Search

For tensor decompositions such as HOSVD and ParaFac, the objective functions are nonconvex. This implies, theoretically, there exists a large number of local optimas: starting from different starting point, the iteratively improved solution will converge to different local solutions. This non-uniqueness present a stability and reliability problem for image compression and retrieval. In this paper, we present the results of a comprehensive investigation of this problem. We found that although all tensor decomposition algorithms fail to reach a unique global solution on random data and severely scrambled data; surprisingly however, on all real life several data sets (even with substantial scramble and occlusions), HOSVD always produce the unique global solution in the parameter region suitable to practical applications, while ParaFac produce non-unique solutions. We provide an eigenvalue based rule for the assessing the solution uniqueness., Submitted to CVPR2009 in Nov. 20, 2008

Community Climate System Model (CCSM) is currently a multi-executable system based on the Multi-Program Multi-Data (MPMD) mechanism. Each component is compiled into a separate executable. MPMD is normally cumbersome in usage and vendor support is sometimes limited or completely unavailable, such as on BlueGene/L. Also smaller groups and institutions would like to run CCSM locally, rather than relying on large computer centers. So, single-executable CCSM is under request. We are developing a multi-executable and single-executable coexisting version of CCSM. In single-executable, each component is organized as a subroutine, which is called from a master program. Different components run simultaneously. This is accomplished by redesigning the top level CCSM structures using the Multi-Program Handshaking (MPH) library.

A growing trend in developing large and complex applications on today's Teraflop scale computers is to integrate stand-alone and/or semi-independent program components into a comprehensive simulation package. One example is the Community Climate System Model which consists of atmosphere, ocean, land-surface and sea-ice components. Each component is semi-independent and has been developed at a different institution. We study how this multi-component, multi-executable application can run effectively on distributed memory architectures. For the first time, we clearly identify five effective execution modes and develop the MPH library to support application development utilizing these modes. MPH performs component-name registration, resource allocation and initial component handshaking in a flexible way.

Coupled climate models are large, multiphysics applications designed to simulate the Earth's climate and predict the response of the climate to any changes in the forcing or boundary conditions. The Community Climate System Model (CCSM) is a widely used state-of-art climate model that has released several versions to the climate community over the past ten years. Like many climate models, CCSM employs a coupler, a functional unit that coordinates the exchange of data between parts of climate system such as the atmosphere and ocean. This paper describes the new coupler, cpl6, contained in the latest version of CCSM, CCSM3. Cpl6 introduces distributed-memory parallelism to the coupler, a class library for important coupler functions, and a standardized interface for component models. Cpl6 is implemented entirely in Fortran 90 and uses Model Coupling Toolkit as the base for most of its classes. Cpl6 gives improved performance over previous versions and scales well on multiple platforms.

Background Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question. Methods Here we provide insight on domain definitions through comparative mapping of two domain classification databases, one sequence-based (Pfam) and the other structure-based (SCOP). A mapping score is defined to indicate the significance of the mapping, and the properties of the mapping matrices are studied. Results The mapping results show a general agreement between the two databases, as well as many interesting areas of disagreement. In the cases of disagreement, the functional and evolutionary characteristics of the domains are examined to determine which domain definition is biologically more informative.

The protein interaction network presents one perspective for understanding cellular processes. Recent experiments employing high-throughput mass spectrometric characterizations have resulted in large datasets of physiologically relevant multi-protein complexes. We present a unified representation of such datasets based on an underlying bipartite graph model that is an advance on existing models of the network. Our unified representation allows for weighting of connections between proteins shared in more than one complex as well as addressing the higher level of organization that occurs when the network is viewed as consisting of protein complexes that share components. This representation also allows for the application of the rigorous MinMaxCut graph clustering algorithm for the determination of relevant protein modules in the networks. Statistically significant annotations of clusters in the protein-protein and complex-complex network using terms from the Gene Ontology suggest that this method will be useful for posing hypothesis about uncharacterized components of protein complexes or uncharacterized relationships between protein complexes.

Many current large and complex HPC applications are based on semi-independent program components developed by different groups or for different purposes. On distributed memory parallel supercomputers, how to perform component-name registration and initialize communications between independent components are among the first critical steps in establishing a distributed multi-component environment. Here we describe MPH, a multi-component handshaking library that resolves these tasks in a convenient and consistent way. MPH uses MPI for high performance and supports many PVM functionality. It supports two major parallel integration mechanism: multi-component multi-executable (MCME) and multi-component single-executable (MCME). It is a simple, easy-to-use module for developing practical codes, or as basis for larger software tools/frameworks.