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New antibiotic targets IBD and AI predicted how it would work

healthsci.mcmaster.ca

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Re: New antibiotic targets IBD and AI predicted how it would work

#31

Post by teiferer »

> Currently, we can’t just assume that these AI models are totally right,

Why could we ever assume that?

> but the notion that it could be right took the guesswork out of our next steps,

Devils advocate here. Couldn't this just be a severe case of confirmation bias? You take 100 such cases, ask AI "how does it work?" and in 99 of those, the answer is somewhere on the spectrum between "total nonsense" and "clever formulation but wrong". One turns out to be right. That's the on we are seeing here, getting confirmed in the lab. That doesn't actually mean AI reduced the time by 75%.

A broken clock is also correct twice a day. We wouldn't say we have invented a clock that works without energy, sure it's wrong sometimes, but when it's correct, it's awesome! No, it's just a broken clock that's wrong most of the time.

I would also love to see that with "generative AI" we have discovered some helpful magic, but as long as we are not honest about those details (which would include publishing and owning up to mishaps), this is all just riding a hype train.

Re: New antibiotic targets IBD and AI predicted how it would work

#34

Post by leakycap »

teiferer wrote: post #31

> Currently, we can’t just assume that these AI models are totally right, Why could we ever assume that? > but the notion that it could be right took the guesswork out of our next steps, Devils advocate here. Couldn't this just be a severe case of confirmation bias? You take 100 such cases, ask AI "how does it work?" and in 99 of those, the answer is somewhere on the spectrum between "total nonsense" and "clever form…

I think this perspective overlooks how human expertise actually works. Humans in cutting-edge research also get things wrong a lot: most hypotheses fail, most experiments don't pan out, and most novel approaches lead nowhere.

When we celebrate a scientist who makes a breakthrough, we're not crediting them for being right 100% of the time. We're recognizing that they were right more often than random chance and earlier in the process than would otherwise occur.

A researcher (or AI) who can identify promising directions at a 2/99 or 3/99 rate instead of 1/99 is genuinely valuable – they're effectively doubling or tripling the efficiency of the discovery process.

Imagine if AI can test theories in under 100 seconds AND is slightly better out of 99 tries at getting things right. Beats the human out of the water.

Re: New antibiotic targets IBD and AI predicted how it would work

#36

Post by heisenbit »

leakycap wrote: post #34
teiferer wrote: post #31

> Currently, we can’t just assume that these AI models are totally right, Why could we ever assume that? > but the notion that it could be right took the guesswork out of our next steps, Devils advocate here. Couldn't this just be a severe case of confirmation bias? You take 100 such cases, ask AI "how does it work?" and in 99 of those, the answer is somewhere on the spectrum between "total nonsense" and "clever form…

I think this perspective overlooks how human expertise actually works. Humans in cutting-edge research also get things wrong a lot: most hypotheses fail, most experiments don't pan out, and most novel approaches lead nowhere. When we celebrate a scientist who makes a breakthrough, we're not crediting them for being right 100% of the time. We're recognizing that they were right more often than random chance and earlie…

This is exactly how I use AI now daily: Provide it with relevant context and help me to troubleshoot some software issue. I found often it casts a wider net and provides good leads to follow up. It balances out my own bias and overall speeds up discovery of the root cause. Admittedly some benefit comes from having to explain the AI the context - half the problems are gone once one can explain them clearly.

Re: New antibiotic targets IBD and AI predicted how it would work

#37

Post by fmbb »

KLK2019 wrote: post #2

Here is the original study published in nature microbiology. https://www.nature.com/articles/s41564-025-02142-0 Wanted to share what I thought the interesting parts. From the university press release. "To date, AI has been leveraged as a tool for predicting which molecules might have therapeutic potential, but this study used it to describe what researchers call “mechanism of action” (MOA) — or how drugs attack disea…

Is DiffDock a large language model?

Because that is what the general public believes AI means, and Open AI say they are building thinking machines with it, and this headline says ”predicted”.

Re: New antibiotic targets IBD and AI predicted how it would work

#38

Post by KLK2019 »

In light of the meta context that this article reinforces the view that ai can replace researchers job I found this part of the artcile very true to how I use AI tools at work.

"Stokes stresses that while the prediction was intriguing, it was just that — a prediction. He would still have to conduct traditional MOA studies in the lab.

“Currently, we can’t just assume that these AI models are totally right, but the notion that it could be right took the guesswork out of our next steps,”...so his team, led in large part by McMaster graduate student Denise Catacutan, began investigating enterololin’s MOA, using MIT’s prediction as a starting point.

Within just a few months, it became clear that the AI was in fact right.

“We did all of our standard MOA workup to validate the prediction — to see if the experiments would back-up the AI, and they did,” says Catacutan, a PhD candidate in the Stokes Lab. “Doing it this way shaved a year-and-a-half off of our normal timeline.”

Re: New antibiotic targets IBD and AI predicted how it would work

#40

Post by rubyfan »

azinman2 wrote: post #17
smeej wrote: post #5

Earlier quoted context omitted.

It's also the case that there is a bewildering variety of things that get sort of lumped together as "IBD." Crohn's and ulcerative colitis are two of them, but there's no particular reason to assume inflammatory bowel diseases all have the same set of causes. Pretty much all of them are made worse by an e. coli infection, though, so a drug that can target just those bacteria is helpful! During my own IBD journey, I'v…

Which markers? What meal? Why that meal? Note it also could return; looks can be deceiving.

Or it was never there to begin with.
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