The inverse RNA folding problem deals with designing a sequence of nucleotides that will fold into a desired target structure. Generalized Nested Rollout Policy Adaptation (GNRPA) is a Monte Carlo search algorithm for optimizing a sequence of choices. It learns a playout policy to intensify the search of the state space near the current best sequence. The algorithm uses a prior on the possible actions so as to perform non uniform playouts when learning the instance of problem at hand. We trained a transformer neural network on the inverse RNA folding problem using the Rfam database. This network is used to generate a prior for every Eterna100 puzzle. GNRPA is used with this prior to solve some of the instances of the Eterna100 dataset. The transformer prior gives better result than handcrafted heuristics.

错误:搜索内容不能为空,请输入英文关键词
错误:关键词超出字数限制,请精简
高级检索

Monte Carlo Inverse RNA Folding

  • Tristan Cazenave,
  • Hamza Touzani

摘要

The inverse RNA folding problem deals with designing a sequence of nucleotides that will fold into a desired target structure. Generalized Nested Rollout Policy Adaptation (GNRPA) is a Monte Carlo search algorithm for optimizing a sequence of choices. It learns a playout policy to intensify the search of the state space near the current best sequence. The algorithm uses a prior on the possible actions so as to perform non uniform playouts when learning the instance of problem at hand. We trained a transformer neural network on the inverse RNA folding problem using the Rfam database. This network is used to generate a prior for every Eterna100 puzzle. GNRPA is used with this prior to solve some of the instances of the Eterna100 dataset. The transformer prior gives better result than handcrafted heuristics.