New data processing pipelines and novel network architectures increasingly drive the success of deep learning. In consequence, the industry considers top-performing architectures as intellectual property and devotes considerable computational resources to discovering such architectures through neural architecture search (NAS). This provides an incentive for adversaries to steal these novel architectures; when used in the cloud, to provide Machine Learning as a Service (MLaaS), the adversaries also have an opportunity to reconstruct the architectures by exploiting a range of hardware side-channels. However, it is challenging to reconstruct novel architectures and pipelines without knowing the computational graph (e.g., the layers, branches or skip connections), the architectural parameters (e.g., the number of filters in a convolutional layer) or the specific pre-processing steps (e.g. embeddings). In this paper, we design an algorithm that reconstructs the key components of a novel deep learning system by exploiting a small amount of information leakage from a cache side-channel attack, Flush+Reload. We use Flush+Reload to infer the trace of computations and the timing for each computation. Our algorithm then generates candidate computational graphs from the trace and eliminates incompatible candidates through a parameter estimation process. We implement our algorithm in PyTorch and Tensorflow. We demonstrate experimentally that we can reconstruct MalConv, a novel data pre-processing pipeline for malware detection, and ProxylessNAS-CPU, a novel network architecture for the ImageNet classification optimized to run on CPUs, without knowing the architecture family. In both cases, we achieve 0% error. These results suggest hardware side channels are a practical attack vector against MLaaS, and more efforts should be devoted to understanding their impact on the security of deep learning systems.