Related papers: Safety and Completeness in Flow Decompositions for…
In Bioinformatics, the applications of flow decomposition in directed acyclic graphs are highlighted in RNA Assembly problem. However, it admits multiple solutions where exactly one solution correctly represents the underlying transcripts.…
Network flow is one of the most studied combinatorial optimization problems having innumerable applications. Any flow on a directed acyclic graph $G$ having $n$ vertices and $m$ edges can be decomposed into a set of $O(m)$ paths. In some…
The Flow Decomposition problem, which asks for the smallest set of weighted paths that "covers" a flow on a DAG, has recently been used as an important computational step in transcript assembly. We prove the problem is in FPT when…
Many important problems in Bioinformatics (e.g., assembly or multi-assembly) admit multiple solutions, while the final objective is to report only one. A common approach to deal with this uncertainty is finding safe partial solutions (e.g.,…
Decomposing a flow on a Directed Acyclic Graph (DAG) into a weighted sum of a small number of paths is an essential task in operations research and bioinformatics. This problem, referred to as Sparse Flow Decomposition (SFD), has gained…
Minimum flow decomposition (MFD) is the strongly NP-hard problem of finding a smallest set of integer weighted $s$-$t$ paths in an $s$-$t$ DAG $G$ whose weighted sum is equal to a given flow $f$ on $G$. Despite its many practical…
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…
It is proven that the connected pathwidth of any graph $G$ is at most $2\cdot\pw(G)+1$, where $\pw(G)$ is the pathwidth of $G$. The method is constructive, i.e. it yields an efficient algorithm that for a given path decomposition of width…
Several modern applications involve huge graphs and require fast answers to reachability queries. In more than two decades since first proposals, several approaches have been presented adopting on-line searches, hop labelling or transitive…
In this paper, we generalize the minimum flow decomposition problem (MFD) to incorporate uncertain edge capacities and tackle it from the perspective of robust optimization. In the classical flow decomposition problem, a network flow is…
In this paper, we propose a deterministic algorithm that approximates the optimal path cover on weighted undirected graphs. Based on the 1/2-Approximation Path Cover Algorithm by Moran et al., we add a procedure to remove the redundant…
We present practical linear and almost linear-time algorithms to compute a chain decomposition of a directed acyclic graph (DAG), $G=(V,E)$. The number of vertex-disjoint chains computed is very close to the minimum. The time complexity of…
Fractures form the main pathways for flow in the subsurface within low-permeability rock. For this reason, accurately predicting flow and transport in fractured systems is vital for improving the performance of subsurface applications.…
We propose a simple and computationally efficient method for dense subgraph discovery, which is a classic problem both in theory and in practice. It is well known that dense subgraphs can have strong correlation with structures of interest…
Tree-width and path-width are widely successful concepts. Many NP-hard problems have efficient solutions when restricted to graphs of bounded tree-width. Many efficient algorithms are based on a tree decomposition. Sometimes the more…
We propose a novel entropy flow on weighted graphs, which provides a principled framework that characterizes the evolution of probability distributions over graph structures while sharing geometric intuition with discrete Ricci flow. We…
Computing a minimum path cover (MPC) of a directed acyclic graph (DAG) is a fundamental problem with a myriad of applications, including reachability. Although it is known how to solve the problem by a simple reduction to minimum flow,…
Finding the optimal embedding of networks into low-dimensional hyperbolic spaces is a challenge that received considerable interest in recent years, with several different approaches proposed in the literature. In general, these methods…
Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…
We present time-efficient distributed algorithms for decomposing graphs with large edge or vertex connectivity into multiple spanning or dominating trees, respectively. As their primary applications, these decompositions allow us to achieve…