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Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Infrared: a declarative tree decomposition-powered framework for bioinformatics
Algorithms Mol Biol. 2024 Mar 16;19(1):13. doi: 10.1186/s13015-024-00258-2.ABSTRACTMOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations.METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a ...
Source: Algorithms for Molecular Biology : AMB - March 17, 2024 Category: Molecular Biology Authors: Hua-Ting Yao Bertrand Marchand Sarah J Berkemer Yann Ponty Sebastian Will Source Type: research

Median quartet tree search algorithms using optimal subtree prune and regraft
Algorithms Mol Biol. 2024 Mar 13;19(1):12. doi: 10.1186/s13015-024-00257-3.ABSTRACTGene trees can be different from the species tree due to biological processes and inference errors. One way to obtain a species tree is to find one that maximizes some measure of similarity to a set of gene trees. The number of shared quartets between a potential species tree and gene trees provides a statistically justifiable score; if maximized properly, it could result in a statistically consistent estimator of the species tree under several statistical models of discordance. However, finding the median quartet score tree, one that maximi...
Source: Algorithms for Molecular Biology : AMB - March 14, 2024 Category: Molecular Biology Authors: Shayesteh Arasti Siavash Mirarab Source Type: research

Median quartet tree search algorithms using optimal subtree prune and regraft
Algorithms Mol Biol. 2024 Mar 13;19(1):12. doi: 10.1186/s13015-024-00257-3.ABSTRACTGene trees can be different from the species tree due to biological processes and inference errors. One way to obtain a species tree is to find one that maximizes some measure of similarity to a set of gene trees. The number of shared quartets between a potential species tree and gene trees provides a statistically justifiable score; if maximized properly, it could result in a statistically consistent estimator of the species tree under several statistical models of discordance. However, finding the median quartet score tree, one that maximi...
Source: Algorithms for Molecular Biology : AMB - March 14, 2024 Category: Molecular Biology Authors: Shayesteh Arasti Siavash Mirarab Source Type: research

Median quartet tree search algorithms using optimal subtree prune and regraft
Algorithms Mol Biol. 2024 Mar 13;19(1):12. doi: 10.1186/s13015-024-00257-3.ABSTRACTGene trees can be different from the species tree due to biological processes and inference errors. One way to obtain a species tree is to find one that maximizes some measure of similarity to a set of gene trees. The number of shared quartets between a potential species tree and gene trees provides a statistically justifiable score; if maximized properly, it could result in a statistically consistent estimator of the species tree under several statistical models of discordance. However, finding the median quartet score tree, one that maximi...
Source: Algorithms for Molecular Biology : AMB - March 14, 2024 Category: Molecular Biology Authors: Shayesteh Arasti Siavash Mirarab Source Type: research

Median quartet tree search algorithms using optimal subtree prune and regraft
Algorithms Mol Biol. 2024 Mar 13;19(1):12. doi: 10.1186/s13015-024-00257-3.ABSTRACTGene trees can be different from the species tree due to biological processes and inference errors. One way to obtain a species tree is to find one that maximizes some measure of similarity to a set of gene trees. The number of shared quartets between a potential species tree and gene trees provides a statistically justifiable score; if maximized properly, it could result in a statistically consistent estimator of the species tree under several statistical models of discordance. However, finding the median quartet score tree, one that maximi...
Source: Algorithms for Molecular Biology : AMB - March 14, 2024 Category: Molecular Biology Authors: Shayesteh Arasti Siavash Mirarab Source Type: research