Efficient algorithms for the gene tree species tree reconciliation problem

... embedding of the gene tree into the species tree [36] In such an embedding, the topology of the gene tree is kept; gene tree leaves are placed at the species tree leaves where they come from; and the ... 2.6.1 The General Reconciliation Problem The species tree inference problem Parsimony-based inference of the species tree from a set of ge...

Ngày tải lên: 09/09/2015, 08:12

... compute the ratio Pxy = Z(πxy)/Z The recursions for the restricted partition function Z(π xy ) can be We implemented the polynomial algorithms for the MPP in the program TARGETING The TARGETING ... graphs These algorithms therefore not appear to give rise to efficient partition function versions The TARGETING software (15) for k Î J Note that these recursions...

Ngày tải lên: 12/08/2014, 17:20

... description of the two new algorithms for Viterbi training and stochastic EM training In addition, we implement all three algorithms, i.e the new algorithms for Viterbi training and stochastic EM training ... , Π s ( X )) and E i (y , L, M) = E iq (y , X , Π s ( X )) , Proof: The proof for this theorem is very similar to the proof of theorem for...

Ngày tải lên: 12/08/2014, 17:20

... Halpern, Fixed points of nonexpanding maps,” Bulletin of the American Mathematical Society, vol 73, pp 957–961, 1967 Fixed Point Theory and Applications 13 F E Browder, Fixed- point theorems for ... Halpern’s property Deduced Theorems Using Theorems 3.1, 3.2, and 3.3, we can obtain many convergence theorems We state some of them We now discuss convergence theorems for f...

Ngày tải lên: 21/06/2014, 20:20

... the 3D wavelet transform, Kutil and Uhl have conducted a study of the software and hardware needs of the 3D wavelet transform [14] They have centered their study on the classic wavelet transform ... speed-up, and the quality of the signal 2.3 GOF-based 3D- WT One of the major challenges to overcome when computing the 3D- WT has to with the developm...

Ngày tải lên: 22/06/2014, 19:20

... in form to those in the real-valued blind source separation case, where the roles of the real-valued amplitudes {Ai } in the complex-valued separation case play identical roles to those of the ... each of the measurements Due to the varying nature of the singular values of A within the measurements, the signal- to-noise ratios (SNRs) of the mixtures...

Ngày tải lên: 22/06/2014, 23:20

... substring is copied from x and inverted before being inserted into the target string y We allow the cost of inversion to be an affine function in the length ℓ of the duplicated inverted string, ... substring of the duplicated string may be inverted before the string is inserted into y For example, we allow (+a +b +c +d +e +f) to become (+a +b -e -d -c +f) before being inserted into y I...

Ngày tải lên: 12/08/2014, 17:20

... studied the strong law of large numbers and Shannon-McMillan for the mth-order nonhomogeneous Markov chains indexed by an m rooted Cayley tree Yang [14] has also studied a class of small deviation theorems ... Shannon-McMillan theorem for nonhomogeneous Markov chains indexed by a homogeneous tree Huang and Yang [11] have studied the strong law of large numb...

Ngày tải lên: 20/06/2014, 23:20

... 22: end for 23: Compute C(M(G), n) = i∈ch(∅) Ci (M(G), n) 24: Outpute PNML (xn | M(G)) = P(xn | M(G))/C(M(G), n) Algorithm 3: The algorithm for computing PNML (xn | M(G)) for a Bayesian forest ... See [16] for more details NML FOR BAYESIAN FORESTS The naive Bayes model discussed in the previous section has been successfully applied in various domains In this section we conside...

Ngày tải lên: 22/06/2014, 00:20

... Cheng, J Sun, M Min, and D.-Z Du, “Energy-efficient broadcast and multicast routing in ad hoc wireless networks,” in Proceedings of the 22nd IEEE International Performance, Computing and Communications ... Leung, and O W W Yang, Distributed multicast algorithms for lifetime maximization in wireless ad hoc networks with omni -directional and directional...

Ngày tải lên: 22/06/2014, 22:20

... is the number of F -structures for which the permutation σ is an automorphism and (σ1 , σ2 , ) is the cycle type of σ [2] In this note, we deal with the special family T of rooted trees Yet another ... Yet another reformulation shows that the cycle index series is also Z(Aut(T )), T ∈T where Z(Aut(T )) is the cycle index of the automorphism group of T...

Ngày tải lên: 07/08/2014, 13:21

... functioning of each method was not deteriorated by the other The relationship obtained with the comparison of the two methods over the whole period (n 589) is presented in figure The slope of the regression ... 2300 and 0400 hours The sap flow rate (F) is calculated lows [2, 10]: as fol- where Cp is the heat capacity of the xylem sap and dT the temper...

Ngày tải lên: 08/08/2014, 23:22

... Multibit tree Again, a too large k will actually slow down the data Figure 11 Fraction of coefficients calculated, different database size The fraction of the database for which the Tanimoto coefficient ... bit In fact we only demand that the data is arranged in some binary tree The match-bits of a given node are computed as all bits that are not a match-bit in any a...

Ngày tải lên: 12/08/2014, 17:20

... of the problem, optimal algorithms can solve some instances of the p- median problem with reasonable effort A typical approach is to combine Lagrangian relaxation with branch-and-bound (see, for ... members of the population after every population update The steps for the replacement operator are as follows Replacement Operator Input: One candidate member Step If fitness value...

Ngày tải lên: 08/08/2013, 08:38