# Genomic Prediction of Complex Disease Risk (bioRxiv)

Our new paper describes over a dozen genomic predictors for common disease risk, constructed via machine learning on hundreds of thousands of genotypes. The predictors use anywhere from a few tens (e.g., 20 or 50) to thousands of SNPs to compute the risk PGS (Poly-Genic Score) for a specific disease. The figure above (Atrial Fibrillation) …

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# Ghosts and Hybrids: Ancient DNA and Human Origins

Take a break from your holiday Netflix binge and learn something about recent breakthroughs in our understanding of human evolution from ancient DNA. John Hawks (UW Madison) is an excellent speaker and this talk is for non-experts. Get the whole family together to watch — it’s a treat to learn from one of the leading …

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# He did it: He Jiankui talk at HKU conference on gene editing

This is He’s talk from a conference on gene editing, in progress now in HK. (Should start at 1h09.) This article describes serious discussions between He and bioethicists over the last year. It’s important to note that CapEx required for this process is quite modest — not beyond the capability of a medium-sized IVF clinic. …

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# Generation CRISPR?

Very strange. This guy left his university a few years ago to concentrate on this research. Are his claims real? Genome-edited baby claim provokes international outcry (Nature News) The startling announcement by a Chinese scientist represents a controversial leap in the use of genome-editing. A Chinese scientist claims that he has helped make the world’s …

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# 1 In 4 Biostatisticians Surveyed Say They Were Asked To Commit Scientific Fraud

In the survey reported below, about 1 in 4 biostatisticians were asked to commit scientific fraud. I don’t know whether this bad behavior was more prevalent in industry as opposed to academia, but I am not surprised by the results. I do not accept the claim that researchers in data-driven areas can be ignorant of …

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# Backpropagation in the Brain?

Ask and ye shall receive :-) In an earlier post I recommended a talk by Ilya Sutskever of OpenAI (part of an MIT AGI lecture series). In the Q&A someone asks about the status of backpropagation (used for training of artificial deep neural nets) in real neural nets, and Ilya answers that it’s currently not …

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# Quantum Information Science Workshop at MSU

Webpage / Program / Abstracts. My opening remarks: On behalf of Michigan State University it is my pleasure to welcome all of you to this workshop on quantum information science. In the fall of 1983 (my freshman year!) Feynman taught a graduate course at Caltech called Potentialities and Limitations of Computing Machines. Chapter 6 of …

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# Intuition and the two brains, revisited

﻿ Iain McGilchrist, author of The Master and His Emissary: The Divided Brain and the Making of the Western World, in conversation with Jordan Peterson. I wrote about McGilchrist in 2012: Intuition and the two brains. Albert Einstein: “The intuitive mind is a sacred gift and the rational mind is a faithful servant. We have …

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# The French Way: Alain Connes interview

I came across this interview with Fields Medalist Alain Connes (excerpt below) via an essay by Dominic Cummings (see his blog here). Dom’s essay is also highly recommended. He has spent considerable effort to understand the history of highly effective scientific / research organizations. There is a good chance that his insights will someday be put …

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# Scientists of Stature

The link below is to the published version of the paper we posted on biorxiv in late 2017 (see blog discussion). Our results have since been replicated by several groups in academia and in Silicon Valley. Biorxiv article metrics: abstract views 31k, paper downloads 6k. Not bad! Perhaps that means the community understands now that genomic …

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# Genomic Prediction: A Hypothetical (Embryo Selection), Part 2

The figures below are from the recent paper Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations (Nature Genetics), discussed previously here. As you can see, genomic prediction of risk allows to identify outliers for conditions like heart disease and diabetes. Individuals who are top 1% in polygenic risk score are …

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# Genomic Prediction of disease risk using polygenic scores (Nature Genetics)

It seems to me we are just at the tipping point — soon it will be widely understood that with large enough data sets we can predict complex traits and complex disease risk from genotype, capturing most of the estimated heritable variance. People will forget that many “experts” doubted this was possible — the term …

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# SSGAC EA3: genomic prediction of educational attainment and related cognitive phenotypes

