Abstract Minimum flow decomposition (MFD) — the problem of finding a minimum set of weighted source-to-sink paths that perfectly decomposes a flow — is a classical problem in Computer Science, and variants of it are powerful models in a different fields such as Bioinformatics and Transportation. Even on acyclic graphs, the problem is NP-hard, and most practical solutions have been via heuristics or approximations. While there is an extensive body of research on acyclic graphs, currently there is no exact solution on graphs with cycles. In this paper we present the first ILP formulation for three natural variants of the MFD problem in graphs with cycles, asking for a decomposition consisting only of weighted source-to-sink paths or cycles, trails, and walks, respectively. On three datasets of increasing levels of complexity from both Bioinformatics and Transportation, our approaches solve any instance in under 12 minutes. Our implementations are freely available at https://github.com/algbio/MFD-ILP .

Abstract To guarantee the safety of flight operations, decision-support systems for air traffic control must be able to improve the usage of airspace capacity and handle increasing demand. This study addresses the aircraft conflict avoidance and trajectory recovery problem. The problem of finding the least deviation conflict-free aircraft trajectories that guarantee the return to a target waypoint is highly complex due to the nature of the nonlinear trajectories that are sought. We present a two-stage iterative algorithm that first solves initial conflicts by manipulating their speed and heading control and then identifying each aircraft’s optimal time to recover its trajectory towards their nominal one. We extend existing mixed-integer programming formulations by modelling speed and heading control as continuous variables while recovery time is treated as a discrete variable. We develop a novel iterative approach which shows that the trajectory recovery costs can be anticipated by inducing avoidance trajectories with higher deviation, therefore obtaining earlier recovery time within a few iterations. Numerical results on benchmark conflict resolution problems show that this approach can solve instances with up to 30 aircraft within 10 min.

Minimum flow decomposition (MFD) is a common problem across various fields of Computer Science, where a flow is decomposed into a minimum set of weighted paths. However, in Bioinformatics applications, such as RNA transcript or quasi-species assembly, the flow is erroneous since it is obtained from noisy read coverages. Typical generalizations of the MFD problem to handle errors are based on least-squares formulations or modelling the erroneous flow values as ranges. All of these are thus focused on error handling at the level of individual edges. In this paper, we interpret the flow decomposition problem as a robust optimization problem and lift error-handling from individual edges to solution paths. As such, we introduce a new minimum path-error flow decomposition problem, for which we give an Integer Linear Programming formulation. Our experimental results reveal that our formulation can account for errors significantly better, by lowering the inaccuracy rate by 30-50% compared to previous error-handling formulations, with computational requirements that remain practical.

MOTIVATION: Many important problems in Bioinformatics (e.g. assembly or multiassembly) 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. contigs) which are common to all solutions. Previous research on safety has focused on polynomially time solvable problems, whereas many successful and natural models are NP-hard to solve, leaving a lack of "safety tools" for such problems. We propose the first method for computing all safe solutions for an NP-hard problem, "minimum flow decomposition" (MFD). We obtain our results by developing a "safety test" for paths based on a general integer linear programming (ILP) formulation. Moreover, we provide implementations with practical optimizations aimed to reduce the total ILP time, the most efficient of these being based on a recursive group-testing procedure. RESULTS: Experimental results on transcriptome datasets show that all safe paths for MFDs correctly recover up to 90% of the full RNA transcripts, which is at least 25% more than previously known safe paths. Moreover, despite the NP-hardness of the problem, we can report all safe paths for 99.8% of the over 27 000 non-trivial graphs of this dataset in only 1.5 h. Our results suggest that, on perfect data, there is less ambiguity than thought in the notoriously hard RNA assembly problem. AVAILABILITY AND IMPLEMENTATION: https://github.com/algbio/mfd-safety.