Publikační činnost Katedry informatiky / Publications of Department of Computer Science (460)

Permanent URI for this collectionhttp://hdl.handle.net/10084/64750

Kolekce obsahuje bibliografické záznamy publikační činnosti (článků) akademických pracovníků Katedry informatiky (460) v časopisech a v Lecture Notes in Computer Science registrovaných ve Web of Science od roku 2003 po současnost.
Do kolekce jsou zařazeny:
a) publikace, u nichž je v originálních dokumentech jako působiště autora (adresa) uvedena Vysoká škola báňská-Technická univerzita Ostrava (VŠB-TUO),
b) publikace, u nichž v originálních dokumentech není v adrese VŠB-TUO uvedena, ale autoři prokazatelně v době jejich zpracování a uveřejnění působili na VŠB-TUO.

Bibliografické záznamy byly původně vytvořeny v kolekci Publikační činnost akademických pracovníků VŠB-TUO, která sleduje publikování akademických pracovníků od roku 1990.

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Now showing 1 - 20 out of 582 results

Impact of antiphospholipid syndrome on placenta and uterine NK cell function: insights from a mouse model
(Springer Nature, 2024) Martirosyan, Anush; Kriegová, Eva; Savara, Jakub; Abroyan, Liana; Ghonyan, Susanna; Slobodová, Zuzana; Nesnadná, Romana; Manukyan, Gayane
Antiphospholipid syndrome (APS) is associated with recurrent pregnancy morbidity, yet the underlying mechanisms remain elusive. We performed multifaceted characterization of the biological and transcriptomic signatures of mouse placenta and uterine natural killer (uNK) cells in APS. Histological analysis of APS placentas unveiled placental abnormalities, including disturbed angiogenesis, occasional necrotic areas, fibrin deposition, and nucleated red blood cell enrichment. Analyses of APS placentas showed a reduced cell proliferation, lower protein content and thinning of endothelial cells. Disturbances in APS trophoblast cells were linked to a cell cycle shift in cytotrophoblast cells, and a reduced number of spiral artery-associated trophoblast giant cells (SpA-TGC). Transcriptomic profiling of placental tissue highlighted disruptions in cell cycle regulation with notable downregulation of genes involved in developmental or signaling processes. Cellular senescence, metabolic and p53-related pathways were also enriched, suggesting potential mechanisms underlying placental dysfunction in APS. Thrombotic events, though occasionally detected, appeared to have no significant impact on the overall pathological changes. The increased number of dysfunctional uNK cells was not associated with enhanced cytotoxic capabilities. Transcriptomic data corroborated these findings, showing prominent suppression of NK cell secretory capacity and cytokine signaling pathways. Our study highlights the multifactorial nature of APS-associated placental pathologies, which involve disrupted angiogenesis, cell cycle regulation, and NK cell functionality.
Complexity of synovial fluid-derived monocyte-macrophage-lineage cells in knee osteoarthritis
(Elsevier, 2024) Mikulková, Zuzana; Gallo, Jiří; Manukyan, Gayane; Trajerová, Markéta; Savara, Jakub; Shrestha, Bishu; Dýšková, Tereza; Nesnadná, Romana; Slobodová, Zuzana; Štefančík, Michal; Kriegová, Eva
Synovial fluid (SF)-derived monocyte-macrophage (MON-Mf)-lineage cells in knee osteoarthritis (KOA) remain poorly understood. We analyzed SF samples from 420 patients with KOA with effusion. The MONMf cells accounted for 47.4% (median; range 7.1%-94.4%) of CD45+ cells and consisted of four subpopulations that correlated with the distribution and activation of other immune cells. The most abundant subpopulation was that of inactive CD11b+CD14-CD16- myeloid dendritic cells (mDCs; cDC2), which exhibited low cytokine production, low T lymphocyte stimulation, and high migratory ability. Other major subpopulations included CD11b+CD14+CD16- monocyte-like cells and CD11b+CD14+CD16+ macrophages, which share a similar transcriptomic profile. A subpopulation of CD11b-CD14-CD16- mDCs (cDC1) was less common. A higher proportion of CD11b+CD14-CD16- mDCs was linked to early-stage KOA and mild joint pain. Dendritic cells were rarely present in KOA synovium. This study revealed the considerable complexity of SF-derived MON-Mf subpopulations and highlighted the role of inactive mDCs in KOA.
