It's named for their company, which does other things too.

Yup. Subgraph is a nearly 7 year old open source software company. We wrote a web scanner (Vega) that's sadly neglected, though still used regularly by thousands of users. We also do consulting, like pentesting, etc.

The name was inspired by work I was following at the time (10 years ago?) by Halvar Flake etc, on applying graph theory methods to reverse engineering / runtime analysis.

It's catchy, sounds technical, and non-technical people can still spell it. Great name. :)

It is a precise technical term, and using it for a company name is unsettling to a graph theorist. But, it's probably cool for almost everyone else.

When the domain was registered by me and idea originally hatched, the vision was to have the company focused on reverse engineering and the application to it of ideas from graph theory. But things change. Name stuck.