sneak preview

blah blah background

mac defaults to zsh, but i resisted changing over right away.

i had a nice dotfiles automation set up (with my terminal timers complete with a custom fun sound when the timer went off). using (someone else’s script) I could clone my dotfiles repo, run a single shell command, and have all my nice terminal customizations.

plus, i had a nice cat.

well, i have not used tt in a while anyway (i really miss working in linux — once i make a bit more, we’re going back to linux haha. though it’s neat the some of the LLMs can run on mac silicon) since it works so-so on my current macbook — mostly, on macbook you can’t force the terminal to stay on top so the timer gets buried anyway.

I also was really happy with autojump. but I had seen brief glimpses of my friends using zsh and it seemed to have really nice tab-completion.

so, zsh time it is!

okay i’m too lazy to write a true write up so i’ll just document what i did for my own reference.

install oh-my-zsh

i’m not sure why oh-my-zsh, but it seems nice. i think it includes a lot of powerful plugins (downloads and lets you one-line activate them).

https://ohmyz.sh

sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)"

out of the bat — git aliases!

i had that in my bashrc manually, but in oh-my-zsh there’s a one-liner.

alias ga='git add'

and already we can see in ~/.zshrc  that we can do

plugins=(git)

and these aliases are included  in oh-my-zsh with that one line!

other oh-my-zsh plugins i enabled:

plugins=(git gitignore 
magic-enter 
colorize 
colored-man-pages 
python 
) 

and then let’s overwrite that (rip) — use random stranger’s plugin pack

okay but i was missing my autojump, and i realized that there are still some manual steps to install extra fancy plugins. i didn’t want to do some comprehensive understanding of competion, tab completion, autocompletion of commands vs files vs folders, frequency-based or history, etc. i just wanted someone to pick a few. and all the different themes, wow.

hence then I used

https://github.com/gustavohellwig/gh-zsh

which includes zsh-completions and zsh-autosuggestions which are not in oh-my-zsh. (completions is in oh-my-zsh).

sudo curl -fsSL https://raw.githubusercontent.com/gustavohellwig/gh-zsh/main/gh-zsh.sh | bash

powerlevel10k — no need for other themes

most importantly, it includes a customizable theme called powerlevel10k. This actually walks you through creating a custom prompt  in detail — everything from what information you want on the right or left, do you want a timestamp (if so in what format), do you want minimalist or maximalist (with all the icons! and colored backgrounds!), if you want a two line prompt or not, how many colors you want, etc.

it was really cool actually!

p10k configure

after all that I ended up with

╭─ ~/Documents/projects/python_fun on main ········· at 22:48:40
╰─❯ 

okay but we need cats: editing the p10k prompt

very importantly, i then spent a while figuring out how to add a cat back into my prompt.

thus

vi ~/.p10k.zsh

it turns out an example of adding to the prompt is given in this line, so lets uncomment it

typeset -g POWERLEVEL9K_RIGHT_PROMPT_ELEMENTS=( 
[...]
example     # example user-defined segment (see prompt_example function below)

way far down we can define it

 # Example of a user-defined prompt segment. Function prompt_example will be called on every 
# prompt if `example` prompt segment is added to POWERLEVEL9K_LEFT_PROMPT_ELEMENTS or # POWERLEVEL9K_RIGHT_PROMPT_ELEMENTS. It displays an icon and orange text greeting th e user. 
# 
# Type `p10k help segment` for documentation and a more sophisticated example. 
function prompt_example() { 
# p10k segment -f 208 -i '⭐' -t 'hello, %n' 
p10k segment -f 208 -i '<hi>' -t 'ฅ^•ﻌ•^ฅ' 
} 

So I put in a cat!  hurray! now on the right hand side my cat friend is back 🙂

this is what the cat looks like

 

╭─ ~/Documents/projects/python_fun on main ········ at 22:58:03
╰─❯ <hi> ฅ^•ﻌ•^ฅ

image: even when my friends are asleep … terminal cat keeps me company

(the <hi>  reminds me of old-school chat logs)

fix the python virtualenvironment display

okay, but what is up with the weird python enviroment display?

╭─ Py py311 ~/Documents/projects/python_fun on main 

There’s a random “Py” and the environment name is sort of just thrown in there, grr.

