Interview Antonio Piccolboni Big Data Analytics RHadoop #rstats

Antonio (AP)- I completed my undergrad in CS in Italy. I liked research and industry didn’t seem so exciting back then, both because of the lack of a local industry and the Microsoft monopoly, so I entered the PhD program.

After a couple of false starts I focused on bioinformatics. I was very fortunate to get involved in an international collaboration and that paved the way for a move to the United States. I wanted to work in the US as an academic, but for a variety of reasons that didn’t work out.

Instead I briefly joined a new proteomics department in a mass spectrometry company, then a research group doing transcriptomics, also in industry, but largely grant-funded. That’s the period when I accumulated most of my citations.

After several years there, I realized that bioinformatics was not offering the opportunities I was hoping for and that I was missing out on great changes that were happening in the computer industry, in particular Hadoop, so after much deliberation I took the plunge and worked first for a web ratings company and then a social network, where I took the role of what is now called a “data scientist”, using the statistical skills that I acquired during the first part of my career. After taking a year off to work on my own idea I became a free lance and Revolution Analytics one of my clients, and I became involved in RHadoop.

As you can see there were several turning points. It seems to me one needs to seek a balance of determination and flexibility, both mental and financial, to explore different options, while trying to make the most of each experience. Also, be at least aware of what happens outside your specialty area. Finally, the mandatory statistical warning: any generalizations from a single career are questionable at best.

2. Test your code. Since proving code correct is unfeasible for the vast majority of projects, development is more like an experimental science, where you assemble programs and then corroborate that they have the desired properties via experiments. Testing can have many forms, but no testing is no option.

3. Many seem to think that programming is an abstract activity somewhere in between mathematics and machines. I think a developer’s constituency are people, be them the millions using a social network or the handful using a specialized API. So I try to understand how people interact with my work, what they try to achieve, what their background is and so forth.

4. Programming is a difficult activity, meaning that failure happens even to the best and brightest. Learning to take risk into account and mitigate it is very important.

5. Programs are dynamic artifacts. For each line of code, one may not only ask if it is correct but for how long, as assumptions shift, or how often it will be executed. For a feature, one could wonder how many will use it, and how many additional lines of code will be necessary to maintain it.

6. Bonus statistical suggestion: check the assumptions. Academic statistics has an emphasis on theorems and optimality, bemoaned already by Tukey over sixty years ago. Theorems are great guides for data analysis, but rely on assumptions being met, and, when they are not, consequences can be unpredictable. When you apply the most straightforward, run of the mill test or estimator, you are responsible for checking the assumptions, or otherwise validating the results. “It looked like a normal distribution” won’t cut it when things go wrong.

AP-Hadoop is for data and R is for statistics, to use slogans, so it’s natural to ask the question of how to combine them, and RHadoop is one possible answer.

We selected a few important components of Hadoop and provided an R API. plyrmr is an offshoot of rmr, which is an API to the mapreduce system. While rmr has enjoyed some success, we received feedback that a simplified API would enable even more people to directly access and analyze the data.Again based on feedback we decided to focus on structured data, equivalent to an R data frame. We tried to reduce the role of user-defined functions as parameters to be fed into the API, and when custom functions are needed they are simpler. Grouping and regrouping the data is fundamental to mapreduce. While in rmr the programmer has to process two data structures, one for the data itself and the other describing the grouping, plyrmr uses a very familiar SQL-like “group” function.

Finally, we added a layer of delayed evaluation that allows to perform certain optimizations automatically and encourages reuse by reducing the cost of abstraction. We found enough commonalities with the popular package plyr that we decided to use it as a model, hence the tribute in the name. This lowers the cognitive burden for a typical user.

AP- It’s always a trade-off between power and ease of use, however I believe that the ability to express analyses in a repeatable and communicable way is fundamental to science and necessary to business and one of the key elements in the success of R. I haven’t seen a point and click GUI that satisfies these requirements yet, albeit it’s not inconceivable. For me, the most fruitful effort is still on languages and APIs. While some people write their own algorithms, the typical data analyst needs a large repertoire of algorithms that can be applied to specific problems. I see a lot of straightforward adaptations of sequential algorithms or parallel algorithms that work at smaller scales, and I think that’s the wrong direction. Extreme data sizes call for algorithms that work within stricter memory, work and communication constraints than before. On the other hand, the abundance of data, at least in some cases, offers the option of using less powerful or efficient statistics. It’s a trade off whose exploration has just started.

AP- I think becoming a freelancer affords me a flexibility that employed work generally lacks. I can put in more or fewer hours depending on competing priorities and can move them around other needs, like being with family in the morning or going for a bike ride while it’s sunny.  I am not sure I manage my time incredibly well, but I try to keep track of where I spend it at least by broad categories, whether I am billing it to a client or not. “If you can not measure it, you can not improve it”, a quote usually attributed to Lord Kelvin.

AP- One of the most interesting things that are happening right now is the development of different R interpreters. A successful language needs at least two viable implementations in my opinion. None of the alternatives is ready for prime time at the moment, but work is ongoing. Some implementations are experimental but demonstrate technological advances that can be then incorporated into the other interpreters. The main challenge is transitioning the language and the community to the world of parallel and distributed programming, which is a hardware-imposed priority. RHadoop is meant to help with that, for the largest data sets. Collaboration and publishing on the web is being addressed by many valuable tools and it looks to me the solutions exist already and it’s more a problem of adoption.  For the enterprise, there are companies offering training, consulting, licensing,  centralized deployments,  database APIs, you name it. It would be interesting to see touch interfaces applied to interactive data visualization, but while there is progress on the latter, touch on desktop is limited to a single platform and R doesn’t run on mobile, so I don’t see it as an imminent development.

About–

Antonio Piccolboni is an  experienced data scientist (Flowingdata, Radar on this emerging role) with industrial and academic backgrounds currently working as an independent consultant on big data analytics. His clients include Revolution Analytics. His other recent work is on social network analysis (hi5) and web analytics (Quantcast). You can contact him via http://piccolboni.info/about.html or his LinkedIn profile