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Afonso Guerra Assunção Senra Paula Freire Susana Barbosa
2nd order .Identifiability of a biological system • A biological system is a group of biomolecules that together perform a certain task. • High throughput technologies generates great amount of data unknown underlying systems. • Data quality observed with noise • A system can be described by a set of mass action equations. • For simplicity: 0th . 1st .
minimum least squares) • Statistical analysis .Identification problem • Equation structure search (model the system.set of ODEs) • Experimental design (inputs .initial concentrations) • Parameter fitting (optimization problem.
Equation structure Ilustrating: A C B D F E .
Hypergraph • Equation system represented by a directed hypergraph • Each edge can involve more than two nodes • Nodes Molecules • Edges Reactions • Real world restrictions apply .
Choose systems of increasing complexity and simulate dynamic trajectories 3. Parameter inference – – – – Perfect observations and complete knowledge of equation structure No knowledge of equation structure With noise: observations and time Partial knowledge of the equation system 1. Generate GMA for a set of components 2. Apply evolutionary model .Project Plan 1.
6 Conc 0.2 50 100 150 200 time .Experimental Design Simulation of dinamic trajectories – A priori estimates for parameters – Initial conditions – Algorithm to numerically solve ODEs 0.4 0.8 0.
Curve fitting • Sampling : CHALLENGE in instationary systems – Simultaneous sampling – Sequential sampling – Parameterized sampling • • Equidistant Exponential • Parameter fitting – Widely applied: local search algorithm requires a good guess! – Estimate parameters one by one each new step use the previous estimate 1-dimensional problem .
Greedy recursive algorithm i. No noise and complete knowledge • Mean least squares distance (MLS) 2.y [X][Y] or kx[X] iii. Predefine a set of realistic reactions (0. No noise and No knowledge of equation structure • Equation Structure Search . Zeros on the rigth side of the equation set ii.05) n components (n+1)n2/2+n2 possibilities • .Curve fitting 1.001 < f < 0. Add a term of the form kx.
Evolutionary Model • Evolution of one model into another • Two models: A and B – Full knowledge of B – PA=PB+ X . X ~ N (0.t) – Stochastic process: Brownian Motion .
Questions • Stiff equations • Nonlinear systems of ODEs – no global optimization guaranteed.stuck in local minima • How sufficient and accurate is the data? • How reliable are the models? • What are the computational challenges? .
Thank you for your attention! Open Discussion .