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A practical fpt algorithm for Flow Decomposition and transcript assembly [article]

Kyle Kloster, Philipp Kuinke, Michael P. O'Brien, Felix Reidl, Fernando Sánchez Villaamil, Blair D. Sullivan, Andrew van der Poel
2017 arXiv   pre-print
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.  ...  We conclude from this table that the Flow Decomposition problem is in fact a useful model for transcript assembly, which underscores the need for efficient algorithms to compute minimum decompositions  ... 
arXiv:1706.07851v3 fatcat:m66yn4yprbg33hfk4w3qk2hzk4

A practical fpt algorithm for Flow Decomposition and transcript assembly [chapter]

Kyle Kloster, Philipp Kuinke, Michael P. O'Brien, Felix Reidl, Fernando Sánchez Villaamil, Blair D. Sullivan, Andrew van der Poel
2018 2018 Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments (ALENEX)  
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.  ...  We conclude from this table that the Flow Decomposition problem is in fact a useful model for transcript assembly, which underscores the need for efficient algorithms to compute minimum decompositions  ... 
doi:10.1137/1.9781611975055.7 dblp:conf/alenex/KlosterKORVSP18 fatcat:dnu5okfyjbenjk5pvdhmchwsbq

Flow Decomposition with Subpath Constraints

Lucia Williams, Alexandru I. Ioan Tomescu, Brendan Mumey
2022 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
For finding a minimum decomposition, we propose both a heuristic and an FPT algorithm.  ...  We formalize the flow decomposition with subpath constraints problem, give the first algorithms for it, and study its usefulness for recovering ground truth decompositions.  ...  Though splice graphs for RNA assembly are usually DAGs, graphs for de novo assembly of viral or other genomes would likely contain cycles due to repeated sequences.  ... 
doi:10.1109/tcbb.2022.3147697 pmid:35104222 fatcat:44gdrbhnd5e7liexfjsjsmkowq

Fast, Flexible, and Exact Minimum Flow Decompositions via ILP [article]

Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
2022 arXiv   pre-print
Minimum flow decomposition (MFD) (the problem of finding a minimum set of paths that perfectly decomposes a flow) is a classical problem in Computer Science, and variants of it are powerful models in multiassembly  ...  We hope that our results can remove the current tradeoff between the complexity of a multi assembly model and its tractability and can lie at the core of future practical RNA assembly tools.  ...  We compare StandardILP with Toboggan, the implementation by [22] for their exact FPT algorithm for MFD, and with Catfish, the implementation by [44] of their heuristic algorithm for MFD.  ... 
arXiv:2201.10923v2 fatcat:kxbxfvy2n5h5jpz4sopdubmcmy

On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly

Romeo Rizzi, Alexandru I Tomescu, Veli Mäkinen
2014 BMC Bioinformatics  
This computational dichotomy between long reads and paired-end reads is also a general insight into multi-assembly problems.  ...  We also consider the weighted case, and show that it can be solved in polynomial-time by a reduction to a min-cost circulation problem.  ...  Acknowledgements We thank Anna Kuosmanen and Ahmed Sobih for their prompt help with the preliminary experiments on RNA-Seq data, which we included as Supplementary Material.  ... 
doi:10.1186/1471-2105-15-s9-s5 pmid:25252805 pmcid:PMC4168716 fatcat:wbkqm7bjlnafbfgfpvodkcxlhq

Width Helps and Hinders Splitting Flows [article]

Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams
2022 arXiv   pre-print
Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow X on directed graph G into weighted source-to-sink paths whose superposition equals X.  ...  For the negative version, we give a (⌈log‖ X ‖⌉ +1)-approximation (‖ X ‖ being the maximum absolute value of X on any edge) using a power-of-two approach, combined with parity fixing arguments and a decomposition  ...  had sped up their FPT algorithm for MFD N .  ... 
arXiv:2207.02136v1 fatcat:4fci3zyduzeornhhctunnkn6fm

Optimizing Safe Flow Decompositions in DAGs [article]

Shahbaz Khan, Alexandru I. Tomescu
2022 arXiv   pre-print
Overall we further develop the theory of safe and complete solutions for the flow decomposition problem, giving an optimal algorithm for the explicit representation, and a near-optimal algorithm for the  ...  Hence, recently flow decomposition was studied [RECOMB22] in the Safe and Complete framework, particularly for RNA Assembly.  ...  Acknowledgements We would like to thank Manuel Cáceres from University of Helsinki, for helpful discussions and for highlighting several errors in our previous approaches.  ... 
arXiv:2102.06480v2 fatcat:a3s5weqdkjanjpal4f7t3y5bmm

Flow Decomposition with Subpath Constraints

Lucia Williams, Alexandru I. Tomescu, Brendan Mumey, Alessandra Carbone, Mohammed El-Kebir
2021
For finding a minimum decomposition, we propose both a heuristic and an FPT algorithm.  ...  We formalize the flow decomposition with subpath constraints problem, give the first algorithms for it, and study its usefulness for recovering ground truth decompositions.  ...  Though splice graphs for RNA assembly are usually DAGs, graphs for de novo assembly of viral or other genomes would likely contain cycles due to repeated sequences.  ... 
doi:10.4230/lipics.wabi.2021.16 fatcat:kojsikknibblnogiy5psgqmz6a

