davidshapiro_youtube_transcripts
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Automating Science with GPT4 attempting and failing to perform autonomous literature review_transcript.csv
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what is up everyone David Shapiro here,0.359,8.16 | |
and we are working on science,4.2,7.68 | |
okay so where we left off what I was,8.519,6.921 | |
working on was my um,11.88,6.06 | |
basically automating science and a lot,15.44,4.48 | |
of you have have pointed out that like,17.94,3.9 | |
you would prefer that I keep working on,19.92,4.019 | |
autonomous cognitive entities and Raven,21.84,4.199 | |
and stuff like that but what I wanted to,23.939,3.84 | |
say is that I'm working with some really,26.039,4.441 | |
like the world leaders in cognitive,27.779,4.32 | |
architecture at least the ones that are,30.48,4.44 | |
not already in Academia and,32.099,5.401 | |
um in in inside the establishment so,34.92,4.86 | |
those of us that are outside are working,37.5,5.18 | |
together and so we'll have some,39.78,6.54 | |
demonstrations in the coming weeks and,42.68,5.08 | |
the stuff that these guys are working on,46.32,4.559 | |
the level of autonomy that these,47.76,6.18 | |
machines have is incredible,50.879,5.041 | |
um so with that being said I am moving,53.94,5.939 | |
on to science and the reason is,55.92,7.439 | |
um one I have an ability to make sign uh,59.879,5.521 | |
make this stuff more accessible and I,63.359,3.661 | |
get so many messages from people that,65.4,3.539 | |
like either have never coded or haven't,67.02,4.62 | |
coded in many years who are inspired by,68.939,5.521 | |
my work to get back in and like the more,71.64,4.74 | |
people we we have participating in,74.46,4.019 | |
artificial intelligence and science the,76.38,3.419 | |
better,78.479,3.601 | |
um yeah so that that's that so that's,79.799,4.32 | |
that's my mission now,82.08,5.96 | |
um with that being said I wanted to,84.119,6.481 | |
revisit this idea of regenerative,88.04,4.66 | |
medicine because that's important to me,90.6,3.42 | |
etc etc,92.7,5.64 | |
so uh last time I I what we did was we,94.02,6.959 | |
found some sources so we've got the the,98.34,4.56 | |
open Journal of regenerative medicine,100.979,5.161 | |
we've got bio archive and then the,102.9,6.6 | |
regenerative medicine topic on on nature,106.14,5.82 | |
that's still really broad,109.5,4.74 | |
um because like let's say you're you're,111.96,4.92 | |
an orthopedic surgeon who focuses on,114.24,4.68 | |
shoulders or you know cervical joints or,116.88,2.879 | |
whatever,118.92,3.42 | |
uh or a researcher who has a particular,119.759,4.621 | |
body part that you're focusing on you're,122.34,3.36 | |
going to want to perform a literature,124.38,2.82 | |
review that's a little bit more narrow,125.7,4.02 | |
so what I started doing was looking for,127.2,4.32 | |
data sources that were going to be a,129.72,3.659 | |
little bit more specific to what we want,131.52,4.799 | |
now I also got access to Bard,133.379,5.58 | |
and I gave Bard and Bing the same exact,136.319,4.621 | |
thing and Bing was just like okay yeah,138.959,3.721 | |
here's here's a few here's a few,140.94,3.9 | |
examples and uh the one that it gave,142.68,3.6 | |
here,144.84,4.92 | |
um was directly relevant and it was,146.28,6.0 | |
um it's over a year old but still,149.76,4.32 | |
um or not over a year old it's about six,152.28,3.0 | |
months old,154.08,3.9 | |
um still not bad and then I asked,155.28,4.44 | |
I asked Barton it's like I can't help,157.98,4.02 | |
what that is I'm only a language model,159.72,5.7 | |
um can you search the internet,162.0,6.3 | |
uh like aren't you a search engine now,165.42,5.76 | |
Bard is still in beta so yes,168.3,4.62 | |
um,171.18,5.72 | |
okay it looks like it doesn't even have,172.92,3.98 | |
yeah it's this is this is like super,176.94,6.18 | |
super basic okay so Bart is not useful,179.58,6.36 | |
um now that being said uh I did find a,183.12,5.1 | |
few things for you know cartilage,185.94,4.079 | |
regeneration,188.22,4.2 | |
um Rehabilitation so this is all,190.019,6.121 | |
specific to shoulders and stem cells,192.42,6.0 | |
