24.4.2024. 18:15h, Faculty of Mathematics (online)

From Climate to Healthcare: Adapting Polar Diagrams for Biomedical and Machine Learning Applications

Aleksandar Anžel

Centre for Artificial Intelligence In Public Health Research, Robert Koch Institute, Berlin, Germany

A meeting of the Bioinformatics seminar will be held on Wednesday, April 24th, starting at 18:15, in online classroom. Teachers and students of doctoral and master studies in computer science, mathematics, biology and other related disciplines are invited to join us.

Abstract

Evaluating the performance of multiple complex models, such as those found in biology, medicine, climatology, and machine learning, using conventional approaches is often challenging when using various evaluation metrics simultaneously. The traditional approach, which relies on presenting multi-model evaluation scores in the table, presents an obstacle when determining the similarities between the models and the order of performance. By combining statistics, information theory, and data visualization, juxtaposed Taylor and Mutual Information Diagrams permit users to track and summarize the performance of one model or a collection of different models. To uncover linear and nonlinear relationships between models, users may visualize one or both charts.

This presentation will delve into the mathematical foundation of both the Taylor and Mutual Information Diagrams, highlighting their distinctions and similarities. Attendees will have the opportunity to view the resulting diagrams generated by the new library named polar-diagrams. This library offers the first publicly available implementation of the Mutual Information Diagram and the first interactive implementation of the Taylor Diagram. Furthermore, the presentation will discuss the additional features recently integrated into both diagrams, enabling the visualization of temporality or specific scalar model attributes like uncertainty. These concepts will be illustrated using sample datasets from diverse fields, including climatology, biomedicine, public health, and machine learning.

Lecturer

Dr. Aleksandar Anžel is a Postdoctoral Researcher at the Robert Koch Institute, where he actively contributes to pioneering research endeavors within the public health domain. His specialization lies in optimizing visualization techniques for AI models, developing early-detection surveillance systems, and improving existing computational workflows, among others.

Aleksandar completed his Ph.D. at Philipps-Universität Marburg, where he focused his research on improving existing and developing new bioinformatics pipelines and tools that leverage machine learning and data science methodologies. His work also revolved around developing, evaluating, and visualizing automated workflows for information storage systems utilizing molecular storage media like DNA. Moreover, he worked on improving existing and developing novel techniques for analyzing and visualizing high-dimensional multi-modal data sets, including temporal multi-omics data. During his Ph.D. Aleksandar was also employed as Technical Lead at eMedicals Healthtech GmbH, where he oversaw the development of the kidi project platform. The project, designed as Software as a Medical Device (Digital Health Application (DiGA)), was developed following rigorous industry standards to ensure patient safety and regulatory compliance.

Furthermore, Aleksandar holds a Master's degree in Mathematics with a specialization in Computer Science and Informatics from the Faculty of Mathematics at the University of Belgrade. He graduated with a Master's Thesis focusing on "Determining Protein N-glycosylation with Machine Learning Methods".

More information about Aleksandar can be found at https://aanzel.github.io/

Seminar

The organizer of the seminar is BIRBI. The heads of the seminar are Prof. dr Nataša Pržulj and dr Jovana Kovačević.

10.4.2024. 18:15h, Faculty of Mathematics (online)

Using random walks to explore complex networks

Alexandre V. Morozov

Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, USA

    Video: Recorded lecture (MP4, 54min, 68MB)

A meeting of the Bioinformatics seminar will be held on Wednesday, April 10th, starting at 18:15, in online classroom. Teachers and students of doctoral and master studies in computer science, mathematics, biology and other related disciplines are invited to join us.

Abstract

Large-scale networks represent a broad spectrum of systems in nature, science, technology, and human and animal societies. The complexity of these networks makes predictions of their properties a challenging task. I will describe a novel computational methodology, based on random walks, for the inference of both local and global properties of complex networks. I will show that our formalism yields reliable estimates of key network properties, such as its size, after only a small fraction of network nodes has been explored. Furthermore, I will introduce a novel algorithm for partitioning network nodes into non-overlapping communities - a key step in revealing network modularity and hierarchical organization. Thus, non-ergodic random walk trajectories help reveal modular organization and global structure of complex networks.

[1] Kion-Crosby, W.B. & Morozov, A.V. (2018). Rapid Bayesian inference of global network statistics using random walks. Phys. Rev. Lett. 121, 038301.

[2] Ballal, A., Kion-Crosby, W.B. & Morozov, A.V. (2022). Network community detection and clustering with random walks. Phys. Rev. Res. 4, 043117.

[3] Yu, J. & Morozov, A.V. (2024). An adaptive Bayesian approach to gradient-free global optimization. New J. Phys. 26, 023027.

Lecturer

Alexandre V. Morozov received his Ph.D. in Physics from the University of Washington, Seattle in 2003. From 2003 to 2007 he was a post-doctoral fellow at the Center for Studies in Physics and Biology, Rockefeller University, New York. In 2007 he joined the Department of Physics and Astronomy at Rutgers University, where he is now Professor and Director of the Center for Quantitative Biology. In 2009, he was a recipient of an Alfred P. Sloan Research Fellowship. His current research interests include non-equilibrium statistical mechanics, machine learning, biological physics, and evolutionary modeling.

Seminar

The organizer of the seminar is BIRBI. The heads of the seminar are Prof. dr Nataša Pržulj and dr Jovana Kovačević.

