# 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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# Survival of the Steepest

Most textbooks tell you that the evolutionary process is really quite simple: three rules are all that’s necessary: inheritance, variation, and selection. It is indeed true that these three rules are all that’s needed for evolution to occur, but that does not mean that the evolutionary process is simple. In fact, quite the opposite. Real systems evolve in …

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# Blade Runner 2049: Demis Hassabis (Deep Mind) interviews director Villeneuve

Hassabis refers to AI in the original Blade Runner, but it is apparent from the sequel that replicants are merely genetically engineered humans. AI appears in Blade Runner 2049 in the form of Joi. There seems to be widespread confusion, including in the movie itself, about whether to think about replicants as robots (i.e., hardware) …

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# Information Theory of Deep Neural Nets: “Information Bottleneck”

This talk discusses, in terms of information theory, how the hidden layers of a deep neural net (thought of as a Markov chain) create a compressed (coarse grained) representation of the input information. To date the success of neural networks has been a mainly empirical phenomenon, lacking a theoretical framework that explains how and why …

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# A Gentle Introduction to Neural Networks

“A gentle introduction to the principles behind neural networks, including backpropagation. Rated G for general audiences.” This very well done. If you have a quantitative background you can watch it at 1.5x or 2x speed, I think :-) A bit more on the history of backpropagation and convexity: why is the error function convex, or nearly …

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# Feynman, Schwinger, and Psychometrics

Slate Star Codex has a new post entitled Against Individual IQ Worries. I write a lot about the importance of IQ research, and I try to debunk pseudoscientific claims that IQ “isn’t real” or “doesn’t matter” or “just shows how well you do on a test”. IQ is one of the best-studied ideas in psychology, one …

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# Is there such a thing as “white hat” research ethics violations?

A couple of weeks ago, I posted about some of the ethical dilemmas involved in using public data for research, using an example of facial recognition researchers who used YouTube videos of people undergoing hormone replacement therapy to improve their algorithms’ ability to recognize faces from pre- and post-transition. Since reading that article, I’ve seen the occasional …

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# Accurate Genomic Prediction Of Human Height

I’ve been posting preprints on arXiv since its beginning ~25 years ago, and I like to share research results as soon as they are written up. Science functions best through open discussion of new results! After some internal discussion, my research group decided to post our new paper on genomic prediction of human height on …

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# Phase Transitions and Genomic Prediction of Cognitive Ability

James Thompson (University College London) recently blogged about my prediction that with sample size of order a million genotypes|phenotypes, one could construct a good genomic predictor for cognitive ability and identify most of the associated common SNPs. The Hsu Boundary … The “Hsu boundary” is Steve Hsu’s estimate that a sample size of roughly 1 …

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# Public data and digital research ethics

The Verge recently posted an article that highlights some of the ethical dilemmas involved in collecting publicly-available data for research purposes. The article begins by describing the work of a researcher working on facial recognition of people before and after hormone replacement therapy: On YouTube, he found a treasure trove. Individuals undergoing HRT often document their progress …

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# BENEFICIAL AI 2017 (Asilomar meeting)

AI researcher Yoshua Bengio gives a nice overview of recent progress in Deep Learning, and provides some perspective on challenges that must be overcome to achieve AGI (i.e., human-level general intelligence). I agree with Bengio that the goal is farther than the recent wave of excitement might lead one to believe. There were many other …

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# Collaboration for Conservation

I pick up the story of my PhD from Nanchong, China, where I have traveled to take a brief break from lab work to have meetings and an interview with representatives from the China Science and Technology Exchange Center (CSTEC). This summer I am here in China on an East Asia and Pacific Institute Summer …

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# Ninety-nine genetic loci influencing general cognitive function

The paper below has something like 200 authors from over 100 institutions worldwide. Many people claimed just a few years ago (or more recently!) that results like this were impossible. Will they admit their mistake? In Scientific Consensus on Cognitive Ability? I described the current consensus among experts as follows. 0. Intelligence is (at least …

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# Meanwhile, down on the Farm

The Spring 2017 issue of the Stanford Medical School magazine has a special theme: Sex, Gender, and Medicine. I recommend the article excerpted below to journalists covering the Google Manifesto / James Damore firing. After reading it, they can decide for themselves whether his memo is based on established neuroscience or bro-pseudoscience. Perhaps top Google …

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# In the matter of James Damore, ex-Googler

James Damore, Harvard PhD* in Systems Biology, and (until last week) an engineer at Google, was fired for writing this memo: Google’s Ideological Echo Chamber, which dares to display the figure above. Here is Damore’s brief summary of his memo (which contains many citations to original scientific research), and the conclusion: Google’s political bias has …