Parameter extraction model of wind turbine based on a novel pigeon-inspired optimization algorithm
(Taiwan Academic Network Executive Committee, 2024) Pan, Jeng-Shyang; Liu, Fei-Fei; Tian, Ai-Qing; Kong, Lingping; Chu, Shu-Chuan
This paper has been designed to address the problems of slow convergence and low convergence accuracy of the pigeon-inspired optimization (PIO) algorithm. The evolutionary mechanism of the PIO algorithm contains two stages, exploration and exploitation, which also exist to solve various numerical optimization problems not well. In order to solve the above problems, this paper proposes a novel pigeon-inspired optimization (NPIO) algorithm, which fuses the two stages of the operator into one stage, where exploitation and exploration are carried out simultaneously, and can assist the algorithm to find the optimal solution better. Numerical optimization problems can be solved with a smaller number of iterations. To verify the performance of the NPIO, standard test functions and practical application scenarios are selected for validation. Firstly, this paper uses 23 test functions to test and cross-sectionally compare with five optimization algorithms. The experimental results show that the NPIO is more competitive than the other five algorithms. Secondly, this paper is based on a high-precision mathematical model commonly used for wind turbines. It uses measurable quantities of wind turbines under actual operating conditions for the theoretical analysis of parameter identifiability. The results show that NPIO has a strong performance in wind turbine parameter identification.
High cumulative glucocorticoid dose is associated with increased levels of inflammation-related mediators in active rheumatoid arthritis
(Frontiers Media S.A., 2024) Petráčková, Anna; Horák, Pavel; Savara, Jakub; Skácelová, Martina; Kriegová, Eva
Glucocorticoids (GCs) are widely used as a treatment for rheumatoid arthritis (RA), leading to high cumulative doses in long-term treated patients. The impact of a high cumulative GC dose on the systemic inflammatory response in RA remains poorly understood. Methods We investigated long-treated patients with RA (n = 72, median disease duration 14 years) through blood counts and the serum levels of 92 inflammation-related proteins, and disease activity was assessed using the Simple Disease Activity Index (SDAI). Patients were grouped based on the cumulative GC dose, with a cut-off value of 20 g (low/high, n = 49/23). Results and discussion Patients with a high cumulative GC dose within the active RA group had elevated serum levels in 23 inflammation-related proteins compared with patients with a low dose (cytokines/soluble receptors: CCL3, CCL20, CCL25, IL-8, CXCL9, IL-17A, IL-17C, IL-18, sIL-18R1, IL-10, sIL-10RB, OSM and sOPG; growth factors: sTGF alpha and sHGF; other inflammatory mediators: caspase 8, STAMBP, sCDCP1, sirtuin 2, 4E-BP1, sCD40, uPA and axin-1; pcorr < 0.05). In non-active RA, the high and low GC groups did not differ in analysed serum protein levels. Moreover, patients with active RA with a high GC dose had an increased white blood cell count, increased neutrophil-lymphocyte and platelet-lymphocyte ratios and a decreased lymphocyte-monocyte ratio compared with the low dose group (p < 0.05). This is the first study to report elevated serum levels in inflammation-related proteins and deregulated blood counts in patients with active RA with a high cumulative GC dose. The elevated systemic inflammation highlights the importance of improving care for patients receiving high cumulative GC doses.
