A fair complaint when seeing yet another “data science” article is to say: “this is just medical statistics” or “this is already part of bioinformatics.” We certainly label many articles as “data science” on this blog. Probably the complaint is slightly cleaner if phrased as “this is already known statistics.” But the essence of the complaint is a feeling of claiming novelty in putting old wine in new bottles. Rob Tibshirani nailed this type of distinction in is famous machine learning versus statistics glossary.
I’ve written about statistics v.s. machine learning , but I would like to explain why we (the authors of this blog) often use the term data science. Nina Zumel explained being a data scientist very well, I am going to take a swipe at explaining data science.
We (the authors on this blog) label many of our articles as being about data science because we want to emphasize that the various techniques we write about are only meaningful when considered parts of a larger end to end process. The process we are interested in is the deployment of useful data driven models into production. The important components are learning the true business needs (often by extensive partnership with customers), enabling the collection of data, managing data, applying modeling techniques and applying statistics criticisms. The pre-existing term I have found that is closest to describing this whole project system is data science, so that is the term I use. I tend to use it a lot, because while I love the tools and techniques our true loyalty is to the whole process (and I want to emphasize this to our readers).
The phrase “data science” as in use it today is a fairly new term (made popular by William S. Cleveland, DJ Patil, and Jeff Hammerbacher). I myself worked in a “computational sciences” group in the mid 1990′s (this group emphasized simulation based modeling of small molecules and their biological interactions, the naming was an attempt to emphasize computation over computers). So for me “data science” seems like a good term when your work is driven by data (versus driven from computer simulations). For some people data science is considered a new calling and for others it is a faddish misrepresentation of work that has already been done. I think there are enough substantial differences in approach between traditional statistics, machine learning, data mining, predictive analytics, and data science to justify at least this much nomenclature. In this article I will try to describe (but not fully defend) my opinion. Read more…
Categories: data science, Expository Writing, Opinion, Pragmatic Data Science, Pragmatic Machine Learning, Statistics Tags: Data Mining, data science, data science project planning, information science, Machine Learning, Project Management, Statistics
Using correlation to track model performance is “a mistake that nobody would ever make” combined with a vague “what would be wrong if I did do that” feeling. I hope after reading this feel a least a small urge to double check your work and presentations to make sure you have not reported correlation where R-squared, likelihood or root mean square error (RMSE) would have been more appropriate.
It is tempting (but wrong) to use correlation to track the performance of model predictions. The temptation arises because we often (correctly) use correlation to evaluate possible model inputs. And the correlation function is often a convenient built-in function. Read more…
Given the range of wants, diverse data sources, required innovation and methods it often feels like data science projects are immune to planning, scoping and tracking. Without a system to break a data science project into smaller observable components you greatly increase your risk of failure. As a followup to the statistical ideas we shared in setting expectations in data science projects we share a few project planning ideas from software engineering. Read more…
It’s often the case that I want to write an R script that loops over multiple datasets, or different subsets of a large dataset, running the same procedure over them: generating plots, or fitting a model, perhaps. I set the script running and turn to another task, only to come back later and find the loop has crashed partway through, on an unanticipated error. Here’s a toy example:
> inputs = list(1, 2, 4, -5, 'oops', 0, 10)
> for(input in inputs) {
+ print(paste("log of", input, "=", log(input)))
+ }
[1] "log of 1 = 0"
[1] "log of 2 = 0.693147180559945"
[1] "log of 4 = 1.38629436111989"
[1] "log of -5 = NaN"
Error in log(input) : Non-numeric argument to mathematical function
In addition: Warning message:
In log(input) : NaNs produced
The loop handled the negative arguments more or less gracefully (depending on how you feel about NaN), but crashed on the non-numeric argument, and didn’t finish the list of inputs.
How are we going to handle this?
Read more…
Model level fit summaries can be tricky in R. A quick read of model fit summary data for factor levels can be misleading. We describe the issue and demonstrate techniques for dealing with them. Read more…
When people ask me what it means to be a data scientist, I used to answer, “it means you don’t have to hold my hand.” By which I meant that as a data scientist (a consulting data scientist), I can handle the data collection, the data cleaning and wrangling, the analysis, and the final presentation of results (both technical and for the business audience) with a minimal amount of assistance from my clients or their people. Not no assistance, of course, but little enough that I’m not interfering too much with their day-to-day job.
This used to be a key selling point, because people with all the necessary skills used to be relatively rare. This is less true now; data science is a hot new career track. Training courses and academic tracks are popping up all over the place. So there is the question: what should such courses teach? Or more to the heart of the question — what does a data scientist do, and what do they need to know?
Read more…
What does a generalized linear model do? R supplies a modeling function called glm() that fits generalized linear models (abbreviated as GLMs). A natural question is what does it do and what problem is it solving for you? We work some examples and place generalized linear models in context with other techniques. Read more…
Categories: data science, Expository Writing, Pragmatic Machine Learning, Statistics, Tutorials Tags: Genearlized Linear Model, GLM, Logistic Regression, logit, R, sigmoid, What does logistic regression do
One of the shortcomings of regression (both linear and logistic) is that it doesn’t handle categorical variables with a very large number of possible values (for example, postal codes). You can get around this, of course, by going to another modeling technique, such as Naive Bayes; however, you lose some of the advantages of regression — namely, the model’s explicit estimates of variables’ explanatory value, and explicit insight into and control of variable to variable dependence.
Here we discuss one modeling trick that allows us to keep categorical variables with a large number of values, and at the same time retain much of logistic regression’s power.
Read more…
A primary problem data scientists face again and again is: how to properly adapt or treat variables so they are best possible components of a regression. Some analysts at this point delegate control to a shape choosing system like neural nets. I feel such a choice gives up far too much statistical rigor, transparency and control without real benefit in exchange. There are other, better, ways to solve the reshaping problem. A good rigorous way to treat variables are to try to find stabilizing transforms, introduce splines (parametric or non-parametric) or use generalized additive models. A practical or pragmatic approach we advise to get some of the piecewise reshaping power of splines or generalized additive models is: a modeling trick we call “masked variables.” This article works a quick example using masked variables. Read more…
The design of the statistical programming language R sits in a slightly uncomfortable place between the functional programming and object oriented paradigms. The upside is you get a lot of the expressive power of both programming paradigms. A downside of this is: the not always useful variability of the language’s list and object extraction operators.
Towards the end of our write-up Survive R we recommended using explicit environments with new.env(hash=TRUE,parent=emptyenv()), assign() and get() to simulate mutable string-keyed maps for storing results. This advice rose out of frustration with the apparent inconsistency with the user facing R list operators. In this article we bite the bullet and discuss the R list operators a bit more clearly. Read more…
