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.
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.
14072276
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees
We present an efficient algorithm for statistical multiple alignment based on the TKF91 model of Thorne, Kishino, and Felsenstein (1991) on an arbitrary k-leaved phylogenetic tree. The existing algorithms use a hidden Markov model approach, which requires at least O( radical 5(k)) states and leads to a time complexity of O(5(k)L(k)), where L is the geometric mean sequence length. Using a combinatorial technique reminiscent of inclusion/exclusion, we are able to sum away the states, thus improving the time complexity to O(2(k)L(k)) and considerably reducing memory requirements. This makes statistical multiple alignment under the TKF91 model a definite practical possibility in the case of a phylogenetic tree with a modest number of leaves.
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
23745644
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks
Under the infinite-sites model of mutation, we consider the problem of finding the minimum number of recombination events which must have occurred in the evolutionary history of sampled DNA sequences. Our approach is deterministic and is based on the combinatorics of leaf-labelled rooted trees. In contrast to previously known approaches, which only yield estimated lower bounds, our approach always gives the exact minimum number of recombination events. Furthermore, our method can be used to reconstruct explicitly evolutionary histories with the minimum number of recombination events. As an additional application, we discuss how our work can be used to define haplotype blocks.
11873336
A concise necessary and sufficient condition for the existence of a galled-tree
Galled-trees are a special class of graphical representation of evolutionary history that has proven amenable to efficient, polynomial-time algorithms. The goal of this paper is to construct a concise necessary and sufficient condition for the existence of a galled-tree for M, a set of binary sequences that purportedly have evolved in the presence of recombination. Both root-known and root-unknown cases are considered here
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.