Transcriptomic profiling of orbital fat tissue and ocular surface wash in active thyroid eye disease requiring urgent orbital decompression
(Association for Research in Vision and Ophthalmology, 2025) Petráčková, Anna; Schovánek, Jan; Karhanová, Marta; Savara, Jakub; Nesnadná, Romana; Kriegová, Eva
PURPOSE. Thyroid eye disease (TED) is an autoimmune disorder characterized by orbital inflammation and tissue remodeling. Although most patients with active TED respond to medical therapy, a subset develops sight-threatening complications which require urgent orbital decompression when conservative treatment fails. This study aimed to elucidate the molecular mechanisms underlying active, moderate-to-severe TED in patients requiring urgent orbital decompression during the active disease stage. METHODS. Transcriptomic profiling was performed on retro-orbital fat samples from 13 patients and ocular surface wash samples from 9 patients undergoing urgent orbital decompression, as well as on samples from control subjects. Differential gene expression, pathway enrichment, cell-type composition, and drug-gene interactions were analyzed. RESULTS. In retro-orbital fat, the majority of differentially expressed genes were upregulated, predominantly mapping to immune system, with a pronounced neutrophilic signature including degranulation and extracellular trap formation. Increased infiltration of neutrophils, B cells, and T cells was observed, whereas ocular surface wash samples exhibited a largely downregulated immune signature, reflecting compartment-specific immune responses. Expression of several transcripts from ocular surface wash correlated with patients' disease activity, suggesting potential use as noninvasive biomarkers with CD151, MAST4, and HPCAL1 genes correlating best. Drug-gene interaction analysis nominated JAK and BTK inhibitors as candidate therapeutics in TED. CONCLUSIONS. This study provides a unique molecular atlas of active, moderate-to-severe TED environment, uncovers the active role of neutrophils in TED pathogenesis, and identifies candidate therapeutic targets and noninvasive biomarkers that may inform future clinical strategies.
Window function expression: Let the self-join enter
(Association for Computing Machinery, 2024) Bača, Radim
Window function expressions (WFEs) became part of the SQL:2003 standard, and since then, they have often been implemented in database systems (DBS). They are especially essential to OLAP DBSs, and people use them daily. Even though WFEs are a heavily used part of the SQL language, the amount of research done on their optimization in the last two decades is not significant. WFE does not extend the expressive power of the SQL language, but it makes writing SQL queries easier and more transparent. DBSs always compile SQL queries with WFE using a sequence of partition-sort-compute operators, which we call a linear strategy. Plans resulting from the linear strategy are robust and, in many cases, efficient. This article introduces an alternative strategy using a self-join, which is not considered in the current DBSs. We call it the self-join strategy, and it is based on an SQL query transformation where the result query uses a self-join query plan to compute WFE. One output of this work is a tool that can automatically perform such SQL query transformations. We created a microbenchmark showing that the self-join strategy is more effective than the linear strategy in many cases. We also performed a cost-based experiment to evaluate the query optimizers' ability to select an appropriate strategy. The article's main aim is to show that usage of the self-join strategy for queries with WFE is beneficial if selected in a cost-based manner.
A novel membrane-inspired evolutionary algorithm framework for VRPTW
(Springer Nature, 2026) Bai, Zhonghai; Snášel, Václav; Mirjalili, Seyedali; Vo, Bay; Kong, Lingping; Wang, Xiaopeng
The vehicle routing problem with time windows (VRPTW) has gained much attention recently due to its wide application in operations research and logistics. VRPTW has been proven to be an NP-hard problem whose optimal solution is computationally costly. Scholars have proposed many methods, such as exact algorithms, heuristics, and metaheuristics, to find near-optimal solutions for the VRPTW. Exact algorithms are limited to small-scale problems, while heuristic algorithms and metaheuristics often converge to locally optimal solutions, despite their applicability to larger-scale problems. This paper proposes a novel membrane-inspired evolutionary algorithm framework (MEAF) consisting of isolated evolutionary rules, communication output rules, communication input rules, fusion-exchange information operation, and membrane dissolution rules. By leveraging the advantages of multiple metaheuristics algorithms and avoiding the pitfalls of local optima, MEAF offers a promising solution to address complex problems. The effectiveness of the proposed MEAF is verified by applying three classical metaheuristics, namely Genetic Algorithm (GA), Ant Colony System (ACS), and Particle Swarm Algorithm (PSO), to solve the VRPTW problem. The experiments are run on 56 instances of Solomon with 100 client benchmarks. The evaluation of the experimental results combined with the mean and standard deviation values show that the algorithm performs better in 54 out of 56 instances, demonstrating the effectiveness and stability of the proposed algorithm.
