ENTRIES TAGGED "pydata"

Scaling up data frames

New frameworks for interactive business analysis and advanced analytics fuel the rise in tabular data objects.

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Long before the advent of “big data,” analysts were building models using tools like R (and its forerunners S/S-PLUS). Productivity hinged on tools that made data wrangling, data inspection, and data modeling convenient. Among R users, this meant proficiency with data frames — objects used to store data matrices that can hold both numeric and categorical data. A data.frame is the data structure consumed by most R analytic libraries.

But not all data scientists use R, nor is R suitable for all data problems. I’ve been watching with interest the growing number of alternative data structures for business analysis and advanced analytics. These new tools are designed to handle much larger data sets and are frequently optimized for specific problems. And they all use idioms that are familiar to data scientists — either SQL-like expressions, or syntax similar to those used for R data.frame or pandas.DataFrame.

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Interface Languages and Feature Discovery

It's easier to "discover" features with tools that have broad coverage of the data science workflow

Here are a few more observations based on conversations I had during the just concluded Strata Santa Clara conference.

Interface languages: Python, R, SQL (and Scala)
This is a great time to be a data scientist or data engineer who relies on Python or R. For starters there are developer tools that simplify setup, package installation, and provide user interfaces designed to boost productivity (RStudio, Continuum, Enthought, Sense).

Increasingly, Python and R users can write the same code and run it against many different execution1 engines. Over time the interface languages will remain constant but the execution engines will evolve or even get replaced. Specifically there are now many tools that target Python and R users interested in implementations of algorithms that scale to large data sets (e.g., GraphLab, wise.io, Adatao, H20, Skytree, Revolution R). Interfaces for popular engines like Hadoop and Apache Spark are also available – PySpark users can access algorithms in MLlib, SparkR users can use existing R packages.

In addition many of these new frameworks go out of their way to ease the transition for Python and R users. wise.io “… bindings follow the Scikit-Learn conventions”, and as I noted in a recent post, with SFrames and Notebooks GraphLab, Inc. built components2 that are easy for Python users to learn.

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Extending GraphLab to tables

The popular graph analytics framework extends its coverage of the data science workflow

GraphLab’s SFrame, an interesting and somewhat under-the-radar tool was unveiled1 at Strata Santa Clara. It is a disk-based, flat table representation that extends GraphLab to tabular data. With the addition of SFrame, users can leverage GraphLab’s many algorithms on data stored as either graphs or tables. More importantly SFrame increases GraphLab’s coverage of the data science workflow: it allows users with terabyte-sized datasets to clean their data and create new features directly within GraphLab (SFrame performance can scale linearly with the number of available cores).

The beta version of SFrame can read data from local disk, HDFS, S3 or a URL, and save to a human-readable .csv or a more efficient native format. Once an SFrame is created and saved to disk no reprocessing of the data is needed. Below is Python code that illustrates how to read a .csv file into SFrame, create a new data feature and save it to disk on S3:

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What I use for data visualization

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

It has roots in academic scientific computing, but has features that appeal to many data scientists

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)

IPython is more than just Python
With an interactive widget architecture that’s 100% language-agnostic, these days IPython is used by many other programming language communities2, including Julia, Haskell, F#, Ruby, Go, and Scala. If you’re a data scientist who likes to mix-and-match languages, you can create, maintain, and share multi-language data projects in IPython:

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A compelling family of DSLs for Data Science

The Delite framework has produced high-performance languages that target data scientists

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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Six reasons why I recommend scikit-learn

It's an extensive, well-documented, and accessible, curated library of machine-learning models

I use a variety of tools for advanced analytics, most recently I’ve been using Spark (and MLlib), R, scikit-learn, and GraphLab. When I need to get something done quickly, I’ve been turning to scikit-learn for my first pass analysis. For access to high-quality, easy-to-use, implementations1 of popular algorithms, scikit-learn is a great place to start. So much so that I often encourage new and seasoned data scientists to try it whenever they’re faced with analytics projects that have short deadlines.

I recently spent a few hours with one of scikit-learn’s core contributors Olivier Grisel. We had a free flowing discussion were we talked about machine-learning, data science, programming languages, big data, Paris, and … scikit-learn! Along the way, I was reminded by why I’ve come to use (and admire) the scikit-learn project.

Commitment to documentation and usability
One of the reasons I started2 using scikit-learn was because of its nice documentation (which I hold up as an example for other communities and projects to emulate). Contributions to scikit-learn are required to include narrative examples along with sample scripts that run on small data sets. Besides good documentation there are other core tenets that guide the community’s overall commitment to quality and usability: the global API is safeguarded, all public API’s are well documented, and when appropriate contributors are encouraged to expand the coverage of unit tests.

