken to reproduce the secondary structure as accurately as possible in the simulations of protein systems. In this chapter, we summarize the physics-based energy terms that govern secondary-structure formation, the auxiliary restraints on secondary structure derived from bioinformatics and from the experimental...
Year 2024
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Convenient and efficient N-methylation of secondary amines under solvent-free ball milling conditions
PublicationIn the present work, we report the development of a rapid, efcient, and solvent-free procedure for the N-methylation of secondary amines under mechanochemical conditions. After optimization of the milling parameters, a vibrational ball mill was used to synthesize 26 tertiary N-methylated amine derivatives in a short time of 20 min (30 Hz frequency) and high yields ranging from 78 to 95%. An exception was compounds having a hydroxyl...
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Dataset Characteristics and Their Impact on Offline Policy Learning of Contextual Multi-Armed Bandits
PublicationThe Contextual Multi-Armed Bandits (CMAB) framework is pivotal for learning to make decisions. However, due to challenges in deploying online algorithms, there is a shift towards offline policy learning, which relies on pre-existing datasets. This study examines the relationship between the quality of these datasets and the performance of offline policy learning algorithms, specifically, Neural Greedy and NeuraLCB. Our results...
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Development of potent and effective SARS-CoV-2 main protease inhibitors based on maleimide analogs for the potential treatment of COVID-19
PublicationIn the present work, we report a new series of potent SARS-CoV-2 Main Protease (Mpro) inhibitors based on maleimide derivatives. The inhibitory activities were tested in an enzymatic assay using recombinant Mpro (3CL Protease from coronavirus SARS-CoV-2). Within the set of new Mpro inhibitors, 6e demonstrated the highest activity in the enzymatic assay with an IC50 value of 8.52 ± 0.44 mM. The IC50 value for Nirmatrelvir (PF-07321332,...
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Investigation of Performance and Energy Consumption of Tokenization Algorithms on Multi-core CPUs Under Power Capping
PublicationIn this paper we investigate performance-energy optimization of tokenizer algorithm training using power capping. We focus on parallel, multi-threaded implementations of Byte Pair Encoding (BPE), Unigram, WordPiece, and WordLevel run on two systems with different multi-core CPUs: Intel Xeon 6130 and desktop Intel i7-13700K. We analyze execution times and energy consumption for various numbers of threads and various power caps and...
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Performance and Energy Aware Training of a Deep Neural Network in a Multi-GPU Environment with Power Capping
PublicationIn this paper we demonstrate that it is possible to obtain considerable improvement of performance and energy aware metrics for training of deep neural networks using a modern parallel multi-GPU system, by enforcing selected, non-default power caps on the GPUs. We measure the power and energy consumption of the whole node using a professional, certified hardware power meter. For a high performance workstation with 8 GPUs, we were...
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Teaching High–performance Computing Systems – A Case Study with Parallel Programming APIs: MPI, OpenMP and CUDA
PublicationHigh performance computing (HPC) education has become essential in recent years, especially that parallel computing on high performance computing systems enables modern machine learning models to grow in scale. This significant increase in the computational power of modern supercomputers relies on a large number of cores in modern CPUs and GPUs. As a consequence, parallel program development based on parallel thinking has become...
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The Big Book of online education for academics and other teaching professionals
PublicationThe Big Book of Online Education to unikatowa, bogata w multimedia publikacja, napisana przez międzynarodowy zespół autorów – ekspertów w dziedzinie metodyki, nowoczesnej edukacji i e-learningu. Znajdziemy w niej mnóstwo porad, inspiracji i informacji o narzędziach użytecznych w dydaktyce, oraz przykładów zastosowania innowacyjnych metod i technik w praktyce akademickiej. Jest to najbogatsza tego typu pozycja na rynku poradników...
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Wyzwania współpracy z robotem jako członkiem zespołu
Publication– Cel: Ocena, jakie są przekonania dotyczące współpracy z robotami w zespole, jakie są obawy i oczekiwania związane z „zatrudnianiem” robotów. – Metodyka badań: Badania ilościowe zrealizowane z zastosowaniem kwestionariusza ankiety w grupie 593 specjalistów IT. – Wyniki badań: Roboty nadal traktowane są głównie jako narzędzia, nie jako podmioty uczestniczące w pracy zespołu. Przekonanie, że obecność robota w zespole nie wyeliminuje...
