6 ms·

How NLP can help cure cancer? [pdf]

98 points by polm23 7y ago

alberto_ol 7y ago
I would like to see the meningof the acronyms in the title. Natural language processing ? Nonlinear programming? Neuro-linguistic programming?
- DonHopkins 7y ago
  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_Magic_I https://www.goodreads.com/book/show/964154.The_Structure_of_... https://www.goodreads.com/book/show/43713.Structure_and_Interpretation_of_Computer_Programs https://www.goodreads.com/book/show/43713.Structure_and_Inte...
- SketchySeaBeast 7y ago
  I thought "that's silly, but I'm sure it's in the article" - I couldn't find it. I flipped (quickly) through every slide and couldn't see what they meant by NLP. We can infer, but I couldn't find a place where we are implicitly told, and for some reason that's maddening to me.
kennethfriedman 7y ago
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
bryanrasmussen 7y ago
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.
makeszerosense2 7y ago
Do people really believe there are serious efforts by modern medicine to "cure cancer", which is a multi trillion dollar franchise to all involved, from universities to pharma companies? In any case, fasting and herbs are already one of the most effective ways to trigger one's own body to rid itself from the damaged cells they like to refer to as "cancer" for scare factor.
DonHopkins 7y ago
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#Alternative_medicine https://en.wikipedia.org/wiki/Neuro-linguistic_programming#A... 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.
- the_seraphim 7y ago
  you could certainly use NLP alongside cancer treatments to help combat the depression and negative emotional state, but you are still going to need radiotherapy
- convery 7y ago
  I second this, had a 100%-off code for udemy courses and picked NLP as it was featured and "bio-hacking" seemed like an interesting subject. Thought the post was going to be a satirical take =P The first 10 hours of the course were literally "when you've finished this course; your life will be perfect and you can spread this information to your friends and be a hero! Here's a success-story about a totally real person that finished the course and rated it 5 stars" - on repeat.
- whenchamenia 7y ago
  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.
KasianFranks 7y ago
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/main.html https://www2.lbl.gov/LBL-Programs/lifesciences/BissellLab/ma... [2] http://www.google.com/patents/US7987191 http://www.google.com/patents/US7987191 [3] https://www.nasa.gov/ames/research/space-biosciences/for-researchers https://www.nasa.gov/ames/research/space-biosciences/for-res...
denzil_correa 7y ago
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.
- untilHellbanned 7y ago
  This is changing.
- heyitsguay 7y ago
  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.
wayoutthere 7y ago
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 7y ago
  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.
- astazangasta 7y ago
  The main problem with this effort is statistical. Medical databases are not accurate samples of the population; they are biased in hundreds of ways (doctor X is running a clinic for disease Y, but doesn't see many poor people because of Medicaid issues, etc.). People get excited about these because there is "so much data", but since it isn't collected prospectively, even if we could bulk extract all the data (which we can't, it's a fucking mess) any conclusions we drew would be invalid.
amelius 7y ago
What could also help cure cancer is to have anonymized medical records on Kaggle. However, I'm pessimistic that this will ever happen.
mark_l_watson 7y ago
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.
jimmaswell 7y ago
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?

98 points by polm23 7y ago

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

DonHopkins 7y ago
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_Magic_I https://www.goodreads.com/book/show/964154.The_Structure_of_... https://www.goodreads.com/book/show/43713.Structure_and_Interpretation_of_Computer_Programs https://www.goodreads.com/book/show/43713.Structure_and_Inte...
SketchySeaBeast 7y ago
I thought "that's silly, but I'm sure it's in the article" - I couldn't find it. I flipped (quickly) through every slide and couldn't see what they meant by NLP. We can infer, but I couldn't find a place where we are implicitly told, and for some reason that's maddening to me.

kennethfriedman 7y ago

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

bryanrasmussen 7y ago

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.

makeszerosense2 7y ago

Do people really believe there are serious efforts by modern medicine to "cure cancer", which is a multi trillion dollar franchise to all involved, from universities to pharma companies? In any case, fasting and herbs are already one of the most effective ways to trigger one's own body to rid itself from the damaged cells they like to refer to as "cancer" for scare factor.

DonHopkins 7y ago

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#Alternative_medicine https://en.wikipedia.org/wiki/Neuro-linguistic_programming#A... 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.

the_seraphim 7y ago
you could certainly use NLP alongside cancer treatments to help combat the depression and negative emotional state, but you are still going to need radiotherapy
convery 7y ago
I second this, had a 100%-off code for udemy courses and picked NLP as it was featured and "bio-hacking" seemed like an interesting subject. Thought the post was going to be a satirical take =P The first 10 hours of the course were literally "when you've finished this course; your life will be perfect and you can spread this information to your friends and be a hero! Here's a success-story about a totally real person that finished the course and rated it 5 stars" - on repeat.
whenchamenia 7y ago
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.

KasianFranks 7y ago

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/main.html https://www2.lbl.gov/LBL-Programs/lifesciences/BissellLab/ma... [2] http://www.google.com/patents/US7987191 http://www.google.com/patents/US7987191 [3] https://www.nasa.gov/ames/research/space-biosciences/for-researchers https://www.nasa.gov/ames/research/space-biosciences/for-res...

denzil_correa 7y ago

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.

untilHellbanned 7y ago
This is changing.
heyitsguay 7y ago
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.

wayoutthere 7y ago

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 7y ago
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.
astazangasta 7y ago
The main problem with this effort is statistical. Medical databases are not accurate samples of the population; they are biased in hundreds of ways (doctor X is running a clinic for disease Y, but doesn't see many poor people because of Medicaid issues, etc.). People get excited about these because there is "so much data", but since it isn't collected prospectively, even if we could bulk extract all the data (which we can't, it's a fucking mess) any conclusions we drew would be invalid.

amelius 7y ago

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

mark_l_watson 7y ago

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.

jimmaswell 7y ago

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?