The design and analysis of communication systems typically rely on the development of mathematical models that describe the underlying communication channel. However, in some systems, such as molecular communication systems where chemical signals are used for transfer of information, the underlying channel models are unknown. In these scenarios, a completely new approach to design and analysis is required. In this work, we focus on one important aspect of communication systems, the detection algorithms, and demonstrate that by using tools from deep learning, it is possible to train detectors that perform well without any knowledge of the underlying channel models. We propose a technique we call sliding bidirectional recurrent neural network (SBRNN) for real-time sequence detection. We evaluate this algorithm using experimental data that is collected by a chemical communication platform, where the channel model is unknown and difficult to model analytically. We show that deep learning algorithms perform significantly better than a detector proposed in previous works, and the SBRNN outperforms other techniques considered in this work.