Safety and Completeness in Flow Decompositions for RNA Assembly [article]

Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu
2022
We evaluated our algorithms against the trivial safe algorithms (unitigs, extended unitigs) and the popularly used heuristic (greedy-width) for flow decomposition on RNA transcripts datasets.  ...  Moreover, it has superior time ($3-5\times$) and space efficiency ($1.2-2.2\times$), resulting in a better and more practical approach for bioinformatics applications of flow decomposition.  ...  Safety in Flow Decomposition for RNA Assembly The prominent application of flow decomposition in bioinformatics is RNA transcript assembly, which is described as follows.  ... 
doi:10.48550/arxiv.2201.10372 fatcat:datbowvkvvfmta7db3se7hceli

BME VIK Annual Research Report on Electrical Engineering and Computer Science 2016

Hassan Charaf, Gábor Harsányi, András Poppe, Sándor Imre, Bálint Kiss, Tamás Dabóczi, Gyula Katona, Lajos Nagy, Gábor Magyar, István Kiss
2017 Periodica Polytechnica Electrical Engineering and Computer Science  
These factors have positioned our Faculty as a significant source of knowledge transfer and a treasured partner in various cooperation activities.The current paper gives a brief account of the results  ...  Thus, participation in these collaborations give a competitive edge and ensure the continuous development of VIK.  ...  For degree parameters, we were able to provide efficient FPT algorithms.  ... 
doi:10.3311/ppee.11067 fatcat:danqnppunnhq3mc2ns3qfhdwy4

On Fitting Finite Dirichlet Mixture Using ECM and MML [chapter]

Nizar Bouguila, Djemel Ziou
2005 Lecture Notes in Computer Science  
Fluid queue models play a vital role in the performance analysis of computer and telecommunication networks.  ...  The system is analysed for different active periods corresponding to the service time of an M/G/1 queue and the busy period of an M/G/1 queue.  ...  A point is fixed on a circle and we assume that Poisson flow of customers arrives for service.  ... 
doi:10.1007/11551188_19 fatcat:gtzi5u6emvfyxea3zbklobnvom

第56回年会予稿集

2018 Seibutsu Butsuri  
Biophysical Society of Japan (BSJ) grants "Early Career Award in Biophysics" and "Early Career Presentation Award" to young BSJ members for their excellent presentations that show great potential to contribute  ...  Up to five awardees of the Early Career Award in Biophysics will be selected and announced at the banquet 3SEA-5 光遺伝子操作による単一の糸球体の活性により誘因される恐怖行動の探索 Immobility responses are induced by photoactivation of  ...  Ke (Emory University) A key challenge in nanotechnology is to design and fabricate nanostructures and nanodevices, for basic science and for practical applications.  ... 
doi:10.2142/biophys.58.s1 fatcat:6slkwnu64fen7cjixehxrcmdzm

Stochastic models of intracellular transport

Paul C. Bressloff, Jay M. Newby
2013 Reviews of Modern Physics  
See text for details.  ...  Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport.  ...  DMS-1120327) and by Award No. KUK-C1-013-4 made by King Abdullah University of Science and Technology (KAUST).  ... 
doi:10.1103/revmodphys.85.135 fatcat:bumcmfjlnnhplf5nyrd6rjavw4

第54回年会予稿集

2016 Seibutsu Butsuri  
Using a quantitative live-cell imaging, we characterized the dynamics of the flow, and proposed a mechanism for the self-organization of the flow.  ...  For control of a linear movement, a pyrene-modified DNA walker and the track were assembled on the DNA origami tile.  ...  3Pos313 Ohashi, Kaoru (大橋 郁) 3Pos279 3Pos284 Ohba, Yasunori (大庭 裕範) 3Pos065 Ohba, Yusuke (大場 雄介) 3SAA-03 Ohgita, Takashi (扇田 隆司) 3Pos072 Ohira, Ayaka (大平 彩花) 1Pos257 Ohki, Mio (大木 規央) 3Pos076 Ohkoshi, A.  ... 
doi:10.2142/biophys.56.s1 fatcat:jxxuc3tfpbhc5isjcmprzec2gi

Dagstuhl Reports, Volume 9, Issue 1, January 2019, Complete Issue [article]

2019
With respect to τ this is an XP algorithm, or an FPT algorithm if p max has size polynomial in the encoding length of the instance. It remains open whether the problem is FPT or W[1]-hard.  ...  For instance, even an f (k)-FPT-approximation (for some function f ) would be very nice, since this would also lead to a g(k)-FPT-approximation (for some function g) for SVP in 2 norm as well.  ...  We establish a new fundamental FPT result on integer programming and hope it will provide a new tool that may allow to establish new FPT results for a variety of combinatorial optimization problems.  ... 
doi:10.4230/dagrep.9.1 fatcat:m3grhk5hanccbg7oxkhos7kv4e
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