The patent, held by Allen's Interval Licensing, relates to the ubiquitous pop-ups that computer users routinely see while surfing the Web or shopping online.
The Court of Appeals for the Federal Circuit said that Chief Judge Marsha Pechman of the federal district court in Seattle had made an "erroneous" interpretation of the patent in 2013 and it sent the case back to her for further hearings.
At the same time, Circuit Judge Raymond Chen agreed with Pechman for invalidating certain claims made over the same Interval patent, and a second one, declaring them too ambiguous.
Interval Licensing is the patent-licensing arm of a Silicon Valley research entity that Allen financed, Interval Research Corp, which shut down in 2000.
Interval Licensing sued the tech companies in 2010 for allegedly infringing four of its patents, although only two became the subject of the appeal. It said they infringed the patents through products and software that use pop-up notifications, court documents said.
Attorneys for Interval could not immediately be reached for comment. Nor could attorneys for the defendants.
Allen and partner David Liddle founded Interval Research in 1992. It employed over 110 scientists and engineers and was granted 300 patents during its existence, according to court documents.
The case is Interval Licensing v. Aol Inc, Apple Inc, Google Inc, and Yahoo! Inc, U.s. Court of Appeals for the Federal Circuit, Nos, 2013-1282, -1283, -1284 and -1285.
(Reporting By Andrew Chung' editing by Andrew Hay)
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