um under regenerative medicine if we go,196.14,4.2 | |
a little bit broader,198.42,4.14 | |
um we get up to actually I guess we,200.34,3.66 | |
still only get five results under the,202.56,3.48 | |
nature Journal of regenerative medicine,204.0,4.56 | |
which is fine uh bio archive gives us a,206.04,4.32 | |
little bit more under stem cell so,208.56,4.02 | |
basically the next step is I'm going to,210.36,5.04 | |
download and process some some uh papers,212.58,4.92 | |
that are specific to this and then I'll,215.4,4.02 | |
show you what happens next,217.5,5.04 | |
um basically I was chatting with some uh,219.42,5.58 | |
some of my friends and we were talking,222.54,6.119 | |
about how loquacious how verbose the,225.0,5.519 | |
models are and we're working on that,228.659,3.121 | |
concept of sparse priming,230.519,3.78 | |
representations and we came up with a,231.78,4.739 | |
conversational model that is also sparse,234.299,4.381 | |
and very concise and that is Morden,236.519,4.261 | |
Solas from Mass Effect so we're,238.68,4.5 | |
basically creating a modern Solis uh,240.78,4.86 | |
chatbot model and it's great it's also,243.18,3.66 | |
really hilarious so I'll show you that,245.64,3.36 | |
in just a moment but yeah we'll be right,246.84,3.72 | |
back,249.0,3.959 | |
okay I wanted to add a quick note I just,250.56,4.98 | |
found journals.sage Pub which has an,252.959,5.161 | |
open access feature and is actually,255.54,3.9 | |
pretty nice so I'm going to download a,258.12,3.06 | |
few more from here also I've got all the,259.44,3.539 | |
sources documented in the readme which I,261.18,3.72 | |
am working on updating so don't worry,262.979,3.961 | |
all of this will be documented,264.9,4.56 | |
um for ease of access all right be right,266.94,3.36 | |
back,269.46,2.94 | |
okay we're about ready to test here let,270.3,4.679 | |
me sit up actually okay,272.4,4.5 | |
um but yeah so here is the system,274.979,5.041 | |
message it doesn't work in 3.5 and,276.9,6.06 | |
that's not uh surprising because 3.5,280.02,4.8 | |
they even documented that it doesn't pay,282.96,4.56 | |
as much attention to the system message,284.82,4.14 | |
um but in this case I say I am more,287.52,3.179 | |
modern soul is scientist solarian,288.96,3.0 | |
currently performing literature review,290.699,3.541 | |
reading many papers taking notes as I go,291.96,4.56 | |
user assisting by submitting research,294.24,4.26 | |
pages incrementally will respond with,296.52,3.72 | |
Salient notes hypotheses possible,298.5,3.3 | |
research questions suspected gaps in,300.24,3.42 | |
scientific literature and so on whatever,301.8,3.42 | |
is most relevant important note,303.66,3.3 | |
responses will be recorded by user to,305.22,3.84 | |
review later responses must include,306.96,4.38 | |
sufficient context to understand goal,309.06,3.72 | |
always same Advanced science solve,311.34,2.7 | |
problems help people respond should,312.78,2.76 | |
follow same linguistic pattern focus on,314.04,3.0 | |
word economy convey much without,315.54,3.06 | |
Superfluous words avoid missing,317.04,3.9 | |
important details so here I've got just,318.6,3.92 | |
a random page,320.94,4.68 | |
from uh from one of the papers that I,322.52,5.56 | |
got and you can see that it the PDF,325.62,4.68 | |
scraping didn't really work because it's,328.08,4.679 | |
missing a lot of spaces so let me just,330.3,3.899 | |
show you how good this is it's a little,332.759,4.801 | |
bit slow because it's gpt4,334.199,7.161 | |
um but yeah so it fix it it,337.56,6.6 | |
fixes the spelling and stuff,341.36,5.38 | |
um and so on,344.16,5.52 | |
and it basically just um summarizing it,346.74,5.58 | |
as it goes let's see post-operative,349.68,4.739 | |
Rehabilitation and mobilization for four,352.32,4.46 | |
weeks,354.419,2.361 | |
so there you go not only is it not only,358.62,6.06 | |
is it re-summarizing it but it is um,361.56,6.66 | |
but it is it's uh like cleaning cleaning,364.68,4.62 | |
it up,368.22,3.84 | |
um and it's posing a research question,369.3,5.04 | |
so if we go back to the file and then,372.06,4.74 | |
add the next page,374.34,5.28 | |
to the chat,376.8,5.94 | |
