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

# Randomness: Friend or Foe?

I spent a chunk of the weekend debugging some code (which involved solving an optimization problem). There was an R script to setup input files and a Java program to process them. The Java program included both a random heuristic to get things going and an integer program solved by CPLEX. Randomness in algorithms is …

More

# Getting Tenure in Digital and Public History, as a Non-Man

Earlier this week, the AHA’s Perspectives on History site published an article from LaDale Winling entitled “Getting Tenure in Digital History: How One Scholar Made His Case.” Dr. Winling presents arc of his career in the history department at Virginia Tech, from his hiring in 2011 to his tenure case in 2017. He suggests that candidates working in digital …

More

# National Council of Urban Indian Health 2d Annual Conference

I am delighted to be presenting a keynote speech titled “Race, Politics, and the Constitution” today for the National Council of Urban Indian Health (PR here). Francys Crevier (PLSI 2010), my former student, is the Executive Director of the organization. My talk will take the theme of my forthcoming paper “Politics, Indian Law, and the …

More

# CPLEX Callbacks: ThreadLocal v. Clone

A while back, I wrote a post about the new (at the time) “generic” callbacks in CPLEX, including a brief discussion of adventures with multiple threads. A key element was that, with generic callbacks, IBM was making the user more responsible for thread safety. In that previous post, I explored a few options for doing …

More

This was originally published at The Sports Column. ‘Enough Already!’ With Big Sports Salaries The elephant in the room is increasing income inequality—the outlandish incomes and escalating growth at the top of the income chain. Perhaps nowhere is that situation more evident than in athletics. Last month we saw two record-breaking salaries. The Phillies’ Bryce Harper signed for …

More

# Scholars, It’s Time to Take Control of Your Online Communities

Crossposted from the Humanities Commons Team blog. A couple of years ago, I got a bit fed up with the ways that certain for-profit networks were purporting to provide scholars with opportunities to share their work openly with one another, and I decided that it was time to mouth off about it a bit: about the fact …

More

# 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 …

More

# 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 …

More

# Pseudocode in LyX Revisited

This post is strictly for users of LyX. In a previous post I offered up a LyX module for typesetting pseudocode. Unfortunately, development of that module bumped up against some fundamental incompatibilities between the algorithmicx package and the way LyX layouts work. The repository for it remains open, but I decided to shift my efforts …

More

# Failures to Listen

One year ago today, Rachael Denhollander addressed the Ingham County court in Michigan, her abuser, and the institutions that failed to protect her and her #SisterSurvivors. Listen again to part of what she said on January 24, 2018: This is what it looks like when institutions create a culture where a predator can flourish unafraid and …

More

# Attitude of Possibility

Putting together a 1,000-piece jigsaw puzzle seems an appropriate metaphor for the challenges ahead of us as a human family. This one took my wife, Ellen, and me, about a week of coming and going. It was a good activity for some frigid, snowy days and evenings. We didn’t count the hours, we simply hovered …

More

# Guessing Pareto Solutions: A Test

In yesterday’s post, I described a simple multiple-criterion decision problem (binary decisions, no constraints), and suggested a possible way to identify a portion of the Pareto frontier using what amounts to guesswork: randomly generate weights; use them to combine the multiple criteria into a single objective function; optimize that (trivial); repeat ad nauseam. I ran …

More

# Guessing Pareto Solutions

One of the challenges of multiple-criteria decision-making (MCDM) is that, in the absence of a definitive weighting or prioritization of criteria, you cannot talk meaningfully about a “best” solution. (Optimization geeks such as myself tend to find that a major turn-off.) Instead, it is common to focus on Pareto efficient solutions. We can say that …

More

# Binary / Integer Conversion in R

I’ve been poking around in R with an unconstrained optimization problem involving binary decision variables. (Trust me, it’s not as trivial as it sounds.) I wanted to explore the entire solution space. Assuming $$n$$ binary decisions, this means looking at the set $$\{0,1\}^n$$, which contains $$2^n$$ 0-1 vectors of dimension $$n$$. For reasons I won’t …

More

# Does Behe’s “First Rule” Really Show that Evolutionary Biology Has a Big Problem?

Michael Behe has a new book coming out this month called Darwin Devolves. Nathan Lents, Joshua Swamidass, and I wrote a review of that book for the journal Science. (You can also find an open-access copy of our review here.) It provides an overview of the problems we see with his thesis and interpretations. As our …

