After three years in the program and $45 million, nine San Francisco schools saw test scores go up and teacher retention improve.

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Seven years and $7 billion wasted.

That was the general reaction to a report released in the final days of the Obama administration that found no proof that a federal program aimed at improving the nation’s lowest-performing schools did any good.

But in a new study co-authored by Min Sun, a professor in the University of Washington’s College of Education, researchers concluded that the grants had significant and positive impact, at least in nine San Francisco schools.

After three years in the program — and millions of dollars in federal grants — researchers said student test scores went up in those nine schools, daily attendance rose and teachers stayed longer.

Education Lab is a Seattle Times project that spotlights promising approaches to persistent challenges in public education. It is produced in partnership with the Solutions Journalism Network and is funded by a grant from the Bill & Melinda Gates Foundation and City University of Seattle. Learn more about Ed Lab 

“Turning around these lowest-performing schools is really a systemic and dramatic undertaking,” Sun said. “Therefore we really need to have patience to allow those (efforts) to make an impact, gradually and over time.”

For their study, Sun and her colleagues at the University of California, Irvine and Stanford University looked at 10 years of data from the San Francisco Unified School District.

As the sixth-largest district in California, it received $45 million under the federal program from 2011 to 2013.

That helped the nine schools install new principals (who were given more flexibility in hiring staff), provide one-on-one coaching for teachers, offer longer school days and summer school, support parent engagement, and more.

After two years under the grant, test scores at the nine schools started to catch up with other schools that weren’t part of the effort.

Sun explained that her research may appear to contradict the federal study because she and her colleagues looked at nine schools in one district, while the U.S. Department of Education examined thousands of schools across the nation.

Congress already eliminated the school-improvement grant program. Under the new Every Student Succeeds Education Act, states will still be required to do something to help low-performing schools, but will have more flexibility in how they do so.

That’s where Sun said her study could come in handy — providing a blueprint of what could work.

“This is a special case study,” Sun said.