Fredrik Wrede
Department Information Technology, Uppsala University
'Motivation:' Discrete stochastic models of biomolecular reaction networks are indispensable tools for biological inquiry since they allow the modeler to predict how molecular interactions give rise to nonlinear system output. Model exploration with the objective of generating qualitative hypotheses about the workings of a pathway is usually the first step in the modeling process. It involves simulating the gene network model under a very large range of conditions, due to the large uncertainty in interactions and kinetic parameters. This makes model exploration highly computational demanding for complex models. Furthermore, with no prior information about the model behavior (e.g lacking real experimental data of the biological processes), labour-intensive manual inspection of very large amounts of simulation results becomes necessary. This limits systematic computational exploration to simplistic models. 'Goal:' Our objective is develop the methodology and toolboxes for model exploration. Even though our focus is in stochastic biochemical reaction networks, the simulator itself is treated as a black-box which enables generalization to other types of stochastic models. The methodology involves adapting machine learning techniques to automate the process of finding different qualitative behaviors of the model and to utilize the embarrassingly parallel parts of the workflow to implement scalable solutions. 'Keywords:' Stochastic biochemical reaction networks, Stochastic simulation algorithm (SSA), Semi-supervised learning, Adaptive sampling, Distributed and cloud computing 'Presentation:' My mid-term seminar will mostly involve the discussion around our human-in-the-loop paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz420/5505421?guestAccessKey=ae154706-b501-46ac-a916-b909e78dddfb I have also contributed a small amount (example VIII) to this paper: https://arxiv.org/pdf/1901.07335.pdf And finally I\u2019m currently finishing up a software paper based on: https://github.com/sciope/sciope which you can also find in TDBs github organization repository https://github.com/scicompuu