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61.
TF-IDF-based classification of Uzbek educational texts
Khabibulla Madatov, Sapura Sattarova, Jernej Vičič, 2025, izvirni znanstveni članek

Opis: This paper presents a baseline study on automatic Uzbek text classification. Uzbek is a morphologically rich and low-resource language, which makes reliable preprocessing and evaluation challenging. The approach integrates Term Frequency–Inverse Document Frequency (TF–IDF) representation with three conventional methods: linear regression (LR), k-Nearest Neighbors (k-NN), and cosine similarity (CS, implemented as a 1-NN retrieval model). The objective is to categorize school learning materials by grade level (grades 5–11) to support improved alignment between curricular texts and students’ intellectual development. A balanced dataset of Uzbek school textbooks across different subjects was constructed, preprocessed with standard NLP tools, and converted into TF–IDF vectors. Experimental results on the internal test set of 70 files show that LR achieved 92.9% accuracy (precision = 0.94, recall = 0.93, F1 = 0.93), while CS performed comparably with 91.4% accuracy (precision = 0.92, recall = 0.91, F1 = 0.92). In contrast, k-NN obtained only 28.6% accuracy, confirming its weakness in high-dimensional sparse feature spaces. External evaluation on seven Uzbek literary works further demonstrated that LR and CS yielded consistent and interpretable grade-level mappings, whereas k-NN results were unstable. Overall, the findings establish reliable baselines for Uzbek educational text classification and highlight the potential of extending beyond lexical overlap toward semantically richer models in future work.
Ključne besede: Uzbek language, text classification, low-resource languages, TF-IDF, cosine similarity, linear regression, k-Nearest Neighbors
Objavljeno v RUP: 17.10.2025; Ogledov: 507; Prenosov: 4
.pdf Celotno besedilo (286,87 KB)
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62.
Evaluation of changes in prediction modelling in biomedicine using systematic reviews
Lara Lusa, Franziska Kappenberg, Gary S. Collins, Matthias Schmid, Willi Sauerbrei, Jörg Rahnenführer, 2025, izvirni znanstveni članek

Opis: The number of prediction models proposed in the biomedical literature has been growing year on year. In the last few years there has been an increasing attention to the changes occurring in the prediction modeling landscape. It is suggested that machine learning techniques are becoming more popular to develop prediction models to exploit complex data structures, higher-dimensional predictor spaces, very large number of participants, heterogeneous subgroups, with the ability to capture higher-order interactions. We examine the changes in modelling practices by investigating a selection of systematic reviews on prediction models published in the biomedical literature. We selected systematic reviews published between 2020 and 2022 which included at least 50 prediction models. Information was extracted guided by the CHARMS checklist. Time trends were explored using the models published since 2005. We identified 8 reviews, which included 1448 prediction models published in 887 papers. The average number of study participants and outcome events increased considerably between 2015 and 2019 but remained stable afterwards. The number of candidate and final predictors did not noticeably increase over the study period, with a few recent studies using very large numbers of predictors. Internal validation and reporting of discrimination measures became more common, but assessing calibration and carrying out external validation were less common. Information about missing values was not reported in about half of the papers, however the use of imputation methods increased. There was no sign of an increase in using of machine learning methods. Overall, most of the findings were heterogeneous across reviews. Our findings indicate that changes in the prediction modeling landscape in biomedicine are smaller than expected and that poor reporting is still common; adherence to well established best practice recommendations from the traditional biostatistics literature is still needed. For machine learning best practice recommendations are still missing, whereas such recommendations are available in the traditional biostatistics literature, but adherence is still inadequate.
Ključne besede: predictive model, medicine, changes
Objavljeno v RUP: 14.10.2025; Ogledov: 416; Prenosov: 8
.pdf Celotno besedilo (6,00 MB)
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63.
Effective cryopreservation of post mortem-collected roe deer gametes by evaluation of post-thaw oocyte and sperm characteristics and in vitro fertilization
Anna Justyna Korzekwa, Elena Bužan, Boštjan Pokorny, Gulsum Ummu Boztepe, Marek Lecewicz, Władysław Kordan, 2025, izvirni znanstveni članek

