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Tech companies like Facebook, Apple, and Google are not the only ones helping U.S. intelligence agencies track citizens.

For years, data scientists have been brought in to brief with the National Security Agency.

The NSA has a massive team of analysts and a huge wiretapping program called PRISM, but it is eager to take advantage of the newest “big data” and machine learning technologies, so it can more easily make sense of millions of phone calls, emails, and text messages.

The goal is to track suspicious activity and create a complex “alerts system” for acts of terrorism, said Sean Gourley, a data scientist and founder of Silicon Valley-based Quid, which provides big-data analysis services, mostly for government customers.

Some of the most innovative technology designed to cope with massive data streams has come out of Silicon Valley. For this reason, the CIA’s venture arm, In-Q-Tel, has an office on the Palo Alto’s famous Sand Hill Road. It makes strategic investments in “big data” startups, like Recorded Future, whose products may come in useful for various government agencies.

“The NSA is naturally interested in data mining; I know of data scientists in Silicon Valley who have helped them,” said Mike Driscoll, chief executive of Silicon Valley-based big data startup Metamarkets.

“They appeal to our sense of patriotism,” said Driscoll.

Driscoll was not surprised by today’s news exposing the government’s PRISM program, which caused a furor among civil liberties activists and the media. He referred to the Echelon Project, the NSA’s clandestine data mining project and spy program that we’ve known about for years, as a precedent.

To recap: The Washington Post reported today that tech companies are participating in a top secret data mining program for the FBI and NSA, dubbed PRISM. Since the news broke, the companies named in the report have almost universally issued statements to the press that they do not provide direct access to their servers.

However, the government is a third party. Facebook’s terms of service, for instance, state that it can share your information with third parties. The assumption most Facebook users make is that the wording refers to marketers or advertisers, not the government.

“We don’t mind little bits of manipulation, but we do mind if it’s on this scale,” said Gourley.

According to Gourley, who regularly works with federal agencies, the NSA is most interested in real-time systems for data analysis. It’s not just what you say — but who you know. In other words, you’ll be flagged if you’ve communicated with a person of interest, or if you share a suspicious tweet.

“The NSA is essentially looking for a needle in a massive, massive haystack,” he said.

Given that technology exists for sophisticated analysis of social networks, “you could be on the list by association,” he warns.

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