Models are chosen and implemented by a dedicated team of experts
scikit-learn’s stable of contributors includes experts in machine-learning and software development. A few of them (including Olivier) are able to devote a portion of their professional working hours to the project.

Covers most machine-learning tasks
Scan the list of things available in scikit-learn and you quickly realize that it includes tools for many of the standard machine-learning tasks (such as clustering, classification, regression, etc.). And since scikit-learn is developed by a large community of developers and machine-learning experts, promising new techniques tend to be included in fairly short order.

As a curated library, users don’t have to choose from multiple competing implementations of the same algorithm (a problem that R users often face). In order to assist users who struggle to choose between different models, Andreas Muller created a simple flowchart for users:

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Data Scientists and Data Engineers like Python and Scala

Python and Scala are popular among members of several well-attended SF Bay Area Meetups

In exchange for getting personalized recommendations many Meetup members declare1 topics that they’re interested in. I recently looked at the topics listed by members of a few local, data Meetups that I’ve frequented. These Meetups vary in size from 600 to 2,000 total (and 400 to 1,100 active2) members.

I was particularly interested in the programming languages members expressed interest in. What I found3 confirmed trends that we’ve noticed in other data sets (online job postings): Python has surpassed R among data scientists and data engineers, Scala is second to Java among JVM languages, and many folks are interested in Javascript. As pydata tools mature, I’ve encountered people who have shifted more of their data workflow from R over to Python.

Popular programming languages for select Meetups

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Data analysis tools target non-experts

Tools simplify the application of advanced analytics and the interpretation of results

A new set of tools make it easier to do a variety of data analysis tasks. Some require no programming, while other tools make it easier to combine code, visuals, and text in the same workflow. They enable users who aren’t statisticians or data geeks, to do data analysis. While most of the focus is on enabling the application of analytics to data sets, some tools also help users with the often tricky task of interpreting results. In the process users are able to discern patterns and evaluate the value of data sources by themselves, and only call upon expert1 data analysts when faced with non-routine problems.

Visual Analysis and Simple Statistics
Three SaaS startups – DataHero, DataCracker, Statwing – make it easy to perform simple data wrangling, visual analysis, and statistical analysis. All three (particularly DataCracker) appeal to users who analyze consumer surveys. Statwing and DataHero simplify the creation of Pivot Tables2 and suggest3 charts that work well with your data. StatWing users are also able to execute and view the results of a few standard statistical tests in plain English (detailed statistical outputs are also available).

Statistics and Machine-learning
BigML and Datameer’s Smart Analytics are examples of recent tools that make it easy for business users to apply machine-learning algorithms to data sets (massive data sets, in the case of Datameer). It makes sense to offload routine data analysis tasks to business analysts and I expect other vendors such as Platfora and ClearStory to provide similar capabilities in the near future.

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Python data tools just keep getting better

A variety of tools are making data science tasks easy to do in Python

Here are a few observations inspired by conversations I had during the just concluded PyData conference1.

The Python data community is well-organized:
Besides conferences (PyData, SciPy, EuroSciPy), there is a new non-profit (NumFOCUS) dedicated to supporting scientific computing and data analytics projects. The list of supported projects are currently Python-based, but in principle NumFOCUS is an entity that can be used to support related efforts from other communities.

It’s getting easier to use the Python data stack:
There are tools that facilitate the dissemination and sharing of code and programming environments. IPython2 notebooks allow Python code and markup in the same document. Notebooks are used to record and share complex workflows and are used heavily for (conference) tutorials. As the data stack grows, one of the major pain points is getting all the packages to work properly together (version compatibility is a common issue). In particular setting up environments were all the pieces work together can be a pain. There are now a few solutions that address this issue: Anaconda and cloud-based Wakari from Continuum Analytics, and cloud computing platform PiCloud.

There are many more visualization tools to choose from:
The 2D plotting tool matplotlib is the first tool enthusiasts turn to, but as I learned at the conference, there are a number of other options available. Continuum Analytics recently introduced companion packages Bokeh and Bokeh.js that simplify the creation of static and interactive visualizations using Python. In particular Bokeh is the equivalent of ggplot (it even has an interface that mimics ggplot). With Nodebox, programmers use Python code to create sketches and interactive visualizations that are similar to those produced by Processing. Read more…

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