I only played a few levels, but I think it works this way: the dots represent hidden numbers that are constant. The pairs of numbers on the beside the rows and columns aren't part of the row/column itself, but instead give information about it. The number on the left/bottom is the number you want to to make the most common number, (i.e. the "target mode"). The number to its right/above it is the current mode.
The numbers with underscores are ones you can alter. An x represents that there is no modal value, and the smaller dots above the numbers indicate where you can move your arrows. Pressing a number changes every underscored number that your arrow is pointing to. You win by making the actual mode the same as the target mode for every sequence that has a target mode.
Hope that helps!