Spartan Ideas is a collection of thoughts, ideas, and opinions independently written by members of the MSU community and curated by MSU Libraries

# 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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# Humanities Commons and the Cultivation of Sustainable Communities

As we navigate the intense period of transformation in human communication through which we are living, identifying ways to nurture sustainable communities through which scholarship can be shared, discovered, and enhanced gains urgency. So many of the platforms through which we might cultivate scholarly lives together — Facebook, Twitter, Google, Academia.edu — are compromised by business models designed to maximize …

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# Dwelling on the Shoreline of Wonder

In one brief sentence, Ralph W. Sockman summarizes the goal of an MSU undergraduate education – Spartans Will. “The larger the island of knowledge, the longer the shoreline of wonder.” –        Ralph W. Sockman I recently ran across this quote from Ralph Sockman, who served as the host of the NBC radio program the National …

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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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# Remarks on the Decline of American Empire

Some gloomy remarks on the decline of the American Empire. 1. US foreign policy over the last decades has been disastrous — trillions of dollars and thousands of lives expended on Middle Eastern wars, culminating in utter defeat. This defeat is still not acknowledged among most of the media or what passes for intelligentsia in …

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# From the Beginning

It was five years ago today I transferred my meanderings since the mid 90s into this blog. 246 blog entries preceded this one with another dozen or so that never got past the draft stage. Probably many of the 246 should have stayed as drafts. So the occasion caused me to go back and look …

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# Practices of Weaving: Arts & Letters at MSU

Late last month, the faculty on the College Advisory Council (CAC) gave me a writing assignment. In preparation for our Fall 2017 faculty meeting on November 17, they asked me to take a step back from the updates on priorities, imperatives, and initiatives that have occupied our more recent faculty meetings, to articulate a broader vision of …

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# DOJ invokes Title VI against Harvard admissions

“Elections have consequences…” — Barack Obama See 20 years @15 percent: does Harvard discriminate against Asian-Americans? CNN: The Justice Department is actively investigating Harvard University’s use of race in its admissions policies and has concluded the school is “out of compliance” with federal law, according to documents obtained by CNN. … [Click through for DOJ …

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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

# MSU Student Success Themes

It is incumbent on all of us who work at MSU to make sure we create realistic pathways so that our students from all backgrounds can meet the learning objectives the faculty have established for MSU programs. At MSU, we believe that all students whom we admit have the ability to learn, persist, and graduate …

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# Article Review – Create Investigation Networks that Mirror the Criminal Network

[This is an excerpt from one of our recent peer-review scholarly journal articles.] Our article focused on a recommendation for how the Public Private Partnership – that is, governments working together with industry and others – could be optimized to reduce the ‘fraud opportunity.’ One co-author was Peter Whelan, who is the head of food …

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# Benders Decomposition with Generic Callbacks

Brace yourself. This post is a bit long-winded (and arguably geekier than usual, which is saying something). Also, it involves CPLEX 12.8, which will not ship until some time next month. I have an updated version of an old example, solving a fixed charge transportation problem using Benders decomposition. The example (using Java, naturally) is …

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# 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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# Review of ‘What’s Worth Teaching: Rethinking Curriculum in the Age of Technology’

I was recently asked to review with Charles Logan the book What’s Worth Teaching: Rethinking Curriculum in the Age of Technology by the incredible scholar Allan Collins. A link to the review and book on the Teachers College Record website here. A pre-print of our review is also available here.   Tweet

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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# What “R” qualitative research methods?

I recently stumbled upon a post on R-bloggers entitled “Qualitative Research in R.” This title got me pretty excited, since I’m generally excited about most things R and since I recently helped teach a qualitative methods course, which has had me thinking about adding more ethnographic and other qualitative elements to my work. I’d also heard of …

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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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# Two data packages: Rail-trails and an assessment of student achievement

Because of interest and the need for better examples (for teaching and for use in tools under development, such as prcr and tidyLPA, I worked to create two data packages, data easily available through an R package. A benefit of the data being in an R package is that it is even easier to access than other formats (in R): …

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# AlphaGo Zero: algorithms over data and compute

AlphaGo Zero was trained entirely through self-play — no data from human play was used. The resulting program is the strongest Go player ever by a large margin, and is extremely efficient in its use of compute (running on only 4 TPUs). Previous versions of AlphaGo initially trained on thousands of human amateur and professional games …

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# Practicing Gratitude

Last weekend was homecoming on the Michigan State University campus, and I found myself reflecting on the meaning and significance of gratitude. So many alumni returned to campus to give thanks for all the ways MSU set them on a meaningful path. In the College of Arts & Letters, we celebrated the generous gifts we received from …

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# Pictures worth thousands of words

The use of whiteboard presentations, especially for short presentations  seems very useful in getting the gyst of a speaker’s intent. Even more so than Powerpoint presentations. I first stumbled on one a few years ago when Sir Kenneth Robinson condense a longer speech into an 11 minute whiteboard presentation that was just brilliant!! When I …

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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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# Talking Ta-Nehisi Coates, Seriously?

Glenn Loury is Merton P. Stoltz Professor of the Social Sciences, Department of Economics, Brown University. John McWhorter is Associate Professor of English and Comparative Literature at Columbia University, where he teaches linguistics, American studies, philosophy, and music history. Loury (@19min): “He’s a good writer but not a deep thinker, and he’s being taken seriously …

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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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# Guns, More Guns – Will We Ever Have Enough?

We were away in Britain when news of the horrific massacre in Las Vegas occurred. We were actually approached on the street in the small Cornish town of Fowey by an older fellow who overheard us chatting and noted our North American accent. He wanted us to try and explain to him how it is …

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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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# Independent Streams (Week of October 2)

Problems Summit Held For Ending Campus Sexual Assault(link is external) IPPSR affiliate Rebecca Campbell explains common trauma-responses in sexual assault victims. ‘Fake News’ Course Aims To Improve Media Consumption And Production(link is external) IPPSR affiliate William Dutton comments on the impact of ‘fake news.’ Cooking Books: DOD, HUD Defrauded Taxpayers Of \$21 Trillion From 1998 to 2015(link …

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# Copyright, Fair Use, and Creative Commons in 7 more videos

Last year, I wrote a post about a series of YouTube videos that I used to give a guest lecture on copyright, fair use, and Creative Commons. It went well enough that I was asked to come back this year and guest lecture again. I made some tweaks to the presentation this time around, switching the order …

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# Where are participants in American and Canadian teacher hashtags?

My dissertation research is focused on Regional Educational Twitter Hashtags (RETHs), which are teacher-focused hashtags that are associated with particular geographic regions, such as American states or Canadian provinces or territories. This isn’t the first time that I’ve done a project on this phenomenon, and it’s rewarding to come back to RETHs to answer some questions that …

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# Sport and Social Justice in South Africa

Nelson Mandela would have been proud of Colin Kaepernick and the black (as well as a few white) U.S. athletes involved in the national anthem demonstrations against police violence and systemic racism. “Sport has the power to change the world,” Mandela believed. “It has the power to inspire. It has the power to unite people in a way that …

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# How Do Michiganders Feel About a Tax Cut? It Depends On What They Know

In March 2017, the Michigan House of Representatives narrowly voted down a proposal to reduce the income tax. But the issue of tax cuts continues to be discussed, both at the state and federal level. To gauge citizen opinions about tax cuts, MSU’s State of the State Survey asked Michigan residents questions about the proposed tax cut …

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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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# Getting started with ‘open science’ through blogging

Through a few different projects and people (such as SIPS and rOpenSci and conversations with friends / colleagues both online and offline), I have been exposed to the idea of open science. I’m actually going to punt for the moment. Here’s a definition that sounds about right to me: Open science is the movement to make scientific research, data and dissemination accessible …

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# A person-in-context approach to student engagement in science (article in JRST)

Over the past few years, I have worked with Jennifer Schmidt and Patrick Beymer to explore student engagement in science using the Experience Sampling Method (ESM). Most recently, we used what scholars have referred to as a “person-in-context” approach, using both ESM and a person-oriented approach. A figure is helpful for conveying how the person-oriented approach can be used to …

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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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# The Vietnam War, Ken Burns and Lynn Novick

Ken Burns’ Vietnam documentary is incredibly good. Possibly the best documentary I’ve ever seen. It’s heartbreaking tragedy, with perspectives from all sides of the conflict: Americans and North and South Vietnamese, soldiers from both sides, war protestors, war planners, families of sons and daughters who died in the war. I was a child when the …

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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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Advisors empower students to make life-altering decisions for themselves, armed with the best possible information. On Thursday, Sept. 21, 2017 I had the opportunity to speak at the first annual MSU Advisor Recognition Ceremony. Advising is a unique academic role on campus: in this role, advisors need to carefully balance giving students accurate and realistic …

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# Minimizing a Median

$$\def\xorder#1{x_{\left(#1\right)}} \def\xset{\mathbb{X}} \def\xvec{\mathbf{x}}$$A somewhat odd (to me) question was asked on a forum recently. Assume that you have continuous variables $$x_{1},\dots,x_{N}$$ that are subject to some constraints. For simplicity, I’ll just write $$\xvec=(x_{1},\dots,x_{N})\in\xset$$. I’m going to assume that $$\xset$$ is compact, and so in particular the $$x_{i}$$ are bounded. The questioner wanted to …

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# Some thoughts on starting year 5 (and French comics)

The image below, from the French comic book Carnets de thèse (“thesis notes”), has been on my mind as I begin my fifth year of grad school. I bought Carnets de thèse as a present for myself for my last birthday, expecting it to be an educational glimpse into the French grad school experience and …

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