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# A day in the field

3:00 a.m. My alarm goes off. I open my eyes and see the Heilongjiang sun starting to rise. I close my eyes just for a minute more… (Editor’s note – China, while geographically spanning five time zones, follows only one for unity. That means far eastern locales like Heilongjiang see daybreak early.) 3:15 a.m. My …

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# Helpful resources for principal components analysis in R

I’m currently working on my dissertation proposal, which has meant exploring principal components analysis. I’ve worked with PCA before, but it’s been a couple of years, so I’m trying to refresh my memory, improve my understanding, and get this proposal moving! Along the way, I’ve found (and been recommended) some helpful resources that I thought …

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# China’s rise in Science and Engineering indicators (NSF)

Data from the 2016 NSF report on global Science & Engineering Indicators shows the rapid rise of China in both academic science and applied technology. Rapid growth in number of Chinese S&E articles, reaching parity with US in 2013, and well ahead of Japan and India. Fraction of high impact (top 1% most cited) papers highest for …

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# Robots taking our jobs

The figures below are from the recent paper Robots and Jobs: Evidence from US Labor Markets, by Acemoglu and Restrepo. VoxEU discussion: … Estimates suggest that an extra robot per 1000 workers reduces the employment to population ratio by 0.18-0.34 percentage points and wages by 0.25-0.5%. This effect is distinct from the impacts of imports, …

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# Like little monkeys: How the brain does face recognition

This is a Caltech TEDx talk from 2013, in which Doris Tsao discusses her work on the neuroscience of human face recognition. Recently I blogged about her breakthrough in identifying the face recognition algorithm used by monkey (and presumably human) brains. The algorithm seems similar to those used in machine face recognition: individual neurons perform …

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# First Human Embryos Edited in U.S. (MIT Technology Review)

It’s only a matter of time… Note this kind of work can be done very secretly and with very modest resources — it does not require banks of centrifuges, big reactors, or ICBM test launches. First Human Embryos Edited in U.S. (MIT Technology Review) Researchers have demonstrated they can efficiently improve the DNA of human …

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# Natural Selection and Body Shape in Eurasia

Prior to the modern era of genomics, it was claimed (without good evidence) that divergences between isolated human populations were almost entirely due to founder effects or genetic drift, and not due to differential selection caused by disparate local conditions. There is strong evidence now against this claim. Many of the differences between modern populations …

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# Back from, and onward to, the Orient

My China fieldwork this year splits into two trips – June to August, then January to October of next year. These will differ from my previous trips in that this time, I am funded directly from government sources (An East Asia and Pacific Summer Institute [EAPSI] fellowship this summer and a Fulbright grant next year). …

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# Don’t Touch the Computer

Under what circumstances should humans override algorithms? From what I have read I doubt that a hybrid team of human + AlphGo would perform much better than AlphaGo itself. Perhaps worse, depending on the epistemic sophistication and self-awareness of the human. In hybrid chess it seems that the ELO score of the human partner is …

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# Going where the questions are… not to mention the funding and position

Once again, I am currently adjusting to the Chinese way of life. Thankfully, this is not my first rodeo in China. I spent two months here last summer, so I am hoping most of the culture shock occurred then. That being said, this summer I will be attempting to collect data for my own dissertation …

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# Genetic variation in Han Chinese population

Largest component of genetic variation is a N-S cline (phenotypic N-S gradient discussed here). Variance accounted for by second (E-W) PC vector is much smaller and the Han population is fairly homogeneous in genetic terms: …while we revealed East-to-West structure among the Han Chinese, the signal is relatively weak and very little structure is discernible …

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# Memory Minimization

As I grow older, I’m starting to forget things (such as all the math I ever learned) … but that’s not the reason for the title of this post. A somewhat interesting question popped up on Mathematics StackExchange. It combines a basic sequencing problem (ordering the processing of computational tasks) with a single resource constraint …

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# Super-human Relational Reasoning (DeepMind)

These neural nets reached super-human (better than an average human) performance on tasks requiring relational reasoning. See the short video for examples. A simple neural network module for relational reasoning https://arxiv.org/abs/1706.01427 Adam Santoro, David Raposo, David G.T. Barrett, Mateusz Malinowski, Razvan Pascanu, Peter Battaglia, Timothy Lillicrap (Submitted on 5 Jun 2017) Relational reasoning is a …

