The arrangement of nucleotides within a bacterial chromosome is influenced by numerous factors. The degeneracy of the third codon within each reading frame allows some flexibility of nucleotide selection; however, the third nucleotide in the triplet of each codon is at least partly determined by the preceding two. This is most evident in organisms with a strong G + C bias, as the degenerate cod...

This paper offers some probabilistic and combinatorial insights into tree formulas for the Green function and hitting probabilities of Markov chains on a finite state space. These tree formulas are closely related to loop-erased random walks by Wilson’s algorithm for random spanning trees, and to mixing times by the Markov chain tree theorem. Let mij be the mean first passage time from i to j f...

A cladogram is an unrooted tree with labeled leaves and unlabeled internal branchpoints of degree 3. Aldous has studied a Markov chain on the set of n-leaf cladograms in which each transition consists of removing a random leaf and its incident edge from the tree and then reattaching the leaf to a random edge of the remaining tree. Using coupling methods, Aldous has shown that a mixing-time para...

Date stream mining techniques can be used in tracking user behaviors as they attempt to achieve their goals. Quality metrics over stream-mined models identify potential changes in user goal attainment. When the quality of some data mined models varies significantly from nearby models—as defined by quality metrics—then the user’s behavior is automatically flagged as a potentially significant beh...

A path reversal is performed in a rooted tree when a node becomes the root of all the nodes along the path from it to the former root. This algorithm on trees is presented as a transition system specified by induction over a convenient view of the tree structure. When each tree node is assigned a fixed weight representing its relative probability to move to the root, the transition system defin...

A calculational framework is proposed for phylogenetics, using nonlocal quantum field theories in hypercubic geometry. Quadratic terms in the Hamiltonian give the underlying Markov dynamics, while higher degree terms represent branching events. The spatial dimension L is the number of leaves of the evolutionary tree under consideration. Momentum conservation modulo Z ×L 2 in L ← 1 scattering co...