First off, I moved it from the right to the left prompt. It’s the virtualenv  not pyenv for reasons i don’t know yet.

typeset -g POWERLEVEL9K_LEFT_PROMPT_ELEMENTS=(
    virtualenv
    [...]
)

Then I set delimiters around the environment name

 typeset -g POWERLEVEL9K_VIRTUALENV_LEFT_DELIMITER='('
typeset -g POWERLEVEL9K_VIRTUALENV_RIGHT_DELIMITER=')' 

I also think it’s handy to have the actual python version, so I’ll try it out, but instead of the “Py” which is super random I’ll use a snake instead.

typeset -g POWERLEVEL9K_VIRTUALENV_SHOW_PYTHON_VERSION=true 
typeset -g POWERLEVEL9K_VIRTUALENV_VISUAL_IDENTIFIER_EXPANSION='🐍

hurray!

there we have it — a zsh prompt I enjoy 🙂

At first I missed autojump, but after typing a few commands in manually, the completion has been great. Very pleased. will report more later (and I can always install autocomplete).

add oh-my-zsh plugins back

oh right — p10k overwrites your zsh, so we have to add them back in.

╰─❯ vi ~/.zshrc
export ZSH="$HOME/.oh-my-zsh" 

[...] 

plugins=(git gitignore 
magic-enter 
colorize 
colored-man-pages 
python 
) 

MAGIC_ENTER_GIT_COMMAND='git status -sb .' 
MAGIC_ENTER_OTHER_COMMAND='ls -la .' 
source $ZSH/oh-my-zsh.sh 

explanation of magic-enter plugin config

so basically when you hit enter on an empty line, zsh will automatically put in this command depending on if you’re in or out of a git directory. (either git status or ls -la)

change git icons to be fancier

okay, this is just because I was really confused to have a ?1 in my prompt and i find it funny that the comment mentions exactly this. in ~/.p10k.sh

 # Branch icon. Set this parameter to '\UE0A0 ' for the popular Powerline branch icon.
# typeset -g POWERLEVEL9K_VCS_BRANCH_ICON= 
typeset -g POWERLEVEL9K_VCS_BRANCH_ICON='\UE0A0 '

# Untracked files icon. It's really a question mark, your font isn't broken.
# Change the value of this parameter to show a different icon. 
# typeset -g POWERLEVEL9K_VCS_UNTRACKED_ICON='?' 
typeset -g POWERLEVEL9K_VCS_UNTRACKED_ICON='…'

all together now

this is the final result (for now)

note that there is an alias of “..” to “cd ..”,  which seems nice. Also, the very last line you c an see how nice the autocompletion is — I only have to type sou and i can tab complete the entire line.

random bugfix: locale

 I did change “C” to “en” in the following variables to fix an issue with showing examples for bash commands, where I would get a random text “failed to set default locale”.

here’s what i mean by showing examples, I can just type “tar” and hit tab and get this:

specifically I changed in my ~/.zshrc:

export LANG="en_US.UTF-8" 
export LC_ALL="en_US.UTF-8" 

bonus: fancy-looking font: fira-code

someone in my past was very excited about ligatures and fancy fonts for coding. most specifically, this font turns !=  into what looks more like ≠while you are typing !

 brew install font-fira-code

well, i don’t think that worked; in the end i downloaded the zip and unziped and opened the fonts.

then i went into terminal settings and set it to use font-fira 🙂

here are some examples of what it looks like. this is what i actually typed

╰─❯ echo 'Example fira-code ! and = is != , > and = >=, = = == => = and = ==, 0 o O lL1

and it shows up like so
here is a video of how the ligatures are rendered on the fly:

 

 

all together now

for reference:

.zshrc

export ZSH="$HOME/.oh-my-zsh" 

[...] 

plugins=(git gitignore 
magic-enter 
colorize 
colored-man-pages 
python 
) 

export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8" 