Opis: The aim was to evaluate the effectiveness of semen cryopreservation and oocyte vitrification in roe deer as a potential method of gamete preservation for endangered deer species. Sperm were isolated from the cauda epididymis of fourteen bucks (n = 14). The motility measure (CASA) and morphology of fresh semen (FS) and frozen–thawed semen (TS) were compared. A hyaluronic binding assay was used to distinguish between mature FS spermatozoa expressing hyaluronan receptors and immature FS lacking these receptors, and the mitochondrial membrane potential (MMP) in TS was determined (flow cytometry). A Sperm–Hyaluronan Binding Assay (HBA) showed a viability rate of 61.9% in FS and 78.2% in TS. Oocytes received from eight does (n = 8) underwent a viability test and vitrification, and fresh oocytes from the other eight does (n = 8) were fertilized with TS and embryos were cultured until the blastocyst stage. The number of isolated oocytes, cumulus–oocyte complexes (COCs), cleaved embryos, and expanded blastocysts was evaluated. Higher percentages of morphological factors (acrosome, head, midpiece, and tail shape) were observed in FS compared to TS, whereas the motility and progressive movement were greater in TS (p ≤ 0.001). The viability was 50.5% and MMP was 40.6% in TS. A total of 311 oocytes were collected and from 150 COCs and 125 blastocysts developed. The viability of thawed oocytes after vitrification was 81%. The viability of vitrified oocytes and cryopreserved sperm confirmed the effectiveness of freezing protocols and highlights the potential for their implementation in other deer species.
Ključne besede: roe deer, semen, oocytes, fertilization
Objavljeno v RUP: 13.10.2025; Ogledov: 461; Prenosov: 14
.pdf Celotno besedilo (1,10 MB)
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64.
The role of community science in DNA-based biodiversity monitoring
Carolina Corrales, Karolina Bacela-Spychalska, Elena Bužan, Torbjørn Ekrem, Sónia Ferreira, William Goodall-Copestake, Elaine van Ommen Kloeke, Peter M. Hollingsworth, Sarah J. Bourlat, 2025, izvirni znanstveni članek

Opis: The mutual interest in nature by the general public and scientists has led to many collaborations, past and present. Community science shows great potential for monitoring species occurrences and distributions, especially in combination with scalable and (semi)-automated methods such as DNA-based monitoring, helping to obtain data from a broader geographic and temporal range than would be possible by the scientific community alone. Here, we present an overview of the complementarity between community science and DNA-based biomonitoring through examples from ongoing projects. The involvement of hobby experts is particularly crucial for building up the necessary species reference databases that enable DNA-based monitoring. Based on this overview, we identify some key points related to learning opportunities and participant recognition to maximise the success, impact and benefit of community participants in DNA-based monitoring.
Ključne besede: eDNA, community science, genetics
Objavljeno v RUP: 13.10.2025; Ogledov: 428; Prenosov: 2
.pdf Celotno besedilo (412,08 KB)
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65.
Deep learning for brain MRI tissue and structure segmentation : a comprehensive review
Nedim Šišić, Peter Rogelj, 2025, pregledni znanstveni članek

Opis: Brain MRI segmentation plays a crucial role in neuroimaging studies and clinical trials by enabling the precise localization and quantification of brain tissues and structures. The advent of deep learning has transformed the field, offering accurate and fast tools for MRI segmentation. Nevertheless, several challenges limit the widespread applicability of these methods in practice. In this systematic review, we provide a comprehensive analysis of developments in deep learning-based segmentation of brain MRI in adults, segmenting the brain into tissues, structures, and regions of interest. We explore the key model factors influencing segmentation performance, including architectural design, choice of input size and model dimensionality, and generalization strategies. Furthermore, we address validation practices, which are particularly important given the scarcity of manual annotations, and identify the limitations of current methodologies. We present an extensive compilation of existing segmentation works and highlight the emerging trends and key results. Finally, we discuss the challenges and potential future directions in the field.
Ključne besede: magnetic resonance imaging, brain, image segmentation, deep learning
Objavljeno v RUP: 10.10.2025; Ogledov: 792; Prenosov: 12
.pdf Celotno besedilo (956,69 KB)
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66.
Reconstructing the post-glacial spread of the sand fly Phlebotomus mascittii Grassi, 1908 (Diptera: Psychodidae) in Europe
Edwin Kniha, Vít Dvořák, Stephan Koblmüller, Jorian Prudhomme, Vladimir Ivović, Ina Hoxha, Sandra Oerther, Anna Heitmann, Renke Lühken, Anne-Laure Bañuls, 2023, izvirni znanstveni članek

Opis: Phlebotomine sand flies (Diptera: Phlebotominae) are the principal vectors of Leishmania spp. (Kinetoplastida: Trypanosomatidae). In Central Europe, Phlebotomus mascittii is the predominant species, but largely understudied. To better understand factors driving its current distribution, we infer patterns of genetic diversity by testing for signals of population expansion based on two mitochondrial genes and model current and past climate and habitat suitability for seven post-glacial maximum periods, taking 19 climatic variables into account. Consequently, we elucidate their connections by environmental-geographical network analysis. Most analyzed populations share a main haplotype tracing back to a single glacial maximum refuge area on the Mediterranean coasts of South France, which is supported by network analysis. The rapid range expansion of Ph. mascittii likely started in the early mid-Holocene epoch until today and its spread possibly followed two routes. The first one was through northern France to Germany and then Belgium, and the second across the Ligurian coast through present-day Slovenia to Austria, toward the northern Balkans. Here we present a combined approach to reveal glacial refugia and post-glacial spread of Ph. mascittii and observed discrepancies between the modelled and the current known distribution might reveal yet overlooked populations and potential further spread.
Ključne besede: Phlebotomus mascittii, modeling, Europe
Objavljeno v RUP: 06.10.2025; Ogledov: 429; Prenosov: 5
.pdf Celotno besedilo (2,55 MB)
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67.
Fed-batch bioreactor modeling
Tilen Gimpelj, Aleksandar Tošić, 2025, izvirni znanstveni članek

