I actually really like that you have to spend a resource to learn new information and that the score is dependent on luck. I.e. you use limited resources to optimize the gamble you are making. That seems like a very good description of how life works, only, it's all transparent and quantified in your game.

Some suggestions:

• In the tutorial, why do I first get to read a description of a picture and then I'm presented with the picture? Obviously, it should be the other way around.
• You should be able to progress the text by mouse.
• It should be easier to distinguish new text from old. I think in visual novels, the text box never "scrolls". If the new text doesn't fit into the text box, or to make a new paragraph, the text box is cleared. You could make separate textboxes for the current message and the history.
• The confusing notation is a real distraction and zaps away a lot of the potential fun. Understanding the notation actually seems more interesting than winning the game, but I have too little information to understand it, which leads to frustration. Why are there two big boxes with normal nodes? Why do normal nodes have all those boxes instead of simple bar that shows the probability? Why do bayes-nodes have all those rows instead of just two bars? What are there grey bars? How do 'and' and 'or' nodes work? I would think that one input corresponds to the vertical division and one input to the horizontal division. It should be more obvious which node is which (by having the input into that side of the box). The connections of nodes did not have arrows. If I understood the game correctly, that would help distinguish inputs from outputs.
• The effect of clicking on one node shouldn't be instant. At first, it should probably go step by step: You click on a node and reveal it's truth-value (some text appears explaining which node changed and why). Press a key -> the next affected node gets updated. Until affected nodes are updated. Later you don't have to click, there is a small pause between each change. That way you could see the effect of measuring a node and understand why the effect was the way it was, instead of ... trying to work that information out for yourself with only being able to see the aftermath.
• You should make it more linear. Put the tutorial and the main game into one. I don't see the use of this decision between introductory and intermediate psychology.
• Have the player start out with much simpler networks and infinite energy.
• Introduce new types of nodes during the game, not all at once in the tutorial. Every time you introduce something new, go back to simple networks with unlimited energy.

Of those, explaining or simplifying the notation seems the most important to me.

I tried it on Ubuntu. The game is practically unplayable. I only see the last line of the text unless I scroll, and most of the bottom box is covered. Is the text supposed to be so huge?

I'm finding the game ... not fun. Here are some reasons.

• The notation for "Bayes nodes" is confusing and figuring out what it's saying requires more conscious thought than I really want to be putting into a game like this.
• There's this menu where I have to choose "go to lectures", "study in the library", or "hang out with friends" all the time -- except that only one choice is actually ever available (so far, at least).
• There's too much now-press-space, somehow.
• In the actual node-guessing game that's the main activity, you usually get to inspect about one node per lecture on average. That's not enough to make it very interesting. (Also: if the idea is to teach people about separation, so that they can figure out when knowing the state of one node means that learning X doesn't tell you anything about Y, wouldn't it be better if that situation were to arise more often?)
• It doesn't feel to me as if any sort of highbrow analysis of the networks provides a substantial advantage, which is a shame if the idea is to make people learn to do it. On the other hand ...
• So far I've played three or four games and been rejected by the academy about halfway through every time. So maybe there are strategic lessons I haven't learned yet. Or maybe it's just that success is too dependent on luck?

Not about the game itself, but the wording of the questions is a bit confusing to me:

In the above network, suppose that we were to observe the variable labeled "A". Which other variables would this influence?

The act of observing a variable doesn't influence any of the variables, it would only change your beliefs about the variables. The only things influencing a variable are its parents in the Bayesian network.

Who's your target audience/guinea pigs? Most normal people would run away screaming after seeing the "This survey tests your understanding of d-separation in Bayesian networks" part.

Ok, I wanted to play it, but the word are too big and/or the textbox is too small. graphics don't run well, and it really needs an exit button. I'm using windows 8. other than that, I think the idea is great.