Related papers: Evaluating Optimal Safe Flows Decomposition for RN…
Decomposing a network flow into weighted paths has numerous applications. Some applications require any decomposition that is optimal w.r.t. some property such as number of paths, robustness, or length. Many bioinformatic applications…
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…
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…
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…
In this work, we present the first algorithm to compute expander decompositions in an m-edge directed graph with near-optimal time \~O(m). Further, our algorithm can maintain such a decomposition in a dynamic graph and again obtains…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
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…
This paper presents a framework that supports the implementation of parallel solutions for the widespread parametric maximum flow computational routines used in image segmentation algorithms. The framework is based on supergraphs, a special…
We present a parallel algorithm for the $(1-\epsilon)$-approximate maximum flow problem in capacitated, undirected graphs with $n$ vertices and $m$ edges, achieving $O(\epsilon^{-3}\text{polylog} n)$ depth and $O(m \epsilon^{-3}…
The coflow scheduling problem has emerged as a popular abstraction in the last few years to study data communication problems within a data center. In this basic framework, each coflow has a set of communication demands and the goal is to…
Several high-throughput distributed data-processing applications require multi-hop processing of streams of data. These applications include continual processing on data streams originating from a network of sensors, composing a multimedia…
A decomposition algorithm for solving large-scale security-constrained AC optimal power flow problems is presented. The formulation considered is the one used in the ARPA-E Grid Optimization (GO) Competition, Challenge 1, held from November…
We introduce a new approach to the maximum flow problem in undirected, capacitated graphs using $\alpha$-\emph{congestion-approximators}: easy-to-compute functions that approximate the congestion required to route single-commodity demands…
Following [21, 23], the present work investigates a new relative entropy-regularized algorithm for solving the optimal transport on a graph problem within the randomized shortest paths formalism. More precisely, a unit flow is injected into…
We give faster algorithms for weak expander decompositions and approximate max flow on undirected graphs. First, we show that it is possible to "warm start" the cut-matching game when computing weak expander decompositions, avoiding the…
Obtaining sparse, interpretable representations of observable data is crucial in many machine learning and signal processing tasks. For data representing flows along the edges of a graph, an intuitively interpretable way to obtain such…
We give the first almost-linear total time algorithm for deciding if a flow of cost at most $F$ still exists in a directed graph, with edge costs and capacities, undergoing decremental updates, i.e., edge deletions, capacity decreases, and…
Maintaining a $k$-core decomposition quickly in a dynamic graph has important applications in network analysis. The main challenge for designing efficient exact algorithms is that a single update to the graph can cause significant global…