Advanced control parameter optimization in DC motors and liquid level systems
(Springer Nature, 2025) Ekinci, Serdar; Izci, Davut; Almomani, Mohammad H.; Saleem, Kashif, kashif; Abu Zitar, Raed; Smerat, Aseel; Snášel, Václav; Ezugwu, Absalom E.; Abualigah, Laith
In recent times, there has been notable progress in control systems across various industrial domains, necessitating effective management of dynamic systems for optimal functionality. A crucial research focus has emerged in optimizing control parameters to augment controller performance. Among the plethora of optimization algorithms, the mountain gazelle optimizer (MGO) stands out for its capacity to emulate the agile movements and behavioral strategies observed in mountain gazelles. This paper introduces a novel approach employing MGO to optimize control parameters in both a DC motor and three-tank liquid level systems. The fine-tuning of proportional-integral-derivative (PID) controller parameters using MGO achieves remarkable results, including a rise time of 0.0478 s, zero overshoot, and a settling time of 0.0841 s for the DC motor system. Similarly, the liquid level system demonstrates improved control with a rise time of 11.0424 s and a settling time of 60.6037 s. Comparative assessments with competitive algorithms, such as the grey wolf optimizer and particle swarm optimization, reveal MGO's superior performance. Furthermore, a new performance indicator, ZLG, is introduced to comprehensively evaluate control quality. The MGO-based approach consistently achieves lower ZLG values, showcasing its adaptability and robustness in dynamic system control and parameter optimization. By providing a dependable and efficient optimization methodology, this research contributes to advancing control systems, promoting stability, and enhancing efficiency across diverse industrial applications.
Spiral-refraction mutation prairie dog algorithm: Optimization framework for engineering design of interconnected multimachine power system
(Elsevier, 2024) Rizk-Allah, Rizk M.; Snášel, Václav; Izci, Davut; Ekinci, Serdar
Many real-world engineering problems, characterized by high-dimensionality, nonlinearity, nonconvexity, and multi-modality, demand advanced optimization methods. Traditional algorithms may struggle with these challenges. Prairie dog optimization (PDO) was proposed for function optimization but faces limitations in balancing exploration and exploitation due to two reasons. The first one is related to diversity features which may not be efficient, and the second one is related to having no leading mechanism for direct search feature towards the promising regions. With that in mind, this study introduces an enhanced PDO variant, improved PDO (IPDO), addressing PDO's drawbacks through two key strategies: refraction-based learning (RBL) and spiral search learning (SSL). RBL enhances exploration by generating refraction solutions, while SSL conducts deep local searches around the best solution, strengthening exploitation. IPDO's performance is evaluated on benchmarks, IEEE CEC2017/CEC2020 test suites, and real-world constraint engineering optimization problems. Comparative analyses, including statistical measures, convergence analysis, and boxplot analysis, demonstrate IPDO's superiority. Besides, the IPDO is applied to estimate more promising parameters of power system stabilizer utilized in an interconnected multimachine power system using Western System Coordinating Council three-machine, ninebus power system. Results illustrate that the IPDO harvests the better estimation among the other methods, making it to be an efficient and powerful tool for dealing with the efficient operation of an interconnected multimachine power system which is a challenging real-world engineering problem.
