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Kanita Karaduzovic-Hadziabdic

Assoc. Professor, Vice-Rector for International Cooperation and Research, International University of Sarajevo

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International University of Sarajevo
Assoc. Professor, Vice-Rector for International Cooperation and Research
Miron Sopić, Kanita Karaduzovic-Hadziabdic, Dimitris Kardassis, Lars Maegdefessel, Fabio Martelli, Ari Meerson, Jelena Munjas, L. Niculescu, Monika Stoll et al.

L. Marcos-Zambrano, Víctor Manuel López-Molina, Burcu Bakir-Gungor, Marcus Frohme, Kanita Karaduzovic-Hadziabdic, Thomas Klammsteiner, Eliana Ibrahimi, Leo Lahti, Tatjana Loncar-Turukalo et al.

The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis.

L. Badimón, E. Robinson, A. Jusic, Irina Carpusca, L. deWindt, C. Emanueli, P. Ferdinandy, Wei Gu, M. Gyöngyösi et al.

Abstract The coronavirus disease 2019 (COVID-19) pandemic has been as unprecedented as unexpected, affecting more than 105 million people worldwide as of 8 February 2020 and causing more than 2.3 million deaths according to the World Health Organization (WHO). Not only affecting the lungs but also provoking acute respiratory distress, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is able to infect multiple cell types including cardiac and vascular cells. Hence a significant proportion of infected patients develop cardiac events, such as arrhythmias and heart failure. Patients with cardiovascular comorbidities are at highest risk of cardiac death. To face the pandemic and limit its burden, health authorities have launched several fast-track calls for research projects aiming to develop rapid strategies to combat the disease, as well as longer-term projects to prepare for the future. Biomarkers have the possibility to aid in clinical decision-making and tailoring healthcare in order to improve patient quality of life. The biomarker potential of circulating RNAs has been recognized in several disease conditions, including cardiovascular disease. RNA biomarkers may be useful in the current COVID-19 situation. The discovery, validation, and marketing of novel biomarkers, including RNA biomarkers, require multi-centre studies by large and interdisciplinary collaborative networks, involving both the academia and the industry. Here, members of the EU-CardioRNA COST Action CA17129 summarize the current knowledge about the strain that COVID-19 places on the cardiovascular system and discuss how RNA biomarkers can aid to limit this burden. They present the benefits and challenges of the discovery of novel RNA biomarkers, the need for networking efforts, and the added value of artificial intelligence to achieve reliable advances.

L. Marcos-Zambrano, Kanita Karaduzovic-Hadziabdic, Tatjana Loncar Turukalo, Piotr Przymus, V. Trajkovik, O. Aasmets, M. Berland, A. Gruca, Jasminka Hasic et al.

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach.

C. Gomes, B. Ágg, Andrejaana Andova, Serdal Arslan, A. Baker, M. Barteková, D. Beis, F. Betsou, S. B. Wettinger et al.

Cardiovascular disease (CVD) remains the leading cause of death worldwide and, despite continuous advances, better diagnostic and prognostic tools, as well as therapy, are needed. The human transcriptome, which is the set of all RNA produced in a cell, is much more complex than previously thought and the lack of dialogue between researchers and industrials and consensus on guidelines to generate data make it harder to compare and reproduce results. This European Cooperation in Science and Technology (COST) Action aims to accelerate the understanding of transcriptomics in CVD and further the translation of experimental data into usable applications to improve personalized medicine in this field by creating an interdisciplinary network. It aims to provide opportunities for collaboration between stakeholders from complementary backgrounds, allowing the functions of different RNAs and their interactions to be more rapidly deciphered in the cardiovascular context for translation into the clinic, thus fostering personalized medicine and meeting a current public health challenge. Thus, this Action will advance studies on cardiovascular transcriptomics, generate innovative projects, and consolidate the leadership of European research groups in the field. COST (European Cooperation in Science and Technology) is a funding organization for research and innovation networks (www.cost.eu).

Kanita Karaduzovic-Hadziabdic, Telalovic J Hasic, Rafał K. Mantiuk

This dataset contains a set of RAW and JPEG image stacks of multi-exposure image sequences that could be used for testing HDR reconstruction and deghosting methods. The unique feature of this dataset is that it contains both test image stacks, with motion and misalignment, and motion-free reference image stacks, which can be used with full-reference image quality metrics. In addition to that, we also provide the results of the subjective quality assessment experiment peformed on the set of merged HDR images. Please check the README.txt file for mode details.

Heart disease is one of the leading causes of deaths worldwide. Several methods have been developed by researchers to support medical diagnosis of heart disease, including artificial intelligence methods. In the past, committee machines have been shown to achieve higher classification accuracy than a single classifier. This study uses a committee of classifiers consisting of a combination of feed-forward multi layer perceptron (MLP) and radial basis functions neural networks (RBF) to diagnose heart disease. The output of the committee has been obtained based on majority voting. Several MLP training algorithms have been analyzed from the viewpoint of learning performance based on the network topology to find the network with the best prediction results. Cleveland heart disease dataset has been used throughout the experiments. The results show that the committee machine approach gives significantly better results than a single neural network. The classification accuracy obtained by the proposed method achieves a high accuracy rate of 95,4545%. This result is better than the results achieved by other methods that use Cleveland dataset reported in literature to this date.

This paper analyses the TLS Handshake protocol in a progressive manner, by gradually building the protocol's messages and message fields. Messages constituting the TLS protocol are described by Casper, a compiler for the analysis of security protocols. FDR, a model checking tool is then used to test whether the protocol achieves its goals. It has been shown that TLS achieves its security goals for the systems tested. By using this progressive approach of the TLS Handshake analysis, this paper identifies the importance of each message and message field to the overall achievement of the security goal of the TLS protocol. The study also shows that the TLS protocol contains much redundancy. A few important points that show how TLS has been carefully designed to thwart some attacks that have appeared in many of the previous security protocols are also emphasized.


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