More

# Food Fraud Education Schedule – Quarterly Update + MOOCs Now On-Demand

REGISTRATION AND COURSES OPEN: MSU Food Fraud MOOC programs – Free Food Fraud Overview Food Fraud Audit Guide Food Defense Audit Guide Food Fraud VACCP Implementation (Food Fraud Vulnerability Assessment FFVA & Food Fraud Prevention Strategy FFPS Development) Each MOOC is offered monthly, with the content available on-demand.  Live lecture webinar updates are offered semiannually. …

More

# 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 …

More

# 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 present 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 …

More

Yesterday I had a rather rude reminder (actually, two) of something I’ve known for a while. I was running a Java program that uses CPLEX to solve an integer programming model. The symptoms were as follows: shortly after the IP solver run started, I ran out of RAM, the operating system started paging memory to …

More

# 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) …

More

# 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 …

More

# Two Books – Real Gifts

I have a pile of about 10 books I’m wading through, but two are of special note as I write this. As I noted in my last blog of 2017 I have the privilege of reading, and especially of reading books. For the past few years I’ve read on average between 20-30 nonfiction works cover-to-cover per year. …

More

# On Fear, Parades of Horribles, and Emotionally Potent Oversimplifications in Tribal Rights Litigation

Will the state of Oklahoma revert back to the Indians? Will tribes veto non-Indian land use decisions? Will thousands of state prisoners go free? Will non-Indians have to give back their lands to Indians? In the last few years, in cases out of Oklahoma, Wyoming, Michigan, Washington, and elsewhere, advocates for states and non-Indian property owners have invoked …

More

# IceCube: neutrino astronomy in Antarctica

Tyce DeYoung (MSU Department of Physics and Astronomy) colloquium on high-energy astrophysics and exploration of the high-energy universe with the IceCube neutrino detector at the South Pole. Several MSU professors are part of the IceCube collaboration. I predict very exciting developments in neutrino astronomy in the coming decade ;-) The situation is similar to that …

More

For almost a decade I’ve been involved with the Football Scholars Forum, an online book club that TV wordsmith Ray Hudson labeled “the soccer think tank.” I also like to think of it as an intellectual pick up game. An informal space to read, reflect, try new things, network, learn, and engage in thoughtful conversations with fútbologists around the …

More

# The President. The Governor. The Economy 2018.

The State of the State Podcast discusses issues, questions, answers, policy and research on the hottest topics on the local, state and national stage. State of the State podcasters Interim IPPSR Director Arnold Weinfeld and Charles Ballard, Director of IPPSR’s State of the State Survey, will talk together and share the air with frequent guests …

More

# Living Values

In the open letter we wrote to the College of Arts & Letters community in January 2018, we promised to look critically at ourselves, recognize our failures, and rebuild the trust that is required of us. This commitment has led to an intense period of critical self-reflection in the Dean’s Office and across the College in …

More

# The Ecosystem for Organized Crime (and how to disrupt Food Fraud vulnerabilities)

This is a summary of Markus Felson’s 2006 report and presentation on The Ecosystem for Organized Crime (Felson, 2006). As is consistent with his other works and Situational Crime Prevention in general, the most efficient focus is on how and why a crime opportunity exists – which is more than just catching bad guys or bad …

More

# The Quantum Theory of Fields

Excerpt from Sidney Coleman’s Erice lectures. The period he describes just predates my entry into physics. This was a great time to be a high-energy theorist, the period of the famous triumph of quantum field theory. And what a triumph it was, in the old sense of the word: a glorious victory parade, full of …

More

# Of Typewriters and Permutations (V)

Okay, this is the last post on the subject. I promise! If you’re coming into this movie on the last reel, you may need to skim the last few posts to see what it’s about. I’m trying not to repeat myself too much. To summarize where we are at: Hardmath123 posted a solution (generated by …

More

# Of Typewriters and Permutations (IV)

I’m continuing the recent theme of solving a quadratic assignment problem that lays out the 26 letters of the English alphabet on a one-dimensional “keyboard” for an 18th century typewriter. I thought this would be the last post, but something new turned up, so there will likely be one more. In the blog post that …

More

# Of Typewriters and Permutations (III)

This continues the discussion (okay, monologue) from the two previous posts about the problem of laying out a one-dimensional typewriter keyboard. This is not the last post in the series, but I can at least guarantee that the series is converging. In the previous post, I gave a MIP model (named MIP1) that used binary …

More

# Of Typewriters and Permutations (II)

This continues my previous post about the problem of optimally laying out a one-dimensional typewriter keyboard, where “optimally” is taken to mean minimizing the expected amount of lateral movement to type a few selected books. As I noted there, Nate Brixius correctly characterized the problem as a quadratic assignment problem (QAP). I’ll in fact try …

