Oblivious Evaluation of Non-deterministic Finite Automata with Application to Privacy-Preserving Virus Genome Detection

Various string matching problems can be solved by means of a deterministic finite automaton (DFA) or a non-deterministic finite automaton (NFA). In non-oblivious cases, DFAs are often preferred for their run-time efficiency despite larger sizes. In oblivious cases, however, the inevitable computation and communication costs associated with the automaton size are more favorable to NFAs. We propose oblivious protocols for NFA evaluation based on homomorphic encryption and demonstrate that our method can be orders of magnitude faster than DFA-based methods, making it applicable to real-life scenarios, such as privacy-preserving detection of viral infection using genomic data.