抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

/pdf/convex-analysisnoer-san-nojin-zhan-nituite-5dl2rbmoyr.pdf

Convex Analysisの二,三の進展について

In this paper we study a first-order primal-dual algorithm for non-smooth convex optimization problems with known saddle-point structure. We prove convergence to a saddle-point with rate O(1/N) in finite dimensions for the complete class of problems. We further show accelerations of the proposed algorithm to yield improved rates on problems with some degree of smoothness. In particular we show that we can achieve O(1/N 2) convergence on problems, where the primal or the dual objective is uniformly convex, and we can show linear convergence, i.e. O(? N ) for some ??(0,1), on smooth problems. The wide applicability of the proposed algorithm is demonstrated on several imaging problems such as image denoising, image deconvolution, image inpainting, motion estimation and multi-label image segmentation.

https://hal.archives-ouvertes.fr/hal-00490826/document

A First-Order Primal-Dual Algorithm for Convex Problems with Applications to Imaging

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software

/pdf/advanced-capabilities-for-materials-modelling-with-quantum-40poaosrve.pdf

Advanced capabilities for materials modelling with Quantum ESPRESSO.

to be done in this area. Face recognition is a problem that scarcely clamoured for attention before the computer age but, having surfaced, has involved a wide range of techniques and has attracted the attention of some fine minds (David Mumford was a Fields Medallist in 1974). This singular application of mathematical modelling to a messy applied problem of obvious utility and importance but with no unique solution is a pretty one to share with students: perhaps, returning to the source of our opening quotation, we may invert Duncan's earlier observation, 'There is an art to find the mind's construction in the face!'.

Linear and nonlinear waves, by G. B. Whitham. Pp.636. £50. 1999. ISBN 0 471 35942 4 (Wiley).

/pdf/analytic-continuation-from-limited-noisy-matsubara-data-3ul71rj8.pdf

Analytic continuation from limited noisy Matsubara data

This paper proposes a new method based on neural networks for computing the high-dimensional committor functions that satisfy Fokker-Planck equations. Instead of working with partial differential equations, the new method works with an integral formulation that involves the semigroup of the differential operator. The variational form of the new formulation is then solved by parameterizing the committor function as a neural network. As the main benefit of this new approach, stochastic gradient descent type algorithms can be applied in the training of the committor function without the need of computing any second-order derivatives. Numerical results are provided to demonstrate the performance of the proposed method.

Solving for high dimensional committor functions using neural network with online approximation to derivatives.

Point-set registration is a classical image processing problem that looks for the optimal transformation between two sets of points. In this work, we analyze the impact of outliers when finding the optimal rotation between two point clouds. The presence of outliers motivates the use of least unsquared deviation, which is a non-smooth minimization problem over non-convex domain. We compare approaches based on non-convex optimization over special orthogonal group and convex relaxations. We show that if the fraction of outliers is larger than a certain threshold, any naive convex relaxation fails to recover the ground truth rotation regardless of the sample size and dimension. In contrast, minimizing the least unsquared deviation directly over the special orthogonal group exactly recovers the ground truth rotation for any level of corruption as long as the sample size is large enough. These theoretical findings are supported by numerical simulations.

Maximizing robustness of point-set registration by leveraging non-convexity

Localized representation of the Kohn-Sham subspace plays an important role in quantum chemistry and materials science. The recently developed selected columns of the density matrix (SCDM) method [J. Chem. Theory Comput. 11, 1463, 2015] is a simple and robust procedure for finding a localized representation of a set of Kohn-Sham orbitals from an insulating system. The SCDM method allows the direct construction of a well conditioned (or even orthonormal) and localized basis for the Kohn-Sham subspace. The SCDM algorithm avoids the use of an optimization procedure and does not depend on any adjustable parameters. The most computationally expensive step of the SCDM method is a column pivoted QR factorization that identifies the important columns for constructing the localized basis set. In this paper, we develop a two stage approximate column selection strategy to find the important columns at much lower computational cost. We demonstrate the effectiveness of this process using the dissociation process of a BH$_3$NH$_3$ molecule, an alkane chain and a supercell with 256 water molecules. Numerical results for the large collection of water molecules show that two stage localization procedure can be more than 30 times faster than the original SCDM algorithm and compares favorably with the popular Wannier90 package.

Computing localized representations of the kohn-sham subspace via randomization and refinement

The boundary integral method is an efficient approach for solving time-harmonic obstacle scattering problems from bounded scatterers. This paper presents the directional preconditioner for the linear systems of the boundary integral method in two dimensions. This new preconditioner builds a data-sparse approximation of the integral operator, transforms it into a sparse linear system, and computes an approximate inverse with efficient sparse linear algebra algorithms. This preconditioner is efficient and results in small and almost frequency-independent iteration counts for nonresonant scatterers when combined with standard iterative solvers. Numerical results are provided to demonstrate the effectiveness of the new preconditioner.

Lexing Ying

Papers

Analytic continuation from limited noisy Matsubara data

Solving for high dimensional committor functions using neural network with online approximation to derivatives.

Maximizing robustness of point-set registration by leveraging non-convexity

Computing localized representations of the kohn-sham subspace via randomization and refinement

Directional Preconditioner for 2D High Frequency Obstacle Scattering