More

# Of Typewriters and Permutations (I)

This is going to be the first of a few posts on the same problem. My efforts are based on a blog post by Nate Brixius (@natebrix) titled “Optimizing 19th Century Typewriters“, which in turn is based on a post titled “Tuning a Typewriter” by “Hardmath123”. As the image in Hardmath123’s post shows, an old …

More

# Time to Empty Your Pockets

I just made my self read the nine page “Executive Summary” of the recently (November 14) released Providing for the Common Defense: The Assessment and Recommendations of the National Defense Strategy Commission . It was all I could do to keep from gagging. I won’t put myself through the full 116 pages, especially as I scanned the …

More

# 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. …

More

# 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 …

More

# Back to Blue; Future Ahead

﻿ The State of the State Podcast discusses issues, questions, answers, policy and research on the hottest topics on the local, state and national stage. State of the State podcasters Interim IPPSR Director Arnold Weinfeld and Charles Ballard, Director of IPPSR’s State of the State Survey, will talk together and share the air with frequent …

More

# In Other Words (Week of November 5)

To the Right: https://rightmi.com/in-the-beginning/ Even from the beginning of Michigan’s current reapportionment process, there was chaos, Right.com notes. https://rightmi.com/michigan-2018-election-results/ A lineup of Michigan’s win’s and losses in Election 2016 with analysis about top races from Right.com. https://www.michigancapitolconfidential.com/whos-moving-up-in-next-years-michigan-legislature Michigan Capitol Confidential.com outlines the new state Legislature broken down by party and notes some key details, after …

More

# The Indian Child Welfare Act at 40

On this date in 1978, President Carter signed the Indian Child Welfare Act into law. Senator Abourezk introduced the bill to the Senate on April 1, 1977, and the Senate voted on it on November 4, 1977. Interestingly, while Sen. Goldwater supported the purpose of the bill, he did not vote on the Senate’s version …

More

# The Narcotic of Power

I still have two chapters to go before I finish Philippe Sands penetrating 2005 book, Lawless World: America and the Making and Breaking of Global Rules, so what follows might have been improved if I had finished before sharing these thoughts.  I can’t be sure if what follows is inspired by that engaging book, or the …

More

# The Limits of Our Thoughts

The reading pile keeps getting bigger. Each morning upon grabbing the coffee and nestling into a corner of the couch, I reach for one of the books in my reading pile. On the coffee table in front of the couch are the magazines that pile up – The Sun, The Atlantic, The Nation, Yes Magazine. Today I grabbed a …

More

Can there be an “adulterated food” that does not include an “adulterant”? Yes. Confused yet? Keep reading. The bottom line is that to avoid confusion it is recommended to use the terms “Food Fraud” or “adulterant-substance” when referring to the type of fraud that is a substance intentionally added for economic gain. This blog post …

More

# 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 …

More

# Stepwise Regression Code Revisited

I’ve added a few more tweaks to the stepwise regression code I published back in 2011. (If you wish, see here for the original post and here for a subsequent update.) The code does stepwise regression using F tests (or, equivalently, p-values of coefficients), which is a bit old fashioned but apparently how it is …

More

# 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 …

More

# Pseudocode in LyX

Fair warning: This post is for LyX users only. When I’m writing a paper or presentation in LaTeX (using LyX, of course) and want to include a program chunk or algorithm in pseudocode, I favor the algorithmicx package (and specifically the algpseudocode style). There being no intrinsic support for the package in LyX, I have …

More

# B.S.-ing Precisely

In a recent blog post titled “Excessive Precision“, John D. Cook points out the foolishness of articulating results to an arbitrarily high degree of precision when the inputs are themselves not that precise. To quote him: Excessive precision is not the mark of the expert. Nor is it the mark of the layman. It’s the …

More

# Physics as a Strange Attractor

Almost every student who attends a decent high school will be exposed to Special Relativity. Their science/physics teacher may not really understand it very well, may do a terrible job trying to explain it. But the kid will have to read a textbook discussion and (in the internet age) can easily find more with a …

More

# Population-wide Genomic Prediction of Health Risks

The UK is ahead of the US in the application of genomics in clinical practice. Part of this is due to their leadership in projects like the UK Biobank (500k genomes with extensive biomedical phenotyping), and part is due to having a single-payer system that can adopt obviously beneficial (and cost-beneficial) practices after some detailed …

More