相关论文: Walks on SPR Neighborhoods

Several cycle lexicographical orders are found to describe the relative likelihood of elements of the random walks on the symmetric group generated by the conjugacy classes of transpositions, 3-cycles, and n-cycles. Spectral analysis finds…

The $k$-th power of the adjacency matrix of a simple undirected graph represents the number of walks with length $k$ between pairs of nodes. As a walk where no node repeats, a path is a walk where each node is only visited once. The set of…

A spanning tree of a graph $G$ is a connected acyclic spanning subgraph of $G$. We consider enumeration of spanning trees when $G$ is a $2$-tree, meaning that $G$ is obtained from one edge by iteratively adding a vertex whose neighborhood…

The co-evolution between network structure and functional performance is a fundamental and challenging problem whose complexity emerges from the intrinsic interdependent nature of structure and function. Within this context, we investigate…

The Neighbor-Joining algorithm is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization of the neighbor-joining transformation, which uses…

We investigate a self-interacting random walk, whose dynamically evolving environment is a random tree built by the walker itself, as it walks around. At time $n=1,2,\dots$, right before stepping, the walker adds a random number (possibly…

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…

Neighborhood finders and nearest neighbor queries are fundamental parts of sampling based motion planning algorithms. Using different distance metrics or otherwise changing the definition of a neighborhood produces different algorithms with…

We present an analytical and numerical study of the paths of self avoiding walks (SAWs) on random networks. Since these walks do not retrace their paths, they effectively delete the nodes they visit, together with their links, thus pruning…

Consider a random walk on a tree $G=(V,E)$. For $v,w \in V$, let the hitting time $H(v,w)$ denote the expected number of steps required for the random walk started at $v$ to reach $w$, and let $\pi_v = \mathrm{deg}(v)/2|E|$ denote the…

Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…

The step-reinforced random walk (SRRW), where each step may replicate a randomly chosen past step, exhibits complex dependencies on the history. This paper introduces a generalized SRRW on groups, incorporating arbitrary transformations of…

In this article, we study the Euclidean minimum spanning tree problem in an imprecise setup. The problem is known as the \emph{Minimum Spanning Tree Problem with Neighborhoods} in the literature. We study the problem where the neighborhoods…

A classical random walk $(S_t, t\in\mathbb{N})$ is defined by $S_t:=\displaystyle\sum_{n=0}^t X_n$, where $(X_n)$ are i.i.d. When the increments $(X_n)_{n\in\mathbb{N}}$ are a one-order Markov chain, a short memory is introduced in the…

Let $S_n$ be a centered random walk with a finite variance, and define the new sequence $A_n:=\sum_{i=1}^n S_i$, which we call an integrated random walk. We are interested in the asymptotics of $$p_N:=P(\min_{1 \le k \le N} A_k \ge 0)$$ as…

We present analytical results for the distribution of first-passage (FP) times of random walks (RWs) on random regular graphs that consist of $N$ nodes of degree $c \ge 3$. Starting from a random initial node at time $t=0$, at each time…

Statistical phylogenetic inference methods use tree rearrangement operations to perform either hill-climbing local search or Markov chain Monte Carlo across tree topologies. The canonical class of such moves are the subtree-prune-regraft…

For a simple (unbiased) random walk on a connected graph with $n$ vertices, the cover time (the expected number of steps it takes to visit all vertices) is at most $O(n^3)$. We consider locally biased random walks, in which the probability…

Small-world graphs, which combine randomized and structured elements, are seen as prevalent in nature. Jon Kleinberg showed that in some graphs of this type it is possible to route, or navigate, between vertices in few steps even with very…

Single particle tracking allows probing how biomolecules interact physically with their natural environments. A fundamental challenge when analysing recorded single particle trajectories is the inverse problem of inferring the physical…