Showing posts with label photos. Show all posts
Showing posts with label photos. Show all posts

Saturday, February 22, 2020

Cold Spring Harbor Laboratory: Seminar and Photos

Last week I visited Cold Spring Harbor Laboratory to give a seminar.

The new material is in slides 13-17. See also Live Long and Prosper: Genetic Architecture of Complex Traits and Disease Risk Predictors. I believe the sibling validation results are extremely important: typically most of the predictive power persists in within-family validation tests. We have not released this paper but will soon -- the slides are a preview. To be honest I fully anticipated these results: the large number of out of sample predictor validations using unrelated individuals strongly suggests that real genetic effects are at work. However, many people are irrationally biased against -- have strong priors against -- genetic causation of complex traits (even disease risks). These family designs provide important "gold standard" evidence, which, one can hope, will enlighten even the most stubborn. The sad alternative is progress one funeral at a time...

Otherwise the talk is similar to the one I gave at the Berkeley/UCSF Innovative Genomics Institute last summer. Video of IGI talk.
Title: Genomic Prediction of Complex Traits and Disease Risks via AI/ML and Large Genomic Datasets

Abstract: The talk is divided into two parts. The first gives an overview of the rapidly advancing area of genomic prediction of disease risks using polygenic scores. We can now identify risk outliers (e.g., with 5 or 10 times normal risk) for about 20 common disease conditions, ranging from diabetes to heart diseases to breast cancer, using inexpensive SNP genotypes (i.e., as offered by 23andMe). We can also predict some complex quantitative traits (e.g., adult height with accuracy of few cm, using ~20k SNPs). I discuss application of these results in precision medicine as well as embryo selection in IVF, and give some details about genetic architectures. The second part covers the AI/ML used to build these predictors, with an emphasis on "sparse learning" and phase transitions in high dimensional statistics.
Some photos. The ones on the wall of the seminar room capture a golden era in molecular biology and the study of DNA. Leo Szilard on the right in the one below. Also, Jacques Monod, Crick and Watson, Wally Gilbert, Max Delbruck, Frank Stahl, Francois Jacob, David Baltimore. Of these individuals I have known four in person. I would give a lot to have met Crick and especially Szilard. While at CSHL I learned that James Watson is still alive and intellectually active.

See H. Judson's The Eighth Day of Creation (PDF) for a brilliant but readable history of the golden age of molecular biology.












Wednesday, July 03, 2019

Beijing 2019 Notes

I'm at Beijing University in Zhongguancun. Some brief notes and photos below.

I had meetings with Beida professors, prominent tech entrepreneurs and VCs, policy analysts, IVF doctors and genetic scientists. I also had conversations with ordinary people -- drivers, maids, hotel and service staff.

I've been traveling to Beijing for about 15 years now and have observed significant improvements in infrastructure, general economic level, civil society, general behavior. This would of course be obvious to people living in China, which presumably explains the confidence people here have in their government and in continued advances in development. The hypothesis that this society is "brittle" or vulnerable to shocks seems unsupported.

The main thing to comprehend about China is scale. There are easily ~350M (i.e., population of US) people here living roughly first world lives: with access to education, good jobs, climate controlled apartment in major city, good public transportation, fast internet access, etc. Probably the number is twice as large depending on how one defines the category. For one thing, this means that the supply of engineers, technologists, lab scientists, project managers, entrepreneurs, etc. is very large. There are certainly poor people who lack opportunity, but the size of the population for which the education and economic system are working reasonably well is very large. Possibly a billion people out of ~1.4B.

Beijing is a microcosm of this phenomenon of scale. It's a huge city (over 20M people) with the kind of modern metro system only to be found in places like Tokyo or perhaps Seoul or Paris or London. One can ride the longer lines for 90 minutes without exiting, covering the entire extent of the city from one side to the other. Despite the public transport system, the roads are clogged with recent model cars, producing traffic conditions reminiscent of Los Angeles. I don't find the city as a whole all that livable -- it's too enormous for me -- but locals know all the many charming locations (see photos below). Beijing is reaching a level of development that reminds me of Tokyo.

