1688557
Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics
Given a set D of input sequences, a genealogy for D can be constructed backward in time using such evolutionary events as mutation, coalescent, and recombination. An ancestral configuration (AC) can be regarded as the multiset of all sequences present at a particular point in time in a possible genealogy for D. The complexity of computing the likelihood of observing D depends heavily on the total number of distinct ACs of D and, therefore, it is of interest to estimate that number. For D consisting of binary sequences of finite length, we consider the problem of enumerating exactly all distinct ACs. We assume that the root sequence type is known and that the mutation process is governed by the infinite-sites model. When there is no recombination, we construct a general method of obtaining closed-form formulas for the total number of ACs. The enumeration problem becomes much more complicated when recombination is involved. In that case, we devise a method of enumeration based on counting contingency tables and construct a dynamic programming algorithm for the approach. Last, we describe a method of counting the number of ACs that can appear in genealogies with less than or equal to a given number R of recombinations. Of particular interest is the case in which R is close to the minimum number of recombinations for D
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
16829828
Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event
The haplotype inference (HI) problem is the problem of inferring 2n haplotype pairs from n observed genotype vectors. This is a key problem that arises in studying genetic variation in populations, for example in the ongoing HapMap project [5]. In order to have a hope of finding the haplotypes that actually generated the observed genotypes, we must use some (implicit or explicit) genetic model of the evolution of the underlying haplotypes. The Perfect Phylogeny Haplotyping (PPH) model was introduced in 2002 [9] to reflect the “neutral coalescent” or “perfect phylogeny” model of haplotype evolution. The PPH problem (which can be solved in polynomial time) is to determine whether there is an HI solution where the inferred haplotypes can be derived on a perfect phylogeny (tree). 
 
Since the introduction of the PPH model, several extensions and modifications of the PPH model have been examined. The most important modification, to model biological reality better, is to allow a limited number of biological events that violate the perfect phylogeny model. This was accomplished implicitly in [7,12] with the inclusion of several heuristics into an algorithm for the PPH problem [8]. Those heuristics are invoked when the genotype data cannot be explained with haplotypes that fit the perfect phylogeny model. In this paper, we address the issue explicitly, by allowing one recombination or homoplasy event in the model of haplotype evolution. We formalize the problems and provide a polynomial time solution for one problem, using an additional, empirically-supported assumption. We present a related framework for the second problem which gives a practical algorithm. We believe the second problem can be solved in polynomial time.
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.
10098796
Constructing Minimal Ancestral Recombination Graphs
By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using the minimum number of recombination events. In contrast to previously known methods, which yield only estimated lower bounds, our method of detecting recombination always gives the minimum number of recombination events if the right kind of rooted trees are used in our algorithm. A new lower bound can be defined if rooted trees with fewer constraints are used. As well as studying how often it actually is equal to the minimum, we test how this new lower bound performs in comparison to some other lower bounds. Our study indicates that the new lower bound is an improvement on earlier bounds. Also, using simulated data, we investigate how well our method can recover the actual site-specific evolutionary relationships. In the presence of recombination, using a single tree to describe the evolution of the entire locus clearly leads to lower average recovery percentages than does our method. Our study shows that recovering the actual local tree topologies can be done more accurately than estimating the actual number of recombination events.
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.
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.
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
7172331
Enhanced Strict Multilevel Successive Elimination Algorithm for Fast Motion Estimation
This paper presents an enhanced strict multilevel successive elimination algorithm (EMSEA) for fast block-matching motion estimation, which is based on the previous strict multilevel successive elimination algorithm (SMSEA) (Song et al., 2006). Different to the SMSEA algorithm with fixed parameters, in EMSEA algorithm, the whole search area is divided into two regions and each region has its own parameters. Therefore, the computation complexity of SMSEA algorithm can be further decreased. Experiments show that the proposed EMSEA algorithm can reduce 16.2% of the SMSEA computation and maintain almost the same image quality, which is better than the TSS and DS algorithms.
2185149
Monocular perception of biological motion-detection and labeling
Computer perception of biological motion is key to developing convenient and powerful human-computer interfaces. Successful body tracking algorithms have been developed; however initialization is done by hand. We propose a method for detecting a moving human body and for labeling its parts automatically. It is based on maximizing the joint probability density function (PDF) of the position and velocity of the body parts. The PDF is estimated from training data. Dynamic programming is used for calculating efficiently the best global labeling on an approximation of the PDF. The computational cost is on the order of N/sup 4/ where N is the number of features detected. We explore the performance of our method with experiments carried on a variety of periodic and non-periodic body motions viewed monocularly for a total of approximately 30,000 frames. Point-markers were strapped to the joints of the subject for facilitating image analysis. We find an average of 2.3% labeling error; the experiments also suggest a high degree of viewpoint-invariance.
25329703
Monocular Perception of Biological Motion in Johansson Displays
Computer perception of biological motion is key to developing convenient and powerful human?computer interfaces. Algorithms have been developed for tracking the body; however, initialization is done by hand. We propose a method for detecting a moving human body and for labeling its parts automatically in scenes that include extraneous motions and occlusion. We assume a Johansson display, i.e., that a number of moving features, some representing the unoccluded body joints and some belonging to the background, are supplied in the scene. Our method is based on maximizing the joint probability density function (PDF) of the position and velocity of the body parts. The PDF is estimated from training data. Dynamic programming is used for calculating efficiently the best global labeling on an approximation of the PDF. Detection is performed by hypothesis testing on the best labeling found. The computational cost is on the order of N4 where N is the number of features detected. We explore the performance of our method with experiments carried on a variety of periodic and nonperiodic body motions viewed monocularly for a total of approximately 30,000 frames. The algorithm is demonstrated to be accurate and efficient.