Pitfalls and Remedies for Cross Validation with Multi-trait Genomic Prediction Methods.

Incorporating measurements on correlated traits into genomic prediction models can increase prediction accuracy and selection gain. However, multi-trait genomic prediction models are complex and prone to overfitting which may result in a loss of prediction accuracy relative to single-trait genomic prediction. Cross-validation is considered the gold standard method for selecting and tuning models for genomic prediction in both plant and animal breeding. When used appropriately, cross-validation gives an accurate estimate of the prediction accuracy of a genomic prediction model, and can effectively choose among disparate models based on their expected performance in real data. However, we show that a naive cross-validation strategy applied to the multi-trait prediction problem can be severely biased and lead to sub-optimal choices between single and multi-trait models when secondary traits are used to aid in the prediction of focal traits and these secondary traits are measured on the individuals to be tested. We use simulations to demonstrate the extent of the problem and propose three partial solutions: 1) a parametric solution from selection index theory, 2) a semi-parametric method for correcting the cross-validation estimates of prediction accuracy, and 3) a fully non-parametric method which we call CV2*: validating model predictions against focal trait measurements from genetically related individuals. The current excitement over high-throughput phenotyping suggests that more comprehensive phenotype measurements will be useful for accelerating breeding programs. Using an appropriate cross-validation strategy should more reliably determine if and when combining information across multiple traits is useful

Lower bounds for the stable marriage problem and its variants

In an instance of the stable marriage problem of size n, n men and n women each ranks members of the opposite sex in order of preference. A stable marriage is a complete matching M = {(m_1, w_i_1), (m_2, w_i_2), ..., (m_n, w_i_n)} such that no unmatched man and woman prefer each other to their partners in M.A pair (m_i, w_j) is stable if it is contained in some stable marriage. In this paper, we prove that determining if an arbitrary pair is stable requires Ω(n^2) time in the worst case. We show, by an adversary argument, that there exists instances of the stable marriage problem such that it is possible to find at least one pair that exhibits the Ω(n^2) lower bound.As corollaries of our results, the lower bound of Ω(n^2) is established for several stable marriage related problems. Knuth, in his treatise on stable marriage, asks if there is an algorithm that finds a stable marriage in less than Θ(n^2) time. Our results show that such an algorithm does not exist

Complexity of the stable marriage and stable roommate problems in three dimensions

The stable marriage problem is a matching problem that pairs members of two sets. The objective is to achieve a matching that satisfies all participants based on their preferences. The stable roommate problem is a variant involving only one set, which is partitioned into pairs with a similar objective. There exist asymptotically optimal algorithms that solve both problems.In this paper, we investigate the complexity of three dimensional extensions of these problems. This is one of twelve research directions suggested by Knuth in his book on the stable marriage problem. We show that these problems are NP-complete, and hence it is unlikely that there exist efficient algorithms for their solutions.Applying the polynomial tranformation developed in this paper, we extend the NP-completeness result to include the problem of matching couples - who are both medical school graduates - to pairs of hospital resident positions. This problem is important in practice and is dealth with annually by NRMP, the centralized program that matches all medical school graduates in the United States to available resident positions

Global existence and decay for solutions of the Hele-Shaw flow with injection

We study the global existence and decay to spherical equilibrium of Hele-Shaw flows with surface tension. We prove that without injection of fluid, perturbations of the sphere decay to zero exponentially fast. On the other hand, with a time-dependent rate of fluid injection into the Hele-Shaw cell, the distance from the moving boundary to an expanding sphere (with time-dependent radius) also decays to zero but with an algebraic rate, which depends on the injection rate of the fluid.Comment: 25 Page

On the Motion of Vortex Sheets with Surface Tension in the 3D Euler Equations with Vorticity

We prove well-posedness of vortex sheets with surface tension in the 3D incompressible Euler equations with vorticity.Comment: 28 page

Navier-Stokes equations interacting with a nonlinear elastic fluid shell

We study a moving boundary value problem consisting of a viscous incompressible fluid moving and interacting with a nonlinear elastic fluid shell. The fluid motion is governed by the Navier-Stokes equations, while the fluid shell is modeled by a bending energy which extremizes the Willmore functional and a membrane energy that extremizes the surface area of the shell. The fluid flow and shell deformation are coupled together by continuity of displacements and tractions (stresses) along the moving material interface. We prove existence and uniqueness of solutions in Sobolev spaces.Comment: 56 pages, 1 figur