Years ago I predicted that: 1. Cognitive ability would turn out to be influenced by many thousands of genetic variants, each of small effect. 2. With large enough sample size we would detect these variants and eventually construct genomic predictors. The Nature Genetics paper (below) from the SSGAC collaboration takes a significant step in that …

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# Some books, NAP reports, and other newer resources related to science education

I’ll be starting a position in STEM Education at the University of Tennessee, Knoxville, beginning this August. As part of this position, I’ll teach science teaching methods (and science and STEM education research-related) courses. Hearing about the course I’ll teach this fall gave me an impetus to begin bto prepare and to read some resources …

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# A Brief History of the (Near) Future: How AI and Genomics Will Change What It Means To Be Human

I’ll be giving the talk below to an audience of oligarchs in Los Angeles next week. This is a video version I made for fun. It cuts off at 17min even though the whole talk is ~25min, because my team noticed that I gave away some sensitive information :-( The slides are here. A Brief …

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# Outlier selection via noisy genomic predictors

We recently used machine learning techniques to build polygenic predictors for a number of complex traits. One of these traits is bone density, for which the predictor correlates r ≈ 0.45 with actual bone density. This is far from perfect, but good enough to identify outliers, as illustrated above. The figures above show the actual bone …

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# The value of a rearview mirror in the field

I am writing from Wolong Nature Reserve, near the tail end of a successful winter field season. Although I previously felt that I had had successful seasons in the past, this has been the most so and has put me close to having enough data to finish my dissertation research (assuming, fingers crossed, successful lab …

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# The Automated Physicist: Experimental Particle Physics in the Era of AI

My office will be recording some of the most interesting of the many talks that happen at MSU. I will post some of my favorites here on the blog. See the MSU Research channel on YouTube for more! Audio for this video isn’t great, but we are making improvements in our process / workflow for capturing these …

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# The science of “Interstellar” revisited: How to travel through a wormhole

The movie “Interstellar” has not only fascinated moviegoers: it also has created a discussion among scientists whether any and all of the science discussed in the movie is accurate. To be sure, this is not the fate that befalls your average Sci-Fi movie where the laws of physics are routinely (and often egregiously) broken over …

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# Stephen Hawking (1942-2018)

Roger Penrose writes in the Guardian, providing a scientifically precise summary of Hawking’s accomplishments as a physicist (worth reading in full at the link). Penrose and Hawking collaborated to produce important singularity theorems in general relativity in the late 1960s. Here is a nice BBC feature: A Brief History of Stephen Hawking. The photo above …

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# Remembering Stephen Hawking

The passing of the great physicist Stephen Hawking today at the age of 76 fills me with sadness for many different reasons. On the one hand, it was inspiring to witness that, seemingly, the power of will and intellect can hold such a serious illness at bay for so long. On the other hand, I …

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# Piecewise Linear Approximations in MIP Models

In the past, I’ve written about piecewise linear approximations of functions of a single variable. (There are too many posts to list here. Just type “piecewise linear” in the search box of my blog if you want to find them.) Handling piecewise linear approximations of multivariable functions is a bit more intimidating. I’ll illustrate one …

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# Genetic testing and embryo selection: current status and ethical issues

This is a conversation with two Stanford students about the current status of genetic testing of embryos in IVF, focusing on related ethical issues. Because there is a lot of interest in this topic I suggested we record the conversation and put it online. I was at Stanford last fall to give a #nofilter talk …

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# AI and Genomics, explained (2 videos)

This video is a nicely done short introduction to AI for non-specialists. It’s part of Shift Change, a six part series on automation and the future of work. I came across the video when creator Joss Fong (Vox) contacted me about her new project on human genomics and genomic prediction. As readers know I think the …

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# US Needs a National AI Strategy: A Sputnik Moment?

