commit e310963b5fe3291d89af7fb3fe4c9926c7bd7a85
parent 34dc579e867c937baeed32cad2e4fbe12b1f86fc
Author: Beau <cbeauhilton@gmail.com>
Date: Thu, 29 Dec 2022 00:25:09 -0600
add some posts
Diffstat:
4 files changed, 223 insertions(+), 0 deletions(-)
diff --git a/index.json b/index.json
@@ -1,5 +1,25 @@
[
{
+ "url": "/posts/medical-humanities-org",
+ "page_file": "site/posts/medical-humanities-org.md",
+ "nav_path": [
+ "posts"
+ ],
+ "excerpt": "About making the med hum website.",
+ "date": "2023-01-22",
+ "title": "<a href=\"https://medical-humanities.org\">medical-humanities.org</a>"
+ },
+ {
+ "url": "/posts/vimbook-org",
+ "page_file": "site/posts/vimbook-org.md",
+ "nav_path": [
+ "posts"
+ ],
+ "excerpt": "About making the Vimbook.",
+ "date": "2023-01-22",
+ "title": "vimbook"
+ },
+ {
"url": "/posts/thanks",
"page_file": "site/posts/thanks.md",
"nav_path": [
diff --git a/site/posts/medical-humanities-org.md b/site/posts/medical-humanities-org.md
@@ -0,0 +1,72 @@
+# [medical-humanities.org](https://medical-humanities.org)
+
+This post is a work in progress.
+
+<time id="post-date">2023-01-22</time>
+
+<p id="post-excerpt">
+I made a static website as an electronic learning system and forum,
+with the option for password protected posts and a controlled editing workflow,
+for free and without a dedicated server. This post has the highlights.
+</p>
+
+
+## First, free as in beer
+
+
+New educational endeavors are, in my experience anyway,
+almost always bootstrapped.
+They start with an idea, passion, even erudition,
+but rarely with money.
+
+This was no different.
+
+There's some funding coming in,
+including some I'm grateful for as it will recompense
+the time I spent building the website,
+but overall this thing needs to run for free.
+
+Because of that, I used the best suite of free tools I know of:
+GitHub, GitHub Actions, Netlify's free tier, NetlifyCMS, Hugo, and digital elbow grease.
+
+
+## Second, free as in freedom (of speech, and the ability to choose what to share on the open web)
+
+
+While we have a strict policy against violating HIPAA,
+we also want an open forum that can be honest,
+vulnerable, critical if need be.
+
+Though the students are encouraged to make their writing available for all to read,
+forming a kind of living magazine from the assignments,
+we also want to make it very easy to keep the assignments
+just within the group if desired.
+
+This combination of desired features led to a need for selective password protection
+of certain pages, opted into or out of by each student writer.
+
+Usually, password protection on a website is akin to a lock on a door,
+beyond which is a table that has the stuff you want to read.
+The routes to sensitive data are locked by the server,
+you need the key to get into the room,
+but once you get in the room you are free to wander over to the table and leaf through the dusty stack of papers.
+Since I'm not paying for a server I fully control,
+this approach is not going to work.
+Every route is accessible by the whole internet,
+every door is open.
+So, instead of worrying about a door and a lock,
+we trade the dusty stack of papers for a Rubix cube with a million facets,
+containing a message that only comes to light when you match up all the pieces.
+Anybody can come and check out the toy,
+but unless you know the secret to solving it,
+it's just a jumble.
+
+To build the Rubix cube I used [Pagecrypt](https://github.com/Greenheart/pagecrypt),
+which encrypts individual HTML pages and provides a dialogue to enter a password to decrypt it.
+To mark which pages should be encrypted,
+I used a simple front-matter key, which a `grep` command picks out on every site rebuild.
+
+Another neat aspect of this is that the *entire* page is encrypted,
+even the comments section, so if a student wants to make a post somewhat private
+and have a personal conversation with the other members of the class,
+it's comfortably hidden from the view of the public internet.
diff --git a/site/posts/oo-et-al.md b/site/posts/oo-et-al.md
@@ -0,0 +1,123 @@
+# good machine learning in medicine
+
+<time id="post-date">2022-12-29</time>
+
+<p id="post-excerpt">
+Because most machine learning in medicine sucks, I thought you might like to see an example of it done well.
+</p>
+
+<https://doi.org/10.1056/CAT.22.0214>
+
+At least on the surface, this looks good.
+The article is paywalled so I haven't gotten to dig into their methods yet,
+but will update when I am able to read the whole thing.
+The approach is the thing I'm keyed in on -
+implementation details of course matter,
+but the biggest problem with machine learning in medicine is not technique, but angle.
+Too often, ML is a new shiny,
+no meat on its bones
+(I'm not discounting some of the delightful advances in e.g. automatic read of ophthalmologic images,
+that's kickass tech and truly practice-changing,
+but it does amount to image processing.
