
How NLP can help cure cancer? [pdf] - polm23
https://people.csail.mit.edu/regina/talks/CNLP.pdf
======
wayoutthere
So, I worked at a startup in the early 00s trying to do exactly this — detect
disease trends from medical chart data. We had an advantage in that all the
data came from a nationalized health care system, so it was relatively
consistent.

We were using slightly different NLP techniques (and were actually a leader in
the NLP space), but ultimately NLP wasn’t really our restriction: we learned
that we couldn’t trust the doctors to enter the data consistently. The data
came in like 8 different versions of HL7 per hospital, and we had to fix our
parsers every time some department decided to upgrade their records systems.
The notes contained so much jargon (that was different in every department and
often using the same acronyms with different meanings in context) that we
ended up pivoting the tech to another industry.

Medical chart data sucks. HL7 sucks. Pretty much everything about doing deep
learning on medical data sucks. Everything about working and selling in the
hospital EMR space sucks. There _might_ be something there, but have fun
building a profitable company around it.

~~~
Amygaz
I did that data curation and analysis in the mid 2000s, before it was all hip
and well paid, and the CS group employed data curators because you need and
experimented human being, to analyze the data in a peer-reviewed paper, and
compare it to the authors’ conclusion. Half the time it doesn’t.

Finding reproducible or reproduced experiments happens at an even lower rate.

Then, context matter, and we know very little about each of our cell, even
less about each one behaves in an ensemble.

So no amount of NLP will cure cancer, currently. It’s a simple garbage-in 101
case. It will hopefully change...

However, there is a good chance that traditional approaches to science will
have worked well enough for most cancers, and NLP will just be a tool to
validate after the fact, build comprehensive database and assist with
incremental update to a treatment.

------
KasianFranks
Great work. At Lawrence Berkeley National Lab in the biosciences (formerly
life sciences) division, headed by Mina Bissell[1], one of the leading
researchers of breast cancer, we developed NLP-based vector space modeling
(embedding) in 2002 to augment genomic research in breast cancer, the
extracellular matrix and aging. That was about 2 years after the first human
genome was sequenced. The Lab patented[2] some of our methods and it helped
pave the way for approaches like word2vec and a few others. There's a lot of
great work yet to be in this area and we continue to make slow and steady
progress defined by generating new insights, hypotheses and sometimes
discoveries using approaches in NLP/NLU. We've recently been applying vector
space modeling in NLU to LET radiation research (DNA damage repair) associated
to space biosciences[3] which is exciting for extending and protecting human
lifespan for space travel. Interdisciplinary aspects are key.

[1] [https://www2.lbl.gov/LBL-
Programs/lifesciences/BissellLab/ma...](https://www2.lbl.gov/LBL-
Programs/lifesciences/BissellLab/main.html)

[2]
[http://www.google.com/patents/US7987191](http://www.google.com/patents/US7987191)

[3] [https://www.nasa.gov/ames/research/space-biosciences/for-
res...](https://www.nasa.gov/ames/research/space-biosciences/for-researchers)

------
kennethfriedman
This looks very interesting, I wonder if anyone has a link to the video
version of these talk slides.

I couldn't find it, but here is the same professor, Regina Barzilay, on the
same topic (but a different talk).

[https://www.youtube.com/watch?v=424zoKmpZvg](https://www.youtube.com/watch?v=424zoKmpZvg)

------
denzil_correa
Slide 12/13 talk about how these areas are "devoid of Computer Scientists". In
traditional areas like Biology and Chemistry, there is an acceptance that
Computer Science is "not a science". They still view CS as IT (service /
software). There are amazing broad applications of advanced computational
techniques like Natural Language Processing, Probabilistic Learning Approach
and Machine Learning within the space but if there's no acceptance of it, we
will hinder progress.

~~~
heyitsguay
For what it's worth, I've been working for a few years in CS + bio at the NIH,
and while demand for CS as IT exists, there's also now a pretty strong and
broad demand for computer scientists for scientific research. Between all of
our institutes there must be a couple dozen labs with projects in the areas
you mention. One of the biggest things holding us back is just finding enough
people with a CS background and interest in bio problems! From what I gather
at conferences, there's a lot of work being done by many groups in the
CS/bio/biostatistics space, and likely more to come.

------
mark_l_watson
I heard the author’s keynote speech at NAACL a few years ago, basically the
material in this paper. I found it inspirational, especially when mixed in her
own story on fighting cancer and disappointments in how much potentially
useful data is “siloed.” An AI system is proposed that can read and understand
all research, lab notes, etc., etc. This may be only achieved in the distant
future, but I believe we will get there.

------
alberto_ol
I would like to see the meningof the acronyms in the title. Natural language
processing ? Nonlinear programming? Neuro-linguistic programming?

~~~
DonHopkins
If there were a Neuro-Linguistic Programming Language, its definitive textbook
would be called "The Structure and Interpretation of Magic".

[https://www.goodreads.com/book/show/964154.The_Structure_of_...](https://www.goodreads.com/book/show/964154.The_Structure_of_Magic_I)

[https://www.goodreads.com/book/show/43713.Structure_and_Inte...](https://www.goodreads.com/book/show/43713.Structure_and_Interpretation_of_Computer_Programs)

------
DonHopkins
The title made me afraid it was about Neuro-Linguistic Programming (a New Age
"psycho-religion") instead of Natural Language Processing:

[https://en.wikipedia.org/wiki/Neuro-
linguistic_programming#A...](https://en.wikipedia.org/wiki/Neuro-
linguistic_programming#Alternative_medicine)

Alternative medicine

NLP has been promoted with claims it can be used to treat a variety of
diseases including Parkinson's disease, HIV/AIDS and cancer.[62] Such claims
have no supporting medical evidence.[62] People who use NLP as a form of
treatment risk serious adverse health consequences as it can delay the
provision of effective medical care.[62]

[62] Russell J; Rovere A, eds. (2009). "Neuro-linguistic programming".
American Cancer Society Complete Guide to Complementary and Alternative Cancer
Therapies (2nd ed.). American Cancer Society. pp. 120–122. ISBN 9780944235713.