IndiVNet A region adaptive semantic image segmentation for autonomous driving in unstructured environments
(Springer Nature, 2025) Chakraborty, Pritam; Bandyopadhyay, Anjan; Bhattacharyya, Siddhartha, Siddhartha; Platoš, Jan
Autonomous navigation in developing regions is challenged by heterogeneous traffic, dynamic occlusions, and weak road structure. Existing segmentation models, largely trained on structured Western datasets, struggle to generalize under these conditions. To address this gap, we propose IndiVNet, a semantic segmentation architecture tailored for unstructured Indian driving environments. IndiVNet introduces a progressive dilation encoder (616) that captures fine-grained details and broad contextual cues without inducing oversparsity. Evaluated on the India Driving Dataset (IDD), it achieves 69.98% mIoU, outperforming CNN and Transformer baselines, and reaches 73.2% mIoU on CAMVID, demonstrating strong cross-domain generalization. By combining contextual adaptability with real-time efficiency, IndiVNet offers a scalable, region-aware solution for robust autonomous navigation in complex environments.
Lexical predicates do substitute in fine-grained attitudes
(Springer Nature, 2025) Jespersen, Bjørn
Let {'is a woodchuck', 'is a groundhog'} be a pair of synonymous lexical predicates. Are they intersubstitutable within a fine-grained attitude ascription without affecting either the truth-value of the ascription or the content of the attitude? I will show that synonymy is sufficient to preserve substitutability within any non-quotational context. Only this requires that substitution is executed within a semantics that observes semantic and epistemic transparency also in contexts such as hyperintensional belief reports. I will develop my argument within Transparent Intensional Logic. I use my pro-substitution claim to argue against one wrong reason for fine-graining, which introduces logical distinctions without semantic differences.
Using synthetic data for pretraining partial discharge detection in overhead transmission lines
(Springer Nature, 2025) Klein, Lukáš; Fulneček, Jan; Kabot, Ondřej; Dvorský, Jiří; Prokop, Lukáš
Accurate detection of partial discharges (PDs) in medium-voltage overhead transmission lines is critical for preemptive maintenance and avoiding costly outages, yet it is challenged by scarce labeled data and pervasive electromagnetic interference. This paper investigates a hybrid simulation-and-data-driven framework in which synthetically generated PD signals are used to pretrain deep neural networks and are subsequently fine-tuned on a limited set of real overhead-line measurements. The synthetic pipeline systematically varies PD repetition rates, amplitude distributions, vegetation-contact scenarios, and noise conditions, producing diverse time-series and spectrogram-like representations that approximate real operating environments. We conduct a comprehensive ablation study across multiple architectures—Convolutional Neural Networks (CNNs), a Vision Transformer (ViT), and a Long Short-Term Memory (LSTM) network—and analyze their sensitivity to granular sweeps of synthetic-data parameters. CNN-based models decisively outperform ViT and LSTM counterparts on the spectrogram-based classification task, while ViT and LSTM fail to learn meaningful representation. For the successful CNNs, pretraining on carefully parameterized synthetic datasets—particularly those reflecting higher PD activity, such as our Datasets 3 and 4—consistently improves downstream performance on real data, boosting the Matthews Correlation Coefficient (MCC) on imbalanced, cost-sensitive test sets by roughly 10–20% compared with training from scratch. At the same time, we show that poorly aligned synthetic data can degrade generalization, underscoring the need for accurate noise calibration and domain-aligned simulation. Overall, the results confirm that (i) architectural choice is pivotal for PD detection in overhead lines and (ii) well-designed synthetic data is a powerful, practical lever for achieving reliable and cost-effective PD monitoring when real labeled data are limited.
