The crucial question for inference is whether you can make the filled-in graph “look like a tree” without the trunk getting too thick. If the megavariable in the trunk has too many possible values, the tree grows out of control until it covers the whole planet, like the baobabs in The Little Prince. In the tree of life, each species is a branch, but inside each branch is a graph, with each creature having two parents, four grandparents, some number of offspring, and so on. The “thickness” of a branch is the size of the species’ population. When the branches are too thick, our only choice is to
The crucial question for inference is whether you can make the filled-in graph “look like a tree” without the trunk getting too thick. If the megavariable in the trunk has too many possible values, the tree grows out of control until it covers the whole planet, like the baobabs in The Little Prince. In the tree of life, each species is a branch, but inside each branch is a graph, with each creature having two parents, four grandparents, some number of offspring, and so on. The “thickness” of a branch is the size of the species’ population. When the branches are too thick, our only choice is to resort to approximate inference. One solution, left as an exercise by Pearl in his book on Bayesian networks, is to pretend the graph has no loops and just keep propagating probabilities back and forth until they converge. This is known as loopy belief propagation, both because it works on graphs with loops and because it’s a crazy idea. Surprisingly, it turns out to work quite well in many cases. For instance, it’s a state-of-the art method for wireless communication, with the random variables being the bits in the message, encoded in a clever way. But loopy belief propagation can also converge to the wrong answers or oscillate forever. Another solution, which originated in physics but was imported into machine learning and greatly extended by Michael Jordan and others, is to approximate an intractable distribution with a tractable one and optimize the latter’s parameters to make it...
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