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Why are cancer guidelines stuck in PDFs?

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Re: Why are cancer guidelines stuck in PDFs?

#81

Post by londons_explore »

epcoa wrote: post #54
epistasis wrote: post #42

Earlier quoted context omitted.

In cancer there's an abundance of clinical trials with high quality data, but it is all very complex in terms of encoding what the clinical trial actually encoded. Go to a clinical cancer conference and you will see the grim reality of 10,000s of people contributing to the knowledge discovery process with their cancer care. There is an inverse relationship between the number of people in a trial and the amount of ris…

By smuggling and bias I meant in an ML model. Smuggling was a bit informal, but referring to models overfit on unintended features or artifacts.

but we have well established ways to deal with those... test/validation sets, n-fold validation, etc.

Even if there was some overfitting or data contamination that was undetected, the result would most probably still be better than a hand-made decision tree over the same data...

Re: Why are cancer guidelines stuck in PDFs?

#82

Post by mav3ri3k »

Excellent read. This consolidated and catalyzed my my spurious thoughts around personal information management. The input is generally markdown/pdf but over time highly useless for a single person. Thete would be value if it is passed through such a system over time.

Re: Why are cancer guidelines stuck in PDFs?

#83

Post by graphviz »

epistasis wrote: post #40
tdeck wrote: post #27

GraphViz has some useful graph schema languages that could be reused for something like this. There's DOT, a delightful DSL, and some kind of JSON format as well. You can then generate a bunch of different output formats and it will lay out the nodes for you.

Of all the challenges with this, graph layout is beyond trivial. It does not rank as a problem, intellectual challenge, or even that interesting. The challenges are all about what goes in the nodes, how to define it, how to standardize it across different institutions, how to compare it to what was tested in two different clinical trials, etc. And if the computerized process goes into clinical practice, how is that n…

Not ... even that interesting?

Re: Why are cancer guidelines stuck in PDFs?

#84

Post by ramoz »

Cool tool. From my experience the PDF was easy to traverse.

The hardest part for me was understanding that treatment options could differ (i.e. between the _top_ hospitals treating the cancer). And there were a few critical options to consider. NCCN paths were traditional, but there is in between decisions to make or alternative paths. ChatGPT was really helpful in that period. "2nd" opinions are important... but again you ask the top 2 hospitals and they differ in opinion, any other hospital is typically in one of those camps.

Re: Why are cancer guidelines stuck in PDFs?

#85

Post by ajsnigrutin »

crazygringo wrote: post #20
prepend wrote: post #4

I’d rather have the pdf than a custom tool. Especially considering the tool will be unique to the practice or emr. And likely expensive to maintain. PDFs suck in many ways but are durable and portable. If I work with two oncologists, I use the same pdf. The author means well but his solution will likely be worse because only he will understand it. And there’s a million edge cases.

Exactly. The PDF's work . They won't break. You can see all the information with your own eyes. You can send them by e-mail. A wizard-type system hides most of the information from you, it might have bugs you aren't aware of, if you want to glance at an alternative path you can't, it's going to be locked into registered users, the system can go down. I think much more intelligent computer systems are the future in he…

> The PDF's work. They won't break.

Not just that, PDFs are one of the few formats, where i'm willing to bet my own money, that they'll still work in 10 or 20 years.

Even basic html has changed, layouts look different depending on many factors, and even the -ing doesn't work anymore.

Re: Why are cancer guidelines stuck in PDFs?

#86

Post by hashishen »

Funny i just had the thought the other day about how we as a society need to move past the pdf format or even just update it to be editable in traditional document software. The fact that Google docs will export as a pdf and not have it saved in the documents is proof its gotten to a point of inefficiency and that's just one example

Re: Why are cancer guidelines stuck in PDFs?

#87

Post by graphviz »

graphviz wrote: post #83
epistasis wrote: post #40

Earlier quoted context omitted.

Of all the challenges with this, graph layout is beyond trivial. It does not rank as a problem, intellectual challenge, or even that interesting. The challenges are all about what goes in the nodes, how to define it, how to standardize it across different institutions, how to compare it to what was tested in two different clinical trials, etc. And if the computerized process goes into clinical practice, how is that n…

Not ... even that interesting?

Modularity is an excellent way of attacking complex problems. We can all play with algorithms that can carry on realistic conversations and create synthetic 3D movies, because people worked on problems like making transistors the size of 10 atoms, figuring out how processors can predict branches with 99% accuracy, giving neural nets self-attention, deploying inexpensive and ridiculously fast networks all over the planet, and a lot of other stuff.

For many of us, curing cancer may someday become more important than almost anything else a computer can help us to do. It's just there are so many building blocks to solving truly complex problems; we must respect all that.

Re: Why are cancer guidelines stuck in PDFs?

#88

Post by easytigerm »

The OP will be pleased to know that they’re not the first person to think of this idea. Searching for “computable clinical guidelines” will unearth a wealth of academic literature on the subject. A reasonable starting point would be this paper [1]. Indeed people have been trying since the 70s, most notably with the famous MYCIN expert system. [2]

As people have alluded to and the history of MYCIN shows, there’s a lot more subtlety to the problem than appears on the surface, with a whole bunch of technical, psychological, sociological and economic factors interacting. This is why cancer guidelines are stuck in PDFs.

Still, none of that should inhibit exploration. After all, just because previous generations couldn’t solve a problem doesn’t mean that it can’t be solved.

[1] https://pmc.ncbi.nlm.nih.gov/articles/PMC10582221/

[2] https://www.forbes.com/sites/gilpress/2020/04/27/12-ai-miles...

Re: Why are cancer guidelines stuck in PDFs?

#89

Post by wizzwizz4 »

londons_explore wrote: post #81
epcoa wrote: post #54

Earlier quoted context omitted.

By smuggling and bias I meant in an ML model. Smuggling was a bit informal, but referring to models overfit on unintended features or artifacts.

but we have well established ways to deal with those... test/validation sets, n-fold validation, etc. Even if there was some overfitting or data contamination that was undetected, the result would most probably still be better than a hand-made decision tree over the same data...

Hand-made decision trees are open to inspection, comprehension, and adaption. There is no way to adapt an opaque ML model to new findings / an experimental treatment except by producing a new model.

Re: Why are cancer guidelines stuck in PDFs?

#90

Post by fasa99 »

WAIT ... Hole up... what have we here: https://www.nccn.org/compendia-templates/compendia/nccn-comp...

TLDR: The NCCN surely has a clean pretty database of these algorithms. They output these junky pdfs for free. Want cleaner "templates" data? Pay the toll please.

What we have here is a walled garden. Want the treatment algorithm? Here muck through this huge disaster of 999 page pdfs. Oh you want the underlying data? Well, well, it's going to cost you.

What we have here is not so much different than the paywalls of an academic journal. Some company running a core service to an altruistic industry and skimming a price. OP is just writing an algorithm to unskim it. And nobody can really use it without making the thing bulletproof lest a physician mistreat a cancer.

To my sentiment this is yet another unethical topic in healthcare. These clunky algorithms, if a physician uses them, slows the process and introduces a potential source of error, ultimately harming patients. Harming patients for increased revenue. The physicians writing and maintaining the guidelines look the other way given they get a paycheck off it, plus the prestige of it all, similar to some scenarios in medicine itself.

The natural thing to do is crack open the database and let algorithms utilize it. This whole thing of dumping data in an obstruse and machine-challenging format, then a rube goldberg machine to reverse the transformation, it's not right.

Anyway I mention this because there seems to be a thought of "these pdfs are messy lets clean them" without looking at what's really going on here.

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