Year 2023
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A multithreaded CUDA and OpenMP based power‐aware programming framework for multi‐node GPU systems
PublicationIn the paper, we have proposed a framework that allows programming a parallel application for a multi-node system, with one or more GPUs per node, using an OpenMP+extended CUDA API. OpenMP is used for launching threads responsible for management of particular GPUs and extended CUDA calls allow to manage CUDA objects, data and launch kernels. The framework hides inter-node MPI communication from the programmer who can benefit from...
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Dataset Related Experimental Investigation of Chess Position Evaluation Using a Deep Neural Network
PublicationThe idea of training Articial Neural Networks to evaluate chess positions has been widely explored in the last ten years. In this paper we investigated dataset impact on chess position evaluation. We created two datasets with over 1.6 million unique chess positions each. In one of those we also included randomly generated positions resulting from consideration of potentially unpredictable chess moves. Each position was evaluated...
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Efficient parallel implementation of crowd simulation using a hybrid CPU+GPU high performance computing system
PublicationIn the paper we present a modern efficient parallel OpenMP+CUDA implementation of crowd simulation for hybrid CPU+GPU systems and demonstrate its higher performance over CPU-only and GPU-only implementations for several problem sizes including 10 000, 50 000, 100 000, 500 000 and 1 000 000 agents. We show how performance varies for various tile sizes and what CPU–GPU load balancing settings shall be preferred for various domain...
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Levels of creativity in architectural education
PublicationArchitectural design combines engineering science and art, thus stimulating creativity is a challenge in the didactic process. There are various levels of creativity that can be attained through architectural education. From idea to architecture (FITA) is a teaching method based on metaphorical and analogical reasoning that was developed, implemented and tested during architectural design classes in the Faculty of Architecture...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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Parallel implementation of a Sailing Assistance Application in a Cloud Environment
PublicationSailboat weather routing is a highly complex problem in terms of both the computational time and memory. The reason for this is a large search resulting in a multitude of possible routes and a variety of user preferences. Analysing all possible routes is only feasible for small sailing regions, low-resolution maps, or sailboat movements on a grid. Therefore, various heuristic approaches are often applied, which can find solutions...
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Performance assessment of OpenMP constructs and benchmarks using modern compilers and multi-core CPUs
PublicationConsidering ongoing developments of both modern CPUs, especially in the context of increasing numbers of cores, cache memory and architectures as well as compilers there is a constant need for benchmarking representative and frequently run workloads. The key metric is speed-up as the computational power of modern CPUs stems mainly from using multiple cores. In this paper, we show and discuss results from running codes such as:...
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The congruence of mental models in entrepreneurial teams – implications for performance and satisfaction in teams operating in an emerging economy
PublicationPurpose – The paper aims to explore the relationship between the congruence of mental models held by the members of entrepreneurial teams operating in an emerging economy (Poland) and entrepreneurial outcomes (performance and satisfaction). Design/methodology/approach – The data obtained from 18 nascent and 20 established entrepreneurial teams was analysed to answer hypotheses. The research was quantitative and was conducted using...
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The Idea of a Student Research Project as a Method of Preparing a Student for Professional and Scientific Work
PublicationIn the paper we present the idea and implementation of a student research project course within the master’s program at the Faculty of Electronics, Telecommunications and Informatics, Gdansk Tech. It aims at preparing students for performing research and scientific tasks in future professional work. We outline the evolution from group projects into research project and the current deployment of both at bachelor’s and master’s levels...
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Visual Features for Improving Endoscopic Bleeding Detection Using Convolutional Neural Networks
PublicationThe presented paper investigates the problem of endoscopic bleeding detection in endoscopic videos in the form of a binary image classification task. A set of definitions of high-level visual features of endoscopic bleeding is introduced, which incorporates domain knowledge from the field. The high-level features are coupled with respective feature descriptors, enabling automatic capture of the features using image processing methods....
