Mixing WIMG and AI

We've been tinkering with incorporating AI (Gemini) with our Fisher app. The idea is not so tricky...you feed the AI an identity/rulebook ("You are the WIMG Bioinformatics Analyst...", etc) and the output of the Fisher test, submit, and then receive some very impressive, formatted output in a minute or less. The AI does not simply make generic observations about the cell cycle, metabolism, etc., but actually notes seemingly paradoxical outputs and attempts to resolve them. It sees rare genes expressed in both user input and database studies of interest, and offers up commentary.

So: enter your genes or a database ID in the Fisher tool. Hit "Run Fisher Analysis", and wait for output. You may then go to "Biological Insight (AI)". Click the "Interpret with AI" button and wait. You should get something that looks like this:

Initially, I was borderline giddy about the awesomeness of this feature. There's a huge difference between merely handing an AI a gene set and handing the AI a gene set + descriptions of 20 overlapping studies + their overlapping genes + 30 keywords of interest. What's more, there are insights that would be difficult or impossible for most biologists to come up with on their own...the AI is not limited by specialization in a particular branch of biology, or a lack of familiarity with 90% of the genes of interest.

The giddiness has now been subdued. One reason is the temperment of the AI. Despite several days of tweaking, the output may lack a beginning (it's "acephalous"), or may be truncated. The output may be disappointingly short, or needlessly long and repetitious. The output depends on up to five rounds of back and forth between WIMG and a Google AI, increasing the possibility of garbage-producing interruptions.

There is, as always, the chance of hallucination. More subtle would be a failure to examine second and third explanations.

Primarily, though, I realize that the user can certainly do a better job of squeezing insights from an AI than WIMG. One reason for this is that the WIMG AI feature is "one shot"...you don't get the chance to converse with it. Also, the AI (Gemini 3.5 flash) is not the high-end tool to which academicians often have access. We're talking about money here. For this reason, you'll see a "Copy Context for External AI" button below the output box:

If you click that, you'll not only receive the AI output, but the data and "rulebook" that goes along with it. You can, of course, edit this (or not), and insert it into your own favorite AI. At some point in the conversation, you could provide the AI with the "true" experimental context that only you know, and/or provide your AI with further data from your lab, from WIMG, from other tools, and from your own grey-matter database. Basically, the WIMG AI tool is a bit superfluous...the main thing is to provide a good AI with good data, which absolutely includes the overlapping studies that WIMG provides.

If the output is flaky or unprofessional, or the tool requires a ludicrous level of maintenence, we'll disable the AI, but retain the "Download Context" capability, making it easy to initiate a conversation with your favorite AI.

In the best cases, the WIMG AI output will be fantastically helpful. Just bear in mind that you can probably do better!

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