um basically I'm having chat gpt4,379.62,7.46 | |
read it and restate it as it goes,382.74,6.84 | |
and it will accumulate more and more,387.08,4.059 | |
insights and what I'm going to do with,389.58,2.64 | |
the script and I'll show you the script,391.139,2.701 | |
in a second is actually record this,392.22,4.5 | |
output along alongside the pages but I'm,393.84,6.799 | |
showing you oh come on,396.72,3.919 | |
there we go statistical analysis,400.86,4.559 | |
performing SPS statistics,402.36,4.5 | |
um,405.419,3.12 | |
paired t-test,406.86,3.48 | |
Etc et cetera so you can see that it it,408.539,5.1 | |
goes uh pretty quickly results,410.34,5.639 | |
um basically restates the results uh,413.639,4.881 | |
pretty quickly,415.979,2.541 | |
um also nice and clean,419.699,3.021 | |
possible research questions factors,423.24,5.48 | |
there you go,426.0,2.72 | |
so there we have it it's ready to go now,429.24,6.36 | |
with 17 PA papers,432.539,5.88 | |
um and quite a bit of text,435.6,3.599 | |
um,438.419,2.701 | |
it's probably going to be prohibitively,439.199,4.22 | |
expensive yeah because you see this is,441.12,5.4 | |
uh two and a half million lines,443.419,3.881 | |
um,446.52,4.32 | |
of uh of text so I'm probably not going,447.3,6.06 | |
to have it read the entire thing,450.84,3.9 | |
um because this,453.36,3.38 | |
let me see how long this original one is,454.74,7.799 | |
2023.01 16 522 18v1,456.74,5.799 | |
so that was oh that was this one that,462.66,4.379 | |
I've Wait no that's the that's the Json,465.0,4.44 | |
I need the text,467.039,4.321 | |
um let's see,469.44,5.599 | |
121 kilobytes,471.36,3.679 | |
so the number of new pages that shows up,475.62,4.859 | |
here oh it's got it at the end so it's,477.78,4.38 | |
only 50 pages,480.479,2.94 | |
um so this will be a little bit,482.16,4.2 | |
expensive but we'll see also one thing,483.419,5.34 | |
that I can probably work to exclude is,486.36,4.44 | |
all the citations,488.759,3.961 | |
um but maybe that's not actually a bad,490.8,5.04 | |
bad thing to to include,492.72,4.86 | |
um but yes let's run the script let me,495.84,4.199 | |
show you the script real quick so read,497.58,4.98 | |
papers it's super straightforward I've,500.039,5.94 | |
got the same chat GPT completion we've,502.56,6.72 | |
got gpt4 I set the temperature to zero,505.979,4.321 | |
um,509.28,4.8 | |
it'll save it all out let's see and then,510.3,7.56 | |
here for file in an OS Lister papers,514.08,6.3 | |
underscore Json if file ends with Json,517.86,5.82 | |
file path join load the load the file,520.38,7.62 | |
and then four page in data Pages which,523.68,6.779 | |
is what you can see here so original,528.0,4.56 | |
file name pages and then there's the,530.459,3.961 | |
embedding page number in text so they,532.56,3.6 | |
are in order so basically it'll be,534.42,4.14 | |
reading each page one at a time and kind,536.16,5.52 | |
of thinking as it goes so this is a very,538.56,5.339 | |
simple cognitive cognitive architecture,541.68,5.4 | |
that will basically just pretend to be,543.899,5.88 | |
a research scientist reading papers as,547.08,5.52 | |
it goes kind of jotting down notes we,549.779,4.861 | |
could probably do a little bit more,552.6,5.22 | |
concise but it's doing a good job of,554.64,6.3 | |
summarizing the most Salient details,557.82,4.38 | |
um and that's probably as far as I'll,560.94,2.64 | |
get today,562.2,3.72 | |
and then it appends it all so on and so,563.58,5.04 | |
forth and then up here uh basically what,565.92,5.7 | |
I do is is I'll I'll try and and do the,568.62,5.76 | |
the output but if it if it is too long,571.62,5.219 | |
then I'll just remove the oldest message,574.38,6.0 | |
so let's see what happens with this,576.839,6.421 | |
um all right so clear screen zoom in a,580.38,6.0 | |
little so you can see it python step,583.26,5.1 | |
three read papers,586.38,4.32 | |
and let's see how it goes so because,588.36,3.9 | |
we're not I'm not using the streaming,590.7,3.24 | |
API we're only going to see the output,592.26,4.56 | |
once uh Morden is done,593.94,3.54 | |
um,596.82,3.18 | |
and then I'll let this run at least for,597.48,4.919 | |