From constraints fusion to manifold optimization: A new directional transport manifold metaheuristic algorithm
(Elsevier, 2024) Snášel, Václav; Kong, Lingping; Das, Swagatam
The ascent of geometry-based models and methodologies, exemplified by geometric deep learning and manifold numerical optimization algorithms, has inaugurated a novel domain across various applications that grapple with geometric data complexities, such as electroencephalogram signals represented by symmetric positive definite matrix manifold, hierarchical data represented by hyperbolic manifold. The imperative fuels this inevitable paradigm shift to encapsulate the intricacies and richness inherent in data, areas where traditional methods prove inadequate. While metaheuristic algorithms are renowned for their versatile adaptability across applications, offering practical solutions within reasonable timeframes. However, the conventional metaheuristic algorithms fail on manifold applications with meaningless solutions. From an extrinsic optimization perspective, we treat manifold optimization problems as general optimization problems with multiple fused constraints that limit the optimization path to the manifold. This study pioneered the proposal and implementation of a metaheuristic manifold optimization, introducing a novel directional transport operator to rectify previously identified issues. Through experimentation across five sets of 25 problems, comparing against five algorithms, including both gradient-free and gradient-dominant counterparts, our proposed algorithm emerges as the optimal performer within the gradient-free category, demonstrating competitiveness even against gradient-dominant algorithms. Furthermore, we applied the proposed algorithm to the robot dynamic manipulation problem, achieving a close-optimal solution that eludes gradient-dominant approaches. This paper delves into the inherent capabilities and establishes the generalization of a metaheuristic algorithm within non-Euclidean functional landscapes. The source code will be available at https://github.com/lingpingfuzzy/metaheuristic-manifold-optimization.
Collaborative filtering by graph convolution network in location-based recommendation system
(KSII, 2024) Tran, Tin T.; Snášel, Václav; Nguyen, Thuan Q.
Recommendation systems research is a subfield of information retrieval, as these systems recommend appropriate items to users during their visits. Appropriate recommendation results will help users save time searching while increasing productivity at work, travel, or shopping. The problem becomes more difficult when the items are geographical locations on the ground, as they are associated with a wealth of contextual information, such as geographical location, opening time, and sequence of related locations. Furthermore, on social networking platforms that allow users to check in or express interest when visiting a specific location, their friends receive this signal by spreading the word on that online social network. Consideration should be given to relationship data extracted from online social networking platforms, as well as their impact on the geolocation recommendation process. In this study, we compare the similarity of geographic locations based on their distance on the ground and their correlation with users who have checked in at those locations. When calculating feature embeddings for users and locations, social relationships are also considered as attention signals. The similarity value between location and correlation between users will be exploited in the overall architecture of the recommendation model, which will employ graph convolution networks to generate recommendations with high precision and recall. The proposed model is implemented and executed on popular datasets, then compared to baseline models to assess its overall effectiveness.
Will dissolved hydrogen reveal the instability of the anaerobic digestion process?
(MDPI, 2025) Platošová, Daniela; Rusín, Jiří; Svoboda, Radek; Vašinková, Markéta
Dissolved hydrogen is a critical factor in maintaining the delicate balance among microbial species that drive anaerobic digestion. Since previous findings have demonstrated a correlation between dissolved hydrogen concentration and volatile fatty acid (VFA) levels, we propose to evaluate the use of dissolved hydrogen concentration in digestate as an alternative to traditional VFA measurements. The aim is to determine whether dissolved hydrogen could serve as a faster, more accurate, and more efficient indicator of process instability in anaerobic digestion. An integral part of this task also involves addressing the technical challenge of identifying a suitable sensor that meets our requirements. In this study, we evaluated the ratio of dissolved hydrogen concentration to Total Inorganic Carbon as a potential alternative to the traditional stability indicator, Volatile Fatty Acids/Total Inorganic Carbon (VFA/TIC), also referred to as Fl & uuml;chtige Organische S & auml;uren/Totales Anorganisches Carbonat (FOS/TAC). The single-stage anaerobic digestion process was carried out in a Terrafors IS rotary drum bioreactor for 150 days at an average temperature of 40 degrees C and an organic volatile load of 0.092 kg m-3 d-1. Corn silage was dosed on weekdays as the substrate. With a theoretical retention time of 45 days, a biogas production of 0.219 Nm3kgVs-1 with a CH4 content of 31.6% was achieved. The values of the determined VFA/TIC stability indicator ranged from 0.22 to 5.66, with the highest values obtained when the reactor was overloaded. The dissolved hydrogen concentration ranged 0.005-0.196 mg dm-3. The Pearson correlation coefficient was 0.337 and the Spearman correlation coefficient was 0.468. The amperometric microsensor has proven to be unsuitable for field applications due to its lack of sensitivity and short lifetime. The proposed ratio of dissolved hydrogen concentration to TIC did not prove to be significantly more effective than the established VFA/TIC indicator.
