Neural network computation by in vitro transcriptional circuits

Title: “Neural network computation by in vitro transcriptional circuits”

Abstract: The structural similarity of neural networks and genetic regulatory net- works to digital circuits, and hence to each other, was noted from the very beginning of their study [1, 2]. In this work, we propose a simple biochemical system whose architecture mimics that of genetic regula- tion and whose components allow for in vitro implementation of arbi- trary circuits. We use only two enzymes in addition to DNA and RNA molecules: RNA polymerase (RNAP) and ribonuclease (RNase). We develop a rate equation for in vitro transcriptional networks, and de- rive a correspondence with general neural network rate equations [3]. As proof-of-principle demonstrations, an associative memory task and a feedforward network computation are shown by simulation. A difference between the neural network and biochemical models is also highlighted: global coupling of rate equations through enzyme saturation can lead to global feedback regulation, thus allowing a simple network without explicit mutual inhibition to perform the winner-take-all computation. Thus, the full complexity of the cell is not necessary for biochemical computation: a wide range of functional behaviors can be achieved with a small set of biochemical components.

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Reference: Kim, Jongmin, John Hopfield, and Erik Winfree. “Neural network computation by in vitro transcriptional circuits.” Advances in neural information processing systems. 2005.