Category: Book Reviews

Reviews of books featuring a summary of the book and links to related material

Book review: The Signal and the Noise by Nate Silver

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This review was first published at Scraperwiki.

Nate Silver first came to my attention during the 2008 presidential election in the US. He correctly predicted the outcome of the November results in 49 of 50 states, missing only on Indiana where Barack Obama won by just a single percentage point. This is part of a wider career in prediction: aside from a job at KPMG (which he found rather dull), he has been a professional poker player and run a baseball statistics website.

His book The Signal and the Noise: The Art and Science of Prediction looks at prediction in a range of fields: economics, disease, chess, baseball, poker, climate, weather, earthquakes and politics. It is both a review and a manifesto; a manifesto for making better prediction.

The opening chapter is on the catastrophic miscalculation of the default rate for collateralized debt obligations (CDO) which led in large part to the recent financial crash. The theme for this chapter is risk and uncertainty. In this instance, risk means the predicted default rate for these financial instruments and uncertainty means the uncertainty in those predictions. For CDOs the problem was that the estimates of risk were way off, and there was no recognition of the uncertainty in those risk estimates.

This theme of unrecognised uncertainty returns for the prediction of macroeconomic indicators such as GDP growth and unemployment. Here again forecasts are made, and practitioners in the field know these estimates are subject to considerable uncertainty, but the market for prediction, and simple human frailty mean that these uncertainties are ignored. I’ve written elsewhere on both the measurement and prediction of GDP. In brief, both sides of the equation are so fraught with uncertainty that you might as well toss a coin to predict GDP!

The psychology of prediction returns with a discussion of political punditry and the idea of “foxes” and “hedgehogs”. In this context “hedgehogs” are people with one Big Idea who make their predictions based on their Big Idea and are unshiftable from it. In the political arena the “Big Idea” may be ideology but as a scientist I can see that science can be afflicted in the same way. To a man with a hammer, everything is a nail. “Foxes”, on the other hand, are more eclectic and combine a range of data and ideas to predict, as a result they are more successful.

In some senses, the presidential prediction is a catching chickens in a coop exercise. There is quite a bit of data to use and your fellow political pundits are typically misled by their own prejudices, they’re “hedgehogs”, so all you, the “fox” needs to do is calculate in a fairly rational manner and you’re there. Silver returns to the idea of diversity in prediction, combining multiple models, or data of multiple types in his manifesto for better prediction.

There are several chapters on scientific prediction, looking at the predictions of earthquakes, the weather, climate and disease. There is not an overarching theme across these chapters. The point about earthquakes is that precise prediction about where, when and how big appears to be impossible. At short range, the weather is predictable but, beyond a few days, seasonal mean predictions and “the same as today” predictions are as good as the best computer simulations.

Other interesting points raised by this chapter are the ideas of judging predictions by accuracy, honesty and economic value. Honesty in this sense means “is this the best model I can make at this point?”. The interesting thing about weather forecasts in the US is that the National Weather Service makes the results of simulations available to all. Big national value-adders such as the Weather Channel produce a “wet bias” forecast which systematically overstates the possibility of rain for lower values of the chances of rain. This is because customers prefer to be told that there is, say, a 20% chance of rain when it actually turns out to be dry, than be told the actual chance of rain (say 5%) and for it to rain. This “wet bias” gives customers what they want.

Finally, there are predictions on games. On poker, baseball, basketball and chess. The benefits of these systems are the large amounts of data available. The US in particular has a thriving “gaming statistics” culture. The problems are closed, in the sense that there are a set of known rules to each game. And finally, there is ample opportunity for testing predictions against outcomes. This final factor is important in improving prediction.

In technical terms, Silver’s call to arms is for the Bayesian approach to predictions. With this approach, an attempt is made to incorporate prior beliefs into prediction through the use of an estimate of the prior probability and Bayes’ Theorem. Silver exemplifies this with a discussion of prediction in poker. Essentially, poker is about predicting your opponents’ hands and their subsequent actions based on those cards. To be successful, poker players must do this repeatedly and intuitively. However, luck still plays a large part in poker and only the very best players make a profit long term.