Opis: This paper describes an open-source computational tool developed for the modeling and simulation of fed-batch bioreactors, particularly for processes employing Chinese Hamster Ovary (CHO) cells, which are integral to biopharmaceutical manufacturing. The software provides a platform for researchers and industry professionals to simulate bioreactor dynamics and investigate the impact of various operational parameters, such as nutrient supply rates, oxygen concentrations, and temperature, prior to physical experimentation. The tool enables users to generate predictions of critical variables including cell density, nutrient consumption, and product concentration profiles over time. These predictions are derived from a mathematical framework based on a system of ordinary differential equations solved using the Runge–Kutta method. A notable capability of the software is the import of experimental data and the application of the Nelder–Mead algorithm for parameter optimization, allowing for the calibration of the model against empirical findings, thereby enhancing its predictive accuracy. The software supports in silico experimentation, which can contribute to reducing the time, cost, and resources associated with optimizing bioreactor configurations and scaling up production processes. By providing a refined and adaptable framework, this instrument assists in improving the understanding of bioreactor dynamics, optimizing biopharmaceutical production methodologies, and correlating theoretical models with practical bioreactor operations. The software is available as an open-source project to promote its adoption and continued development within the scientific community.
Ključne besede: bioreaktor, mathematical modeling, CHO
Objavljeno v RUP: 29.09.2025; Ogledov: 707; Prenosov: 5
.pdf Celotno besedilo (939,94 KB)
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68.
Polycyclic geometric realizations of the Gray configuration
Leah Berman, Gábor Gévay, Tomaž Pisanski, 2025, izvirni znanstveni članek

Opis: The Gray configuration is a (27_3) configuration which typically is realized as the points and lines of the 3×3×3 integer lattice. It occurs as a member of an infinite family of configurations defined by Bouwer in 1972. Since their discovery, both the Gray configuration and its Levi graph (i.e., its point-line incidence graph) have been the subject of intensive study. Its automorphism group contains cyclic subgroups isomorphic to Z3 and Z9, so it is natural to ask whether the Gray configuration can be realized in the plane with any of the corresponding rotational symmetry. In this paper, we show that there are two distinct polycyclic realizations with Z3 symmetry. In contrast, the only geometric polycyclic realization with straight lines and Z9 symmetry is only a “weak” realization, with extra unwanted incidences (in particular, the realization is actually a (27_4) configuration).
Ključne besede: Gray graph, Gray configuration, polycirculant, polycyclic configuration
Objavljeno v RUP: 29.09.2025; Ogledov: 597; Prenosov: 4
.pdf Celotno besedilo (2,95 MB)

69.
A lightweight deep learning model for profiled SCA based on random convolution kernels
Yu Ou, Yongzhuang Wei, René Rodríguez, Fengrong Zhang, 2025, izvirni znanstveni članek

Opis: In deep learning-based side-channel analysis (DL-SCA), there may be a proliferation of model parameters as the number of trace power points increases, especially in the case of raw power traces. Determining how to design a lightweight deep learning model that can handle a trace with more power points and has fewer parameters and lower time costs for profiled SCAs appears to be a challenge. In this article, a DL-SCA model is proposed by introducing a non-trained DL technique called random convolutional kernels, which allows us to extract the features of leakage like using a transformer model. The model is then processed by a classifier with an attention mechanism, which finally outputs the probability vector for the candidate keys. Moreover, we analyze the performance and complexity of the random kernels and discuss how they work in theory. On several public AES datasets, the experimental results show that the number of required profiling traces and trainable parameters reduce, respectively, by over 70% and 94% compared with state-of-the-art works, while ensuring that the number of power traces required to recover the real key is acceptable. Importantly, differing from previous SCA models, our architecture eliminates the dependency between the feature length of power traces and the number of trainable parameters, which allows for the architecture to be applied to the case of raw power traces.
Ključne besede: side-channel analysis, deep learning, convolution neural networks, random convolution kernel
Objavljeno v RUP: 26.09.2025; Ogledov: 1680; Prenosov: 7
.pdf Celotno besedilo (1,75 MB)
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70.
Extreme hollow hexagons with respect to the Mostar index
Roberto Cruz, Andrés Santamaría-Galvis, 2025, izvirni znanstveni članek

Opis: The Mostar index of a connected graph is a well-known distance-based topologicalindex. Hollow hexagons are coronoid systems that represent coronoid hydrocarbons be-longing to the class of cycloarenes. They are formed by a single chain in a macro-cyclicarrangement consisting of linearly and angularly annelated hexagons, with exactly six an-gular hexagons. In this paper, we compute the Mostar index of hollow hexagons and findmaximal and minimal values of the Mostar index over the set of hollow hexagons with afixed number of hexagons.
Ključne besede: Mostar index, hollow hexagons, cut method, extremal values
Objavljeno v RUP: 26.09.2025; Ogledov: 527; Prenosov: 12
.pdf Celotno besedilo (850,33 KB)
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