2088404
A dispatching mechanism providing REMPLI applications with QoS
For supporting applications with different timing constraints, a PLC (power line communication) system must provide differentiated QoS (quality of service). In this paper a traffic dispatching policy is specified and implemented which guarantees both required periodic data update and short end-to-end delay of aperiodic data request services. This policy is compared with the classic dual-priority one showing its good performance
15862894
Quantitative evaluation of the safety of X-by-Wire architecture subject to EMI perturbations
The X-by-Wire systems in cars can only be accepted if they provide at least the same dependability than the traditional ones. In this paper we propose a new approach to evaluate the impact of the EMI perturbations on the dependability of an X-by-Wire architecture. The considered X-by-Wire architecture is distributed around a TDMA-like communication protocol. So a perturbation causes the loss of a communication cycle with a certain probability. The vehicle level failure is then defined as the consecutive loss of a certain number of communication cycles. Its reliability is modeled as that of the well-known consecutive-k-out-of-n:F systems. A case study, together with the EMI perturbations collected on the roads in France, is used to illustrate our approach
7144496
Loss-tolerant QoS using firm constraints in guaranteed rate networks
We propose a trade-off between hard and soft real-time guarantees to maintain an acceptable QoS guarantee in overload condition and maximize efficiently the utilization of network resources. The key of our solution is that many real-time applications are loss-tolerant, but the loss profile must be well defined since successive packet losses are not suitable. We use the concept of (m,k)-firm timing constraints to define a novel guaranteed loss-tolerant QoS. Therefore, we extend the basic WFQ algorithm to take into account the firm timing constraints to provide lower delay guarantees without violating bandwidth fairness or misusing network resources. The proposal is called (m,k)-WFQ. Using network calculus formalism, analytic study gives the deterministic delay bound provided by the (m,k)-WFQ algorithm for upper bounded arrival curve traffic. Theoretical results and simulations show a noticeable improvement on delay guarantee made by (m,k)-WFQ compared to standard WFQ algorithm without much degrading bandwidth fairness.
16612931
Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution
MOTIVATION
We are interested in studying the evolution of DNA single nucleotide polymorphism sequences which have undergone (meiotic) recombination. For a given set of sequences, computing the minimum number of recombinations needed to explain the sequences (with one mutation per site) is a standard question of interest, but it has been shown to be NP-hard, and previous algorithms that compute it exactly work either only on very small datasets or on problems with special structure.


RESULTS
In this paper, we present efficient, practical methods for computing both upper and lower bounds on the minimum number of needed recombinations, and for constructing evolutionary histories that explain the input sequences. We study in detail the efficiency and accuracy of these algorithms on both simulated and real data sets. The algorithms produce very close upper and lower bounds, which match exactly in a surprisingly wide range of data. Thus, with the use of new, very effective lower bounding methods and an efficient algorithm for computing upper bounds, this approach allows the efficient, exact computation of the minimum number of needed recombinations, with high frequency in a large range of data. When upper and lower bounds match, evolutionary histories found by our algorithm correspond to the most parsimonious histories.


AVAILABILITY
HapBound and SHRUB, programs implementing the new algorithms discussed in this paper, are available at http://wwwcsif.cs.ucdavis.edu/~gusfield/lu.html
11425513
Graceful degradation of loss-tolerant QoS using (m, k)-firm constraints in guaranteed rate networks
The Weighted Fair Queueing (WFQ) scheduling algorithm and its variants can be used to provide real-time guarantees by making bandwidth reservation. However, while hard guarantees are based on a peak workload model that leads to underutilize network resources, soft guarantees, based on average workload model, are not always sufficient to maintain acceptable Quality-of-Service (QoS) since consecutive packet losses or deadline misses may occur, which are not suitable for real-time applications. In this paper, we propose a trade-off between hard and soft real-time guarantees to maintain an acceptable QoS in overload conditions and efficiently maximize the utilization of network resources. The key to our solution is based on the fact that many real-time applications, such as voice and video, are loss-tolerant. The loss profile must be well defined, and such a profile can be easily specified using the (m,k)-firm model. Therefore, we propose the (m,k)-WFQ algorithm to take into account (m,k)-firm timing constraints to provide delay guarantees of at least m packets out of any k consecutive packets without violating bandwidth fairness or misusing network resources. Using the Network Calculus theory, an analytic study gives the deterministic delay bound provided by the (m,k)-WFQ algorithm for upper bounded arrival curve traffic. We extend our analytic results for guaranteed-rate networks, such as the IntServ QoS model and ATM networks, and the DiffServ QoS model. Analytic results and simulations show a noticeable improvement in delay guarantee made by (m,k)-WFQ compared to WFQ without much degradation of bandwidth fairness.
9240638
An Irregular Search Window Reuse Scheme for Motion Estimation in MPEG-2 to H.264 Transcoding
Motion estimation (ME) is a computation-intensive operation in video coding system. In MPEG-2 to H.264 transcoding, motion vector (MV) from MPEG-2 reused as search center in H.264 encoder is a simple but effective technique to simplify ME procedure. However directly introducing MPEG-2 MV will bring irregular overlapping between search windows of successive macroblocks (MB) which invalidates the data reuse scheme in hardware design of ME module. In this paper, the authors propose a search window reuse scheme for transcoding in HDTV application. By utilizing the similarity between neighboring MVs, overlapping of search windows between successive MBs can be regularized. Experiment results show that our method achieve average 93.1% search window reuse rate in HDTV sequence with almost no video quality degradation. And the bandwidth can be reduced to 92.5 Mbytes/s based on theoretical calculation which is only 40.6% of that without this scheme.
40339335
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations
Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is “association mapping” in populations, which is widely hoped to help find genes that influence genetic diseases [3, 4]. Hence, a great deal of recent attention has focused on problems of inferring the historical derivation of sequences in populations when both mutations and recombinations have occurred. In the algorithms literature, most of that recent work has been directed to single-crossover recombination. However, gene-conversion is an important, and more common, form of (two-crossover) recombination which has been much less investigated in the algorithms literature. 
 
In this paper we explicitly incorporate gene-conversion into discrete methods to study historical recombination. We are concerned with algorithms for identifying and locating the extent of historical crossing-over and gene-conversion (along with single-nucleotide mutation), and problems of constructing full putative histories of those events. The novel technical issues concern the incorporation of gene-conversion into recently developed discrete methods [20, 26] that compute lower and upper-bound information on the amount of needed recombination without gene-conversion. We first examine the most natural extension of the lower bound methods from [20], showing that the extension can be computed efficiently, but that this extension can only yield weak lower bounds. We then develop additional ideas that lead to higher lower bounds, and show how to solve, via integer-linear programming, a more biologically realistic version of the lower bound problem. We also show how to compute effective upper bounds on the number of needed single-crossovers and gene-conversions, along with explicit networks showing a putative history of mutations, single-crossovers and gene-conversions. 
 
We validate the significance of these methods by showing that they can be effectively used to distinguish simulation-derived sequences generated without gene-conversion from sequences that were generated with gene-conversion. We apply the methods to recently studied sequences of Arabidopsis thaliana, identifying many more regions in the sequences than were previously identified [22], where gene-conversion may have played a significant role. Demonstration software is available at www.cs. ucdavis.edu/~gusfield.