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

Asymmetric Traveling Salesman Path and Directed Latency Problems

We study integrality gaps and approximability of two closely related problems on directed graphs. Given a set V of n nodes in an underlying asymmetric metric and two specified nodes s and t, both problems ask to find an s-t path visiting all other nodes. In the asymmetric traveling salesman path problem (ATSPP), the objective is to minimize the total cost of this path. In the directed latency problem, the objective is to minimize the sum of distances on this path from s to each node. Both of these problems are NP-hard. The best known approximation algorithms for ATSPP had ratio O(log n) until the very recent result that improves it to O(log n/ log log n). However, only a bound of O(sqrt(n)) for the integrality gap of its linear programming relaxation has been known. For directed latency, the best previously known approximation algorithm has a guarantee of O(n^(1/2+eps)), for any constant eps > 0. We present a new algorithm for the ATSPP problem that has an approximation ratio of O(log n), but whose analysis also bounds the integrality gap of the standard LP relaxation of ATSPP by the same factor. This solves an open problem posed by Chekuri and Pal [2007]. We then pursue a deeper study of this linear program and its variations, which leads to an algorithm for the k-person ATSPP (where k s-t paths of minimum total length are sought) and an O(log n)-approximation for the directed latency problem

Searching for Realizations of Finite Metric Spaces in Tight Spans

An important problem that commonly arises in areas such as internet traffic-flow analysis, phylogenetics and electrical circuit design, is to find a representation of any given metric $D$ on a finite set by an edge-weighted graph, such that the total edge length of the graph is minimum over all such graphs. Such a graph is called an optimal realization and finding such realizations is known to be NP-hard. Recently Varone presented a heuristic greedy algorithm for computing optimal realizations. Here we present an alternative heuristic that exploits the relationship between realizations of the metric $D$ and its so-called tight span $T_D$. The tight span $T_D$ is a canonical polytopal complex that can be associated to $D$, and our approach explores parts of $T_D$ for realizations in a way that is similar to the classical simplex algorithm. We also provide computational results illustrating the performance of our approach for different types of metrics, including $l_1$-distances and two-decomposable metrics for which it is provably possible to find optimal realizations in their tight spans.Comment: 20 pages, 3 figure

Chordal Decomposition in Rank Minimized Semidefinite Programs with Applications to Subspace Clustering

Semidefinite programs (SDPs) often arise in relaxations of some NP-hard problems, and if the solution of the SDP obeys certain rank constraints, the relaxation will be tight. Decomposition methods based on chordal sparsity have already been applied to speed up the solution of sparse SDPs, but methods for dealing with rank constraints are underdeveloped. This paper leverages a minimum rank completion result to decompose the rank constraint on a single large matrix into multiple rank constraints on a set of smaller matrices. The re-weighted heuristic is used as a proxy for rank, and the specific form of the heuristic preserves the sparsity pattern between iterations. Implementations of rank-minimized SDPs through interior-point and first-order algorithms are discussed. The problem of subspace clustering is used to demonstrate the computational improvement of the proposed method.Comment: 6 pages, 6 figure

A novel evolutionary formulation of the maximum independent set problem

We introduce a novel evolutionary formulation of the problem of finding a maximum independent set of a graph. The new formulation is based on the relationship that exists between a graph's independence number and its acyclic orientations. It views such orientations as individuals and evolves them with the aid of evolutionary operators that are very heavily based on the structure of the graph and its acyclic orientations. The resulting heuristic has been tested on some of the Second DIMACS Implementation Challenge benchmark graphs, and has been found to be competitive when compared to several of the other heuristics that have also been tested on those graphs