Automatic Task-Based Code Generation for High Performance Domain Specific Embedded Language

Providing high level tools for parallel programming while sustaining a high level of performance has been a challenge that techniques like Domain Specific Embedded Languages try to solve. In previous works, we investigated the design of such a DSEL—NT\(^2\)—providing a Matlab -like syntax for parallel numerical computations inside a C++ library. In this paper, we show how NT\(^2\!\) has been redesigned for shared memory systems in an extensible and portable way. The new NT\(^2\!\) design relies on a tiered Parallel Skeleton system built using asynchronous task management and automatic compile-time taskification of user level code. We describe how this system can operate various shared memory runtimes and evaluate the design by using two benchmarks implementing linear algebra algorithms.     

Enhanced ground support: lessons from work on reduced crew operations

Cognition, Technology & Work - From the 1950s through the 1980s, aircraft design was marked by an increase in reliability and automation, and, correspondingly, a decrease in the crew complement...     

Optimizing latency and throughput of application workflows on clusters

Scheduling, in many application domains, involves optimization of multiple performance metrics. For example, application workflows with real-time constraints have strict throughput requirements and also desire a low latency or response time. In this paper, we present a novel algorithm for the scheduling of workflows that act on a stream of input data. Our algorithm focuses on the two performance metrics, latency and throughput, and minimizes the latency of workflows while satisfying strict throughput requirements. We also describe steps to use the above approach to solve the problem of meeting latency requirements while maximizing throughput. We leverage pipelined, task and data parallelism in a coordinated manner to meet these objectives and investigate the benefit of task duplication in alleviating communication overheads in the pipelined schedule for different workflow characteristics. The proposed algorithm is designed for a realistic bounded multi-port communication model, where each processor can simultaneously communicate with at most k distinct processors. Experimental evaluation using synthetic benchmarks as well as those derived from real applications shows that our algorithm consistently produces lower latency schedules that meet throughput requirements, even when previously proposed schemes fail.     

Template-based quadrilateral mesh generation from imaging data

This paper describes a novel template-based meshing approach for generating good quality quadrilateral meshes from 2D digital images. This approach builds upon an existing image-based mesh generation technique called Imeshp, which enables us to create a segmented triangle mesh from an image without the need for an image segmentation step. Our approach generates a quadrilateral mesh using an indirect scheme, which converts the segmented triangle mesh created by the initial steps of the Imesh technique into a quadrilateral one. The triangle-to-quadrilateral conversion makes use of template meshes of triangles. To ensure good element quality, the conversion step is followed by a smoothing step, which is based on a new optimization-based procedure. We show several examples of meshes generated by our approach, and present a thorough experimental evaluation of the quality of the meshes given as examples.     

On the complexity of binary samples

Consider a class of binary functions h: X→{ − 1, + 1} on an interval . Define the sample width of h on a finite subset (a sample) S ⊂ X as ω _S (h) =  min _x ∈ S |ω _h (x)| where ω _h (x) = h(x) max {a ≥ 0: h(z) = h(x), x − a ≤ z ≤ x + a}. Let be the space of all samples in X of cardinality ℓ and consider sets of wide samples, i.e., hypersets which are defined as Through an application of the Sauer-Shelah result on the density of sets an upper estimate is obtained on the growth function (or trace) of the class , β > 0, i.e., on the number of possible dichotomies obtained by intersecting all hypersets with a fixed collection of samples of cardinality m. The estimate is .      

Reconstruction of cellular biological structures from optical microscopy data

Developments in optical microscopy imaging have generated large high-resolution data sets that have spurred medical researchers to conduct investigations into mechanisms of disease, including cancer at cellular and subcellular levels. The work reported here demonstrates that a suitable methodology can be conceived that isolates modality-dependent effects from the larger segmentation task and that 3D reconstructions can be cognizant of shapes as evident in the available 2D planar images. In the current realization, a method based on active geodesic contours is first deployed to counter the ambiguity that exists in separating overlapping cells on the image plane. Later, another segmentation effort based on a variant of Voronoi tessellations improves the delineation of the cell boundaries using a Bayesian formulation. In the next stage, the cells are interpolated across the third dimension thereby mitigating the poor structural correlation that exists in that dimension. We deploy our methods on three separate data sets obtained from light, confocal, and phase-contrast microscopy and validate the results appropriately.     

Computer program for automated sleep depth estimation

In this article, we present a new implementation of an amplitude-independent method for continuous-scale sleep depth estimation. Having been implemented as an add-on analysis module under commercially available biosignal recording and analysis software, it can be easily applied in clinical routine. The software gives the user full freedom to change all the analysis parameters inside theoretical limits. Computational sleep depth profiles produced by the presented software compare favourably with visual classifications. Future work will concentrate on systematic optimization of analysis parameters, further evaluation of the method with disturbed sleep and application of the method for automated adaptive sleep analysis.     

A theory of mode of action of azolylalkylquinolines as DNA binding agents using automated flexible ligand docking

Azolylalkylquinolines (AAQs) are a family of quinolines with varying degrees of cytotoxic activity (comparable or moderately superior to adriamycin in some cases) developed in the past decade in our group where their exact mode of action is still unclear. In this study the most probable DNA binding mode of AAQs was investigated employing a novel flexible ligand docking approach by using AutoDock 3.0. Forty-nine AAQs with known experimental inhibitory activity were docked onto d(CGCAAATTTGCG)(2), d(CGATCG)(2) and d(CGCG)(2) oligonucleotides retrieved from the Protein Data Bank (PDB IDs: 102D, 1D12 and 1D32, respectively) as the representatives of the three plausible models of interactions between chemotherapeutic agents and DNA (groove binding, groove binding plus intercalation and bisintercalation, respectively). Good correlation (r(2)=0.64) between calculated binding energies and experimental inhibitory activities was obtained using groove binding plus intercalation model for phenyl-azolylalkylquinoline (PAAQ) series. Our findings show that the most probable mode of action of PAAQs as DNA binding agents is via intercalation of quinolinic moiety between CG base pairs with linker chain and azole moiety binding to the minor groove.     

Fluorescence in situ hybridization of three oncogenes on a leiomyoma

Using fluorescence in situ hybridization technique, expression of three oncogenes, C-myc, RARa, and cyclin-D was tested on a uterine leiomyoma. C-myc and RARa were amplified in approximately 30% and 90% of the cells, respectively. Numerous small signals of C-myc were indicative of the presence of double minutes. Amplification of RARa is being reported for the first time in a leiomyoma. Cyclin-D was normal in diploid cells while it was highly amplified in polyploid cells. Low levels of amplified C-myc and cyclin-D cells seem to be the reason for this tumor to be benign, while RARa could not be effective without the association of some other gene such as PML. Information presented here are significant toward developing new curative strategies such as gene-specific drugs and molecular manipulation to stop the activity of cancer gene. Further study may elucidate that how fibroids grow and maintain their rare benign nature.