JavaScript: Faster way to create and initialize two dimensional array (matrix)

You could use the Array.prototype.fill method:

var nodes = Array(ast.length).fill(Array(ast.length).fill(0));

jsperf test: http://jsperf.com/fill-array-matrix

You can create array of zeros once and create copies of it:

var length = 10;

var zeros = Array.apply(null, Array(length)).map(Number.prototype.valueOf, 0);
var nodes = zeros.map(function(i) {
    return zeros.slice();
});

console.log(nodes);

Since you asked for "faster", it looks like you can gain some speed by creating a single initalized array and then using .slice() to copy it rather than initializing each array itself:

var nodes = new Array(ast.length);
var copy = new Array(ast.length);
for (var i = 0; i < ast.length; i++) {
    copy[i] = 0;
}

for (var i=0; i < nodes.length; i++){
    nodes[i] = copy.slice(0);
}

jsperf test: http://jsperf.com/slice-vs-for-two-d-array/2

This method looks to be 10-20% faster in all three major browsers.