Hunting binary code difference without source code (i.e., binary diffing) has compelling applications in software security. Due to the high variability of binary code, existing solutions have been driven towards measuring semantic similarities from syntactically different code. Since compiler optimization is the most common source contributing to binary code differences in syntax, testing the resilience against the changes caused by different compiler optimization settings has become a standard evaluation step for most binary diffing approaches. For example, 47 top-venue papers in the last 12 years compared different program versions compiled by default optimization levels (e.g., -Ox in GCC and LLVM). Although many of them claim they are immune to compiler transformations, it is yet unclear about their resistance to non-default optimization settings. Especially, we have observed that adversaries explored non-default compiler settings to amplify malware differences.

The discrete logarithm problem is one of the well-known NP problems. It has important applications in such fields as cryptography. The discrete logarithm problem is the basis for the security of many cryptosystems including the Elliptic Curve Cryptosystem and Diffie-Hellman protocol. In this paper, we proposed newly developed parallel bio-molecular logic computing algorithms based on bio-molecular logic computing model to solve discrete logarithm problem.

Any protein is a linear chain of amino acid, and under specific conditions it folds into a unique native three-dimensional structure. Based upon thermodynamical hypothesis, the native structure of a protein always achieves the global minimum of free energy. The hydrophobic-hydrophilic model [1] for predicting the protein native structure is perhaps one of the most successful and best-studied models. The protein folding problem [2] in the hydrophobic-hydrophilic (HP) model has been proved as an NP-complete problem. This paper is the first one in which we demonstrate that bio-molecular operations with basic logical operations can be used to solve the three dimensional protein folding problem in the HP model. In order to achieve the goal, intelligent bioinformatics logic algorithms are proposed.