An activity level based surrogate-assisted evolutionary algorithm for many-objective optimization
(Elsevier, 2024) Pan, Jeng-Shyang; Zhang, An-Ning; Chu, Shu-Chu; Zhao, Jia; Snášel, Václav
Addressing expensive many-objective optimization problems (MaOPs) is a formidable challenge owing to their intricate objective spaces and high computational demands. Surrogate-assisted evolutionary algorithms (SAEAs) have gained prominence because of their ability to tackle MaOPs efficiently. They achieve this by using surrogate models to approximate objective functions, significantly reducing their reliance on costly evaluations. However, the effectiveness of many SAEAs is hampered by their reliance on various surrogate models and optimization strategies, which often result in suboptimal prediction accuracy and optimization performance. This study introduces a novel approach: an activity level based surrogate-assisted reference vector guided evolutionary algorithm specifically designed for expensive MaOPs. Utilizing the Kriging model and an angle penalty distance criterion, this algorithm effectively filters solutions that require evaluation using the original function. It employs a fixed number of training sets,that are updated via a two-screening strategy that leverages activity levels to refine population screening. This process ensures that the reference vector progressively aligns more closely with the Pareto fronts,which is enhanced by the deployment of adjusted adaptive reference vectors, thereby improving the screening precision. The proposed algorithm was tested against six contemporary algorithms using the DTLZ, WFG, and MaF test suites. The experimental results show that the proposed method outperforms other algorithms in most problems. Furthermore, its application to the cloud computing task scheduling problem underscores its practical value, demonstrating its notable effectiveness. The experimental outcomes attest to the robust performance of the algorithm across both test scenarios and real-world applications.
A brief review on quantum computing based drug design
(Wiley, 2024) Das, Poulami; Ray, Avishek; Bhattacharyya, Siddhartha; Platoš, Jan; Snášel, Václav; Mršić, Leo; Huang, Tingwen; Zelinka, Ivan
Design and development of new drug molecules are essential for the survival of human society. New drugs are designed for therapeutic purposes to combat new diseases. Besides treating new diseases, new drug development is also needed to treat pre-existing diseases more effectively and reduce the existing drugs' side effects. The design of drugs involves several steps, from the discovery of the drug molecule to its commercialization in the market. One of the most critical steps in drug design is to find the molecular interactions between the target (infected) molecule and the drug molecule. Several complex chemical equations need to be solved to determine the molecular interactions. In the late 20th Century, the advancement of computational technologies has made the solution of chemical equations relatively easier and faster. Moreover, the design of drug molecules involves multi-criteria optimization. Classical computational methodologies have been used for drug design since the end of the 20th Century. However, nowadays, more advanced computational methodologies are inevitable in designing drugs for new diseases and drugs with fewer side effects. In this context, the quantum computing paradigm has proved beneficial in drug design due to its advanced computational capabilities. This paper presents a state-of-the-art comprehensive review of the quantum computing-based methodologies involved in drug design. A comparative study is made about the different quantum-aided drug design methods, stating each methodology's merits and demerits. The review work presented in this manuscript will help new researchers assess the present state-of-the-art concept of quantum-based drug design. This article is categorized under: Technologies > Structure Discovery and Clustering Technologies > Computational Intelligence Application Areas > Health Care
Association of selected adipokines with vitamin D deficiency in children with inflammatory bowel disease
