6081722
Factoring zero-dimensional ideals of linear partial differential operators
We present an algorithm for factoring a zero-dimensional left ideal in the ring <b>Q</b>(<i>x, y</i>) [∂<inf><i>x</i></inf>, ∂<inf><i>y</i></inf>], i.e. factoring a linear homogeneous partial differential system whose coefficients belong to <b>Q</b>(<i>x, y</i>), and whose solution space is finite-dimensional over <b>Q.</b> The algorithm computes all the zero-dimensional left ideals containing the given ideal. It generalizes the Beke-Schlesinger algorithm for factoring linear ordinary differential operators, and uses an algorithm for finding hyperexponential solutions of such ideals.
6468095
Factoring systems of linear PDEs with finite-dimensional solution spaces
A D-finite system is a finite set of linear homogeneous partial differential equations in several independent and dependent variables, whose solution space is of finite dimension. Let L be a D-finite system with rational function coefficients. We present an algorithm for computing all hyperexponential solutions of L, and an algorithm for computing all D-finite systems whose coefficients are also rational functions, and whose solutions are contained in the solution space of L.
10936659
Haplotype reconstruction from SNP fragments by minimum error correction
MOTIVATION
Haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the minimum error correction (MEC) model, which has been mentioned in several literatures. The model retrieves a pair of haplotypes by correcting minimum number of SNPs in given genome fragments coming from an individual's DNA.


RESULTS
In the first part of this paper, an exact algorithm for the MEC model is presented. Owing to the NP-hardness of the MEC model, we also design a genetic algorithm (GA). The designed GA is intended to solve large size problems and has very good performance. The strength and weakness of the MEC model are shown using experimental results on real data and simulation data. In the second part of this paper, to improve the MEC model for haplotype reconstruction, a new computational model is proposed, which simultaneously employs genotype information of an individual in the process of SNP correction, and is called MEC with genotype information (shortly, MEC/GI). Computational results on extensive datasets show that the new model has much higher accuracy in haplotype reconstruction than the pure MEC model.
18036140
Reducing cache conflicts by partitioning and privatizing shared arrays
Parallelizing compilers for shared-memory multiprocessors typically generate fork-join programs in which multiple threads may access different sections of shared arrays. Each thread tends to access discontiguous addresses due to the gap between sections which belong to different arrays. Such interarray discontiguity often causes cache-set conflicts even when the private cache is large enough to hold the working set. A compiler technique, called array partition and privatization (or APP), is proposed to correct this problem. The APP technique partitions a shared array into sections, one for each computing thread, and then maps each section to the private stack of the corresponding thread. Interarray discontiguity is thus removed and the cache performance improved. This paper presents a compiler algorithm for APP and preliminary experimental results based on four benchmark programs running on an SGI Origin 2000 multiprocessor.
17055037
Efficient thermal-oriented 3D floorplanning and thermal via planning for two-stacked-die integration
New three-dimensional (3D) floorplanning and thermal via planning algorithms are proposed for thermal optimization in two-stacked die integration. Our contributions include (1) a two-stage design flow for 3D floorplanning, which scales down the enlarged solution space due to multidevice layer structure; (2) an efficient thermal-driven 3D floorplanning algorithm with power distribution constraints; (3) a thermal via planning algorithm considering congestion minimization. Experiments results show that our approach is nine times faster with better solution quality compared to a recent published result. In addition, the thermal via planning approach is proven to be very efficient to eliminate localized hot spots directly.
3173724
Buffer insertion in large circuits with constructive solution search techniques
Most existing buffer insertion algorithms, such as van Ginneken's algorithm, consider only individual nets. As a result, these algorithms tend to over buffer when applied to combinational circuits, since it is difficult to decide how many buffers to insert in each net. Recently, Sze, et al. (Sze, 2005) proposed a path-based algorithm for buffer insertion in combinational circuits. However their algorithm is inefficient for large circuits when there are many critical paths. In this paper, we present a new buffer insertion algorithm for combinational circuits such that the timing requirements are met and the buffer cost is minimized. Our algorithm iteratively inserts buffers in the circuit to improve the circuit delay. The core of this algorithm is simple but effective technique that guides the search for a good buffering solution. Experimental results on ISCAS85 circuits show that our new algorithm on average uses 36% less buffers and runs 3 times faster than Sze's algorithm
9219226
iFlow: Middleware-assisted Rendezvous-based Information Access for Mobile Ad Hoc Applications
Due to node mobility and limitations on bandwidth availability in wireless channels, there exist unique challenges towards achieving efficient and effective information access in wireless ad hoc networks with mobile nodes. In this paper, we address two critical questions: (1) How may information be accessed with the highest degree of bandwidth efficiency? and (2) How should algorithms be designed so that node mobility contributes positively towards high performance and efficiency? We present iFlow, a middleware-based framework for bandwidth-efficient and delay-aware information access for mobile ad hoc applications. We present the case of information rendezvous, where the demands for information are satisfied by the supplies in a fully distributed fashion, across third-party nodes beyond information suppliers and consumers. Such rendezvous is achieved via controlled diffusion of information from the suppliers, matched by the gleaning process on the consumers. We validate our claims using simulation and experimental results.