February 2012
39 posts
The case for open computer programs →
According to an editorial in Nature, all scientific code should be released open source so that independent researchers can reproduce the results of a paper.
Here’s a link to the original Nature article (you will need a subscription). I appreciate the authors’ recognition of the work that we’ve done at Biostatistics.
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Statistics project ideas for students
Here are a few ideas that might make for interesting student projects at all levels (from high-school to graduate school). I’d welcome ideas/suggestions/additions to the list as well. All of these ideas depend on free or scraped data, which means that anyone can work on them. I’ve given a ballpark difficulty for each project to give people some idea.
Happy data crunching!
Data...
Gulf on Open Access to Federally Financed Research →
Advocates and opponents of “open access” for government-financed scientific research are girding for a long battle before Congress, which has little enthusiasm for either extreme.
Duke Taking New Steps to Safeguard Research... →
Here is a link to the press release from Duke regarding Anil Potti and the Duke Saga.
It’s impossible to develop a system that will completely eliminate academic fraud if a researcher is intent on misconduct, said Sally Kornbluth, vice dean for the basic sciences in the School of Medicine. “But this case highlighted that we can take a hard look at the infrastructure and the culture...
The Duke Saga Starter Set
A few of our recent posts relate to the Duke trial saga. For those that want to learn more, Baggerly and Coombes have put together a “starter set”. It includes
1. a video of one of their talks
2. the 60 Minutes episode and clip
3. slides from a recent presentation with some new details
4. their Annals of Applied Statistics paper
5. a editorial they wrote for Clinical Chemistry...
Graham & Dodd's Security Analysis: Moneyball...
The last time I posted something about finance I got schooled by people who actually know stuff. So let me just say that I don’t claim to be an expert in this area, but I do have an interest in it and try to keep up the best I can.
One book I picked up a little while ago was Security Analysis by Benjamin Graham and David Dodd. This is the “bible of value investing” and so I...
'WaterBillWoman' pestered city for years over... →
An interesting story about faulty water bills in Baltimore discovered via some shoe-leather data analysis.
In 2006, Stewart was running a business, the Gaslight Tavern, and managing two rental properties. Water bills weren’t exactly foremost in her mind.
Then the water bill for one of her rental properties jumped from $40 to $800, while her business received a bill showing it had used no...
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Prediction: the Lasso vs. just using the top 10...
One incredibly popular tool for the analysis of high-dimensional data is the lasso. The lasso is commonly used in cases when you have many more predictors than independent samples (the n « p) problem. It is also often used in the context of prediction.
Suppose you have an outcome Y and several predictors X1,…,XM, the lasso fits a model:
Y = B0 + B1 X1 + B2 X2 + … + BM XM +...
Monitoring Your Health With Mobile Devices →
Smartphones may some day help people take better control of their health by tracking it with increasing precision and convenience.
The question for me is will simply collecting more data make things better?
Professional statisticians agree: the knicks...
A week ago, Nate Silver tweeted this:
Since Lin became starting PG, Knicks have outscored opponents by 63 with Novak on the floor. Been outscored by 8 when he isn’t.
In a previous post we showed the plot below. Note that Carmelo Anthony is in ball hog territory. Novak plays the same position as Anthony but is a three point specialist. His career three point FG% of 42% (253-603) puts him...
Air Pollution Linked to Heart and Brain Risks →
Three studies published this week found that people exposed to pollutants have a higher risk of stroke, heart attacks and cognitive deterioration.
One study in particular by Jennifer Weuve at Rush University Medical Center examined fine PM and cognition in older women.
Dr. Weuve’s research followed 19,409 women in the United States between the ages of 70 and 81 for about a decade, looking at...
Interracial Couples Who Make the Most Money →
Among newlyweds, Asian grooms and white brides earn the most money between them, followed by white grooms and Asian brides.
Here is a link to the original report if you want to skip right to it.
Scientists Find New Dangers in Tiny but Pervasive... →
Gaseous byproducts that were thought to dissipate quickly are now found to evaporate more slowly and persist longer than anyone had thought.