The US needs a national AI strategy. Many academic researchers that could contribute to AI research — including to fundamental new ideas and algorithms, mathematical frameworks for better understanding why some algorithms and architectures work better than others, etc. — are not able to get involved at the real frontier because they lack the kind …

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# Steve Pinker and Joe Rogan

I’ve just started watching this so I can’t give you an evaluation of the whole conversation. Looks promising — they jump right in on topics like sex differences, political correctness, internet flame wars, the Trump candidacy, social media, … (I’m skipping the Super Bowl, by the way. I stopped watching the NFL and NBA years …

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# When climate change is a given

My childhood home sits on a big hill just outside Portland, Oregon. From my bedroom window I often gazed at the familiar and pointy snow-capped peak of Mt. Hood looming in the distance. If I turned northward on a clear day, I could just make out the peaks of Mts. Rainier and St. Helens. These …

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# New publication: Strategies, Use, and Impact of Social Media for Supporting Teacher Community within Professional Development: The Case of One Urban STEM Program

Just over a month ago, an article by Josh Rosenberg, me, Leigh Graves Wolf, and Matt Koehler appeared in the Journal of Computers in Mathematics and Science Teaching. This is—perhaps obviously—a continuation of some of our previous work on Twitter hashtags in graduate education, but this piece took a particular look at social media use, …

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# Counting branches of the black hole wave function

When I was at Caltech a few weeks ago I had a chance to discuss the recent paper below by Sean Carroll and collaborators. (Authors are at Caltech, Berkeley, and UBC.) Their paper is very clearly written, but probably suitable only for experts who are already familiar with the black hole information paradox. I discussed …

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# Allen Institute meeting on Genetics of Complex Traits

You can probably tell by all the photos below that I am in love with their new building :-) I was a participant in this event: What Makes Us Human? The Genetics of Complex Traits (Allen Frontiers Group), including in a small second day workshop with just the speakers and the AI leadership. This workshop …

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# Institute for Advanced Study: Genomic Prediction of Complex Traits (seminar)

Genomic Prediction of Complex Traits After a brief review (suitable for physicists) 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 …

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# Gork revisited, 2018

It’s been almost 10 years since I made the post Are you Gork? Over the last decade, both scientists and non-scientists have become more confident that we will someday create: A. AGI (= sentient AI, named “Gork” :-)  See Rise of the Machines: Survey of AI Researchers. B. Quantum Computers. See Quantum Computing at a Tipping …

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# Grain size, where species are and where they might be

A large body of work in the ecology of conservation is devoted to figuring out where species truly are and what causes them to be in some places and not others. Termed species distribution modeling, or SDM for short, this endeavor involves looking at the environment where species are known to occur compared to the …

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# Low SES does not decrease heritability of cognitive ability (N=300k)

These researchers, from Stanford, Northwestern, and the University of Florida, analyze a large population of twins and siblings (~24k twins and ~300k children in total, born 1994-2002 in Florida). They find no evidence of SES (Socio-Economic Status) moderation of genetic influence on test scores (i.e., cognitive ability). The figure above shows the usual pattern of lower pairwise …

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# Big Ed

Today I came across a recent interview with Ed Witten in Quanta Magazine. The article has some nice photos like the one above. I was struck by the following quote from Witten (“It from Qubit!”): When I was a beginning grad student, they had a series of lectures by faculty members to the new students about …

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# Heilongjiang is for the birds

My friends are used to my frequent and sometimes infuriating habit of stopping whatever I am doing (be it walking, talking or driving) to look at and identify any birds. I have even been known to pull to the side of the road to ogle particularly interesting species, a habit I picked up from my …

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# CMSE (Computational Mathematics, Science and Engineering) at MSU

At Oregon I was part of an interdisciplinary institute that included theoretical physicists and chemists, mathematicians, and computer scientists. We tried to create a program (not even a new department, just an interdisciplinary program) in applied math and computation, but failed due to lack of support from higher administration. When I arrived at MSU as …

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# IQ (Institute for Quantitative Health Science and Engineering) at MSU

Chris Contag is the founding director of the Institute for Quantitative Health Science and Engineering and the chairperson of the new Department of Biomedical Engineering in the College of Engineering. Contag was previously a professor in the Departments of Pediatrics, Radiology, Bioengineering and Microbiology and Immunology at Stanford University. He held the titles of …

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# On developing my dissertation

