Related papers: Minimum length RNA folding trajectories

Geodesic distance, sometimes called shortest path length, has proven useful in a great variety of applications, such as information retrieval on networks including treelike networked models. Here, our goal is to analytically determine the…

The All-Pairs Shortest Paths (APSP) problem is one of the fundamental problems in theoretical computer science. It asks to compute the distance matrix of a given $n$-vertex graph. We revisit the classical problem of maintaining the distance…

The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…

Native shortcut networks (SCN0) are sub-graphs of native protein residue networks (PRN0). In this paper, we propose the Network Dynamics (ND) model, which reconstructs a PRN0 by adding back its edges according to some recipe, while its…

In this work we study shortest path problems in multimode graphs, a generalization of the min-distance measure introduced by Abboud, Vassilevska W. and Wang in [SODA'16]. A multimode shortest path is the shortest path using one of multiple…

We propose a new way of looking at global optimization of off-lattice protein models. We present a dual optimization concept of predicting optimal sequences as well as optimal folds. We validate the utility of the recently introduced…

The min-distance between two nodes $u, v$ is defined as the minimum of the distance from $v$ to $u$ or from $u$ to $v$, and is a natural distance metric in DAGs. As with the standard distance problems, the Strong Exponential Time Hypothesis…

The single-source shortest path problem (SSSP) with nonnegative edge weights is a notoriously difficult problem to solve efficiently in parallel---it is one of the graph problems said to suffer from the transitive-closure bottleneck. In…

The approximate single-source shortest-path problem is as follows: given a graph with nonnegative edge weights and a designated source vertex $s$, return estimates of the distances from~$s$ to each other vertex such that the estimate falls…

In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…

We give an algorithm that takes a directed graph $G$ undergoing $m$ edge insertions with lengths in $[1, W]$, and maintains $(1+\epsilon)$-approximate shortest path distances from a fixed source $s$ to all other vertices. The algorithm is…

Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…

We present a reduction of Milestoning (ReM) algorithm to analyze the high-dimensional Milestoning kinetic network. The algorithm reduces the Milestoning network to low dimensions but preserves essential kinetic information, such as local…

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…

The shortest-path distance is a fundamental concept in graph analytics and has been extensively studied in the literature. In many real-world applications, quality constraints are naturally associated with edges in the graphs and finding…

Persistence diagrams (PD)s play a central role in topological data analysis. This analysis requires computing distances among such diagrams such as the $1$-Wasserstein distance. Accurate computation of these PD distances for large data sets…

RNA polymerase (RNAP) elongates RNA by walking along a DNA template and selectively incorporating ribonucleoside triphosphates (rNTPs). Rather than mechanically replicating the base sequence, RNAP conditions binding and chemistry on the…

Flip graphs are a ubiquitous class of graphs, which encode relations induced on a set of combinatorial objects by elementary, local changes. Skeletons of associahedra, for instance, are the graphs induced by quadrilateral flips in…

We present a general framework of designing efficient dynamic approximate algorithms for optimization on undirected graphs. In particular, we develop a technique that, given any problem that admits a certain notion of vertex sparsifiers,…

Computing the optimal transport distance between statistical distributions is a fundamental task in machine learning. One remarkable recent advancement is entropic regularization and the Sinkhorn algorithm, which utilizes only matrix…