How to defend a US patent for software considered patent ineligible

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Some software inventions that embody computational methods which can be formed entirely in the human mind are considered to be abstract and patent ineligible in the US.  These inventions have been said to embody the “basic tools of scientific and technological work” that are free to all men and reserved exclusively to none [1], or consist solely of mental steps which can be carried out by a human using pen and paper [2].
The recent US court decision VERACODE [3], however, successfully defended an attack on the above grounds, and provides valuable guidance on defending a US software patent or software patent application.
The VERACODE invention subject of US patent 7,752,609 is to a software analysis framework that consists of a method of decompiling binary machine code – which humans cannot interpret – into an intermediate form that one of a certain skill can analyse. A software developer can reverse engineer the intermediate code to reconstruct or approximate a program’s original source code.
It was argued that the invention is directed to a computerized, automated approach to software analysis that is based on longstanding technological approaches (data flow and control flow), which were previously done by hand using human mental processes, and are therefore patentable ineligible. 
While it was conceded that the invention was directed to an abstract idea and a building block of computer science and a fundamental practice in the industry, it was determined that the invention was more than merely requiring a generic computer implementation of the abstract idea. 
The court appeared to be particularly persuaded by the evidence that decompiling the binary code was impossible without the assistance of a decompiler. The evidence also showed that the algorithm was an improvement in the technical field and existing technology.
[1] Cybersource Corp. v. Retail Decisions, INC., 654 F.3D 1366, 1372-73 (Fed. Cir. 2011), citing Gottschalk 409 US at 67.
[2] Planet Bingo, LLC v. VKGS LLC, 576 F. App’x 1005, 1006 (Fed. Cir. 2014)

[3] Veracode et al. v. Appthority, 12-10487-DPW

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