Many software engineering tasks, such as testing, and anomaly detection can benefit from the ability to infer a behavioral model of the software.Most existing inference approaches assume access to code to collect execution sequences. In this paper, we investigate a black-box scenario, where the system under analysis cannot be instrumented, in this granular fashion.This scenario is particularly prevalent with control systems log analysis in the form of continuous signals. In this situation, an execution trace amounts to a multivariate time-series of input and output signals, where different states of the system correspond to different `phases` in the time-series. The main challenge is to detect when these phase changes take place. Unfortunately, most existing solutions are either univariate, make assumptions on the data distribution, or have limited learning power.Therefore, we propose a hybrid deep neural network that accepts as input a multivariate time series and applies a set of convolutional and recurrent layers to learn the non-linear correlations between signals and the patterns over time.We show how this approach can be used to accurately detect state changes, and how the inferred models can be successfully applied to transfer-learning scenarios, to accurately process traces from different products with similar execution characteristics. Our experimental results on two UAV autopilot case studies indicate that our approach is highly accurate (over 90% F1 score for state classification) and significantly improves baselines (by up to 102% for change point detection).Using transfer learning we also show that up to 90% of the maximum achievable F1 scores in the open-source case study can be achieved by reusing the trained models from the industrial case and only fine tuning them using as low as 5 labeled samples, which reduces the manual labeling effort by 98%.