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A compilation technique for reliability-aware software transformations is presented. An instruction-level reliability estimation technique quantifies the effects of hardware-level faults at the instruction-level while considering spatial and temporal vulnerabilities. It bridges the gap between hardware - where faults occur according to our fault model - and software (the abstraction level where we aim to increase reliability). For a given tolerable performance overhead, an optimization algorithm compiles an application software with respect to a tradeoff between performance and reliability. Compared to performance-optimized compilation, our method incurs 60%-80% lower application failures, averaged over various fault injection scenarios and fault rates.