A practical fpt algorithm for Flow Decomposition and transcript assembly

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 parameterized by the number of paths by giving a practical linear fpt algorithm. Further, we implement and engineer a Flow Decomposition solver based on this algorithm, and evaluate its performance on RNA-sequence data. Crucially, our solver finds exact solutions while achieving runtimes competitive with a state-of-the-art heuristic. Finally, we contextualize our design choices with two hardness results related to preprocessing and weight recovery. Specifically, $k$-Flow Decomposition does not admit polynomial kernels under standard complexity assumptions, and the related problem of assigning (known) weights to a given set of paths is NP-hard.Comment: Introduces software package Toboggan: Version 1.0. http://dx.doi.org/10.5281/zenodo.82163

Pseudo-Separation for Assessment of Structural Vulnerability of a Network

Based upon the idea that network functionality is impaired if two nodes in a network are sufficiently separated in terms of a given metric, we introduce two combinatorial \emph{pseudocut} problems generalizing the classical min-cut and multi-cut problems. We expect the pseudocut problems will find broad relevance to the study of network reliability. We comprehensively analyze the computational complexity of the pseudocut problems and provide three approximation algorithms for these problems. Motivated by applications in communication networks with strict Quality-of-Service (QoS) requirements, we demonstrate the utility of the pseudocut problems by proposing a targeted vulnerability assessment for the structure of communication networks using QoS metrics; we perform experimental evaluations of our proposed approximation algorithms in this context

A Polynomial-time Bicriteria Approximation Scheme for Planar Bisection

Given an undirected graph with edge costs and node weights, the minimum bisection problem asks for a partition of the nodes into two parts of equal weight such that the sum of edge costs between the parts is minimized. We give a polynomial time bicriteria approximation scheme for bisection on planar graphs. Specifically, let $W$ be the total weight of all nodes in a planar graph $G$. For any constant $\varepsilon > 0$, our algorithm outputs a bipartition of the nodes such that each part weighs at most $W/2 + \varepsilon$ and the total cost of edges crossing the partition is at most $(1+\varepsilon)$ times the total cost of the optimal bisection. The previously best known approximation for planar minimum bisection, even with unit node weights, was $O(\log n)$. Our algorithm actually solves a more general problem where the input may include a target weight for the smaller side of the bipartition.Comment: To appear in STOC 201

Setting Parameters by Example

We introduce a class of "inverse parametric optimization" problems, in which one is given both a parametric optimization problem and a desired optimal solution; the task is to determine parameter values that lead to the given solution. We describe algorithms for solving such problems for minimum spanning trees, shortest paths, and other "optimal subgraph" problems, and discuss applications in multicast routing, vehicle path planning, resource allocation, and board game programming.Comment: 13 pages, 3 figures. To be presented at 40th IEEE Symp. Foundations of Computer Science (FOCS '99

Improved Approximation Algorithms for Computing k Disjoint Paths Subject to Two Constraints

For a given graph $G$ with positive integral cost and delay on edges, distinct vertices $s$ and $t$, cost bound $C\in Z^{+}$ and delay bound $D\in Z^{+}$, the $k$ bi-constraint path ($k$BCP) problem is to compute $k$ disjoint $st$-paths subject to $C$ and $D$. This problem is known NP-hard, even when $k=1$ \cite{garey1979computers}. This paper first gives a simple approximation algorithm with factor-$(2,2)$, i.e. the algorithm computes a solution with delay and cost bounded by $2*D$ and $2*C$ respectively. Later, a novel improved approximation algorithm with ratio $(1+\beta,\,\max\{2,\,1+\ln\frac{1}{\beta}\})$ is developed by constructing interesting auxiliary graphs and employing the cycle cancellation method. As a consequence, we can obtain a factor-$(1.369,\,2)$ approximation algorithm by setting $1+\ln\frac{1}{\beta}=2$ and a factor-$(1.567,\,1.567)$ algorithm by setting $1+\beta=1+\ln\frac{1}{\beta}$. Besides, by setting $\beta=0$, an approximation algorithm with ratio $(1,\, O(\ln n))$, i.e. an algorithm with only a single factor ratio $O(\ln n)$ on cost, can be immediately obtained. To the best of our knowledge, this is the first non-trivial approximation algorithm for the $k$BCP problem that strictly obeys the delay constraint.Comment: 12 page