Gradient computation in JavaScript

Question

I'm working with some math-heavy code in JavaScript. I just realized that there's a render that currently takes about 30 minutes. 95% of that time is spent in a single ~40 line function that I've pasted below. I am not extremely well-versed in JavaScript math optimization, so my first attempts to optimize this code haven't gone wonderfully.

I would love any pointers as to what in here is slowing things down. I have good reason to believe that things are non-optimal because the same code in Python runs about 30x faster and JS is not a slow language.

// return cost and gradient, given an arrangement
costGrad: function(Y) {
  var N = this.N; // About 5000 long
  var dim = this.dim; // About 300 long
  var P = this.P; // About 5000^2 long

  var pmul = this.iter < 100 ? 4 : 1; // trick that helps with local optima

  // compute current Q distribution, unnormalized first
  var Qu = zeros(N * N);
  var qsum = 0.0;
  for(var i=0;i<N;i++) {
    for(var j=i+1;j<N;j++) {
      var dsum = 0.0;
      for(var d=0;d<dim;d++) {
        var dhere = Y[i][d] - Y[j][d];
        dsum += dhere * dhere;
      }
      var qu = 1.0 / (1.0 + dsum); // Student t-distribution
      Qu[i*N+j] = qu;
      Qu[j*N+i] = qu;
      qsum += 2 * qu;
    }
  }
  // normalize Q distribution to sum to 1
  var NN = N*N;
  var Q = zeros(NN);
  for(var q=0;q<NN;q++) { Q[q] = Math.max(Qu[q] / qsum, 1e-100); }

  var cost = 0.0;
  var grad = [];
  for(var i=0;i<N;i++) {
    var gsum = new Array(dim); // init grad for point i
    for(var d=0;d<dim;d++) { gsum[d] = 0.0; }
    for(var j=0;j<N;j++) {
      cost += - P[i*N+j] * Math.log(Q[i*N+j]); // accumulate cost (the non-constant portion at least...)
      var premult = 4 * (pmul * P[i*N+j] - Q[i*N+j]) * Qu[i*N+j];
      for(var d=0;d<dim;d++) {
        gsum[d] += premult * (Y[i][d] - Y[j][d]);
      }
    }
    grad.push(gsum);
  }

  return {cost: cost, grad: grad};
}

For those that are curious to see more, this is from the wonderful tsnejs library from Andrej Karpathy.