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I don't think it means what ESPN thinks it means
Given ESPN’s recent headline difficulties it seems like they might want a headline editor or something…
60 Lives, 30 Kidneys, All Linked →
A record chain of kidney transplants resulted from a mix of medical need, pay-it-forward selflessness and lockstep coordination among 17 hospitals over four months.
This is a fascinating story of the longest “domino chain” of kidney transplantations yet done.
Domino chains, which were first attempted in 2005 at Johns Hopkins, seek to increase the number of people who can be helped...
Company Unveils DNA Sequencing Device Meant to Be... →
A British company plans to sell a disposable gene sequencing device that is the size of a USB memory stick and plugs into a laptop computer to deliver its results.
The latest in vaporware technology. Sounds cool, but
A drawback is that the Oxford machine has a 4 percent error rate, too high for many applications, including diagnosis.
How Companies Learn Your Secrets →
Your shopping habits reveal even the most personal information — like when you’re going to have a baby.
Andrew Pole had just started working as a statistician for Target in 2002, when two colleagues from the marketing department stopped by his desk to ask an odd question: “If we wanted to figure out if a customer is pregnant, even if she didn’t want us to know, can you do that?”
The real...
I.B.M.: Big Data, Bigger Patterns →
I.B.M. is the world’s largest employer of Ph.D.’s. It has plenty of businesses it can throw them at, but the trick is figuring out which ones will yield the best return. That happens by finding the algorithms for one industry, like power generation, that will work in another, like traffic management.
I.B.M., Mr. Mills [I.B.M.’s senior vice president for software and systems] said, is...
A Flat Budget for NIH in 2013 - ScienceInsider →
The President’s budget proposal would hold the National Institutes of Health’s (NIH’s) budget at the current level of $30.86 billion.
In order to squeeze more grants out of the flat budget—the target is an 8% increase in new grants, to 672, for a total of 9415—NIH will put in place new grant management policies. Continuing grants will be cut 1% below the 2012 level,...
Harvard's Stat 110 is now a course on iTunes
Back in January we interviewed Joe Blitzstein and pointed out that he made his lectures freely available on iTunes. Now it is a course on iTunes and the format has been upgraded to work better with iPhones and iPads. Enjoy!
Mathematicians Organize Boycott of a Publisher →
More than 5,700 researchers are denouncing the pricing policies of the journal publisher Elsevier in a growing furor over open access to the fruits of scientific research.
Mortimer Spiegelman Award: Call for Nominations....
The Statistics Section of the American Public Health Association invites nominations for the 2012 Mortimer Spiegelman Award honoring a statistician aged 40 or younger who has made outstanding contributions to health statistics, especially public health statistics. The award was established in 1970 and is presented annually at the APHA meeting. The award serves three purposes: to honor the...
The Duke Clinical Trials Saga: What Really... →
Following up on the 60 Minutes segment on the Duke Clinical Trials Saga, here’s a video of Keith Baggerly giving talk about his and Kevin Coombes’ investigation of the data and the methods. Thanks to Andrew J. for the link.
WatchDuke clinical trials saga on 60 Minutes. First, the back-to-back shot of Keith and Kevin is priceless. Second, I’ve never seen a cleaner desk in my life.
At MSNBC, a Professor as TV Host →
Melissa Harris-Perry, with her progressive talk show of the same name, is set to join MSNBC’s weekend lineup of cable news shows beginning Saturday.
Ms. Harris-Perry will be the only tenured professor in the United States — and one of a very small number of African-American women — who serves as a cable news host.
The article talks about how Ms. Harris-Perry had given a specific lecture at Tulane...
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Sunday Data/Statistics Link Roundup (2/12)
An awesome alternative to D3.js - R’s svgAnnotation package. Here’s the paper in JSS. I feel like this is one step away from gaining broad use in the statistics community - it still feels a little complicated building the graphics, but there is plenty of flexibility there. I feel like a great project for a student at any level would be writing some easy wrapper functions for these...
The Age of Big Data →
For those who can make sense of the explosion of data, there are job opportunities in fields as diverse as crime, retail and dating.