“What are you researching?” Since starting my PhD program at MSU this fall, I have been asked this question countless times, but it is one to which I have no definite answer yet. Some grad students start their studies by joining an ongoing project, while others begin from scratch and create their own project. I fall …

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# Ex Laboratorium

The E. coli long-term evolution experiment, or LTEE for short, is approaching its 30th birthday, which will be on February 24th, 2018. In honor of all the people who have worked on this project, I thought it would be neat to commission a special, but shareable, piece of art. Given the history of science and …

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# The nuclear physics of neutron star mergers at MSU’s FRIB

Science reports on MSU’s Facility for Rare Isotope Beams, which will probe the properties of nuclear matter. Science: Last month, astronomers wowed the world when they announced that they had seen two neutron stars merge, apparently creating heavy elements such as gold and platinum and spewing them into space. Nuclear physicists here at Michigan State …

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# Behold, the Super Cow

Hmm… how do they compute the Net Merit and GTPI? (But, but, what about all of that missing heritability?) See also Applied genomics: the genetic “super cow” Genomic prediction: no bull. Attention climate virtue signalers: more efficient cows produce less methane per liter of milk! Drink milk from genetically engineered cows :-) Tweet

# 23andme

I’m in Mountain View to give a talk at 23andMe. Their latest funding round was $250M on a (reported) valuation of$1.5B. If I just add up the Crunchbase numbers it looks like almost half a billion invested at this point… Slides: Genomic Prediction of Complex Traits Abstract: We apply methods from Compressed Sensing (L1-penalized regression; Donoho-Tanner …

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As I noted in yesterday’s post, one of the major changes associated with the new “generic” callback structure in CPLEX is that users now bear the responsibility of making their callbacks thread-safe. As I also noted yesterday, this is pretty new stuff for me. So I’m going to try to share what I know about thread …

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# CPLEX 12.8: Generic Callbacks

IBM is getting ready to release CPLEX 12.8, and I had the opportunity to attend a presentation about by Xavier Nodet at the 2017 INFORMS annual meeting. Here are links to two presentations by Xavier: CPLEX Optimization Studio 12.8 – What’s New and CPLEX 12.8 – the Generic Callback. As with any new release, there …

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# The Future is Here: Genomic Prediction in MIT Technology Review

MIT Technology Review reports on our startup Genomic Prediction. Some basic points worth clarifying: 1. GP’s first product, announced at the annual ASRM (American Society of Reproductive Medicine) meeting this week, tests chromosomal abnormality. It is a less expensive but more accurate version of existing tests. 2. The polygenic product, to be launched in 2018, checks …

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# Time fleas, with apologies to Jonathan Swift

Over on twitter, Kyle Card posted a photo of Halloween in the Lenski lab. That prompted Morgan Feeney to reply: “You mean you don’t all dress up as different generations of the LTEE? I am SHOCKED.” And that got me thinking about Jonathan Swift’s rhapsody on fleas: So nat’ralists observe, a flea Has smaller fleas that on him prey; And these have …

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# The Physicist and the Neuroscientist: A Tale of Two Connectomes

This is video of an excellent talk on the human connectome by neuroscientist Bobby Kasthuri of Argonne National Lab and the University of Chicago. (You can see me sitting on the floor in the corner :-) The story below is for entertainment purposes only. No triggering of biologists is intended. The Physicist and the Neuroscientist: A …

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# The Philosophers’ Way

Sometimes we forget … forget to take a break, forget to get outside, and forget to reflect on our individual and collective pasts. After an intense three days of talks at EMBO—hearing about exciting work by diverse and superb biologists in 13-minute chunks (plus Q&A); seeing dear friends Santiago Elena, Sebastian Bonhoeffer, and Roy Kishony; …

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# Steven Weinberg: What’s the matter with quantum mechanics?

In this public lecture Weinberg explains the problems with the two predominant interpretations of quantum mechanics, which he refers to as Instrumentalist (e.g., Copenhagen) and Realist (e.g., Many Worlds). The term “interpretation” may be misleading because what is ultimately at stake is the nature of physical reality. Both interpretations have serious problems, but the problem …

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