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# Waves of grain

My car packed with too many clothes, an extremely terrified cat and a live Kombucha culture, I headed west to my summer field site. Oddly enough, my summer field site is also where I grew up. The endless waves of grain remind me of my labor-intensive childhood detasseling corn,1 walking beans2 and bucking bales.3  I …

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# Probing deep networks: inside the black box

See also AI knows best: AlphaGo “like a God”: Humans are going to have to learn to “trust the AI” without understanding why it is right. I often make an analogous point to my kids — “At your age, if you and Dad disagree, chances are that Dad is right” :-) Of course, I always …

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# Building the Gadget: A Technical History of the Atomic Bomb

This is the best technical summary of the Los Alamos component of the Manhattan Project that I know of. It includes, for example, detail about the hydrodynamical issues that had to be overcome for successful implosion. That work drew heavily on von Neumann’s expertise in shock waves, explosives, numerical solution of hydrodynamic partial differential equations, …

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# Machine intelligence threatens overpriced aircraft carriers

The excerpt below is from a recent comment thread, arguing that the US Navy should de-emphasize carrier groups in favor of subs and smaller surface ships. Technological trends such as rapid advancement in machine learning (ML) and sensors will render carriers increasingly vulnerable to missile attack in the coming decades. 1. US carriers are very …

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# How the brain does face recognition

This is a beautiful result. IIUC, these neuroscientists use the terminology “face axis” instead of (machine learning terminology) variation along an eigenface vector or feature vector. Scientific American: …using a combination of brain imaging and single-neuron recording in macaques, biologist Doris Tsao and her colleagues at Caltech have finally cracked the neural code for …

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# Face Recognition applied at scale in China

The Chinese government is not the only entity that has access to millions of faces + identifying information. So do Google, Facebook, Instagram, and anyone who has scraped information from similar social networks (e.g., US security services, hackers, etc.). In light of such ML capabilities it seems clear that anti-ship ballistic missiles can easily target …

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# An evolutionary theory of music

“The beauty of music is in the ear of the beholder”, we are always told. Or perhaps we are not always told this, but I imagine that we should be told that. Because while I like a lot of music that other people like, I don’t always agree with what other people say is–not just …

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# Premature Obituaries

[T]he report of my death was an exaggeration. (Mark Twain, 1897) In a recent blog post, “Data Science Is Not Dead“, Jean-Francois Puget discussed and dissented with a post by Jeroen ter Heerdt titled “Data Science is dead.” Barring the possibility that Schroedinger shoved data science into a box and sealed it, both assertions cannot …

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# What can the physics of spin crystals tell us about how we cooperate?

In the natural world, cooperation is everywhere. You can see it among people, of course, but not everybody cooperates all the time. Some people, as I’m sure you’ve heard or experienced, don’t really care for cooperation. Indeed, if cooperation were something that everybody does all the time, we wouldn’t even talk about it: we’d take …

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# Scientific Consensus on Cognitive Ability?

From the web site of the International Society for Intelligence Research (ISIR): a summary of the recent debate involving Charles Murray, Sam Harris, Richard Nisbett, Eric Turkheimer, Paige Harden, Razib Khan, Bo and Ben Winegard, Brian Boutwell, Todd Shackelford, Richard Haier, and a cast of thousands! ISIR is the main scientific society for researchers of …

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# Climate Risk and AI Risk for Dummies

The two figures below come from recent posts on climate change and AI. Please read them. The squiggles in the first figure illustrate uncertainty in how climate will change due to CO2 emissions. The squiggles in the second figure illustrate uncertainty in the advent of human-level AI.   Many are worried about climate change because …

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# Rise of the Machines: Survey of AI Researchers

These predictions are from a recent survey of AI/ML researchers. See SSC and also here for more discussion of the results. When Will AI Exceed Human Performance? Evidence from AI Experts Katja Grace, John Salvatier, Allan Dafoe, Baobao Zhang, Owain Evans Advances in artificial intelligence (AI) will transform modern life by reshaping transportation, health, science, …

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# Complex Trait Adaptation and the Branching History of Mankind

A new paper (94 pages!) investigates signals of recent selection on traits such as height and educational attainment (proxy for cognitive ability). Here’s what I wrote about height a few years ago in Genetic group differences in height and recent human evolution: These recent Nature Genetics papers offer more evidence that group differences in a …

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# Epistemic Caution and Climate Change

I have not, until recently, invested significant time in trying to understand climate modeling. These notes are primarily for my own use, however I welcome comments from readers who have studied this issue in more depth. I take a dim view of people who express strong opinions about complex phenomena without having understood the underlying …

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