+The stuff I'm talking about here is not a smarter camera,
+but automated gestalt handed to you by a mechanical Turk).
+
+
+## ML is mostly for automation, but automating medicine is scary
+
+
+The big idea is that
+while machine learning is great for many things,
+the most important thing in industrial machine learning is
+teaching a machine to make independent decisions
+to make things easier for humans who already have too much cognitive load,
+or not enough hands,
+and a pesky attachment to oxygen, food, and sleep.
+E.g. if there's a knob someone needs to turn when a certain complex set of things happens,
+and sometimes the human forgets because they were occupied with all the switches and buttons instead,
+or they were on lunch,
+or sleeping off the Superbowl party,
+it sure would be nice to make an algorithm
+that can independently assess whether the complex condition has been sufficiently met,
+and go ahead and turn the knob for you
+(and maybe, while it's at it, get you a few ibuprofen for that hangover headache).
+
+In medicine we usually don't want a bot making independent decisions,
+but this paper from UPMC is a great example of the kind of independent decision we could stomach, or even welcome.
+
+
+## build a model that is high-yield and low-risk
+
+
+This system builds a mortality model, which is fun in itself, but then goes to the next level to automate an e-consult to the palliative care team for patients at highest risk of mortality after discharge.
+
+(Avati et al did the same basic thing at Stanford using a neural network,
+which is a fine technology,
+but their explanatory models were these shitty,
+ugly text-based tables that make you want to stab yourself in the eyes - <https://doi.org/10.1186%2Fs12911-018-0677-8>).
+
+It's beautiful.
+Nothing bad bubbles up if the algorithm falls down altogether (we're just back where we were before the model went live).
+Nothing horrible happens if the algorithm makes a weird claim (every consult will still be triaged through a human).
+Possible positives are numerous.
+The conversation itself may be one of the most pivotal in the patient's end-of-life journey,
+the hospital system will likely have reduced readmissions for cases that should be managed at home with hospice,
+and we will have more data to put towards figuring out how to identify the modifiable risk factors for early post-discharge death.
+
+This team used the same tech I did when I built a mortality model for CCF,
+my favorite kind of algorithm,
+tree-based models called gradient-boosting machines (GBMs).
+
+
+## interpretability - gotta do it, maybe they did
+
+
+What I can't see yet is if they took the next obvious step,
+which is to apply interpretability models on top.
+The main reason to use a GBM,
+in my mind, other than they're fast to train compared to neural networks
+and perform the same if there's enough data and you tune them properly,
+is that they're inherently compatible with the best meta-models that allow you to interrogate,
+both on a per-prediction and cohort level,
+why the model is saying whatever it's saying -
+they're actually less of a black box than many standard statistical models,
+believe it or not.
+
+The best tool for doing this is called SHAP,
+and the output is gorgeous - [check it out](https://shap.readthedocs.io/en/latest/example_notebooks/overviews/An%20introduction%20to%20explainable%20AI%20with%20Shapley%20values.html).
+We used it here,
+I think to lovely effect:
+<https://www.nature.com/articles/s41746-020-0249-z>,
+and it's only gotten better since then)
+
+The other thing I love about pairing the interpretability models
+with the predictive models
+is now you have something you can really learn from, and, hence, teach from.
+
+
+## but, will this worsen burnout?
+
+
+The main issue, (given that the model works and has been proven trustworthy)
+and which I don't think I've heard anyone talk about in great depth,
+is the new alert fatigue this kind of system would make,
+for already overworked palliative care teams,
+and what mitigations they are taking to keep the firehose of new possible consults manageable.
+One thing we could do,
+and I have faith our house staff could do it well,
+would be to implement the same system and have it first trigger an alert to the primary team,
+with a recommendation to have the convo and reach out to pall care if there is any hint of a loose end,
+or an automated pivot to pall care if the notes don't document GOC within a certain number of days of the alert
+(or could pop up one of those boxes we love so fucking much with a radio button asking you if you've had "the talk" yet).
+
+Anywho,
+I'm not saying I want to actually do this project,
+I've got other stuff going on,
+but if you're reading this you're the kind of person who is interested in what tech can do for a hospital system,
+and this is a model combination of the very cutting edge of tech
+and the oldest technique we have,
+which is to offer a hand to the dying and with them face the abyss.
+My vision of the future is less Skynet, cold and isolated,
+but rather humans forefront,
+with machines that run in the background to nudge us into and help make room for more
+(non-digital, non-Apple mediated) facetime.
diff --git a/site/posts/vimbook-org.md b/site/posts/vimbook-org.md
@@ -0,0 +1,8 @@
+# vimbook
+
+<time id="post-date">2023-01-22</time>
+
+<p id="post-excerpt">
+About making the Vimbook.
+</p>
+
