First some background on these conferences quoted from the preface of David Johnson's 1991 STOC/FOCS Bibliography.
Since the 1960's, two of the most important venues for presenting new results in theoretical computer science have been the annual STOC and FOCS conferences sponsored respectively by the Association for Computing Machinery and the IEEE Computer Society. "STOC" is an acronym standing for the ACM Symposium on Theory of Computing and "FOCS" stands for what is now called the IEEE Symposium on Foundations of Computer Science. The STOC Conference is organized by ACM's Special Interest Group on Automata and Computability Theory (SIGACT) and has been held every spring since 1969. The FOCS conference is organized by what is now called the IEEE Technical Committee on Mathematical Foundations of Computer Science (TC-MFCS) and is held in the fall. It began in 1960 as a "Symposium on Switching Circuit Theory and Logic Design" (SCT&LD), changed its name in 1966 to "Symposium on Switching and Automata Theory" (SWAT), and assumed its current name in 1975.
A few updates: SIGACT now stands for the Special Interest Group on Algorithms and Computation Theory. The 33rd STOC in 2001, besides being the first held outside the US or Canada, is also the first held in the summer. The SWAT acronym has been appropriated by the Scandinavian Workshop on Algorithm Theory.
FOCS and STOC have changed in other ways. Until the 80's, they were the only major outlet for conference papers in theoretical computer science. Now there are several specialized conferences including, of course, the IEEE Conference on Computational Complexity. Many researchers put a greater emphasis on their specialized conference than STOC and FOCS. This is somewhat true in complexity but much more so in say computational learning theory.
While most, but not all, of the best papers in theory still appear in STOC and FOCS, these conferences no longer reflect the broad interests of theoretical computer scientists. This was probably an inevitable outcome of a field maturing and becoming more specialized.
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