In this paper, we tackle the problem of automatically generating algorithms
for linear algebra operations by taking advantage of problem-specific
knowledge. In most situations, users possess much more information about the
problem at hand than what current libraries and computing environments accept;
evidence shows that if properly exploited, such information leads to
uncommon/unexpected speedups. We introduce a knowledge-aware linear algebra
compiler that allows users to input matrix equations together with properties
about the operands and the problem itself; for instance, they can specify that
the equation is part of a sequence, and how successive instances are related to
one another. The compiler exploits all this information to guide the generation
of algorithms, to limit the size of the search space, and to avoid redundant
computations. We applied the compiler to equations arising as part of
sensitivity and genome studies; the algorithms produced exhibit, respectively,
100- and 1000-fold speedups