MAGIC_ENTER_GIT_COMMAND='git status -sb .' 
MAGIC_ENTER_OTHER_COMMAND='ls -la .' 
source $ZSH/oh-my-zsh.sh 

and  edits to .p10k.zsh

typeset -g POWERLEVEL9K_LEFT_PROMPT_ELEMENTS=(
    virtualenv
    [...]
)

typeset -g POWERLEVEL9K_RIGHT_PROMPT_ELEMENTS=( 
    [...]
    example
)
function prompt_example() { 
    p10k segment -f 208 -i '<hi>' -t 'ฅ^•ﻌ•^ฅ' 
} 

typeset -g POWERLEVEL9K_VIRTUALENV_LEFT_DELIMITER='('
typeset -g POWERLEVEL9K_VIRTUALENV_RIGHT_DELIMITER=')' 

typeset -g POWERLEVEL9K_VIRTUALENV_SHOW_PYTHON_VERSION=true 
typeset -g POWERLEVEL9K_VIRTUALENV_VISUAL_IDENTIFIER_EXPANSION='🐍

typeset -g POWERLEVEL9K_VCS_BRANCH_ICON='\UE0A0 '

hurray!

oracle

i started off with oracle session as i hadn’t really attended industry panels. i enjoyed some of the acronyms, like “stormed and normed.” also, the idea that oracle as a big company was late to the cloud / others had years ahead, so to catch up they hire the eng that build other clouds and ask for better faster cheaper. (?!)

from words to wonder

i dropped by there – so it appears that for some tasks fine-tuned bert is still performing better even than latest llm on token-level NER vs. document level NER (not entirely sure what this means). this makes sense since llm is trained for causal prediction (next token) vs . embeddings may have more sense of individual words (bidirectional) and may be better suited for such classifciation tasks. i found it interesting that they point out limitations that there are other ways to instruct llms – for my own research i found it difficult to figure out how many prompts i should use to feel confident in my results. i guess … just one lol

food entities

this paper looked more at zero shot and one shot for identifying food entities from patient generated data. chatgpt performed a lot better than rule-based systems trained on fairly clean data, since it could handle stuff like “bbq” for barbecue and “happy meal” for mcdonalds. the research was excited that we can now use more varied data without tailoring algorithms across datasets.

bioner

i finally got an order of magnitude sense, the presenter said that fine tuning the llm directly took around 30 mins on 4x A100 18 GB gpus. but other methods include llora and parameter efficient fine tuning (peft). interesting point to just say that there was not statistically significance for some of comparisions

nih common data element normalization

again emphasis that ensemble methods perform better. i guess this is true for humans too!

nabla

i also went to Q&A part of nabla, it was cool to sit in a room of practicing clinicians vs. rooms of fellow researchers that are slightly adjacent to my work. (i also miss the extremely technical nerds sometimes). i created a mastodon account (to use every half year or so between conferences? next time i’ll add it to my badge):

TIL: paperwork burden big driver of provider burnout (!), and “Ambient AI” shortens from 90 mins to 30 mins = can go home and spend time with family in evening, can see more patients #amia2024 nrobot@mastodon.social

https://mastodon.social/@nrobot/113467025691843019

i had no idea that the paperwork was so severe that it actually drives burnout. but it makes sense if it’s taking an extra 1.5 hrs of your life after work to catch up on all the paperwork !!

also this interesting quote “gen AI scribing [note to summary] is like ice cream — there’s some people who like it, but not many!”

WIG NLP

then i learned a bit about working groups, still not entirely sure what they are, but i have to be an AMIA member to access anyway (vs just attending the conference). they were trying to set up a mentor / mentee network but kind of struggling. in general i’ve noticed there’s less willingness to randomly connect and mentor than i expect. especially i heard fabled west coast startups willingness to help each other out. maybe it’s that there are many high level industry execs here.

yale – emulated clinical trial

trying to find cohort retrospectively — realized the biggest issue (spent years) is the messiness of the data. normal clinical trial is 100% accurate. if you have 6 parameters that have to be pulled out with nlp, and the current state of art is 80-90% accuracy, that comes down to 30-50% accuracy which is unacceptable for running an emulated clinical trial.

generally

i’ve heard a lot about how finding patients (and others aspects) of clinical trials are slowing down research in a major way. so there’s a ton of research into how to address this.

