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Register a new userAn Optimal Mass Transport Method for Random Genetic Drift
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Added by
Jose A. Carrillo
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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We propose and analyze an optimal mass transport method for a random genetic drift problem driven by a Moran process under weak-selection. The continuum limit, formulated as a reaction-advection-diffusion equation known as the Kimura equation, inherits degenerate diffusion from the discrete stochastic process that conveys to the blow-up into Dirac-delta singularities hence brings great challenges to both the analytical and numerical studies. The proposed numerical method can quantitatively capture to the fullest possible extent the development of Dirac-delta singularities for genetic segregation on one hand, and preserves several sets of biologically relevant and computationally favored properties of the random genetic drift on the other. Moreover, the numerical scheme exponentially converges to the unique numerical stationary state in time at a rate independent of the mesh size up to a mesh error. Numerical evidence is given to illustrate and support these properties, and to demonstrate the spatio-temporal dynamics of random generic drift.
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We introduce a simple, accurate, and extremely efficient method for numerically solving the multi-marginal optimal transport (MMOT) problems arising in density functional theory. The method relies on (i) the sparsity of optimal plans [for $N$ marginals discretized by $ell$ gridpoints each, general Kantorovich plans require $ell^N$ gridpoints but the support of optimizers is of size $O(ellcdot N)$ [FV18]], (ii) the method of column generation (CG) from discrete optimization which to our knowledge has not hitherto been used in MMOT, and (iii) ideas from machine learning. The well-known bottleneck in CG consists in generating new candidate columns efficiently; we prove that in our context, finding the best new column is an NP-complete problem. To overcome this bottleneck we use a genetic learning method tailormade for MMOT in which the dual state within CG plays the role of an adversary, in loose similarity to Wasserstein GANs. On a sequence of benchmark problems with up to 120 gridpoints and up to 30 marginals, our method always found the exact optimizers. Moreover, empirically the number of computational steps needed to find them appears to scale only polynomially when both $N$ and $ell$ are simultaneously increased (while keeping their ratio fixed to mimic a thermodynamic limit of the particle system).
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