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We develop a novel method to remove injected backdoors in deep learning models. It works by cloning the benign behaviors of a trojaned model to a new model of the same structure. It trains the clone model from scratch on a very small subset of samples and aims to minimize a cloning loss that denotes the differences between the activations of important neurons across the two models. The set of important neurons varies for each input, depending on their magnitude of activations and their impact on the classification result. We theoretically show our method can better recover benign functions of the backdoor model. Meanwhile, we prove our method can be more effective in removing backdoors compared with fine-tuning. Our experiments show that our technique can effectively remove nine different types of backdoors with minor benign accuracy degradation, outperforming the state-of-the-art backdoor removal techniques that are based on fine-tuning, knowledge distillation, and neuron pruning.