This is a nice article in the popular press that talks about some of the problems with “black box” models (in particular deep neural nets) used extensively in many big data projects. It is a bit shy on technical details, which is understandable for a paper like the New York Times. Even so, the stories are quite intriguing. This is a wake up call for those people who fail to recognize the serious problems with many big data models. Continue reading

# Tag Archives: Big data

# Recommended: beanumber repository

This is the github repository of Ben Baumer. He is one of the co-authors of “Modern Data Science with R” and the data and code from that book is available here. He also provides code and data for OpenWAR, an open source method for calculating a baseball statistic, Wins Above Replacement. Finally, there is an R library for extracting, transforming, and loading “medium” sized datasets into SQL. Medium here means multi-gigabyte sized files. Related to this are a couple of “medium” sized data sets from the Internet Movie Database and from the NYC CitiBike dataset. Continue reading

# Recommended: Teaching precursors to data science in introductory and second courses in statistics

This paper talks about how to get students to think about large databases in an introductory class that normally uses “toy” problems with a few dozen rows of data. Continue reading

# Recommended: This is your machine learning system?

This xkcd cartoon by Scott Munro is open source, so I can hotlink the image directly. But if you go to the source, https://xkcd.com/1838/, be sure to hover over the image for a second punch line.

# Recommended: ROSE: A package for binary imbalanced learning

Logistic regression and other statistical methods for predicting a binary outcome run into problems when the outcome being tested is very rare, even in data sets big enough to insure that the rare outcome occurs hundreds or thousands of times. The problem is that attempts to optimize the model across all of the data will end up looking predominantly at optimizing the negative cases, and could easily ignore and misclassify all or almost all of the positive cases since they consistute such a small percentage of the data. The ROSE package generates artificial balanced samples to allow for better estimation and better evaluation of the accuracy of the model. Continue reading

# Recommended: How Bright Promise in Cancer Testing Fell Apart

A nice overview of the problems with shoddy research in genetics testing. It highlights the work of “forensic statistics” of Keith Baggerly and Kevin Coombes. Continue reading

# Recommended: Standards and guidelines for the interpretation of sequence variants

This article outlines a standardized way to describe genetic variants.

# Recommended: Genetics: Clues in the code

If you want to understand the value of genomic medicine, you can learn a lot by reviewing the case of Nicholas Volker, one of the first success stories in this area. Here’s a nice review. Continue reading

# Recommended: Text Mining with R

This is an O’Reilly book (cute animal on the cover is a rabbit) that is available online for free. It’s a great resource for someone just getting started with text mining. Continue reading

# PMean: Examining the storage format for sparse matrices in R

I’ve been working with sparse matrices a bit for my work with the Greater Plains Collaborative. They are a very useful way of storing matrices where most of the entries are zero. This occurs quite often in medical data. There are thousands of medical procedures that you can torture your patients with, so any matrix that has indicator variables for every medical procedure will be quite big. Fortunately, both for us and for the patients, the number of procedures that a particular patient has to endure is quite a bit smaller. So for each row of the matrix, the number of non-zero entries will be very small, probably in the single digits. A sparse matrix will be much smaller because it stores only the location of the non-zero entries. Here’s some R code that shows how this works. I have the code available at my new github site. Continue reading