Claire Shipman, the acting president of Columbia University, was met with a chorus of boos on Wednesday from some of the 12,000 graduates at the school’s main commencement ceremony as she took the podium to deliver remarks.

The graduates of Columbia’s class of 2025 had taken meaningful classes and made lifelong friends. But they had also lived through campus lockdowns, the arrests of hundreds of students at pro-Palestinian protests and a revolving door of university presidents.

So it was with a mixture of gratitude and relief that the graduates gathered for a massive ceremony in the rain. Last year’s commencement was canceled in the aftermath of pro-Palestinian encampments and police crackdowns.

Ms. Shipman kept talking over the boos, praising the families, teachers and graduates. “Graduates, it is time to give the world your gifts,” she said.

Amid a clampdown by the Trump administration on international students involved in pro-Palestinian activism, Ms. Shipman spoke in favor of the rights of those students, saying, “We firmly believe that our international students have the same rights to free speech as everyone else.” She said they should not be punished for exercising those rights.

The president noted that many graduates were “mourning” that Mahmoud Khalil, a new graduate who continues to be detained in Louisiana by Immigration and Customs Enforcement officials, was not there.