MSU Research Update (video)

Remarks at a recent Michigan State University leadership meeting. MSU is currently #1 in the US in annual Department of Energy (DOE) and DOE + NSF (National Science Foundation) funding. There are ~30 institutions in the US with larger annual research expenditures than MSU, however in all but a few cases (e.g., MIT and UC …

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Interview with Genetic Engineering & Biotechnology News

  Polygenic Risk Scores and Genomic Prediction: Q&A with Stephen Hsu In this exclusive interview, Stephen Hsu (Michigan State University and co-founder of Genomic Prediction) discusses the application of polygenic risk scores (PRS) for complex traits in pre-implantation genetic screening. Interview conducted by Julianna LeMieux (GEN). GEN: What motivated you to start Genomic Prediction? STEVE …

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Precision Genomic Medicine and the UK

I just returned from the UK, where I attended a Ditchley Foundation Conference on machine learning and genetic engineering. The attendees included scientists, government officials, venture capitalists, ethicists, and medical professionals. The UK could become the world leader in genomic research by combining population-level genotyping with NHS health records. The application of AI to datasets …

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The Future of Genomic Precision Medicine

As I mentioned in this earlier post, I’ll be in the UK next week for a Ditchley Foundation conference on the intersection of machine learning and genetic engineering. I’ll presentĀ these slides at the meeting. The slides review the rapidly evolving situation in genomic prediction, focusing on disease risk predicted using inexpensive genotyping. There are now …

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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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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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The French Way: Alain Connes interview

I came across this interview with Fields Medalist Alain ConnesĀ (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 biorxivĀ 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 previouslyĀ 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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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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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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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 isā€”perhaps obviouslyā€”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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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” :-) Ā SeeĀ Rise of the Machines: Survey of AI Researchers. B. Quantum Computers. See Quantum Computing at a Tipping …

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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 findĀ no evidenceĀ 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 recentĀ 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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IQ (Institute for Quantitative Health Science and Engineering) at MSU

Ā  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

ā€œWhat are you researching?ā€ 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 anĀ 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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Behold, the Super Cow

Hmm… how do they compute the Net Merit andĀ GTPI? (But, but, what about all of thatĀ 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. TheirĀ latest funding roundĀ 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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Thread Safety

As I noted inĀ 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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