What is the operation you are expecting in
tt.batched_dot(Xs, weights_in_1) + biases_in_1
?
Specifically, looking at the shape:
Xs_train.shape, weights_in_1.tag.test_value.shape, biases_in_1.tag.test_value.shape
# ==> ((2, 1167, 11), (2, 11, 5), (2, 5))
are you expecting the output to have a shape of (2, 5) or (2, 1167, 5)?