posters

then i caught up with my coworkers posters! since i have most reference on this i’ll post more later. basically presenting on the system side of a pilot to rank patients for screening, anecdotal catching patient with cancer that wouldn’t have been caught by old system. rolling out pilot to 28 hospitals soon. the clinicians present on the outcomes side of impact on patients, vs the informatics group presenting on rapid system roll-out

here i’ve started talking to random posters and connecting with people. i think i was just talking to people that were too busy / high level before. humbling for sure, and also confusing coming from socializing in startup circles i guess as i never integrated well into higher education :'(

TIL: paperwork burden big driver of provider burnout (!), and “Ambient AI” shortens from 90 mins to 30 mins = can go home and spend time with family in evening, can see more patients

generally

the nicest seminar was still the keynote on sunday, not sure if that’s because i’m flitting in and out of sessions instead of sticking in one session and talking to people

i skipped out on an entire half session, just went to sit and read a book. the sensory room is just a small conference room set on a different floor, but it was chairs at tables, no comfy couches, so i went to the lobby and sat in a comfy couch instead and put in headphones. actually that place was incredibly loud but it worked haha

dei event

i would not have gone on my own, at this conference i feel like not-minority lmao. but i went with my coworkers and the industry sponsor provided good food. at first it was just a few people and we stood by ourselves, but the chair / co-chair came to talk to us, and by the time that finished the room was incredibly full. i was really impressed by one of them who could tell that ray and rui are pronounced differently (rui has the tongue further back), legit thought he did linguistics. he connected it to christian beliefs which i found interesting, that the lord knew our true name before we were born, so really pronouncing names is important to him. i didn’t connect with anyone new (too burnt out) but i reconnected with folks from WINE.

career talk

i talked to one person about my life goals, and that was a good talk. i should likely not treat my supervisor as anything adversarial. i admit that it threw me off for him to say that i would be working under my coworker so that was the more important opinion for performance evals. and it has made me mrrr to hear that i should be doing the work of the position i want when i am being paid half the cost of that position to do that much work. but i do not think my supervisor meant to imply i would be working under my coworker no matter what.

VA event

there was also a VA event that we dropped by, but everyone there was super tired so we talked to one group of people and left. i again felt some regional politics at play slightly.

personal

okay, i feel like i’m totally at failing at connecting with people, but have to remind myself i’m like … 2 days into getting to know people here. and two months into having some new blurb to write about myself.

it’s been incredibly relaxing even if possibly fool hardy to not go around the exhibition hall trying to connect with companies.

also there is so much i need to learn, that i can feel free to list now that i have a job and a foot in the door (and emotional reserves). likert, rouge, llora, spearman, these are all terms i need to learn. maybe i’ll install chat on my phone just so i can learn those in the moment as i’m motivated and there’s context for how it’s used …

prior self

i can see how i must have come across to people before i got a job now. just kind of emotionally disconnected from everyone else, not wanting people’s pity and knowing they can’t help right away, and feeling so hopelessly caught up in my own life issues. i keep trying to remind myself. one day when i struggle to go to the bathroom on my own i’ll look back on this time in my life and be like “wow that was such a good time.”

or maybe i’ll get cancer earlier and just wish i had such normal problems where i thought i would live to old age. i’ll miss the time when i could still just call my parents and they didn’t have major health problems and i still had hope for them to live to 120. who knows, who knows.

general state of the world

i feel surprisingly detached from all my anger and fear about the elections in the united states. it barely takes up 1% of my mental headspace. it’s like 50% industry career new job, 30% technical skills worry, 15% relationships, 4% excitement about extremely random stuff on my backburner, 1% state of domestic and international world affairs / bitterness (how could we have someone who molests women as our president? and millions of people turned out to vote for him? i feel such shame and horror and despair and hopelessness that kamala harris is not our next president. all my degrees and accomplishments feel utterly useless. i feel so angry, so angry at anyone in my life that doesn’t hate trump. but remember — the world is not ending today or tomorrow, my friends can ally with me on other things, and my life will be okay).