Trump, the trade war, and US-China relations came up frequently in discussion. Chinese opinion tends to focus on the long term. Our driver for a day trip to the Great Wall was an older man from the countryside, who has lived only 3 years in Beijing. I was surprised to hear him expressing a very balanced opinion about the situation. He understood Trump's position remarkably well -- China has done very well trading with the US, and owes much of its technological and scientific development to the West. A recalibration is in order, and it is natural for Trump to negotiate in the interest of US workers.

China's economy is less and less export-dependent, and domestic drivers of growth seem easy to identify. For example, there is still a lot of low-hanging fruit in the form of "catch up growth" -- but now this means not just catching up with the outside developed world, but Tier 2 and Tier 3 cities catching up with Tier 1 cities like Beijing, Shanghai, Shenzhen, etc.

China watchers have noted the rapidly increasing government and private sector debt necessary to drive growth here. Perhaps this portends a future crisis. However, I didn't get any sense of impending doom for the Chinese economy. To be fair there was very little inkling of what would happen to the US economy in 2007-8.  Some of the people I met with are highly placed with special knowledge -- they are among the most likely to be aware of problems. Overall I had the impression of normalcy and quiet confidence, but perhaps this would have been different in an export/manufacturing hub like Shenzhen. [ Update: Today after posting this I did hear something about economic concerns... So situation is unclear. ]

Innovation is everywhere here. Perhaps the most obvious is the high level of convenience from the use of e-payment and delivery services. You can pay for everything using your mobile (increasingly, using just your face!), and you can have food and other items (think Amazon on steroids) delivered quickly to your apartment. Even museum admissions can be handled via QR code.

A highly placed technologist told me that in fields like AI or computer science, Chinese researchers and engineers have access to in-depth local discussions of important arXiv papers -- think StackOverflow in Mandarin. Since most researchers here can read English, they have access both to Western advances, and a Chinese language reservoir of knowledge and analysis. He anticipates that eventually the pace and depth of engineering implementation here will be unequaled.

IVF and genetic testing are huge businesses in China. Perhaps I'll comment more on this in the future. New technologies, in genomics as in other areas, tend to be received more positively here than in the US and Europe.


National Museum



Bookstore and Cafe on the grounds of the National Art Museum.







Tiananmen Square (see below for historical note)


An email sent to Julian Assange's attorney, whom I met at CogX in London:
Hi Jen,

I really enjoyed your Q&A today. Keep fighting the good fight.

Wikileaks diplomatic cables reveal no mass shootings in Tiananmen Square:

https://wikileaks.org/plusd/cables/89BEIJING18828_a.html

https://www.telegraph.co.uk/news/worldnews/wikileaks/8555142/Wikileaks-no-bloodshed-inside-Tiananmen-Square-cables-claim.html

Our media has been misrepresenting this historical event for 30 years
now. There was certainly violence, but not in the square itself.

Best wishes,
Steve
Columbia Journalism Review (1998): The Myth of Tiananmen. See comments for further discussion...

Note Added: In the comments AG points to a Quora post by a user called Janus Dongye Qimeng, an AI researcher in Cambridge UK, who seems to be a real China expert. I found these posts to be very interesting.

Infrastructure development in poor regions of China

Size of Chinese internet social network platforms

Can the US derail China 2025? (Core technology stacks in and outside China)

Huawei smartphone technology stack and impact of US entity list interdiction (software and hardware!)

Agriculture at Massive Scale

US-China AI competition


More recommenations: Bruno Maçães is one of my favorite modern geopolitical thinkers. A Straussian of sorts (PhD under Harvey Mansfield at Harvard), he was Secretary of State for European Affairs in Portugal, and has thought deeply about the future of Eurasia and of US-China relations. He spent the last year in Beijing and I was eager to meet with him while here. His recent essay Equilibrium Americanum appeared in the Berlin Policy Journal. Podcast interview -- we hope to have him on Manifold soon :-)

Friday, January 04, 2019

The Golden State

Apologies for the lack of posts. I've been enjoying some time with the family in CA :-) Kids have the MI middle school state swimming championships coming up and we got some good training done in a beautiful outdoor pool. I'm using USRPT methods, which seem to work well for my kids. I wish we had it when I was competing.

We had really good luck with the weather, sunny and 60s every day on the central coast.




