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Deep learning speech separation algorithms have achieved great success in improving the quality and intelligibility of separated speech from mixed audio. Most previous methods focused on generating a single-channel output for each of the target speakers, hence discarding the spatial cues needed for the localization of sound sources in space. However, preserving the spatial information is important in many applications that aim to accurately render the acoustic scene such as in hearing aids and augmented reality (AR). Here, we propose a speech separation algorithm that preserves the interaural cues of separated sound sources and can be implemented with low latency and high fidelity, therefore enabling a real-time modification of the acoustic scene. Based on the time-domain audio separation network (TasNet), a single-channel time-domain speech separation system that can be implemented in real-time, we propose a multi-input-multi-output (MIMO) end-to-end extension of TasNet that takes binaural mixed audio as input and simultaneously separates target speakers in both channels. Experimental results show that the proposed end-to-end MIMO system is able to significantly improve the separation performance and keep the perceived location of the modified sources intact in various acoustic scenes.