I/O reduction has been a major focus in optimizing data-parallel programs for big-data processing. While the current state-of-the-art techniques use static program analysis to reduce I/O, Cybertron proposes a new direction that incorporates runtime mechanisms to push the limit further on I/O reduction. In particular, Cybertron tracks how data is used in the computation accurately at runtime to filter unused data at finer granularity dynamically, beyond what current static-analysis based mechanisms are capable of, and to facilitate a new mechanism called constraint based encoding for more efficient encoding. Cybertron has been implemented and applied to production data-parallel programs; our extensive evaluations on real programs and real data have shown its effectiveness on I/O reduction over the existing mechanisms at reasonable CPU cost, and its improvement on end-to-end performance in various network environments.