Now I'm in the bay area for this meeting:

37th Annual J.P. Morgan HEALTHCARE CONFERENCE
January 7 - 10, 2019
Westin St. Francis Hotel | San Francisco, California


Sunday, December 09, 2018

Paris 2018: Global Capital and Its Discontents



Is she shooting video of the riot outside, or is she video chatting with a friend, oblivious? Did she just have the Royale with Cheese? :-)

My suggested title is Global Capital and Its Discontents.

Amazing work by this photographer.








Paris in happier times.
“If you are lucky enough to have lived in Paris as a young man, then wherever you go for the rest of your life, it stays with you, for Paris is a moveable feast.” ― Ernest Hemingway, A Moveable Feast

A meal by the Seine.



Les Deux Magots.



Le Louvre.







View from Sacre Coeur.

Wednesday, November 14, 2018

London / DeepMind photos

I've been very lucky with the London weather on this trip -- in the 50s and sunny.



These were taken from the roof terrace of the Google building that houses DeepMind:





These are from the nearby area: St. Pancras, Granary Square, in King's Cross.







More photos from the area.


Photos below from The Economist (also rooftop views of London, but not as posh as GOOG) and BBC visits.

This Economist article on Genomic Prediction has been in waiting for weeks, to appear in The World in 2019 special issue. I spent a couple hours briefing their science team on what is coming in AI and genomics -- I would guess there will be more coverage of polygenic scores and health care in the future.

See also this New Scientist article on GP.

2019 may be the Year of the Designer Baby, if journos are to be believed ;-)  Of course, this is sensationalism. It is more accurate to say that 2019 will see the first deployment of advanced genetic tests which can be used to screen against complex disease and health risks. Already today ~1 million IVF embryos per year are screened worldwide using less sophisticated genetic tests for single gene disease mutations and chromosomal abnormality.

The Economist:
In 2019, ... those with the cash to do so will have an opportunity to give their offspring a greater chance of living a long and healthy life.

"Expert" opinion seems to have evolved as follows:
1. Of course babies can't be "designed" because genes don't really affect anything -- we're all products of our environment!

2. Gulp, even if genes do affect things it's much too complicated to ever figure out!

3. Anyone who wants to use this technology (hmm... it works) needs to tread carefully, and to seriously consider the ethical issues.

Only point 3 is actually correct, although there are still plenty of people who believe 1 and 2   :-(
BBC wanted me for their Radio 4 Today show. I went in and recorded some clips, but the broadcast may be delayed due to all the Brexit excitement -- Theresa May has finally revealed the proposed EU-UK agreement her administration negotiated. Angry Brexiteer Tory MPs may vote her out. I had a ringside seat to all this thanks to my friend Dominic Cummings!






Friday, November 09, 2018

DeepMind Talk: Genomic Prediction of Complex Traits and Disease Risks via Machine Learning


I'll be at DeepMind in London next week to give the talk below. Quite a thrill for me given how much I've admired their AI breakthroughs in recent years. Perhaps AlphaGo can lead to AlphaGenome :-)

Hope the weather holds up!
Title: Genomic Prediction of Complex Traits and Disease Risks via Machine Learning

Abstract: After a brief review (suitable for non-specialists) of computational genomics and complex traits, I describe recent progress in this area. Using methods from Compressed Sensing (L1-penalized regression; Donoho-Tanner phase transition with noise) and the UK BioBank dataset of 500k SNP genotypes, we construct genomic predictors for several complex traits. Our height predictor captures nearly all of the predicted SNP heritability for this trait -- actual heights of most individuals in validation tests are within a few cm of predicted heights. I also discuss application of these methods to cognitive ability and polygenic disease risk: sparsity estimates (of the number of causal loci), combined with phase transition scaling analysis, allow estimates of the amount of data required to construct good predictors. We can now identify risk outliers for conditions such as heart disease, diabetes, breast cancer, hypothyroidism, etc. using inexpensive genotyping. Finally, I discuss how these advances will affect human reproduction (embryo selection for In Vitro Fertilization (IVF); gene editing) in the coming decade.

Bio: Stephen Hsu is VP for Research and Professor of Theoretical Physics at Michigan State University. He is also a researcher in computational genomics and founder of several Silicon Valley startups, ranging from information security to biotech. Educated at Caltech and Berkeley, he was a Harvard Junior Fellow and held faculty positions at Yale and the University of Oregon before joining MSU.

Action Photos!







Blog Archive

Labels