Related papers: Minimum length RNA folding trajectories
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
For given a pair of nodes in a graph, the minimum non-separating path problem looks for a minimum weight path between the two nodes such that the remaining graph after removing the path is still connected. The balanced connected bipartition…
Given an edge-weighted graph and a set of known seed vertices, a network scientist often desires to understand the graph relationships to explain connections between the seed vertices. When the seed set is 3 or larger Steiner minimal tree -…
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…
This work addresses weight optimization problem for fully-connected feed-forward neural networks. Unlike existing approaches that are based on back-propagation (BP) and chain rule gradient-based optimization (which implies iterative…
A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has…
In this thesis, we present new techniques to deal with fundamental algorithmic graph problems where graphs are directed and partially dynamic, i.e. undergo either a sequence of edge insertions or deletions: - Single-Source Reachability…
This work presents a maximum entropy principle based algorithm for solving minimum multiway $k$-cut problem defined over static and dynamic {\em digraphs}. A multiway $k$-cut problem requires partitioning the set of nodes in a graph into…
An $N$-point FFT admits many valid implementations that differ in radix choice, stage ordering, and register-blocking strategy. These alternatives use different SIMD instruction mixes with different latencies, yet produce the same…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…
Understanding cellular trajectories via time-resolved single-cell transcriptomics is vital for studying development, regeneration, and disease. A key challenge is inferring continuous trajectories from discrete snapshots. Biological…
We present an iterative inverse reinforcement learning algorithm to infer optimal cost functions in continuous spaces. Based on a popular maximum entropy criteria, our approach iteratively finds a weight improvement step and proposes a…
We study the 2-Disjoint Shortest Paths (2-DSP) problem: given a directed weighted graph and two terminal pairs $(s_1,t_1)$ and $(s_2,t_2)$, decide whether there exist vertex-disjoint shortest paths between each pair. Building on recent…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
A network topology with low average shortest path length (ASPL) provides efficient data transmission while the number of nodes and the number of links incident to each node are often limited due to physical constraints. In this paper, we…
The Euclidean Steiner Minimal Tree problem takes as input a set $\mathcal P$ of points in the Euclidean plane and finds the minimum length network interconnecting all the points of $\mathcal P$. In this paper, in continuation to the works…
This paper presents an approximation algorithm for finding a shortest path between two points $s$ and $t$ in a weighted planar subdivision $\PS$. Each face $f$ of $\PS$ is associated with a weight $w_f$, and the cost of travel along a line…
We study the minimum Manhattan network problem, which is defined as follows. Given a set of points called \emph{terminals} in $\R^d$, find a minimum-length network such that each pair of terminals is connected by a set of axis-parallel line…