The book is structured around a series of interviews with workers in the field, and partly as a result of this it reads rather nicely – it’s not just a dry exposition of facts, but has some human elements too. Though it’s no replacement for a technical reference, it’s worth as a survey of prediction, as well as for the human interest stories.

Book review: Darwin’s Ghosts by Rebecca Stott

darwinsghosts_bookcoverCharles Darwin’s On the Origin of Species was rushed into print after a very long gestation when it became clear that Alfred Russell Wallace was close to publishing the same ideas on evolution. Lacking from the first edition was a historical overview of what went before, pertinent to the ideas of evolution. On the occasion of the publication of the first American edition, Darwin took the opportunity to address the lack. Darwin’s Ghosts: In search of the first evolutionists by Rebecca Stott is a modern look at those influences.

After an introductory, motivating chapter Darwin’s Ghosts works in approximately chronological order.  Each chapter introduces a person, or group of people, who did early work in areas of biology which ultimately related to evolution. The first characters introduced are Aristotle, and then Jahiz, a Persian scholar working around 860AD. Aristotle brought systematic observation to biology, a seemingly basic concept which was not then universal. He wrote The History of Animals in about 350BC. The theme of systematic observation and experimentation continues through the book. Jahiz extended Aristotle’s ideas to include interactions of species, or webs. His work is captured in The Book of Living Beings.

Next up was a curiosity over fossils, and the inklings that things had not always been as they were now. Leonardo Da Vinci (1452-1519) and, some time later, Bernard Palissy (1510-1590) are used to illustrate this idea. Everyone has heard of da Vinci. Palissy was a Hugenot who lived in the second half of the 16th century. He was a renowned potter, and commissioned by Catherine de Medici to build the Tuileries gardens in Paris but in addition he lectured on natural sciences.

I must admit to being a bit puzzled at the introduction of Abraham Trembley (1710-1784), he was the tutor of two sons of a prominent Dutch politician. He worked on hydra, a very simple aquatic organism and his wikipedia page credits him as being one of the first experimental zoologists. He discovered that whole hydra could regenerated from parts of a “parent”.

Conceptually the next developments were in hypothesising a great age for the earth coupled to ideas that species were not immutable, they change over time. Benoît de Maillet (1656-1739) wrote on this but only posthumously. Similarly Robert Chambers (1802-1871) was to write anonymously about evolution in Vestiges of the Natural History of Creation first published in 1844. Note that this publication date is only 15 years before the first publication of the Origin of Species.

The reasons for this reticence on the part of a number of writers is that these ideas of mutability and change collide with major religions, they are “blasphemous”. This becomes a serious issue over the years spanning 1800. Erasmus Darwin, Charles’s grandfather, was something of an evolutionist but wrote relatively cryptically about it for fear of his career as a doctor. I reviewed Desmond King-Hele’s biography of Erasmus Darwin some time ago. At the time when Erasmus wrote evolution was considered a radical idea, both in political and religious senses. This at a time when the British establishment was feeling vulnerable following the Revolution in France and the earlier American revolution.

I have some sympathy with the idea that religion suppressed evolutionary theory, however it really isn’t as simple as that. The part religion plays is as a support to wider cultural and political movements.

The core point of Darwin’s Ghosts is that a scientist working in the first half of the 19th century was standing on the shoulders of giants or at least on top of a pile of people the lowest strata of which date back a couple of millennia. Not only this, they are not on an isolated pinnacle, around them are others also standing. Culturally we are fond of stories of lone geniuses but practically they don’t exist.

In fact the theory of evolution is a nice demonstration of this interdependence – Darwin was forced to publish his theory because Wallace had essentially got the gist of it entirely independently – his story is the final chapter in the book. For Wallace the geographic ranges of species were a key insight into forming the theory. A feature very apparent in the area of southeast Asia where he was working as a freelance specimen collector.

Once again I am caught out by my Kindle – the book proper ends at 66% of the way through, although Darwin’s original essay is included as an appendix taking us to 70%. Darwin’s words are worth reading, if only for his put-down of Richard Owen for attempting to claim credit for evolutionary theory, despite being one of those who had argued against it previously.