high level planner

i’ve been trying to move in the opposite direction of my natural instincts. if i’m drawn to the climate and diversity and equity talks, i’ve been forcing myself to go in more purely technical directions. i would like to find my own pure happiness in technical implementation for the next few years independent of the impact. of course, from my perspective any work i do on AI is work I’m not doing on equity in AI and contributing to climate change in data centers. i’m not living up to my principles and the emotional energy i directed at it. but reminding myself that the alternate pathway is: get rich, make changes, donate to causes and empower others to work on these topics. i feel after my thesis on illicit massage industry and the energy i put into supporting my ex partner, it’s time to focus on just me. and nothing has to be permanent. it’s like i constantly have a higher-level planner — what should i be spending my time thinking about? usually the answer is, not what i’m thinking about right now. and it’s important but hopefully i can start tuning it down some day soon. i want to be thinking about interesting technical papers, where the field is going, cool packages i learned about recently, learning about monads and the latest bug in some code i wrote. hopefully next week i can finally start doing that.

my brain is totally fried

right, saturday was workshops were i was upskilling and connecting with people on linkedin and sort of my coworkers

sunday — when i really started to dive into informatics. sunday was infinitely more exhausting, just way more people. interesting thoughts but no one to talk to about them, not possible to go to all the sessions. but i did learn yesterday (saturday at WINE, the women .. informatics… networking thing) you can swap between sessions during paper presentations, so i marked mine out carefully and have been going in and out of sessions.

sunday morning

morning i went to sessions on social media research. as usual i was late, insomnia and turning off my alarm and i find it really hard to stop ironing once i start but i’m also bad at it. but it was freeing that no one knowed or cared if i showed up on time, since my lab group went to alcatraz without me … first half of workshop was a bunch of paper presentations. afterward was group discussion. and at the end there was coffee break, so you could stick around and talk to people.

i learned through brief chat after: best practice is to contact a forum moderator and explain what research you want to do. if they don’t respond, tell university irb. university irb will likely say exempt since it’s social media research. prior big discussion on whether this is reasonable, observation that junior faculty are encouraged to use social media if irb approvals taking too long. note that irbs are overworked, so either have inter-institutional irb focused on this, or perhaps have subject matter experts to call in on these topics. dataset release: also occurs, and just run an off-the-shelf name stripper. (i stressed that names will slip through, but i guess… it’s… fine?)

i went over my idea of how to flip the legal power dynamic: companies agree to users’ privacy policy when we agree to theirs. incentive: perhaps just that

keynote

the keynote in the early afternoon was a really good crash course on theoretical ethics. no longer felt so obscure and hard to understand. i should start watching more talks.

–> differential privacy — the simplest example is randomized response. for a survey about behavior people might lie about, e,g, their social distancing habits, we can give people plausible deniability. tell them to flip a coin, if it’s heads tell the truth, if it’s tails, flip the coin again: if it’s heads, tell the truth, if it’s tails, tell the predetermined response. that default response is yes to illegal behavior, so you have plausible deniability. on the individual level, who knows; at the aggregate level, you can work out mathematically an estimate of the truth.

i’d heard of this technique long ago, but never realized it counted as a differential privacy algorithm.

throw money at it, aka bug bounties, and concatenate models for more accuracy without less fairness

bounty a: find subgroup with different outcomes. bounty b: if not only subgroup where outcomes different for current model, but also find model with optimal performance on that subgroup;

then you can just concatenate models! and don’t have to trade fairness with accuracy — strict (theoretically proven) increase in accuracy. if it’s in subgroup z then use model B, otherwise use model A. downside: do not know full model complexity ahead of time so risk overfitting.

bug bounties in traditional security: avoid adversarial interaction (propublica, facebook, compas) and shift to more collaborative interaction.

(will insert rest of summary of talk tomorrow)

sunday afternoon

i flitted between sessions.

demos: people’s screens were illegibly tiny, and i couldn’t get my camera to zoom enough. next time i’m bringing binoculars or a phone camera binocular attachment. one presentation was mostly a webapp llm, but the enthusiasm was catchy. (the topic was connecting pregnant women to sources of info). little practical tidbits, like they tried conversation history but the llm tended to stop referring to primary srcs and start reflecting user inaccuracies. makes sense since the user input will be the most recent input. the other was a recommendation for LLM engineers handbook. also, models can run on laptops (macbook m series i’m guessing?).

