President Trump released a $4.8 trillion budget proposal on Monday that includes a familiar list of deep cuts to student loan assistance, affordable housing efforts, food stamps and Medicaid, reflecting Mr. Trump’s election-year effort to continue shrinking the federal safety net.

Congress has rejected President Trump’s plan to cut funds for biomedical research and would instead increase spending by the National Institutes of Health. The appropriations committees in both houses rejected Mr. Trump’s proposal to slash payments to universities for overhead — the “indirect costs” of research financed by the health institutes. These include the cost of utilities, internet service, data storage, the construction and upkeep of laboratories and compliance with federal rules protecting human subjects of clinical research.

President Trump’s proposal on Thursday for deep cuts to the budgets of a broad part of the federal bureaucracy was billed as a tough-minded and necessary corrective to the growth of the government’s power. But even  members of his own party questioned some of the cuts — and what was not being cut. “While we have a responsibility to reduce our federal deficit, I am disappointed that many of the reductions and eliminations proposed in the president’s skinny budget are draconian, careless and counterproductive,” said Representative Harold Rogers, Republican of Kentucky and a former chairman of the House Appropriations Committee.