What I use for data visualization

[A version of this post appears on the O’Reilly Data blog.]

Depending on the nature of the problem, data size, and deliverable, I still draw upon an array of tools for data visualization. As I survey the Design track at next month’s Strata conference, I see creators and power users of visualization tools that many data scientists have come to rely on. Several pioneers will lead sessions on (new) tools for creating static and interactive charts, against small and massive data sets.

The Grammar of Graphics
To this day, I find R (specifically ggplot2) to be a tool I turn to for producing static visualizations. Even the simplest charts allow me to quickly spot data problems and anomalies, and a tool like ggplot2 can accomplish a lot in very few lines of code. Charts produced by ggplot2 look much nicer than simple R plots and once you get past the initial learning curve, they are easy to fine-tune and customize.

Hadley Wickham1, the creator of ggplot2, is speaking on two new domain specific languages (ggvis and dplyr) that make it easy for R users to declaratively create interactive web graphics. As Hadley describes it, ggvis is interactive Grammar of Graphics for R. As more data scientists turn to interactive visualizations that can be shared through web browsers, ggvis is the natural next tool for ggplot2 users.

Leland Wilkinson, the primary author of The Grammar of Graphics2, will also be at Strata to lead a tutorial on an interesting expert system that lets machine-learning techniques be accessible to business users. Leland’s work has influenced many other visualization tools including Polaris (from the Stanford team that founded Tableau), Bokeh, and ggbio (for genomics data). Effective visualization techniques will be an important component of his Strata tutorial.

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IPython: A unified environment for interactive data analysis

[A version of this post appears on the O’Reilly data blog and Forbes.]

As I noted in a recent post on reproducing data projects, notebooks have become popular tools for maintaining, sharing, and replicating long data science workflows. Much of that is due to the popularity of IPython1. In development since 2001, IPython grew out of the scientific computing community and has slowly added features that appeal to data scientists.

Roots in academic scientific computing
As IPython creator Fernando Perez noted in his “historical retrospective”, exploratory analysis in a scientific setting requires a solid interactive environment. After years of development IPython has become a great tool for interacting with data. IPython also addresses other important pain points for scientists – reproducibility and collaboration – issues that are equally important to data scientists working in industry.

The Lifecycle of a Scientific Idea (schematically)

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Big Data systems are making a difference in the fight against cancer

[A version of this post appears on the O’Reilly Data blog and Forbes.]

As open source, big data tools enter the early stages of maturation, data engineers and data scientists will have many opportunities to use them to “work on stuff that matters”. Along those lines, computational biology and medicine are areas where skilled data professionals are already beginning to make an impact. I recently came across a compelling open source project from UC Berkeley’s AMPLab: ADAM is a processing engine and set of formats for genomics data.

Second-generation sequencing machines produce more detailed and thus much larger files for analysis (250+ GB file for each person). Existing data formats and tools are optimized for single-server processing and do not easily scale out. ADAM uses distributed computing tools and techniques to speedup key stages of the variant processing pipeline (including sorting and deduping):

Variant Calling Pipeline

Very early on the designers of ADAM realized that a well-designed data schema (that specifies the representation of data when it is accessed) was key to having a system that could leverage existing big data tools. The ADAM format uses the Apache Avro data serialization system and comes with a human-readable schema that can be accessed using many programming languages (including C/C++/C#, Java/Scala, php, Python, Ruby). ADAM also includes a data format/access API implemented on top of Apache Avro and Parquet, and a data transformation API implemented on top of Apache Spark. Because it’s built with widely adopted tools, ADAM users can leverage components of the Hadoop (Impala, Hive, MapReduce) and BDAS (Shark, Spark, GraphX, MLbase) stacks for interactive and advanced analytics.

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A compelling family of DSLs for Data Science

[A version of this post appears on the O’Reilly Data blog.]

An important reason why pydata tools and Spark appeal to data scientists is that they both cover many data science tasks and workloads (Spark users can move seamlessly between batch and streaming). Being able to use the same programming style and syntax for workflows that span a variety of tasks is a huge productivity boost. In the case of Spark (and Hadoop), the emergence of a variety of scalable analytic engines have made distributed computing applications much easier to build.

Delite: a framework for embedded, parallel, and high-performance DSLs
Another way to boost productivity is to use a family of high-performance languages that cover many data science tasks. Ideally you want languages that allow programmers to focus on applications (not on low-level details of parallel programming) and that can run efficiently on different machines and architectures1 (CPU, GPU). And just like pydata and Spark, syntax and context-switching shouldn’t get in the way of tackling complex data science workflows.

The Delite framework from Stanford’s Pervasive Parallelism Lab (PPL) has been used to produce a family of high-performance domain specific languages (DSLs) that target different data analysis tasks. DSLs are programming languages2 with restricted expressiveness (for a particular domain) and tend to be high-level in nature (they are often declarative and deterministic). Delite is a compiler and runtime infrastructure that allows language designers to use aggressive, domain-specific optimizations to deliver high-performance DSLs. Using Delite, the team at Stanford produced DSLs embedded in a functional language (Scala) with performance results comparable to hand-optimized implementations (e.g. MATLAB, LINQ) across different domains.

Delite DSLs

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