I enjoyed this book, much of my reading is scientific mono-biography which misses the ensemble nature of science which this book demonstrates.

Book review: Hadoop in Action by Chuck Lam

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This review was first published at ScraperWiki.

Hadoop in Action by Chuck Lam provides a brief, fairly technical introduction to the Hadoop Big Data ecosystem. Hadoop is an open source implementation of the MapReduce framework originally developed by Google to process huge quantities of web search data. The name MapReduce, refers to dividing up jobs amongst multiple processors (“Mapping”) and then recombining results to provide an answer to the problem (“Reducing”). Hadoop, allows users to process large quantities of data by distributing it across a network of relatively cheap computers. Each computer in the network has a portion of the data to process, and at the end it is combined together to give the final reult. Hadoop provides the infrastructure to enable this. In a sense it is a distributed operated system which provides fundamental services to applications such as Hive and Pig.

At ScraperWiki we’ve had many philosophical discussions about the meaning of Big Data. What size is Big Data? Is it one million lines? Is it one billion lines? Should we express it in terms of gigabytes and terabytes rather than lines?

For many, Big Data is data that requires you use Hadoop or similar to process.

Our view is that Big Data is data big enough to break the tools or hardware you commonly use, so for many of our customers this is a software limit based on Microsoft Excel. Technically Excel can handle a million or so lines but practically speaking life gets uncomfortable as you go above a few tens of thousands of rows.

The largest dataset a customer has come to us with so far is the UK MOT test data – results of the roadworthiness test for every vehicle on the road in the UK, over three years old. This dataset is about 100 million lines and 4 gigabytes per year, it’s available back to 2005 giving a total of approximately 1 billion lines and 32GB. A single year can be readily analysed on an Intel i7 laptop with 8GB RAM, MySQL and Tableau by readily I mean that some indexing jobs can take up to an hour but once indexed most queries are 10 – 20 minutes maximum.

At ScraperWiki a number of us have backgrounds in the physical sciences where we’ve been interested in computational intensive simulations involving clusters of commodity hardware which pre-date Hadoop (Beowulf), or big data from the Large Hadron Collider. Physical scientists have long been interested in parallel computing where the amount of data to move around is small but the amount of calculation to do is large. The point here is that parallel computing is possible for a subset of problems where a task can be divided up into smaller chunks of data and processing to be distributed amongst multiple processors or machines. In the case of photorealistic computer graphics rendering this might be frames of video, or a portion of a whole scene. Software like Matlab, Fortran and computer graphics renderers can parallelise certain operations with relative ease. The difficulty has always been turning your big computing problem into one of those “certain operations”. The Large Hadron Collider is an example more suited to the Hadoop style approach, the data flows are enormous but the calculations performed on that data are, comparatively less troublesome.

Hadoop in Action spends a significant amount of time discussing the core Hadoop system and MapReduce processing framework. I must admit to finding this part rather dull. I perked up when we reached Pig, described as a data processing language and Hive, a SQL-like system. One gets the impression the Pig system was built around a naming convention pushed too far: the Pig commandline is called Grunt and the language used by Pig is Pig Latin. Pig and Hive look like systems where I could sit down and run some queries with a language looks like my old friend, SQL.

The book finishes with some case studies, these are an image conversion problem, machine learning and data processing at China Mobile, the Stumbleupon social bookmarking system and providing search for IBM’s intranet. In the latter three cases users were migrating from SQL based systems running on monolithic hardware. To give an idea of scale: China Mobile collect terabytes of data per day across 100s of millions of customers, the IBM intranet has something like 100 million pages and 16 million documents and Stumbupon has 25 million users clicking their Stumble buttons about 1 billion times in a month.

Overall, a handy introduction to Hadoop although perhaps oddly pitched – it’s probably too technical for most managers, not technical enough for system administrators and with insufficient applications for data scientists. If you want to get hands on experience of Hadoop, then the Hortonworks Sandbox provides a pre-packaged virtual machine with a web interface for you to try out the various technologies.

If you want us to help you get value out of your big data or even Big Data, please get in touch!

Book review: Python for Data Analysis by Wes McKinney

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This review was first published at ScraperWiki.

As well as developing scrapers and a data platform, at ScraperWiki we also do data analysis. Some of this is just because we’re interested, other times it’s because clients don’t have the tools or the time to do the analysis they want themselves. Often the problem is with the size of the data. Excel is the universal solvent for data analysis problems – go look at any survey of data scientists. But Excel has it’s limitations. There are the technical limitations of something like a million rows maximum size but well before this size Excel becomes a pain to use.

There is another path – the programming route. As a physical scientist of moderate age I’ve followed these two data analysis paths in parallel. Excel for the quick look see and some presentation. Programming for bigger tasks, tasks I want to do repeatedly and types of data Excel simply can’t handle – like image data. For me the programming path started with FORTRAN and the NAG libraries, from which I moved into Matlab. FORTRAN is pure, traditional programming born in the days when you had to light your own computing fire. Matlab and competitors like Mathematica, R and IDL follow a slightly different path. At their core they are specialist programming languages but they come embedded in graphical environments which can be used interactively. You type code at a prompt and stuff happens, plots pop up and so forth. You can capture this interaction and put it into scripts/programs, or simply write programs from scratch.

Outside the physical sciences, data analysis often means databases. Physical scientists are largely interested in numbers, other sciences and business analysts are often interested in a mixture of numbers and categorical things. For example, in analysing the performance of a drug you may be interested in the dose (i.e. a number) but also in categorical features of the patient such as gender and their symptoms. Databases, and analysis packages such as R and SAS are better suited to this type of data. Business analysts appear to move from Excel to Tableau as their data get bigger and more complex. Tableau gives easy visualisation of database shaped data. It provides connectors to many different databases. My workflow at ScraperWiki is often Python to SQL database to Tableau.

Python for Data Analysis by Wes McKinney draws these threads together. The book is partly about the range of tools which make Python an alternative to systems like R, Matlab and their ilk and partly a guide to McKinney’s own contribution to this area: the pandas library. Pandas brings R-like dataframes and database-like operations to Python. It helps keep all your data analysis needs in one big Python-y tent. Dataframes are 2-dimensional tables of data whose rows and columns have indexes which can be numeric but are typically text. The pandas library provides a great deal of functionality to process Dataframes, in particular enabling filtering and grouping calculations which are reminiscent of the SQL database workflow. The indexes can be hierarchical. As well as the 2-dimensional Dataframe, pandas also provides 1-dimensional Series and a 3-dimensional Panel data structures.

I’ve already been using pandas in the Python part of my workflow. It’s excellent for importing data, and simplifies the process of reshaping data for upload to a SQL database and onwards to visualisation in Tableau. I’m also finding it can be used to help replace some of the more exploratory analysis I do in Tableau and SQL.

Outside of pandas the key technologies McKinney introduces are the ipython interactive console and the NumPy library. I mentioned the ipython notebook in my previous book review. ipython gives Python the interactive analysis capabilities of systems like Matlab. The NumPy library is a high performance library providing simple multi-dimensional arrays, comforting those who grew up with a FORTRAN background.

Why switch from commercial offerings like Matlab to the Python ecosystem? Partly it’s cost, the pricing model for Matlab has a moderately expensive core (i.e. $1000) with further functionality in moderately expensive toolboxes (more $1000s). Furthermore, the most painful and complex thing I did at my previous (very large) employer was represent users in the contractual interactions between my company and Mathworks to license Matlab and its associated tool boxes for hundreds of employees spread across the globe. These days Python offers me a wider range of high quality toolboxes, at it’s core it’s a respectable programming language with all the features and tooling that brings. If my code doesn’t run it’s because I wrote it wrong, not because my colleague in Shanghai has grabbed the last remaining network license for a key toolbox. R still offers statistical analysis with greater gravitas and some really nice, publication quality plotting but it does not have the air of a general purpose programming language.

The parts of Python for Data Analysis which I found most interesting, and engaging, were the examples of pandas code in “live” usage. Early in the book this includes analysis of first names for babies in the US over time, with later examples from the financial sector – in which the author worked. Much of the rest is very heavy on showing code snippets which is distracting from a straightforward reading of the book.  In some senses Mining the Social Web has really spoiled me – I now expect a book like this to come with an Ipython Notebook!

Book review: Mining the Social Web by Matthew A. Russell

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This review was first published at ScraperWiki.

The twitter search and follower tools are amongst the most popular on the ScraperWiki platform so we are looking to provide more value in this area. To this end I’ve been reading “Mining the Social Web” by Matthew A. Russell.

In the first instance the book looks like a run through the APIs for various social media services (Twitter, Facebook, LinkedIn, Google+, GitHub etc) but after the first couple of chapters on Twitter and Facebook it becomes obvious that it is more subtle than that. Each chapter also includes material on a data mining technique; for Twitter it is simply counting things. The Facebook chapter introduces graph analysis, a theme extended in the chapter on GitHub. Google+ is used as a framework to introduce term frequency-inverse document frequency (TF-IDF), an information retrieval technique and a basic, but effective, way to process natural language. Web pages scraping is used as a means to introduce some more ideas about natural language processing and summarisation. Mining mailboxes uses a subset of the Enron mail corpus to introduces MongoDB as a document storage system. The final chapter is a twitter cookbook which includes lots of short recipes for simple twitter related activities but no further analysis. The coverage of each topic isn’t deep but it is practical – introducing the key libraries to do tasks. And it’s alive with suggests for further work, and references to help with that.

The examples in the book are provided as IPython Notebooks which are supplied, along with a Notebook server on a virtual machine, from a GitHub repository. IPython notebooks are interactive Python sessions run through a browser interface. Content is divided into cells which can either be code or simple descriptive text. A code cell can be executed and the output from the code appears in an output cell. These notebooks are a really nice way to present example code since the code has some context. The virtual machine approach is also a great innovation since configuring Python libraries and the IPython server itself, in a platform agnostic manner, is really difficult and this solution bypasses most of those problems. The system makes it incredibly easy to run the example code for yourself, almost too easy in fact, I found myself clicking blindly through some of the example code. Potentially the book could have been presented simply as an IPython notebook, this is likely not economically practical but it would be nice to collect the links to further reading there where they would be more usable. The GitHub repository also provides a great place for interaction with the author: I filed a couple of issues regarding setting the system up and he responded unerringly quickly – as he did for many other readers. Also I discovered incidentally, through being subscribed to the repository, that one of the people I follow on Twitter (and a guest blogger here) was also reading the book. An interesting example of the social web in action!

Mining the social web covers some material I had not come across in my earlier machine learning/ data mining reading. There are a couple of chapters containing material on graph theory using data from Facebook and GitHub data. In the way of benefitting from reading about the same material in different places, Russell highlights that cluster and de-duplication are of course facets of the same subject.

I read with interest the section on using a MongoDB database as a store for tweets and other data in the form of JSON objects. Currently I am bemused by MongoDB. The ScraperWiki platform uses it to store user profile information. I have occasional recourse to try to look things up there. I’ve struggled to see the benefit of MongoDB over a SQL database. Particularly having watched two of my colleagues spend a morning working out how to do a what would be a simple SQL join in MongoDB. Mining the social web has made me wonder about giving MongoDB another chance.

The penultimate chapter is a discussion of the semantic web, introducing both microformats as well as RDF technology, although the discussion is much less concrete than earlier chapters. Microformats are HTML elements which hold semantic information about a page using an agreed schema, to give an example: the geo microformat encodes geographic information. In the absence of such a microformat, geographic information such as latitude and longitude could be encoded in pretty much any way, making it necessary to either use custom scrapers on a page by page basis or complex heuristics to infer the presence of such information. RDF is one of the underpinning technologies for the semantic web: a shorthand for a worldwide web marked up such that machines can understand the meaning of webpages. This touches on the EU Newsreader project on which we are collaborators, and which seeks to generate this type of semantic mark up for news articles using natural language processing.

Overall, definitely worth reading. We’re interested in extending our tools for social media and with this book in hand I’m confident we can do it and be aware of more possibilities.