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Sorry to pull up an old post, it just might be relevant for something else I'm chasing down. @Jonathan Edwards did you ever get more details as to whether it is likely the signal came from nerves? I'd be very interested if it wasn't in fact nerves

It is an interesting tidbit, it just has so little strength that I can’t confidently say it isn’t due to pure chance and the relative overrepresentation of synapse-related pathways in the database (even if they don’t contain the same genes). Viewed in light of the Zhang et al findings, it’s...

Looking through I would say the synapse-related findings are quite weak. CC pathways are quite small to begin with, I imagine there would be difficulty getting much signal from them from a Genebass dataset. Few pathways pass the FDR cutoff, and only 3-4 genes are driving the enrichment that...

Yeah it is an artificially small confidence interval, but in my opinion you don’t particularly need one for validating on an independent test cohort. And even increasing the confidence interval by an order of magnitude wouldn’t put the AUC in the range of being no better than random assignment...

More or less. I suspect that there are no particularly strong associations to begin with—I’d be quite surprised if one gene had more than 2-3 associated mutations present in the dataset at all. Rather, what the algorithm seems to be doing is leveraging attention across neighborhoods of nodes...

Yes that's definitely a concern, which is why I was hoping to get a sense of which genes are driving the validation in the test cohort. If it was clear from the training weights that only a few top genes were driving most of the predictive power, that would be fairly straightforward since it...

The structure of a mendelian randomization study enables you to claim causation, but only if certain criteria are adequately met. There was some discussion of MR studies in this thread...

Yes thank you, he's on my list as well1

Yes in agreement, @Creekside several research groups are quite ahead of you on that. More comprehensive in silico models are becoming all the rage. I think the problem is simply that modeling the whole human body is a computational task of unimaginable complexity, even to get the most basic...

I apologize for what will probably be too blunt of an answer, I’m running low on energy for refining my language this morning. I hope nothing is taken as a personal attack. To answer your question, that proposal is an extremely generic word salad. Unfortunately, I’ve had the displeasure of...

I’ve been planning on reaching out to Rob Wust anyway, I will ask about that as well!

Thank you, I will add them to my list!

I’m most interested in muscle. Whether they have to be fresh depends on a few details that haven’t been hammered out yet. My main concern is that for my particular hypothesis, participant selection is quite important. For something like a bio bank I may not be able to confirm that the...

I think the main disconnect is between what an AI model theoretically could do, and what it actually ends up doing. Many of my rabbit holes are things that are, in an abstract sense, possible for an AI to figure out. It would be extremely useful if e.g. AI was able to look at existing papers...

In all honesty I think it is quite a vague conclusion. Glycosylation is simply the process of conjugating proteins and carbohydrates, it’s a broad biological process with extremely wide applicability in various biological contexts. The connection between fibrinogen, collagen, and P-selectin is...

I think so. The main issue would be that it’s not only training the AI to understand what makes a “good” study (i.e. ranking diagnostic criteria or checking for double blinding in a clinical trial). For the search for a biological mechanism, it would also have to be aware of all the potential...

Thanks! Unfortunately, blood samples will probably not be able to address the hypothesis I have in mind. Though it’s possible they could be used for something supplemental.

I’m meeting with a couple potential collaborators in the next few weeks to sort out exactly what would be feasible to do experimentally—the cost might vary quite a bit based on this. But I’m happy to keep folks on here updated as I know more! Unfortunately I’m also limited by time and energy...