Privacy preserving error resilient dna searching through oblivious automata

Human Desoxyribo-Nucleic Acid (DNA) sequences offer a wealth of information that reveal, among others, predisposition to various diseases and paternity relations. The breadth and personalized nature of this information highlights the need for privacy-preserving protocols. In this paper, we present a new error-resilient privacy-preserving string searching protocol that is suitable for running private DNA queries. This protocol checks if a short template (e.g., a string that describes a mutation leading to a disease), known to one party, is present inside a DNA sequence owned by another party, accounting for possible errors and without disclosing to each party the other party's input. Each query is formulated as a regular expression over a finite alphabet and implemented as an automaton. As the main technical contribution, we provide a protocol that allows to execute any finite state machine in an oblivious manner, requiring a communication complexity which is linear both in the number of states and the length of the input string.

[1]  Sean R Eddy,et al.  What is dynamic programming? , 2004, Nature Biotechnology.

[2]  Mehryar Mohri,et al.  On some applications of finite-state automata theory to natural language processing , 1996, Nat. Lang. Eng..

[3]  Sheng Yu,et al.  The State Complexities of Some Basic Operations on Regular Languages , 1994, Theor. Comput. Sci..

[4]  Mehryar Mohri,et al.  Finite-State Transducers in Language and Speech Processing , 1997, CL.

[5]  Klaus U. Schulz,et al.  Fast string correction with Levenshtein automata , 2002, International Journal on Document Analysis and Recognition.

[6]  Vladimir I. Levenshtein,et al.  Binary codes capable of correcting deletions, insertions, and reversals , 1965 .

[7]  Mikhail J. Atallah,et al.  Secure outsourcing of sequence comparisons , 2004, International Journal of Information Security.

[8]  Pascal Paillier,et al.  Public-Key Cryptosystems Based on Composite Degree Residuosity Classes , 1999, EUROCRYPT.

[9]  Baruch Awerbuch,et al.  Verifiable secret sharing and achieving simultaneity in the presence of faults , 1985, 26th Annual Symposium on Foundations of Computer Science (sfcs 1985).

[10]  Moni Naor,et al.  Communication preserving protocols for secure function evaluation , 2001, STOC '01.

[11]  T. K. Vintsyuk.  Speech discrimination by dynamic programming , 1968 .

[12]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .

[13]  Silvio Micali,et al.  How to play ANY mental game , 1987, STOC.

[14]  Markus Jakobsson,et al.  Mix and Match: Secure Function Evaluation via Ciphertexts , 2000, ASIACRYPT.

[15]  Jeffrey D. Ullman,et al.  Introduction to Automata Theory, Languages and Computation , 1979 .

[16]  Wenliang Du,et al.  Secure and private sequence comparisons , 2003, WPES '03.

[17]  Moni Naor,et al.  Communication Complexity and Secure Function Evaluation , 2001, Electron. Colloquium Comput. Complex..

[18]  Silvio Micali,et al.  Probabilistic Encryption , 1984, J. Comput. Syst. Sci..

[19]  Andrew Chi-Chih Yao,et al.  Protocols for secure computations , 1982, FOCS 1982.

[20]  Somesh Jha,et al.  Secure function evaluation with ordered binary decision diagrams , 2006, CCS '06.

[21]  I. Damglurd.  Unconditionally secure constant-rounds multi-party computation for equality, comparison, bits and exponentiation , 2006 .

[22]  Moni Naor,et al.  Efficient oblivious transfer protocols , 2001, SODA '01.