Nonlinear Low-dimensional Structures in High-dimensions for Biological Data
Many problems in biology, particularly at the molecular level, involve very high dimensions. Traditional methods, such as principal component analysis provide, an important first step toward understanding the underlying lower dimensional structure. Nevertheless, finding even lower-dimensional and possibly nonlinear structures requires more qualitative procedures. Some possible candidates, among others, include geodesic principal component analysis, SiZER analysis, and persistent homology. The aim of this Working Group will be to describe and understand the nature of certain biological data coming from areas such as brain artery tree networks, gene networks, biomechanical motion data, and metagenomics, to name a few. We will explore and formulate strategies to best apply these qualitative procedures. In addition, a recent insight into a connection between SiZER analysis and persistent
homology will be discussed.
Discussion
Date: Wednesday, April 9, 2014
Time: 11:00 am, Eastern Daylight Time (New York, GMT-04:00)
Meeting Room: SAMSI 203
Meeting Number: 688 972 210
Meeting Password: Nonlinear1
Phone: 919-685-9399, ext 9338#
Current Direction
Now tha we are near the end of the program, we will discuss what analysis we wish to collaborate on.
Date: Wednesday, March 26, 2014
Time: 11:00 am, Eastern Daylight Time (New York, GMT-04:00)
Meeting Room: SAMSI 203
Meeting Number: 688 972 210
Meeting Password: Nonlinear1
Phone: 919-685-9399, ext 9338#
Dirichlet-Multinomial Regression and Simulated CDI
This week we review DM-Regression and discuss simulated CDI data. The simulated data to be released after the meeting.
Date: Wednesday, March 19, 2014
Time: 11:00 am, Eastern Daylight Time (New York, GMT-04:00)
Meeting Room: SAMSI 203
Meeting Number: 688 972 210
Meeting Password: Nonlinear1
Phone: 919-685-9399, ext 9338#
Dirichlet-Multinomial with Metagenomic Data
This week Jungsik Noh will be presenting some analysis he performed with the HMP package.
Date: Wednesday, March 4, 2014
Time: 11:00 am, Eastern Daylight Time (New York, GMT-04:00)
Meeting Room: SAMSI 203
Meeting Number: 688 972 210
Meeting Password: Nonlinear1
Phone: 919-685-9399, ext 9338#
Nonlinear strucutre in biology
Date: Wednesday, February 19, 2014
Time: 11:00 am, Eastern Daylight Time (New York, GMT-04:00)
Meeting Room: SAMSI 203
Meeting Number: 688 972 210
Meeting Password: Nonlinear1
Phone: 919-685-9399, ext 9338#
Sparse DM Regression
Date: Wednesday, January 22, 2014
Time: 11:00 am, Eastern Daylight Time (New York, GMT-04:00)
Meeting Room: SAMSI 203
Meeting Number: 688 972 210
Meeting Password: Nonlinear1
Phone: 919-685-9399, ext 9338#
We'll discuss the attached paper by Chen and Li, "Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis"