The Year in Machine Learning (Part Two)

This is the second installment in a four-part review of 2016 in machine learning and deep learning. Part One, here, covered general trends. In Part Two, we review the year in open source machine learning and deep learning projects. Parts Three and Four will cover commercial machine learning and deep learning software and services.

There are thousands of open source projects on the market today, and we cannot cover them all. We’ve selected the most relevant projects based on usage reported in surveys of data scientists, as well as development activity recorded in OpenHub.  In this post, we limit the scope to projects with a non-profit governance structure, and those offered by commercial ventures that do not also provide licensed software. Part Three will include software vendors who offer open source “community” editions together with commercially licensed software.

R and Python maintained their leadership as primary tools for open data science. The Python versus R debate continued amid an emerging consensus that data scientists should consider learning both. R has a stronger library of statistics and machine learning techniques and is agiler when working with small data. Python is better suited to developing applications, and the Python open source license is less restrictive for commercial application development.

Not surprisingly, deep learning frameworks were the most dynamic category, with TensorFlow, Microsoft Cognitive, and MXNet taking leadership away from more mature tools like Caffe and Torch. It’s remarkable that deep learning tools introduced as recently as 2014 now seem long in the tooth.

The R Project

The R user community continued to expand in 2016. It ranked second only to SQL in the 2016 O’Reilly Data Science Salary Survey; first in the KDNuggets poll; and first in the Rexer survey. R ranked fifth in the IEEE Spectrum ranking.

R functionality grew at a rapid pace. In April, Microsoft’s Andrie de Vries reported that there were more than 8,000 packages in CRAN, R’s primary repository for contributed packages. As of mid-December, there are 9,737 packages.  Machine learning packages in CRAN continued to grow in number and functionality.

The R Consortium, a Collaborative Project of the Linux Foundation, made some progress in 2016. IBM and ESRI joined the Consortium, whose membership now also includes Alteryx, Avant, DataCamp, Google, Ketchum Trading, Mango Solutions, Microsoft, Oracle, RStudio, and TIBCO. There are now three working groups and eight funded projects.

Hadley Wickham had a good year. One of the top contributors to the R project, Wickham co-wrote R for Data Science and released tidyverse 1.0.0 in September. In The tidy tools manifesto, Wickham explained the four basic principles to a tidy API.

Max Kuhn, the author of Applied Predictive Modeling and developer of the caret package for machine learning, joined RStudio in November. RStudio previously hired Joseph Rickert away from Microsoft.

AT&T Labs is doing some impressive work with R, including the development of a distributed back-end for out-of-core processing with Hadoop and other data platforms. At the UseR! Conference, Simon Urbanek presented a summary.

It is impossible to enumerate all of the interesting analysis performed in R this year. David Robinson’s analysis of Donald Trump’s tweets resonated; using tidyverse, tidytext, and twitteR, Robinson was able to distinguish between the candidate’s “voice” and that of his staffers on the same account.

On the Revolutions blog, Microsoft’s David Smith surveyed the growing role of women in the R community.

Microsoft and Oracle continued to support enhanced R distributions; we’ll cover these in Part Three of this survey.


Among data scientists surveyed in the 2016 KDNuggets poll, 46% said they use Python for analytics, data mining, data science or machine learning projects in the past twelve months. That figure was up from 30% in 2015, and second only to R. In the 2016 O’Reilly Data Science Salary Survey, Python ranked third behind SQL and R.

Python Software Foundation (PSF) expanded the number and dollar value of its grants. PSF awarded many small grants to groups around the world that promote Python education and training. Other larger grants went to projects such as the design of the Python in Education site, improvements to the packaging ecosystem (see below), support for the Python 3.6 beta 1 release sprint, and support for major Python conferences.

The Python Packaging Authority launched the Warehouse project to replace the existing Python Packaging Index (PyPI.) Goals of the project include updating the visual identity, making packages more discoverable and improving support for package users and maintainers.

PSF released Python 3.6.0 and Python 2.7.13 in December.  The scikit-learn team released Version 0.18 with many enhancements and bug fixes; maintenance release Version 0.18.1 followed soon after that.

Many of the key developments for machine learning in Python were in the form of Python APIs to external packages, such as Spark, TensorFlow, H2O, and Theano. We cover these separately below.

Continuum Analytics expanded its commercial support for Python during the year and added commercially licensed software extensions which we will cover in Part Three.

