Comments on "parallel algorithms for finding a near-maximum independent set of a circle graph" [with reply

Abstract

The authors refers to the work of Y. Takefuji et al. (see ibid., vol.1, pp. 263-267, Sept. (1990)), which is concerned with the problem of RNA secondary structure prediction, and draws the reader's attention to his own model and experiments in training the neural networks on small tRNA subsequences. The author admits that Takefuji et al. outline an elegant way to map the problem onto neural architectures, but suggests that such mappings can be augmented with empirical knowledge (e.g., free energy values of base pairs and substructures) and the ability to learn. In their reply, Y. Takefuji and K.-C. Lee hold that the necessity of the learning capability for the RNA secondary structure prediction is questionable. They believe that the task is to build a robust parallel algorithm considering more thermodynamic properties in the model.