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Wykorzystanie klasyfikacji funkcjonalnej usług do efektywnego zarządzania zasobami chmurowymi
PublicationWykazano jak istotnym problemem jest zarzadzanie chmurą obliczeniową, w tym alokacja zasobów do wykonania usług (workloadów) zgłoszonych przez użytkownika. Przeanalizowano problem podziału usług wdrażanych w środowiskach chmurowych na klasy określające ich funkcjonalność. Zaproponowano oryginalną metodę alokacji workloadów wykorzystującą wprowadzoną klasyfikację funkcjonalną oraz identyfikację tych klas na podstawie wielkości generowanego...
Year 2022
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Algorytm mrówkowy do zarządzania zasobami sprzętowymi chmury obliczeniowej w przypadku różnych kategorii usług
PublicationZarządzanie chmurą obliczeniową odbywa się na dwóch poziomach: zarządzanie żądaniami klientów chmury oraz zarządzanie jej infrastrukturą, na której te usługi są realizowane. Analizując standardy dotyczące zarządzania usługami, w niniejszym rozdziale skoncentrowano się na drugim poziomie zarządzania, którego głównym celem jest efektywne wykonanie wskazanej usługi (lub usług) na dostępnych zasobach sprzętowych, tak by spełnione zostały...
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Development of Sulfamoylated 4‑(1-Phenyl‑1H‑1,2,3-triazol-4-yl)phenol Derivatives as Potent Steroid Sulfatase Inhibitors for Efficient Treatment of Breast Cancer
PublicationWe present here the advances achieved in the development of new sulfamoylated 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives as potent steroid sulfatase (STS) inhibitors for the treatment of breast cancer. Prompted by promising biological results and in silico analysis, the initial series of similar compounds were extended, appending a variety of m-substituents at the outer phenyl ring. The inhibition profiles of the newly...
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Edu Inspiracje WZiE: Technologia XR w edukacji. Czy jesteśmy na nią gotowi?
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Featured based CAVE software factory
PublicationIn the paper we convey the lessons learned along the path we have gone through several years since establishing a room-sized CAVE installation at our university, from craft manufacturing and ad-hoc software reuse of VR software products to the robust feature driven software product line (SPL) implementing the Product Line Engineering (PLE) factory paradigm. With that we can serve all our departments and other entities from the...
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Food Classification from Images Using a Neural Network Based Approach with NVIDIA Volta and Pascal GPUs
PublicationIn the paper we investigate the problem of food classification from images, for the Food-101 dataset extended with 31 additional food classes from Polish cuisine. We adopted transfer learning and firstly measured training times for models such as MobileNet, MobileNetV2, ResNet50, ResNet50V2, ResNet101, ResNet101V2, InceptionV3, InceptionResNetV2, Xception, NasNetMobile and DenseNet, for systems with NVIDIA Tesla V100 (Volta) and...
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Inteligentne zarządzanie usługami chmurowymi
PublicationRozwój chmur obliczeniowych stanowi wyzwanie dla nowych efektywnych metod zarządzania zasobami chmurowymi, zwłaszcza, że oprócz usług typu SaaS rozwija się nowe kategorie usług jak obliczenia brzegowe czy wielochmurowe. W pracy zaproponowano ogólny model zarządzania usługami oraz efektywne procedury alokacji zasobów. Podkreślono potrzebę oszacowania parametrów zasobów chmury by zapewnić wykonanie żądanych usług. Przedstawiono również...
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Investigation of Performance and Configuration of a Selected IoT System—Middleware Deployment Benchmarking and Recommendations
PublicationNowadays Internet of Things is gaining more and more focus all over the world. As a concept it gives many opportunities for applications for society and it is expected that the number of software services deployed in this area will still grow fast. Especially important in this context are properties connected with deployment such as portability, scalability and balance between software requirements and hardware capabilities. In...
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Performance Assessment of Using Docker for Selected MPI Applications in a Parallel Environment Based on Commodity Hardware
PublicationIn the paper, we perform detailed performance analysis of three parallel MPI applications run in a parallel environment based on commodity hardware, using Docker and bare-metal configurations. The testbed applications are representative of the most typical parallel processing paradigms: master–slave, geometric Single Program Multiple Data (SPMD) as well as divide-and-conquer and feature characteristic computational and communication...
Year 2021
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All-gather Algorithms Resilient to Imbalanced Process Arrival Patterns
PublicationTwo novel algorithms for the all-gather operation resilient to imbalanced process arrival patterns (PATs) are presented. The first one, Background Disseminated Ring (BDR), is based on the regular parallel ring algorithm often supplied in MPI implementations and exploits an auxiliary background thread for early data exchange from faster processes to accelerate the performed all-gather operation. The other algorithm, Background Sorted...
