Related papers: Minimum length RNA folding trajectories
Given two labeled data-sets $\mathcal{S}$ and $\mathcal{T}$, we design a simple and efficient greedy algorithm to reweigh the loss function such that the limiting distribution of the neural network weights that result from training on…
We initiate the study of the shortest reconfiguration problem for independent sets under the adjacency relation derived from the independent set polytope. Given a graph and two independent sets, the problem asks for a shortest sequence…
Maximum-distance-separable (MDS) codes are a class of erasure codes that are widely adopted to enhance the reliability of distributed storage systems (DSS). In (n, k) MDS coded DSS, the original data are stored into n distributed nodes in…
We present fast algorithms for approximate shortest paths in the massively parallel computation (MPC) model. We provide randomized algorithms that take $poly(\log{\log{n}})$ rounds in the near-linear memory MPC model. Our results are for…
In the Minimum Clique Routing Problem on Cycles \textsc{MCRPC} we are given a cycle together with a set of demands (weighted origin-destination pairs) and the goal is to route all the pairs minimizing the maximum weighted clique of the…
We present a deterministic (1+sqrt(5))/2-approximation algorithm for the s-t path TSP for an arbitrary metric. Given a symmetric metric cost on n vertices including two prespecified endpoints, the problem is to find a shortest Hamiltonian…
Binary neural networks (BNNs) have been widely adopted to reduce the computational cost and memory storage on edge-computing devices by using one-bit representation for activations and weights. However, as neural networks become…
In literature, Clustered Shortest-Path Tree Problem (CluSPT) is an NP-hard problem. Previous studies often search for an optimal solution in relatively large space. To enhance the performance of the search process, two approaches are…
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where…
In this paper, we propose the neural shortest path (NSP), a vector-valued implicit neural representation (INR) that approximates a distance function and its gradient. The key feature of NSP is to learn the exact shortest path (ESP), which…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
We study the NP-hard Shortest Path Most Vital Edges problem arising in the context of analyzing network robustness. For an undirected graph with positive integer edge lengths and two designated vertices $s$ and $t$, the goal is to delete as…
The 2-Wasserstein distance (or RMS distance) is a useful measure of similarity between probability distributions that has exciting applications in machine learning. For discrete distributions, the problem of computing this distance can be…
We develop faster approximation algorithms for Metric-TSP building on recent, nearly linear time approximation schemes for the LP relaxation [Chekuri and Quanrud, 2017]. We show that the LP solution can be sparsified via cut-sparsification…
Maximum distance separable (MDS) codes are widely used in distributed storage systems as they provide optimal fault tolerance for a given amount of storage overhead. The seminal work of Dimakis~\emph{et al.} first established a lower bound…
A problem of reconstruction of the topology and the respective edge resistance values of an unknown circular planar passive resistive network using limitedly available resistance distance measurements is considered. We develop a multistage…
The current best practice for computing optimal transport (OT) is via entropy regularization and Sinkhorn iterations. This algorithm runs in quadratic time as it requires the full pairwise cost matrix, which is prohibitively expensive for…
The min-sum (MS) algorithm is arguably the second most fundamental algorithm in the realm of message passing due to its optimality (for a tree code) with respect to the {\em block error} probability \cite{Wiberg}. There also seems to be a…
Despite the rapid progress of neuromorphic computing, inadequate capacity and insufficient representation power of spiking neural networks (SNNs) severely restrict their application scope in practice. Residual learning and shortcuts have…
The Clustered Shortest-Path Tree Problem (CluSPT) plays an important role in various types of optimization problems in real-life. Recently, some Multifactorial Evolutionary Algorithm (MFEA) have been introduced to deal with the CluSPT,…