27.3.2024. 18:15h, Faculty of Mathematics (online)

Computational image analysis of cell nuclei textures in pediatric patients suffering from inflammatory bowel disease

Vedrana Makević, Dr. Anđelija Ilić

Faculty of Medicine, University of Belgrade, Serbia
Institute of Physics, University of Belgrade, Serbia

    Video: Recorded lecture (MP4, 60min, 101MB)

A meeting of the Bioinformatics seminar will be held on Wednesday, March 27th, starting at 18:15, in online classroom. Teachers and students of doctoral and master studies in computer science, mathematics, biology and other related disciplines are invited to join us.

Abstract

We will present our recent research results obtained in collaboration of Faculty of Medicine, University of Belgrade (UB), and Institute of Physics Belgrade, UB, with the Department of Gastroenterology, Hepatology, and Endoscopy, University Children’s Hospital, UB, namely Dr. Ivan Milovanovich, MD, PhD, and N. Popovac, MD. We focused on the inflammatory bowel disease (IBD) in pediatric population. The incidence of IBD has been in increase in recent years, with 20–30% of cases beginning in pediatric age. While an early diagnosis is essential for obtaining timely treatment and preventing more permanent consequences, it can be very challenging. In particular, discerning between the two different disease phenotypes, Crohn’s disease (CD) and ulcerative colitis (UC), often presents a problem even to the experienced pathologists. We complemented standard biochemical and immunohistochemical analyses with the extraction of morphological and textural features from the high-resolution digitalized micrographs of intestinal cell nuclei. The aim was to check out the possibility to discern the IBD patients from the healthy controls based on some of the studied parameters, as well as to hopefully find the combinations of parameters which could help differentiate between the Crohn’s disease and ulcerative colitis. Our motivation to use the intestinal cell nuclei extracted from the crypt glandular epithelium arose from the prior investigations of our own as well as of other groups, showing significantly altered textural features of cell nuclei chromatin in cancers. Given the role of genetic, immune, and environmental factors in IBD, we presumed that the analysis of intestinal cell nuclei might show the existence of modified cell nuclei textures in IBD. Each of the seven distinct intestinal tissues was considered separately and in addition to the intergroup comparisons, we also showed intersegmental comparisons of the selected cell nuclei features. Very promising results, in agreement and additionally supporting other analyses were obtained. Some of the observed correlations with other studied manifestations of IBD will be discussed. The conducted comprehensive investigation showed some promise of the use of the proposed methodology as one of the constituent parts in the development of computer assisted IBD diagnosis tools.

Lecturers

Vedrana Makević was born in Belgrade, Serbia, on July 7th 1988. She received the MD degree in 2013 from the Faculty of Medicine, University of Belgrade (MFUB). Since 2014, she is enrolled into the MFUB graduate school program on Physiological sciences, towards obtaining her PhD degree. During the same period, she was employed at the Institute of Pathological Physiology at MFUB, where she currently works. Since 2022, she took part in the currently ongoing project of the Science Fund of the Republic of Serbia, program IDEAS, grant No. 7673781, “Polyphenols as potential targeted treatments in D. melanogaster model of fragile X syndrome”, as well as (since 2023.) in the ERASMUS+ project “Development and implementation of metacognitive problem-based modules in blended learning courses in medical sciences, ProBLeMS”. Within her PhD research, under the guidance of Prof. Dr. Silvio de Luka (MFUB) and Dr. Andjelija Ilić (Inst. of Physics Belgrade, UB), she studied pediatric IBD cases, combining standard methodology with innovative methods such as determining metal and trace element contents in intestinal tissues and conducting digital image analyses of intestinal cell nuclei morphology and texture.

Dr. Andjelija Ilić was born in Belgrade, Serbia, in 1973. She received the Dipl. Eng., M.Sc., and Ph.D. degrees in electrical engineering in 1998, 2004, and 2010, from the University of Belgrade (Belgrade, Serbia), the University of Massachusetts Dartmouth (MA, USA), and the University of Belgrade (Belgrade, Serbia), respectively. She is currently an Associate Research Professor with the Institute of Physics, University of Belgrade. In 2013 and 2014, she was a Postdoctoral Research Associate with the School of Science and Technology, University of Westminster, London, UK. Her research interests are in the fields of applied physics and electromagnetics, including numerical methods, microwave circuits, accelerator technology, application of novel materials in electrical engineering, and electromagnetic field interaction with biological systems. Since 2012, she collaborates with MFUB, in diverse studies including the biomedical image analysis focused onto specific problems in medical sciences, which can be challenging in practice, and could therefore benefit mostly from the accurate and quantitative analysis.

She holds two patents in biomedical engineering. She was the principal investigator of the Innovation project for 2018–2019, No. 391-00-16/2017-16/27, “Development of a new type of device for electroporation of cells and tissues using ultra short electric pulses”, financed by the Ministry of Education, Science, and Technological Development of the Republic of Serbia. Currently, she participates in two projects funded by the Science Fund of the Republic of Serbia, Green project No. 5661, IonCleanTech, “Elimination of respirable airborne particles, microplastics, microorganisms, and VOCs by ionization of indoor air and filtration systems: comprehensive investigation for reliable technological answers”, and PRISMA project No. 7328, ToxoReTREAT, “Reinvention of the diagnostic algorithm and treatment options for reactivated toxoplasmosis”.

Dr. Ilić is the Senior Member of IEEE. She was the recipient of the 2006 Young Scientist and the 2014 Best Paper ETRAN Awards, as well as the “Prof. Aleksandar Marinčić” Award given annually by the IEEE MTTS Serbia chapter, for the best journal paper in 2016.

Seminar

The organizer of the seminar is BIRBI. The heads of the seminar are Prof. dr Nataša Pržulj and dr Jovana Kovačević.