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Early run-time prediction of co-running independent applications prior to application integration becomes challenging in multi-core processors. One of the most notable causes is the interference at the main memory subsystem, which results in significant degradation in application performance and response time in comparison to standalone execution. Currently available techniques for run-time prediction like traditional cycle-accurate simulations are slow, and analytical models are not accurate and time-consuming to build. By contrast, existing machine-learning-based approaches for run-time prediction simply do not account for interference. In this paper, we use a machine learning- based approach to train a model to correlate performance data (instructions and hardware performance counters) for a set of benchmark applications between the standalone and interference scenarios. After that, the trained model is used to predict the run-time of co-running applications in interference scenarios. In general, there is no straightforward one-to-one correspondence between samples obtained from the standalone and interference scenarios due to the different run-times, i.e. execution speeds. To address this, we developed a simple yet effective sample alignment algorithm, which is a key component in transforming interference prediction into a machine learning problem. In addition, we systematically identify the subset of features that have the highest positive impact on the model performance. Our approach is demonstrated to be effective and shows an average run-time prediction error, which is as low as 0.3% and 0.1% for two co-running applications.