Veteran data analysts tell of friends who were long bored by discussions of their work but now are suddenly curious. “Moneyball” helped, they say, but things have gone way beyond that. “The culture has changed,” says Andrew Gelman, a statistician and political...
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Peter Thiel on Peer Review/Science
Peter Theil gives his take on science funding/peer review:
My libertarian views are qualified because I do think things worked better in the 1950s and 60s, but it’s an interesting question as to what went wrong with DARPA. It’s not like it has been defunded, so why has DARPA been doing so much less for the economy than it did forty or fifty years ago? Parts of it have become politicized. You...
Data says Jeremy Lin is for real
Nate Silver makes a table of all NBA players that have had four games in a row with 20+ points, 6+ assists, 50%+ shooting. The list is short (and it doesn’t include Kobe).
Duke Saga on 60 Minutes this Sunday
This Sunday February 12, the news magazine 60 Minutes will have a feature on the Duke Clinical Trials saga. Will Dr. Potti himself make an appearance? This is from the 60 Minutes web site:
Deception at Duke - Scott Pelley reports on a Duke University oncologist whose supervisor says he manipulated the data in his study of a breakthrough cancer therapy. Kyra Darnton is the producer.
The word on...
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An example of how sending a paper to a statistics...
In a previous post I complained about statistics journals taking way too long rejecting papers. Today I am complaining because even when everything goes right —better than above average review time (for statistics), useful and insightful comments from reviewers— we can come out losing.
In May 2011 we submitted a paper on removing GC bias from RNAseq data to Biostatistics. It was...
Statisticians and Clinicians: Collaborations Based... →
Don Berry, former head of the division of quantitative sciences and chair of the department of biostatistics at the M.D. Anderson Cancer Center has a great column in Amstat News discussing collaborations between statisticians and clinicians. There are a few very nice bits, but do read the full column.
The first is
We send clear messages to our clinical collaborators that we are as interested in...
DealBook: Illumina Formally Rejects Roche's... →
The battle for Illumina continues.
The genetic analysis services provider said that Roche’s $5.7 billion takeover offer was “grossly inadequate” and that the Swiss drug maker’s director candidates should be rejected.
Wolfram, a Search Engine, Finds Answers Within... →
Wolfram Alpha Pro’s creator wants his “computational knowledge engine” to appeal to more than math and science enthusiasts.
Is it me, or is there a nascent boomlet in “anti-search engines” like Wolfram Alpha?
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An R script for estimating future inflation via...
One factor that is critical for any financial planning is estimating what future inflation will be. For example, if you’re saving money in an instrument that gains 3% per year, and inflation is estimated to be 4% per year, well then you’re losing money in real terms.
There are a variety of ways to estimate the rate of future inflation. You could, for example, use past rates as an...
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Sunday Data/Statistics Link Roundup (2/5)
Cool app, you can write out an equation on the screen and it translates the equation to latex. Via Andrew G.
Yet another D3 tutorial. Stay tuned for some cool stuff on this front here at Simply Stats in the near future. Via Vishal.
Our favorite Greek statistician in the news again.
How measurement of academic output harms science. Related: is submitting scientific papers too time consuming?...
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Why don't we hear more about Adrian Dantley on...
In my last post I complained about efficiency not being discussed enough by NBA announcers and commentators. I pointed out that some of the best scorers have relatively low FG% or TS%. However, via the comments it was pointed out that top scorers need to take more difficult shots and thus are expected to have lower efficiency. The plot below (made with this R script) seems to confirm this (click...
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Cleveland's (?) 2001 plan for redefining...
This plan has been making the rounds on Twitter and is being attributed to William Cleveland in 2001 (thanks to Kasper for the link). I’m not sure of the provenance of the document but it has some really interesting ideas and is worth reading in its entirety. I actually think that many Biostatistics departments follow the proposed distribution of effort pretty closely.
One of the most...
Evidence-based Music
There was recently a fascinating article published in PNAS that compared the sound quality of different types of violins. In this study, researchers assembled a collection of six violins, three of which were made by Stradivari and Guarneri del Gesu and three made by modern luthiers (i.e. 20th century). The combined value of the “old” violins was $10 million, about 100 times greater...