Apache Software Foundation

There are ten Apache projects with machine learning capabilities. Of these, Spark has the most users, active contributors, commits, and lines of code added. Flink is a close second in active development, although most Flink devotees care more about its event-based streaming than its machine learning capabilities.

Top-Level Projects

There are four top-level Apache projects with machine learning functionality: Spark, Flink, Mahout, and OpenNLP.

Apache Spark

The Spark team delivered Spark 2.0, a major release, and six maintenance releases. Key enhancements to Spark’s machine learning capabilities in this release included additional algorithms in the DataFrames-based API, in PySpark and in SparkR, as well as support for saving and loading ML models and pipelines. The DataFrames-based API is now the primary interface for machine learning in Spark, although the team will continue to support the RDD-based API.

GraphX, Spark’s graph engine, remained static. Spark 2.0 included many other enhancements to Spark’s SQL and Streaming capabilities.

Third parties added 24 machine learning packages to Spark Packages in 2016.

The Spark user community continued to expand. Databricks reported 30% growth in Spark Summit attendees and 240% growth in Spark Meetup members. 18% of respondents to Databricks’ annual user survey reported using Spark’s machine learning library in production, up from 13% in 2015. Among data scientists surveyed in the 2016 KDNuggets poll, 22% said they use Spark; in the 2016 O’Reilly Data Science Salary Survey, 21% of the respondents reported using Spark.

The Databricks survey also showed that 61% of users work with Spark in the public cloud, up from 51% in 2015. As of December 2016, there are Spark services available from each of the major public cloud providers (AWS, Microsoft, IBM and Google), plus value-added managed services for data scientists from Databricks, Qubole, Altiscale and Domino Data.

Apache Flink

dataArtisans’ Mike Winters reviewed Flink’s accomplishments in 2016 without using the words “machine learning.” That’s because Flink’s ML library is still pretty limited, no doubt because Flink’s streaming runtime is the primary user attraction.

While there are many use cases for scoring data streams with predictive models, there are few real-world use cases for training predictive models on data streams. Machine learning models are useful when they generalize to a population, which is only possible when the process that creates the data is in a steady state. If a process is in a steady state, it makes no difference whether you train on batched data or streaming data; the latest event falls into the same mathematical space as previous events. If recent events produce major changes to the model, the process is not in a steady state, so we can’t rely on the model to predict future events.

Flink does not yet support PMML model import, a relatively straightforward enhancement that would enable users to generate predictions on streaming data with models built elsewhere. Most streaming engines support this capability.

There may be use cases where Flink’s event-based streaming is superior to Spark’s micro-batching. For the most part, though, Flink strikes me as an elegant solution looking for a problem to solve.

Apache Mahout

The Mahout team released four double-dot releases. Key enhancements include the Samsara math environment and support for Flink as a back end. Most of the single machine and MapReduce algorithms are deprecated, so what’s left is a library of matrix operators for Spark, H2O, and Flink.

Apache OpenNLP

OpenNLP is a machine learning toolkit for processing natural language text. It’s not dead; it’s just resting.

Incubator Projects

In 2016, two machine learning projects entered the Apache Incubator, while no projects graduated, leaving six in process at the end of the year: SystemML, PredictionIO, MADLib, SINGA, Hivemall, and SAMOA. SystemML and Hivemall are the best bets to graduate in 2017.

Apache SystemML

SystemML is a library of machine learning algorithms that run on Spark and MapReduce, originally developed by IBM Research beginning in 2010. IBM donated the code to Apache in 2015; since then, IBM has committed resources to developing the project. All of the major contributors are IBM employees, which begs the question: what is the point of open-sourcing software if you don’t attract a community of contributors?

The team delivered three releases in 2016, adding algorithms and other features, including deep learning and GPU support. Given the support from IBM, it seems likely that the project will hit Release 1.0 this year and graduate to top-level status.

Usage remains light among people not employed by IBM. There is no “Powered By SystemML” page, which implies that nobody else uses it. IBM added SystemML to BigInsights this year, which expands the potential reach to IBM-loyal enterprises if there are any of those left. It’s possible that IBM uses the software in some of its other products.

Apache PredictionIO

PredictionIO is a machine learning server built on top of an open source stack, including Spark, HBase, Spray, and Elasticsearch. An eponymous startup began work on the project in 2013; Salesforce acquired the company earlier this year and donated the assets to Apache. Apache PredictionIO entered the Apache Incubator in May.

Apache PredictionIO includes many templates for “prebuilt” applications that use machine learning. These include an assortment of recommenders, lead scoring, churn prediction, electric load forecasting, sentiment analysis, and many others.

Since entering the Incubator, the team has delivered several minor releases. Development activity is light, however, which suggests that Salesforce isn’t doing much with this.

Apache SINGA

SINGA is a distributed deep learning project originally developed at the National University of Singapore and donated to Apache in 2015. The platform currently supports feed-forward models, convolutional neural networks, restricted Boltzmann machines, and recurrent neural networks.  It includes a stochastic gradient descent algorithm for model training.

The team has delivered three versions in 2016, culminating with Release 1.0.0 in September. The release number suggests that the team thinks the project will soon graduate to top-level status; they’d better catch up with paperwork, however, since they haven’t filed status reports with Apache in eighteen months.

Apache MADLib

MADLib is a library of machine learning functions that run in PostgreSQL, Greenplum Database and Apache HAWQ (incubating). Work began in 2010 as a collaboration between researchers at UC-Berkeley and data scientists at EMC Greenplum (now Pivotal Software). Pivotal donated the software assets to the Apache Software Foundation in 2015, and the project entered Apache incubator status.

In 2016, the team delivered three minor releases. The active contributor base is tiny, averaging three contributors per month.

According to a survey conducted by the team, most users have deployed the software on Greenplum database. Since Greenplum currently ranks 35th in the DB-Engines popularity ranking and is sinking fast, this project doesn’t have anywhere to go unless the team can port it to a broader set of platforms.

Apache Hivemall

Originally developed by Treasure Data and donated to the Apache Software Foundation, Hivemall is a scalable machine learning library implemented as a collection of Hive UDFs designed to run on Hive, Pig or Spark SQL with MapReduce, Tez or Spark. The team organized in September 2016 and plans an initial release in Q1 2017.

Given the relatively mature state of the code, large installed base for Hive, and high representation of Spark committers on the PMC, Hivemall is a good bet for top-level status in 2017.

Apache SAMOA

SAMOA entered the Apache Incubator two years ago and died. It’s a set of distributed streaming machine learning algorithms that run on top of S4, Storm, and Samza.

As noted above, under Flink, there isn’t much demand for streaming machine learning. S4 is moribund, Storm is old news and Samza is going nowhere; so, you can think of SAMOA as like an Estate Wagon built on an Edsel chassis. Unless the project team wants to port the code to Spark or Flink, this project is toast.

Machine Learning Projects

This category includes general-purpose machine learning platforms that support an assortment of algorithms for classification, regression, clustering and association. Based on reported usage and development activity, we cover H2O, XGBoost, and Weka in this category.

Three additional projects are worth noting, as they offer graphical user interfaces and appeal to business users. KNIME and RapidMiner provide open-source editions of their software together with commercially licensed versions; we cover these in Part Three of this survey. Orange is a project of the Bioinformatics Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Slovenia.

Vowpal Wabbit gets an honorable mention. Known to Kaggleists as a fast and efficient learner, VW’s user base is currently too small to warrant full coverage. The project is now domiciled at Microsoft Research. It will be interesting to see if MSFT does anything with it.


H2O is an open source machine learning project of, a commercial venture. (We’ll cover’s business accomplishments in Part Three of this report.)

In 2016, the H2O team updated Sparkling Water for compatibility with Spark 2.0. Sparkling Water enables data scientists to combine Spark’s data ingestion and ETL capabilities with H2O machine learning algorithms. The team also delivered the first release of Steam, a component that supports model management and deployment at scale, and a preview of Deep Water for deep learning.

For 2017, plans to add an automated machine learning capability and deliver a production release of Deep Water, with support for TensorFlow, MXNet and Caffe back ends.

According to, H2O more than doubled its user base in 2016.


A project of the University of Washington’s Distributed Machine Learning Common (DMLC), XGBoost is an optimized distributed gradient boosting library used by top data scientists, who appreciate its scalability and accuracy. Tianqi Chen and Carlos Guestrin published a paper earlier this year describing the algorithm. Machine learning startups DataRobot and Dataiku added XGBoost to their platforms in 2016.


Weka is a collection of machine learning algorithms written in Java, developed at the University of Waikato in New Zealand and distributed under GPU license. Pentaho and RapidMiner include the software in their commercial products.

We include Weka in this review because it is still used by a significant minority of data scientists; 11% of those surveyed in the annual KDnuggets poll said they use the software. However, reported usage is declining rapidly, and development has virtually flatlined in the past few years, which suggests that this project may go the way of the eponymous flightless bird.

Deep Learning Frameworks

We include in this category software whose primary purpose is deep learning. Many general-purpose machine learning packages also support deep learning, but the packages listed here are purpose-built for the task.

Since they were introduced in late 2015, Google’s TensorFlow and Microsoft’s Cognitive Toolkit have rocketed from nothing to leadership in the category. With backing from Amazon and others, MXNet is coming on strong, while Theano and Keras have active communities in the Python world. Meanwhile, older and more mature frameworks, such as Caffe, DL4J, and Torch, are getting buried by the new kids on the block.

Money talks; commercial support matters. It’s a safe bet that projects backed by Google, Microsoft and Amazon will pull away from the pack in 2017.


TensorFlow is the leading deep learning framework, measured by reported usage or by development activity. Launched in 2015, Google’s deep learning platform went from zero to leadership in record time.

In April, Google released TensorFlow 0.8, with support for distributed processing. The development team shipped four additional releases during the year, with many additional enhancements, including:

  • Python 3.5 support
  • iOS support
  • Microsoft Windows support (selected functions)
  • CUDA 8 support
  • HDFS support
  • k-Means clustering
  • WALS matrix factorization
  • Iterative solvers for linear equations, linear least squares, eigenvalues and singular values

Also in April, DeepMind, Google’s AI research group, announced plans to switch from Torch to TensorFlow.

Google released its image captioning model in TensorFlow in September. The Google Brain team reported that this model correctly identified 94% of the images in the ImageNet 2012 benchmark.

In December, Constellation Research selected TensorFlow as 2016’s best innovation in enterprise software, citing its extensive use in projects throughout Google and strong developer community.

Microsoft Cognitive Toolkit

In 2016, Microsoft rebranded its deep learning framework as Microsoft Cognitive Toolkit (MCT) and released Version 2.0 to beta, with a new Python API and many other enhancements. In VentureBeat, Jordan Novet reports.

At the Neural Information Processing Systems (NIPS) Conference in early December, Cray announced that it successfully ran MCT on a Cray XC50 supercomputer with more than 1,000 NVIDIA Tesla P100 GPU accelerators.

Separately, Microsoft and NVIDIA announced a collaborative effort to support MCT on Tesla GPUs in Azure or on-premises, and on the NVIDIA DGX-1 supercomputer with Pascal GPUs.


Theano, a project of the Montreal Institute for Learning Algorithms at the University of Montreal, is a Python library for computationally intensive scientific investigation. It allows users to efficiently define, optimize and evaluate mathematical expressions with multi-dimensional arrays. (Reference here.) Like CNTK and TensorFlow, Theano represents neural networks as a symbolic graph.

The team released Theano 0.8 in March, with support for multiple GPUs. Two additional double-dot releases during the year added support for CuDNN v.5 and fixed bugs.


MXNet, a scalable deep learning library, is another project of the University of Washington’s Distributed Machine Learning Common (DMLC). It runs on CPUs, GPUs, clusters, desktops and mobile phones, and supports APIs for Python, R, Scala, Julia, Matlab, and Javascript.

The big news for MXNet in 2016 was its selection by Amazon Web Services. Craig Matsumoto reports; Serdar Yegulalp explains; Eric David dives deeper; Martin Heller reviews.


Keras is a high-level neural networks library that runs on TensorFlow or Theano. Originally authored by Google’s Francois Chollet, Keras had more than 200 active contributors in 2016.

In the Huffington Post, Chollet explains how Keras differs from other DL frameworks. Short version: Keras abstracts deep learning architecture from the computational back end, which made it easy to port from Theano to TensorFlow.


Updated, based on comments from Skymind CEO Chris Nicholson.

Deeplearning4j (DL4J) is a project of Skymind, a commercial venture. IT is an open-source, distributed deep-learning library written for Java and Scala. Integrated with Hadoop and Spark, DL4J runs on distributed GPUs and CPUs. Skymind benchmarks well against Caffe, TensorFlow, and Torch.

While Amazon, Google, and Microsoft promote deep learning on their cloud platforms, Skymind seeks to deliver deep learning on standard enterprise architecture, for organizations that want to train models on premises. I’m skeptical that’s a winning strategy, but it’s a credible strategy. Skymind landed a generous seed round in September, which should keep the lights on long enough to find out. Intel will like a deep learning framework that runs on Xeon boxes, so there’s a possible exit.

Skymind proposes to use Keras for a Python API, which will make the project more accessible to data scientists.


Caffe, a project of the Berkeley Vision and Learning Center (BVLC) is a deep learning framework released under an open source BSD license.  Stemming from BVLC’s work in vision and image recognition, Caffe’s core strength is its ability to model a Convolutional Neural Network (CNN). Caffe is written in C++.  Users interact with Caffe through a Python API or through a command line interface.  Deep learning models trained in Caffe can be compiled for operation on most devices, including Windows.

I don’t see any significant news for Caffe in 2016.

Big Analytics Roundup (March 14, 2016)

HPE wins the internet this week by announcing the re-re-release of Haven, this time on Azure.  The other big story this week: Flink announces Release 1.0.

Third Time’s a Charm

Hewlett Packard Enterprise (HPE) announces Haven on Demand on Microsoft Azure; PR firestorm ensues.  Haven  is a loose bundle of software assets salvaged from the train wreck of Autonomy, Vertica, ArcSight and HP Operations Management machine learning suite, originally branded as HAVEn and announced by HP in June, 2013.  Since then, the software hasn’t exactly gone viral; Haven failed to make KDnuggets’ list of the top 50 machine learning APIs last December, a list that includes the likes of Ersatz, Hutoma and Skyttle.

One possible reason for the lack of virality: although several analysts described Haven as “open source”, HP did not release the Haven source code, and did not offer the software under an open source license.

Other than those two things, it’s open source.

In 2015, HP released Haven on Helion Public Cloud, HP’s failed cloud platform.

So this latest announcement is a re-re-release of the software. On paper, the library looks like it has some valuable capabilities in text, images video and audio analytics.  The interface and documentation look a bit rough, but, after all, this is a first third release.

Jim’s Latest Musings

Angus Loten of the WSJ’s CIO Journal interviews SAS CEO Jim Goodnight, who increasingly sounds like your great-uncle at Thanksgiving dinner, the one who complains about “these kids today.”  Goodnight compares cloud computing to mainframe time sharing.  That’s ironic, because although SAS runs in AWS, it does not offer elastic pricing, the one thing that modern cloud computing shares with timesharing.

Goodnight also pooh-poohs IoT, noting that “we don’t have any major IoT customers, and I haven’t seen a good example of IoT yet.”  SAS’ Product Manager for IoT could not be reached for comment.

Meanwhile, SAS held its annual analyst conference at a posh resort in Steamboat Springs, Colorado; in his report for Ventana Research, David Menninger gushes.

Herbalife Messes Up, Blames Data Scientists

Herbalife discloses errors reporting non-financial information, blames “database scripting errors.” The LA Times reports; Kaiser Fung comments.


— Several items from the morning paper this week:

  • Adrian Colyer explains CryptoNets, a combination of Deep Learning and homohorphic encryption.  By encrypting your data before you load it into the cloud, you make it useless to a hacker.
  • Adrian explains Neural Turing Machines.
  • Adrian explains Memory Networks.
  • Citing a paper published by Google last year, Adrian explains why using personal knowledge questions for account recovery is a really bad thing.

— Data Artisans’ Robert Metzger explains Apache Flink.

— In a video, Eric Kramer explains how to leverage patient data with Dataiku Data Science Studio.


— In InfoWorld, Serdar Yegulalp examines Flink 1.0 and swallows whole the argument that Flink’s “pure” streaming is inherently superior to Spark’s microbatching.

— On the MapR blog, Jim Scott offers a more balanced view of Flink, noting that streaming benchmarks are irrelevant unless you control for processing semantics and fault tolerance.  Scott is excited about Flink ease of use and CEP API.

— John Leonard interviews Vincent de Lagabbe, CTO of bitcoin tracker Kaiko, who argues that Hadoop is unnecessary if you have less than a petabyte of data.  Lagabbe prefers Datastax Enterprise.

— Also in InfoWorld, Martin Heller reviews Azure Machine Learning, finds it too hard for novices.  I disagree.  I used AML in a classroom lab, and students were up and running in minutes.

Open Source Announcements

— Flink announces Release 1.0.  DataArtisans celebrates.

Teradata Watch

CEO Mike Koehler demonstrates confidence in TDC’s future by selling 11,331 shares.

Commercial Announcements

— Objectivity announces that Databricks has certified ThingSpan, a graph analytics platform, to work with Spark and HDFS.

— Databricks announces that adtech company Sellpoints has selected the Databricks platform to deliver a predictive analytics product.