-> lost-in-the-middle: issue with RAG where references at the beginning (ranked relevant) and end (due to how llms are trained to predict next token) are highly rated but ones in the middle are ignored.

epic: packed. the ten minutes i heard were a lot of “physicians hate changes usually but they actually sometimes liked this!” a lot of focus on a. we have so many users! and b. they’re happy with us! and not a lot of mention of hallucinations and integrity checking. i will have to find someone who went to the epic session to debrief me. otherwise, it matched my fears of industry: focused on putting gen AI in everything regardless of if reasonable or not and not really caring about unknown bugs.

~ epic: my own thoughts on ethics: i find there are multiple “choice” frames to approach this from. one: if it makes care 1% better for 1000 patients and 50% worse for one patient, is it worth it? two: if taking an extra month to implement some quality assurance avoids that one bad outcome, is the extra month worth it? three: what if it means we can provide care for one person we couldn’t see at all before due to lack of physician time? etc.

JAMA: i learned that physicians are exhausted and frankly rather scared of how AI is taking over. the FDA has approved over a thousand devices with AI components the past year. there is work on a podcast to explain recent research to physicians.

JAMA – methods move fast: if used same methods as five years ago in a paper submitted today, paper would be returned with tons of methods critiques

child maltreatment public (state-level) policy analysis: how different state laws correlated with different pediatric outcomes.

used LLMs to summarize a bunch of public policies. does maltreatment definition include physical abuse? is reporting centralized or not (hotline)? then factor analysis to find factors to make cohorts (find underlying patterns in policies): mandated reporter? reporter training? then cluster around to find specific factor combinations (few/moderate/high levels of training, or penalties, etc.). then look at outcome differences. (will insert screenshots later)

policy -> difference-in-difference: check if results still hold between 2019 and 2021 when policies were in-place and not-in-place.

dinner / expo

they have free headshots! i desperately need one, but [tmi] i have a giant pimple right now :'( maybe that’s what AI is for lol. the expo … somehow i was completely uninterested. i think i felt rejected by my coworkers. i called a friend for moral support lol

personal thoughts

overall the conference is more diverse than i expected (which isn’t saying that much though tbh). i wonder how the stats compare to IROS/RSS/ICRA.

i need to remind myself i’m utterly new to this field and i’m not here presenting a paper or poster. of course, i will have to work harder to connect technically with people, and surface a whole different set of my interests than i usually nerd out about. people here are not excited about welding robots or maker faire or engineering education. nor are they nerding out about the latest theoretical advances and architectures and benchmark leaderboards. people here talk about weird interesting healthcare things.

i’ve only officially been to robotics conferences as a presenter

so there’s multiple factors at play here for my social sore thumb feeling.

mostly, i was really surprised when a fellow attendee who also went to the boston VA for many years declined to connect on linkedin. but i guess we exchanged conference app qr codes? in any case – the main thing i learned talking to her is that there a huge disparity in resources in regional VAs. i thought it was a national organization but apparently not. we in boston have the resources to figure out how to get at data sets but researchers in other VA regional sites do not. even though the data sets are VA datasets! at least, this was her experience a decade ago. also, generally feeling a bit surprised that my coworkers are not meeting up between sessions and discussing topics in real time constantly. i guess we are not really in the same lab. i gave up on organizing meals with my labmates and just messaged randomly people (around my career level) to find someone to go to dinner with. a person from WINE invited me to a dinner with a bunch of student volunteers for the conference. note: if you join the working group, there’s a chance you can be invited to volunteer for the conference and the registration fee is waived. (but travel, hotel, food not covered).

people expect postdocs to have a research idea and focus, so i need a different self-intro hook.

that makes sense. i’m not really working with a professor directly on a specific idea. as a result of my lack of topic, i need a different self blurb than “i do data science at the VA.” i think the only thing i’ve done of interest to folks is my thesis research topic.

alternatively, i could just not talk to anyone and do my own work. but oh, i felt a bit sad to not have people to compare notes with after the sessions. i really wanted those interesting and thought-provoking technical conversations i would have late at night in undergrad. (i never really got that in grad school except for classes, not research). i really did yesterday. but y’know, this is like one day into the field for me depending on how you count lol

grad school – i wish that after leave of absence they’d invested in my success instead of throwing me in and asking me to perform better than other people with a handicap already. i learned so much in so little time from this conference ! !

i guess for many of the older/senior folks, AMIA is like putzgiving, where people fly in every year and it’s a reunion.