(BMC, 2024) Geryk, Miloš; Kučerová, Veronika; Velgáňová-Véghová, Mária; Foltenová, Hana; Bouchalová, Kateřina; Karásek, David; Radvansky Jr., Martin; Karásková, Eva
Background: Adipose tissue is significantly involved in inflammatory bowel disease (IBD). Vitamin D can affect both adipogenesis and inflammation. The aim of this study was to compare the production of selected adipokines, potentially involved in the pathogenesis of IBD - adiponectin, resistin, retinol binding protein 4 (RBP-4), adipocyte fatty acid binding protein and nesfatin-1 in children with IBD according to the presence of 25-hydroxyvitamin D (25(OH)D) deficiency. Methods: The study was conducted as a case-control study in pediatric patients with IBD and healthy children of the same sex and age. In addition to adipokines and 25(OH)D, anthropometric parameters, markers of inflammation and disease activity were assessed in all participants. Results: Children with IBD had significantly higher resistin levels regardless of 25(OH)D levels. IBD patients with 25(OH)D deficiency only had significantly lower RBP-4 compared to healthy controls and also compared to IBD patients without 25(OH)D deficiency. No other significant differences in adipokines were found in children with IBD with or without 25(OH)D deficiency. 25(OH)D levels in IBD patients corelated with RBP-4 only, and did not correlate with other adipokines. Conclusions: Whether the lower RBP-4 levels in the 25(OH)D-deficient group of IBD patients directly reflect vitamin D deficiency remains uncertain. The production of other adipokines does not appear to be directly related to vitamin D deficiency.
Retinal image dataset of infants and retinopathy of prematurity
(Springer Nature, 2024) Timkovič, Juraj; Nowaková, Jana; Kubíček, Jan; Hasal, Martin; Varyšová, Alice; Kolarčík, Lukáš; Maršolková, Kristýna; Augustynek, Martin; Snášel, Václav
Retinopathy of prematurity (ROP) represents a vasoproliferative disease, especially in newborns and infants, which can potentially affect and damage the vision. Despite recent advances in neonatal care and medical guidelines, ROP still remains one of the leading causes of worldwide childhood blindness. The paper presents a unique dataset of 6,004 retinal images of 188 newborns, most of whom are premature infants. The dataset is accompanied by the anonymized patients' information from the ROP screening acquired at the University Hospital Ostrava, Czech Republic. Three digital retinal imaging camera systems are used in the study: Clarity RetCam 3, Natus RetCam Envision, and Phoenix ICON. The study is enriched by the software tool ReLeSeT which is aimed at automatic retinal lesion segmentation and extraction from retinal images. Consequently, this tool enables computing geometric and intensity features of retinal lesions. Also, we publish a set of pre-processing tools for feature boosting of retinal lesions and retinal blood vessels for building classification and segmentation models in ROP analysis.
Fast bicriteria streaming algorithms for submodular cover problem under noise models
(Elsevier, 2024) Nguyen, Bich-Ngan T.; Pham, Phuong N. H.; Pham,Canh V.; Snášel, Václav
The Submodular Cover (SC) problem has attracted the attention of researchers because of its wide variety of applications in many domains. Previous studies on this problem have focused on solving it under the assumption of a non-noise environment or using the greedy algorithm to solve it under noise. However, in some applications, the data is often large-scale and brings a noisy version, so the existing solutions are ineffective or not applicable to large and noisy data. Motivated by this phenomenon, we study the Submodular Cover under Noises (SCN) problem and propose two efficient streaming algorithms, which provide a solution with theoretical bounds under two common noise models, multiplicative and additive noises. The experimental results indicate that our proposed algorithms not only provide the solution with a high objective function value but also outperform the state-of-the-art algorithm in terms of both the number of queries and the running time.

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