a little bit because gpt4 is so,600.0,5.36 | |
expensive I probably won't do all 17,602.399,5.641 | |
Pages let's see so we're all night 28,605.36,5.26 | |
cents right now so we'll see about how,608.04,5.58 | |
expensive they are per run,610.62,4.98 | |
um there we go,613.62,4.38 | |
objective methods results conclusion,615.6,4.44 | |
okay cool,618.0,5.04 | |
so just restates it very very succinctly,620.04,4.68 | |
we'll watch it a couple more times,623.04,3.78 | |
you're probably watching on 2x anyways,624.72,4.619 | |
so and actually some of you watch on 3x,626.82,4.38 | |
I don't know how you understand me if,629.339,3.781 | |
you watch that fast,631.2,5.759 | |
um but yeah so while that's running,633.12,6.48 | |
let's see,636.959,5.641 | |
do a quick refresh it takes what like,639.6,5.28 | |
five minutes to update,642.6,4.2 | |
so we'll see,644.88,2.959 | |
um,646.8,5.039 | |
objective design and exosuit there we go,647.839,6.881 | |
conclusion exomuscle design,651.839,5.521 | |
so it looks like it's kind of restating,654.72,5.34 | |
it it could it could be problematic to,657.36,4.52 | |
keep feeding it in,660.06,4.62 | |
talks about the design,661.88,7.44 | |
thermoplastic polyurethane TPU coated,664.68,4.64 | |
and also we should have the uh chat logs,672.48,4.919 | |
here,676.32,3.24 | |
okay so the chat logs are just are are,677.399,4.56 | |
just um saving the whole thing I guess,679.56,5.219 | |
what I should do is also save the um,681.959,7.641 | |
save the user input but let's see,684.779,4.821 | |
so it keep keeps restating the whole,694.98,6.06 | |
paper which I don't think is a good use,697.92,4.32 | |
of,701.04,3.12 | |
of time,702.24,4.64 | |
all right,704.16,2.72 | |
it's not not a good use of tokens here,710.399,3.12 | |
I'm going to pause it real quick and see,712.44,2.399 | |
if I can investigate what's going on,713.519,2.88 | |
here,714.839,3.421 | |
okay I changed the system message a,716.399,3.601 | |
little bit and it works um much better,718.26,4.74 | |
so basically I just added a um a note,720.0,4.68 | |
here at the end focus on last page no,723.0,3.18 | |
need to restate all notes every time,724.68,4.68 | |
prefer to keep notes concise succinct,726.18,5.279 | |
um and then the exponential back off,729.36,4.68 | |
that I added last time is actually,731.459,5.94 | |
really helpful because the gpt4 API is,734.04,6.6 | |
so busy it you're liable to time out but,737.399,6.06 | |
also you might also get rate limited so,740.64,6.0 | |
the longer between times but so anyways,743.459,5.761 | |
here let me show you what I mean,746.64,4.439 | |
um,749.22,4.64 | |
there we go,751.079,2.781 | |
it's better it's not perfect so in this,754.56,4.44 | |
case it summarizes the first page and,757.079,3.481 | |
then we move on to the second page where,759.0,3.959 | |
it talks about the design comparison and,760.56,3.54 | |
findings,762.959,3.361 | |
so we're getting there,764.1,5.88 | |
and then uh testing and testing results,766.32,6.24 | |
conclusion it's a pretty short paper one,769.98,4.32 | |
thing that occurs to me is that with the,772.56,3.36 | |
longer because I started this experiment,774.3,4.2 | |
before I had access to gpt4 so I might,775.92,5.039 | |
need to go back to the drawing board and,778.5,5.16 | |
make use of that 8 000 token,780.959,5.101 | |
um window so rather than submitting it,783.66,4.859 | |
one page at a time which was you know,786.06,5.82 | |
when I only had 4 000 tokens what I,788.519,6.541 | |
might do is redo this and kind of do it,791.88,5.88 | |
as like one big chunk,795.06,6.36 | |
um to to summarize it but another rule,797.76,6.3 | |
of thumb that I have is is don't try to,801.42,5.159 | |
force the context window because if it,804.06,5.459 | |
doesn't work it doesn't work and the,806.579,4.38 | |
fact that it keeps restating this I,809.519,2.521 | |
think this might not be the right,810.959,4.32 | |
approach but the idea is still there,812.04,5.64 | |
where it's like let's let's use the,815.279,4.141 | |
model to do as much of the science as,817.68,5.339 | |
possible so today was kind of a wash but,819.42,7.34 | |
we'll see all right thanks for watching,823.019,3.741 | |