Hua-Ting Yao, Bertrand Marchand, Sarah J Berkemer, Yann Ponty, Sebastian Will
MOTIVATION: 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 generalization of constraint networks...
March 16, 2024: Algorithms for Molecular Biology: AMB