2011 Spring: 生命科学中的随机动力学模型

生命科学中的随机动力学模型
Spring 2011

Course Information

Synopsis (摘要)

本课程主要覆盖在生命科学中的高维动态数据分析及相关的数学统计模型，包括 Markov models, Michalis-Menton Equation, 等。

Time and Place:

Tuesday 3:10-6:00pm, Rm 425, Ying Jie Exchange Center; 数院本科生机房, 英杰交流中心 425

Schedule (时间表)

Date	Topic	Presenters
02/22/2011	Lecture 01: Introduction, clustering in biomolecular folding [slides]	Y.Y.
03/01/2011	Lecture 02: Kcenter lab session, Spectral Clustering [slides] [data] www.math.pku.edu.cn/teachers/yao/Spring2011/data or download from stanford [matlab] www.math.pku.edu.cn/teachers/yao/Spring2011/matlab or download from stanford	Y.Y.
03/08/2011	Lecture 03: Spectral Clustering, Nystrom Method, and Lab Session [slides] [data] www.math.pku.edu.cn/teachers/yao/Spring2011/data [matlab] www.math.pku.edu.cn/teachers/yao/Spring2011/matlab	Y.Y.
03/15/2011	Lecture 04: Cover Tree -- an hierarchical online k-center [slides] [data] ./data/confs_3D.txt ./data/confs_partial.txt [C++ codes by Ying Chen] www.math.pku.edu.cn/teachers/yao/Spring2011/covertree	CHEN, Ying Y.Y.
03/22/2011	Lecture 05: Bayesian Inference for (reversible) Markov Chains [slides] [data] ./data/motor_stepsize.txt [Python codes by Sergio Bacallado, with partial Matlab translations] ./msmbayes ./matlab/MultinomialLogLik.m ./matlab/MarkovChainLogLik.m ./matlab/RevChainLogLik.m [New Reference for Projects] Sun et al. Nature Structural & Molecular Biology, 17(4):485-491, 2010.	Y.Y.
03/29/2011	Lecture 06: Systems Neuroscience Modeling [slides]	Louis L.-T. Tao (CBI, PKU)
04/12/2011	Lecture 07: Mathematics of Data -- Introduction, PCA, MDS, and Graph Realization [slides]	Y. Y.
04/19/2011	Lecture 08: Mathematics of Data -- ISOMAP and LLE [slides] [Matlab Toolbox for Dimensionality Reduction] ./matlab/drtoolbox/ ./matlab/isomap.m (isomap by Tennenbaum, de Silva) ./matlab/isomapII.m (isomap by Tennenbaum, de Silva with sparsity, fast mex with dijkstra.cpp fibheap.h) ./matlab/lle.m (lle)	Y. Y.
04/26/2011	Lecture 09: Study of Molecular Motor Proteins Using Single Molecule Fluorescence Microscopy (slides unreleased due to speaker's request) [Reference] Sun et al. Nature Structural & Molecular Biology, 17(4):485-491, 2010. A Preliminary Markov Model Analysis for Myosin Stepsizes (slides by Y.Y.)	SUN, Yujie (BIOPIC, PKU)
05/03/2011	Lecture 10: Mathematics of Data -- Laplacian, Diffusion, and Hessian LLE [slides] [Matlab] ./matlab/hlle.m (Hessian LLE)	Y.Y.
05/10/2011	Lecture 11: Mathematics of Data 1. Heat Kernals and Shape Analysis [ SUN, Jian's slides ] 2. Local Tangent Space Alignment (LTSA) [ slides ] 3. Comparisons of Manifold Learning Techniques [ Todd Wittman's slides ] [Matlab] ./matlab/mani.m (Todd Wittman's comparisons of 8 techniques)	SUN, Jian (Tsinghua) Y.Y.
05/17/2011	Lecture 12: HMM in Bioinformaces [slides]	DENG, Minghua
05/24/2011	Lecture 13: Topics on BioPIC	HUANG, Yanyi (BIOPIC, PKU)
05/31/2011	Lecture 14: Introduction to Topological Data Analysis [Reference] Topology and Data , by Gunnar Carlsson at MMDS'2008 Dimitry Morozov's course web at Stanford 2009 [Matlab] ./matlab/PlexMatlabTutorialFiles/ -- by Henry Adams 2009	Y.Y.
6/07/2011	Lecture 15: Combinatorial Hodge Theory and Applications [slides]	Y.Y.

Reading list

To-be-announced

Required

[label]