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Anticancer Properties of Amino Acid and Peptide Derivatives of Mycophenolic Acid
PublicationBackground: Although Mycophenolic Acid (MPA) is applied as prodrugs in clinic as an immunosuppressant, it also possesses anticancer activity. MPA acts as Inosine-5’-Monophosphate Dehydrogenase (IMPDH) inhibitor, where the carboxylic group at the end of the side chain interacts with Ser 276 of the enzyme via hydrogen bonds. Therefore, MPA derivatives with other polar groups indicated high inhibition too. On the other hand, potent...
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Assessment of OpenMP Master–Slave Implementations for Selected Irregular Parallel Applications
PublicationThe paper investigates various implementations of a master–slave paradigm using the popular OpenMP API and relative performance of the former using modern multi-core workstation CPUs. It is assumed that a master partitions available input into a batch of predefined number of data chunks which are then processed in parallel by a set of slaves and the procedure is repeated until all input data has been processed. The paper experimentally...
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Benchmarking Scalability and Security Configuration Impact for A Distributed Sensors-Server IOT Use Case
PublicationInternet of Things has been getting more and more attention and found numerous practical applications. Especially important in this context are performance, security and ability to cope with failures. Especially crucial is to find good trade-off between these. In this article we present results of practical tests with multiple clients representing sensors sending notifications to an IoT middleware – DeviceHive. We investigate performance...
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Human awareness versus Autonomous Vehicles view: comparison of reaction times during emergencies
PublicationHuman safety is one of the most critical factors when a new technology is introduced to the everyday use. It was no different in the case of Autonomous Vehicles (AV), designed to replace generally available Conventional Vehicles (CV) in the future. AV rules, from the start, focus on guaranteeing safety for passengers and other road users, and these assumptions usually work during normal traffic conditions. However, there is still...
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Improving Clairvoyant: reduction algorithm resilient to imbalanced process arrival patterns
PublicationThe Clairvoyant algorithm proposed in “A novel MPI reduction algorithm resilient to imbalances in process arrival times” was analyzed, commented and improved. The comments concern handling certain edge cases in the original pseudocode and description, i.e., adding another state of a process, improved cache friendliness more precise complexity estimations and some other issues improving the robustness of the algorithm implementation....
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Interval Edge Coloring of Bipartite Graphs with Small Vertex Degrees
PublicationAn edge coloring of a graph G is called interval edge coloring if for each v ∈ V(G) the set of colors on edges incident to v forms an interval of integers. A graph G is interval colorable if there is an interval coloring of G. For an interval colorable graph G, by the interval chromatic index of G, denoted by χ'_i(G), we mean the smallest number k such that G is interval colorable with k colors. A bipartite graph G is called (α,β)-biregular...
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Just look at to open it up: A biometric verification facility for password autofill to protect electronic documents
PublicationElectronic documents constitute specific units of information, and protecting them against unauthorized access is a challenging task. This is because a password protected document may be stolen from its host computer or intercepted while on transfer and exposed to unlimited offline attacks. The key issue is, therefore, making document passwords hard to crack. We propose to augment a common text password authentication interface...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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New potent steroid sulphatase inhibitors based on 6-(1-phenyl-1H-1,2,3-triazol-4-yl)naphthalen-2-yl sulphamate derivatives
PublicationIn the present work, we report a new class of potent steroid sulphatase (STS) inhibitors based on 6-(1-phenyl-1H-1,2,3-triazol-4-yl)naphthalen-2-yl sulphamate derivatives. Within the set of new STS inhibitors, 6-(1-(1,2,3-trifluorophenyl)-1H-1,2,3-triazol-4-yl)naphthalen-2-yl sulphamate 3L demonstrated the highest activity in the enzymatic assay inhibiting the STS activity to 7.98% at 0.5 µM concentration. Furthermore, to verify...
