Computer Science
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The Computer Science Department at Montana State University supports the Mission of the College of Engineering and the University through its teaching, research, and service activities. The Department educates undergraduate and graduate students in the principles and practices of computer science, preparing them for computing careers and for a lifetime of learning.
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Item Improving RNA Assembly via Safety and Completeness in Flow Decompositions(Mary Ann Liebert Inc, 2022-12) Khan, Shahbaz; Kortelainen, Milla; Cáceres, Manuel; Williams, Lucia; Tomescu, Alexandru I.Decomposing a network flow into weighted paths is a problem with numerous applications, ranging from networking, transportation planning, to bioinformatics. In some applications we look for a decomposition that is optimal with respect to some property, such as the number of paths used, robustness to edge deletion, or length of the longest path. However, in many bioinformatic applications, we seek a specific decomposition where the paths correspond to some underlying data that generated the flow. In these cases, no optimization criteria guarantee the identification of the correct decomposition. Therefore, we propose to instead report the safe paths, which are subpaths of at least one path in every flow decomposition. In this work, we give the first local characterization of safe paths for flow decompositions in directed acyclic graphs, leading to a practical algorithm for finding the complete set of safe paths. In addition, we evaluate our algorithm on RNA transcript data sets against a trivial safe algorithm (extended unitigs), the recently proposed safe paths for path covers (TCBB 2021) and the popular heuristic greedy-width. On the one hand, we found that besides maintaining perfect precision, our safe and complete algorithm reports a significantly higher coverage ( = 50% more) compared with the other safe algorithms. On the other hand, the greedy-width algorithm although reporting a better coverage, it also reports a significantly lower precision on complex graphs (for genes expressing a large number of transcripts). Overall, our safe and complete algorithm outperforms (by = 20%) greedy-width on a unified metric (F-score) considering both coverage and precision when the evaluated data set has a significant number of complex graphs. Moreover, it also has a superior time (4 - 5x) and space performance (1.2 - 2.2x), resulting in a better and more practical approach for bioinformatic applications of flow decomposition.Item Efficient Minimum Flow Decomposition via Integer Linear Programming(Mary Ann Liebert Inc, 2022-11) Dias, Fernando H.C.; Williams, Lucia; Mumey, Brendan; Tomescu, Alexandru I.Minimum flow decomposition (MFD) is an NP-hard problem asking to decompose a network flow into a minimum set of paths (together with associated weights). Variants of it are powerful models in multiassembly problems in Bioinformatics, such as RNA assembly. Owing to its hardness, practical multiassembly tools either use heuristics or solve simpler, polynomial time-solvable versions of the problem, which may yield solutions that are not minimal or do not perfectly decompose the flow. Here, we provide the first fast and exact solver for MFD on acyclic flow networks, based on Integer Linear Programming (ILP). Key to our approach is an encoding of all the exponentially many solution paths using only a quadratic number of variables. We also extend our ILP formulation to many practical variants, such as incorporating longer or paired-end reads, or minimizing flow errors. On both simulated and real-flow splicing graphs, our approach solves any instance in <13 seconds. We hope that our formulations can lie at the core of future practical RNA assembly tools. Our implementations are freely available on Github.