Digital Bifurcation Analysis

Samuel Pastva

SAMUEL PASTVA

Faculty of Informatics, Masaryk University

• Mgr. in Parallel and Distributed Systems, graduated with honours in 2017.
• Member of the Sybila systems biology laboratory since 2015.
• PhD student and researcher since 2017, with prof. Luboš Brim as advisor.

ACADEMIC BACKGROUND

SYSTEMS BIOLOGY

• Biological systems can be studied via computational models.
• Models are predictive and explainable.
• In silico analysis is faster and cheaper than in vivo experiments.

BIFURCATION ANALYSIS

• Models often contain unknown or uncertain elements ⇒ parameters.
• Bifurcation analysis: inspect which parameters (and for what values) lead to significant change in model behaviour.

RESEARCH PROBLEM

• Bifurcation is only defined in quantitative models (how much?), not qualitative (yes/no?) models.
• For large systems, qualitative (or hybrid) approach is often necessary.
• How to study bifurcation in qualitative models?

METHODOLOGY

• Qualitative models correspond to directed graphs, or sets of runs over directed graphs.
• Long-term behaviour of the graph corresponds to SCCs (strongly connected components), especially BSCCs.
• Bifurcation analysis: identify which parameter values lead to a change in SCC/BSCC structure.

METHODOLOGY

• Development of new symbolic algorithms that can detect (B)SCCs in very large graphs with parameters (up to 2^100 - 2^1000 states).
• A new interactive visualisation technique based on decision trees for identification of critical parameter values.

Application

• AEON: Bifurcation analysis of Boolean networks.
• Online editor of parametrised models with static validation of structural properties.
• Compute types of possible behaviour and explore dependence on parameters as a decision tree.

FUTURE PROSPECTS

• Case study showcasing bifurcation analysis of interferon type-1 inflammation model.
• New collaboration started with Faculty of Medicine at MUNI.
• AEON used by students of bioinformatics at MUNI and VUT.
• Possible future collaboration with Boolean network research at JAIST in Ishikawa.

other EXPERIENCE

• Co-author of 15 ranked conference papers (7 A-ranked) and 4 journal papers.
• Supervisor of three successful Bc. students, two of these later resulted in conference publications.
• Artefact evaluation chair (CMSB '18,'21), program committee member (CIBCB, ICONS) and reviewer for other conferences and journals.
• Seminar tutor for Computability and Complexity as well as Advanced Algorithms and Data Structures courses since 2015.
• Oracle Labs research internship on VM tooling team (2020).
• Brno PhD Talent scholarship (2018-2020).