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Novel 1,2,3-Triazole Derivatives as Mimics of Steroidal System—Synthesis, Crystal Structures Determination, Hirshfeld Surfaces Analysis and Molecular Docking
PublicationHerein, we present the synthesis and crystal structures determination of five 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives containing halogen atoms, 6a–e, which may be used as an excellent mimic of steroids in the drug development process. Good quality crystals obtained for all of the synthesized compounds allowed the analysis of their molecular structures. Subsequently, the determined crystal structures were used to calculate...
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O neutralności, prezydencie, portalach społecznościowych i edukacji
PublicationArtykuł dotyczy neutralności sieci, która omówiona jest w kontekście zablokowania kont prezydenta USA w mediach społecznościowych. Odnosząc się do różnych znaczeń neutralności i opinii zebranych wśród informatyków, autorzy sformułowali rekomendacje dotyczące miejsca neutralności w edukacji informatycznej studentów.
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Optimization of Data Assignment for Parallel Processing in a Hybrid Heterogeneous Environment Using Integer Linear Programming
PublicationIn the paper we investigate a practical approach to application of integer linear programming for optimization of data assignment to compute units in a multi-level heterogeneous environment with various compute devices, including CPUs, GPUs and Intel Xeon Phis. The model considers an application that processes a large number of data chunks in parallel on various compute units and takes into account computations, communication including...
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Paradoks decyzyjny – racjonalne i intuicyjne podejmowanie decyzji
PublicationW pracy scharakteryzowano poszczególne etapy działań prowadzące do znajdowania najlepszych rozwiązań dla rozpatrywanego problemu. Zwrócono uwagę na paradoks decyzyjny który wskazuje, że mądre rozwiązanie problemu wymaga zarówno racjonalnego, jak i intuicyjnego podejścia. Na przykładzie sortowania obrazów zaprezentowano niezależnie oba podejścia podkreślając potrzebę ich wzajemnego uzupełniania się. Podkreślono trudność budowy algorytmów,...
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Total chromatic sum for trees
PublicationThe total chromatic sum of a graph is the minimum sum of colors (natural numbers) taken over all proper colorings of vertices and edges of a graph. We provide infinite families of trees for which the minimum number of colors to achieve the total chromatic sum is equal to the total chromatic number. We construct infinite families of trees for which these numbers are not equal, disproving the conjecture from 2012.
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Zasady efektuacji w działaniach początkujących przedsiębiorców
PublicationArtykuł dotyczy efektuacyjnego, dynamicznego modelu przedsiębiorczości stanowiącego odpowiedź na wymagania zmiennego, niepewnego otoczenia biznesowego, w którym funkcjonują współcześni przedsiębiorcy. We wcześniejszych badaniach, obejmujących stosowanie pięciu zasad efektuacji w prowadzeniu firm, różni autorzy odnosili się głównie do dojrzałych przedsiębiorców, charakteryzujących się doświadczeniem w zakładaniu i prowadzeniu własnego...
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Znaczenie i dynamika efektuacji w działaniach zespołów projektowych IT
PublicationCel: Celem opracowania jest sprawdzenie, na ile wdrażanie zasad efektuacji jest korzystne dla efektywności zespołów projektowych pracujących nad innowacyjnymi rozwiązaniami i czy wpływa na ich satysfakcję. Metodyka badań: Badania ilościowe zrealizowano w studenckich zespołach projektowych z branży IT, opracowujących rozwiązania na zlecenie interesariuszy zewnętrznych. Do pomiaru zmiennych wykorzystano autorskie kwestionariusze....
Year 2020
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A Universal Theory of Wisdom . A Mind - oriented Approach
PublicationThe purpose of the paper is to synthesize the issues of human wisdom in terms of minds which create knowledge-based judgment. We form a transdisciplinary, big-picture view of the wisdom of humans. Findings: Wisdom is the right judgment and choice in the context of the art of living. Practical implications: Wisdom can be developed within the set of minds. Social implications: To pursue wisdom in thinking and action, one must extend...
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Auto-tuning methodology for configuration and application parameters of hybrid CPU + GPU parallel systems based on expert knowledge
PublicationAuto-tuning of configuration and application param- eters allows to achieve significant performance gains in many contemporary compute-intensive applications. Feasible search spaces of parameters tend to become too big to allow for exhaustive search in the auto-tuning process. Expert knowledge about the utilized computing systems becomes useful to prune the search space and new methodologies are needed in the face of emerging heterogeneous...