Selecting Relevant Genes with a Spectral Approach

Array technologies have made it possible to record simultaneously the expression pattern of thousands of genes. A fundamental problem in the analysis of gene expression data is the identification of highly relevant genes that either discriminate between phenotypic labels or are important with respect to the cellular process studied in the experiment: for example cell cycle or heat shock in yeast experiments, chemical or genetic perturbations of mammalian cell lines, and genes involved in class discovery for human tumors. In this paper we focus on the task of unsupervised gene selection. The problem of selecting a small subset of genes is particularly challenging as the datasets involved are typically characterized by a very small sample size ?? the order of few tens of tissue samples ??d by a very large feature space as the number of genes tend to be in the high thousands. We propose a model independent approach which scores candidate gene selections using spectral properties of the candidate affinity matrix. The algorithm is very straightforward to implement yet contains a number of remarkable properties which guarantee consistent sparse selections. To illustrate the value of our approach we applied our algorithm on five different datasets. The first consists of time course data from four well studied Hematopoietic cell lines (HL-60, Jurkat, NB4, and U937). The other four datasets include three well studied treatment outcomes (large cell lymphoma, childhood medulloblastomas, breast tumors) and one unpublished dataset (lymph status). We compared our approach both with other unsupervised methods (SOM,PCA,GS) and with supervised methods (SNR,RMB,RFE). The results clearly show that our approach considerably outperforms all the other unsupervised approaches in our study, is competitive with supervised methods and in some case even outperforms supervised approaches.

Output from the 1998 Product Development Value Stream Workshop: A Framework for Understanding Information Flow in the Product Development Process

The descriptions below and the attached diagrams are outputs of the 1998 LAI Product Development Focus Team workshop on the Value Chain in Product Development. A working group at that workshop was asked to model the product development process: in terms of the phases of product development and their interfaces, boundaries and outputs. Their work has proven to be generally useful to LAI researchers and industry members, and so is formalized here.

Benefits of Implementing Lean Practices and the Impact of the Lean Aerospace Initiative in the Defense Aerospace Industry and Government Agencies

In the 1980’s, many United States industrial organizations started developing new production processes to improve quality, reduce cost, and better respond to customer needs and the pressures of global competition. This new paradigm was coined Lean Production (or simply “Lean”) in the book The Machine That Changed The World published in 1990 by researchers from MIT’s International Motor Vehicle Program. In 1993, a consortium of US defense aerospace firms and the USAF Aeronautical Systems Center, together with the AFRL Materials and Manufacturing Directorate, started the Lean Aircraft Initiative (LAI) at MIT. With expansion in 1998 to include government space products, the program was renamed the Lean Aerospace Initiative. LAI’s vision is to “Significantly reduce the cost and cycle time for military aerospace products throughout the entire value chain while continuing to improve product performance.” By late 1998, 23 industry and 13 government organizations with paying memberships, along with MIT and the UAW were participating in the LAI.

Preliminary Observations on Program Instability

This white paper reports emerging findings at the end of Phase I of the Lean Aircraft Initiative in the Policy focus group area. Specifically, it provides details about research on program instability. Its objective is to discuss high-level findings detailing: 1) the relative contribution of different factors to a program’s overall instability; 2) the cost impact of program instability on acquisition programs; and 3) some strategies recommended by program managers for overcoming and/or mitigating the negative effects of program instability on their programs. Because this report comes as this research is underway, this is not meant to be a definitive document on the subject. Rather, is it anticipated that this research may potentially produce a number of reports on program instability-related topics. The government managers of military acquisition programs rated annual budget or production rate changes, changes in requirements, and technical difficulties as the three top contributors, respectively, to program instability. When asked to partition actual variance in their program’s planned cost and schedule to each of these factors, it was found that the combined effects of unplanned budget and requirement changes accounted for 5.2% annual cost growth and 20% total program schedule slip. At a rate of approximately 5% annual cost growth from these factors, it is easy to see that even conservative estimates of the cost benefits to be gained from acquisition reforms and process improvements can quickly be eclipsed by the added cost associated with program instability. Program management practices involving the integration of stakeholders from throughout the value chain into the decision making process were rated the most effective at avoiding program instability. The use of advanced information technologies was rated the most effective at mitigating the negative impact of program instability.

Preliminary Observations on Program Instability

This white paper reports emerging findings at the end of Phase I of the Lean Aircraft Initiative in the Policy focus group area. Specifically, it provides details about research on program instability. Its objective is to discuss high-level findings detailing: 1) the relative contribution of different factors to a program’s overall instability; 2) the cost impact of program instability on acquisition programs; and 3) some strategies recommended by program managers for overcoming and/or mitigating the negative effects of program instability on their programs. Because this report comes as this research is underway, this is not meant to be a definitive document on the subject. Rather, is it anticipated that this research may potentially produce a number of reports on program instability-related topics. The government managers of military acquisition programs rated annual budget or production rate changes, changes in requirements, and technical difficulties as the three top contributors, respectively, to program instability. When asked to partition actual variance in their program’s planned cost and schedule to each of these factors, it was found that the combined effects of unplanned budget and requirement changes accounted for 5.2% annual cost growth and 20% total program schedule slip. At a rate of approximately 5% annual cost growth from these factors, it is easy to see that even conservative estimates of the cost benefits to be gained from acquisition reforms and process improvements can quickly be eclipsed by the added cost associated with program instability. Program management practices involving the integration of stakeholders from throughout the value chain into the decision making process were rated the most effective at avoiding program instability. The use of advanced information technologies was rated the most effective at mitigating the negative impact of program instability.