Inferring Causal Protein Signaling Networks with Reinforcement Learning via Artificial Bee Colony Neural Architecture Search

Jihao Zhai, Junzhong Ji, Jinduo Liu

Abstract: Inferring causal protein signaling networks from human immune system cellular data is an important approach to reveal underlying tissue signaling biology and dysfunction in diseased cells. In recent years, reinforcement learning (RL) methods have shown excellent performance in the field of causal protein signaling network inference. However, the complexity of RL models and the need for manual hyperparameter tuning can hinder performance. In this paper, we propose a actor-critic RL model via artificial bee colony (ABC) neural architecture search, called ABCNAS-RL. Specifically, the entire method is divided into two phases: ABC neural architecture search and actor-critic RL search. In phase one, we represent each bee as a set of hyperparameter, utilizing the ABC algorithm searching for optimal hyperparameters of the actor-critic RL model on the training set. In phase two, we use the actor-critic RL model to infer the causal protein signaling network on the test set. The actor network consists of an encoder-decoder architecture, composed of a transformer and a bidirectional gated recurrent unit (BiGRU) with an integrated attention mechanism. The critic network consists of a fully connected neural network that estimates the output state of the actor network. By maximizing cumulative rewards, we ultimately derive the causal protein signaling network. Extensive experimental results on simulated and real datasets verify that ABCNAS-RL outperforms the comparison methods and has superior performance.