Abstract: Fault-tolerant deep learning accelerator is the basis for highly reliable deep learning processing, and is also critical to deploy deep learning in safety-critical applications such as avionics and robotics. Since deep learning is known to be both computing-intensive and memory-intensive, traditional fault-tolerant approaches based on redundant computing will incur substantial overhead including power consumption and chip area. To this end, we propose to characterize deep learning vulnerability difference across both neurons and bits of each neuron, and leverage the vulnerability difference to enable selective protection of the deep learning processing components from the perspective of architecture layer and circuit layer respectively for the sake of lower fault-tolerant design overhead. At the same time, we observe the correlation between model quantization and bit protection overhead of the underlying processing elements of deep learning accelerators, and propose to reduce the bit protection overhead by adding additional quantization constrain without compromising the model accuracy. Finally, we employ Bayesian optimization strategy to co-optimize the correlated cross-layer design parameters at algorithm layer, architecture layer, and circuit layer to minimize the hardware resource consumption while fulfilling multiple user constraints including reliability, accuracy, and performance of the deep learning processing at the same time.