~~~
whenchamenia
Thats sad. NLP started off as a more scientific take on Hypnosis, as
california required certification for hypno, but none for other, identical
processes, hence the name change. However the 'inventors' left it in the hands
of people who made it a sketchy MLM pyramid of trainers trainings. There IS
some good insight, but most of it ia just rehashed lessons from Milton H
Erickson retold by Richard Bandler. Then came the pickup artist trend, also
latching on to similar techniques. That said, most 'Neuro Linguistic
Programming' published in the last 20 years is mostly crap.

~~~
DonHopkins
Sad they were eventually exposed and debunked? Nope. I'm just sad it took so
long.

The inventors, Richard Bandler and John Grinder, were greedy bickering
charlatans, both just trying to make a buck from the very start. It was pure
crap from day one.

[https://en.wikipedia.org/wiki/Neuro-
linguistic_programming#I...](https://en.wikipedia.org/wiki/Neuro-
linguistic_programming#Intellectual_property_disputes)

>On this matter Stollznow (2010)[18] comments, "[i]ronically, Bandler and
Grinder feuded in the 1980s over trademark and theory disputes. Tellingly,
none of their myriad of NLP models, pillars, and principles helped these
founders to resolve their personal and professional conflicts."

>[...] In 2009, a British television presenter was able to register his pet
cat as a member of the British Board of Neuro Linguistic Programming (BBNLP),
which subsequently claimed that it existed only to provide benefits to its
members and not to certify credentials.

[http://news.bbc.co.uk/2/hi/8303126.stm](http://news.bbc.co.uk/2/hi/8303126.stm)

[https://neurobollocks.wordpress.com/2013/03/29/neuro-
linguis...](https://neurobollocks.wordpress.com/2013/03/29/neuro-linguistic-
programming-the-1970s-neurobollocks-that-just-refuses-to-die/)

>Despite being nearly 40 years old, and a ridiculous, facile hodge-podge of
concepts from psychology, philosophy, linguistics and new-age twaddle with
absolutely no support from any reputable sources, amazingly, NLP is still very
much alive and kicking. Bandler has kept on developing (and ruthlessly
trademarking) a load of new techniques including ‘Design Human Engineering™’,
or ‘Charisma Enhancement™’. A lot of his recent work also appears to include
hypnosis. His website is essentially one big advertisement for his books, CDs
and speaking gigs; and there are literally thousands of individuals,
businesses, and ‘institutes’ offering NLP training for a bewildering variety
of purposes and people. Bandler has even latterly jumped on the ‘Brain
training’ trend with a new company called ‘QDreams‘ (‘Quantum brain
training!’; ‘Success at the speed of thought!’ FFS…). Searching on Twitter
turns up many, many people earnestly tweeting away about the benefits of NLP.
Why is it so persistent? Partly this is because of Bandler’s clear talent for
slick marketing, re-invention and dedication to innovative bull-shittery, and
partly because NLP was never really clearly defined in the first place, which
makes it highly malleable and adaptable to any pseudo-scientific new-age
trends that come along. Despite a hiccup in the mid-90s (when Bandler tried to
sue Grinder for ninety million dollars) it seems to be as popular as ever, and
to be attracting new adherents all the time.

>In my opinion the real stroke of genius in NLP, and perhaps the reason why
it’s been so successful, is simply the name. These days we’re used to putting
the ‘neuro-‘ prefix in front of everything, but back in the ’70s, this was way
ahead of its time. Obviously there’s nothing remotely ‘neuro’ about it,
though. Plus the ‘programming’ bit has a deliciously Orwellian appeal;
promising the potential to effect change in oneself or others, if you just
know the right techniques.

[http://skepdic.com/neurolin.html](http://skepdic.com/neurolin.html)

>"For example, I believe it was very useful that neither one of us were
qualified in the field we first went after - psychology and in particular, its
therapeutic application; this being one of the conditions which Kuhn
identified in his historical study of paradigm shifts. Who knows what Bandler
was thinking?" -John Grinder

>postscript: On a more cheerful note, Bandler has sued Grinder for millions of
dollars. Apparently, the two great communicators and paradigm innovators
couldn't follow their own advice or perhaps they are modeling their behavior
after so many other great Americans who have found that the most lucrative way
to communicate is by suing someone with deep pockets. NLP is big on metaphors
and I doubt whether this nasty lawsuit is the kind of metaphor they want to be
remembered by. Is Bandler's action of putting a trademark on half a dozen
expressions a sign of a man who is simply protecting the integrity of NLP or
is it a sign of a greedy megalomaniac?

------
amelius
What could also help cure cancer is to have anonymized medical records on
Kaggle. However, I'm pessimistic that this will ever happen.

------
jimmaswell
I've wondered - what if Facebook for example found a typing pattern that
predicted something like Alzheimers in 95% of cases, but couldn't tell any
users because of GDPR, or GDPR prevented these typing patterns from being
analyzed for this purpose in the first place?

------
bryanrasmussen
I would personally expect how NLP can help detect cancer as being more
rewarding - and cynically speaking that Obama quote in the presentation about
America being the country to cure cancer, hell America it seems can't even
cure measels. Maybe I'm just having a bad day though.

