Related papers: Minimum length RNA folding trajectories
The significant progress in constructing graph spanners that are sparse (small number of edges) or light (low total weight) has skipped spanners that are everywhere-sparse (small maximum degree). This disparity is in line with other network…
The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the…
We study the problem of computing a minimum equivalent digraph (also known as the problem of computing a strong transitive reduction) and its maximum objective function variant, with two types of extensions. First, we allow to declare a set…
We present an algorithm to find an {\it Euclidean Shortest Path} from a source vertex $s$ to a sink vertex $t$ in the presence of obstacles in $\Re^2$. Our algorithm takes $O(T+m(\lg{m})(\lg{n}))$ time and $O(n)$ space. Here, $O(T)$ is the…
RNA inverse folding, designing sequences to form specific 3D structures, is critical for therapeutics, gene regulation, and synthetic biology. Current methods, focused on sequence recovery, struggle to address structural objectives like…
Let $S$ be a set of $n$ points in a polygon $P$ with $m$ vertices. The geodesic unit-disk graph $G(S)$ induced by $S$ has vertex set $S$ and contains an edge between two vertices whenever their geodesic distance in $P$ is at most one. In…
A fundamental problem associated with the task of network reconstruction from dynamical or behavioral data consists in determining the most appropriate model complexity in a manner that prevents overfitting, and produces an inferred network…
For two multisets $S$ and $T$ of points in $[\Delta]^2$, such that $|S| = |T|= n$, the earth-mover distance (EMD) between $S$ and $T$ is the minimum cost of a perfect bipartite matching with edges between points in $S$ and $T$, i.e.,…
The concept of Reload cost in a graph refers to the cost that occurs while traversing a vertex via two of its incident edges. This cost is uniquely determined by the colors of the two edges. This concept has various applications in…
We revisit the problem of privately releasing the all-pairs shortest path distances of a weighted undirected graph up to low additive error, which was first studied by Sealfon [Sea16]. In this paper, we improve significantly on Sealfon's…
Reducing the running time of graph algorithms is vital for tackling real-world problems such as shortest paths and matching in large-scale graphs, where path information plays a crucial role. To address this critical challenge, this paper…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
Given a weighted $n$-vertex graph $G$ with integer edge-weights taken from a range $[-M,M]$, we show that the minimum-weight simple path visiting $k$ vertices can be found in time $\tilde{O}(2^k \poly(k) M n^\omega) = O^*(2^k M)$. If the…
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
We present an optimal and efficient algorithm for finding a shortest path in an elastic optical network. The algorithm is an adaptation of the Dijkstra shortest path algorithm, where we take into account the spectrum continuity and…
Network applications, such as multimedia streaming and video conferencing, impose growing requirements over Quality of Service (QoS), including bandwidth, delay, jitter, etc. Meanwhile, networks are expected to be load-balanced,…
This paper focuses on designing edge-weighted networks, whose robustness is characterized by maximizing algebraic connectivity, or the second smallest eigenvalue of the Laplacian matrix. This problem is motivated by cooperative vehicle…
We study the NP-hard problem of approximating a Minimum Routing Cost Spanning Tree in the message passing model with limited bandwidth (CONGEST model). In this problem one tries to find a spanning tree of a graph $G$ over $n$ nodes that…
This paper is devoted to advancing the theoretical understanding of the iterated immediate snapshot (IIS) complexity of the Weak Symmetry Breaking task (WSB). Our rather unexpected main theorem states that there exist infinitely many values…