Related papers: Minimum length RNA folding trajectories
Gaussian Process (GP) formulation of continuoustime trajectory offers a fast solution to the motion planning problem via probabilistic inference on factor graph. However, often the solution converges to in-feasible local minima and the…
Consider the following distance query for an $n$-node graph $G$ undergoing edge insertions and deletions: given two sets of nodes $I$ and $J$, return the distances between every pair of nodes in $I\times J$. This query is rather general and…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
In this paper we provide new randomized algorithms with improved runtimes for solving linear programs with two-sided constraints. In the special case of the minimum cost flow problem on $n$-vertex $m$-edge graphs with integer…
Base polytopes of polymatroids, also known as generalized permutohedra, are polytopes whose edges are parallel to a vector of the form $\mathbf{e}_i - \mathbf{e}_j$. We consider the following computational problem: Given two vertices of a…
Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow/circulation $X$ on a directed graph $G$ into weighted source-to-sink paths whose superposition equals $X$. We show that, for…
We introduce stronger notions for approximate single-source shortest-path distances, show how to efficiently compute them from weaker standard notions, and demonstrate the algorithmic power of these new notions and transformations. One…
An efficient algorithm to solve the $k$ shortest non-homotopic path planning ($k$-SNPP) problem in a 2D environment is proposed in this paper. Motivated by accelerating the inefficient exploration of the homotopy-augmented space of the 2D…
Finding efficient routes for data packets is an essential task in computer networking. The optimal routes depend greatly on the current network topology, state and traffic demand, and they can change within milliseconds. Reinforcement…
The multiscale simplicial flat norm (MSFN) of a d-cycle is a family of optimal homology problems indexed by a scale parameter {\lambda} >= 0. Each instance (mSFN) optimizes the total weight of a homologous d-cycle and a bounded (d +…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
The Constraint Shortest Path (CSP) problem is as follows. An $n$-vertex graph is given, each edge/arc assigned two weights. Let us call them "cost" and "length" for definiteness. Finding a min-cost upper-bounded length path between a given…
Given a directed graph of nodes and edges connecting them, a common problem is to find the shortest path between any two nodes. Here we show that the shortest path distances can be found by a simple matrix inversion: If the edges are given…
Minimum flow decomposition (MFD) -- the problem of finding a minimum set of weighted source-to-sink paths that perfectly decomposes a flow -- is a classical problem in Computer Science, and variants of it are powerful models in different…
It is $\mathsf{NP}$-hard to determine the minimum number of branching vertices needed in a single-source distance-preserving subgraph of an undirected graph. We show that this problem can be solved in polynomial time if the input graph is…
Shortest path algorithms have played a key role in the past century, paving the way for modern day GPS systems to find optimal routes along static systems in fractions of a second. One application of these algorithms includes optimizing the…
Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…