Monthly Archives: May 2012

Connectograms and Circos Visualization Tool

Connectograms and Circos Visualization Tool

Yesterday (May 16) the Public Library of Science (PLoS) published a fascinating article titled “Mapping Connectivity Damage in the Case of Phineas Gage“. It analyzes the brain damage which the famous trauma victim sustained after an accident drove a steel rod through his skull. Railroad worker Phineas Gage survived the accident and continued to live for another 12 years, albeit with significant behavioral changes and anomalies. Those changes were severe enough for him to have to discontinue his work and also get estranged from his friends who stated he was “no longer Gage”. This has become a much studied case about the impact of brain damage on behavior anomalies. Since the accident happened more than 150 years ago there are no autopsy data or brain scans from Phineas Gage’s brain. So how did the scientists reconstruct the likely damage?

Since a few years there has been interest in the human connectome. Just like the genome is a map of human genes, the connectome is a map of the connectivity in the human brain. The human brain is enormously complex. Most estimates put the number of neurons in the hundreds of billions and the synaptic interconnections in the hundreds of trillions! Using diffusion weighted (DWI) and magnetic resonance imaging (MRI) one can identify detailed neuron connectivity. This is such a challenging endeavor that it drives the development of many new technologies, including the data visualization. The image resolution and post-processing power of modern instruments is now large enough to create detailed connectomes that show major pathways of neuronal fibers within the human brain.

The authors of the Laboratory of Neuro Imaging (LONI) in the Neurology Department at UCLA have studied the connectomes of a population of N=110 healthy young males (similar in age and dexterity to Phineas Gage at the time of his accident). From this they constructed a typical healthy connectome and visualized it as follows:

Circular representation of cortical anatomy of normal males (Source: PLoS ONE)

Details of the graphic are explained in the PLoS article. The outermost ring shows the various brain regions by lobe (fr – frontal, ins – insula etc.). The left (right) half of the connectogram figure represents the left (right) hemisphere of the brain and the brain stem is at the bottom, 6 o’clock position of the graph.

Connectograms are circular representations introduced by LONI researchers in their NeuroImage article “Circular representation of human cortical networks for subject and population-level connectomic visualization“:

This article introduces an innovative framework for the depiction of human connectomics by employing a circular visualization method which is highly suitable to the exploration of central nervous system architecture. This type of representation, which we name a ‘connectogram’, has the capability of classifying neuroconnectivity relationships intuitively and elegantly.

Back to Phineas Gage: His skull has been preserved and is on display at a museum. Through sophisticated spatial and neurobiological reasoning the researchers reconstructed the pathway of the steel rod and thus the damaging effects on white matter structure.

Phineas Gage Skull with reconstructed steel rod pathway and damage (Source: PLoS ONE)

Based upon this geospatial model of the damaged brain overlaid against the typical brain connectogram from the healthy population they created another connectogram indicating the connections between brain regions lost or damaged in the accident.

Mean connectivity affected in Phineas Gage by the accident damage (Source: PLoS ONE)

From the article:

The lines in this connectogram graphic represent the connections between brain regions that were lost or damaged by the passage of the tamping iron. Fiber pathway damage extended beyond the left frontal cortex to regions of the left temporal, partial, and occipital cortices as well as to basal ganglia, brain stem, and cerebellum. Inter-hemispheric connections of the frontal and limbic lobes as well as basal ganglia were also affected. Connections in grayscale indicate those pathways that were completely lost in the presence of the tamping iron, while those in shades of tan indicate those partially severed. Pathway transparency indicates the relative density of the affected pathway. In contrast to the morphometric measurements depicted in Fig. 2, the inner four rings of the connectogram here indicate (from the outside inward) the regional network metrics of betweenness centrality, regional eccentricity, local efficiency, clustering coefficient, and the percent of GM loss, respectively, in the presence of the tamping iron, in each instance averaged over the N = 110 subjects.

The point of the above quote is not to be precise in terms of neuroscience. Experts can interpret these images and advance our understanding of how the brain works – I’m certainly not an expert in this field, not even close. The point is to show how advances in imaging and data visualization technologies enable inter-disciplinary research which just a decade ago would have been impossible to conduct. There is also a somewhat artistic quality to these images, which reinforces the notion of data visualization being both art and science.

The tool used for these visualizations is called Circos. It was originally developed for genome and cancer research by Martin Krzywinski at the Genome Sciences Center in Vancouver, CA. Circos can be used for circular visualizations of any tabular data, and the above connectome visualization is a great application. Martin’s website is very interesting in terms of both visualization tools as well as projects. I have already started using Circos – which is available both for download and in an online tableviewer version – for some visualization experiments which I may blog about in the future.


Posted by on May 17, 2012 in Scientific


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Faceplant with Facebook?

With the Facebook IPO coming up this Friday there is a lot of attention around its business model and financials. I’m not an expert in this area, but my hunch is that a lot of people will lose a lot of money by chasing after Facebook shares. Why?

I think there are two types of answers. One from reasoning and one from intuition.

For reasoning one needs to look at a more technical assessment of the business model and financials. Some have written extensively about the comparative lack of innovation in Facebook’s business model and core product. Some have compared Facebook’s performance in advertising to Google – the estimates are that Google’s ad performance is 100x better than that of Facebook. Some have pointed out that many of Facebook’s core metrics such as visits/person, pages/visit or Click-Through-Rates have been declining for two years and go as far as calling this the Facebook ad scam. One can question the wisdom of the Instagram acquisition, buying a company with 12 employees and zero revenues for $1B. One can question the notion that the 28 year old founder will have 57% of the voting rights of the public company. One could look at stories about companies discontinuing their ad Facebook efforts such as the Forbes article about GM pulling a $10m account because they found it ineffective. The list goes on.

Here is a more positive leaning infographic from an article looking at “Facebook: Business Model, Hardware Patents and IPO“:

Analysis Infographic of pre-IPO Facebook (source: Gina Smith,

To value a startup at 100x last year’s income seems just extremely high – but then Amazon’s valuation is in similarly lofty territory. As for reasoning and predicting the financial success of Facebook’s IPO, people can cite numbers to justify their beliefs both ways. At the end of the day, it’s unpredictable and nobody can know for sure.

The other answer to why I am not buying into the hype is more intuitive and comes from my personal experience. Here is a little thought experiment as to how valuable a company is for your personal life: Imagine for a moment if the company with all its products and services would disappear overnight. How much of an impact would it have for you as an individual? If I think about companies like Apple, Google, Microsoft, or Amazon the impact for me would be huge. I use their products and services every day. Think about it:

No Apple = no iPhone, no iPad, no iTunes music on the iPod or via AppleTV on our home stereo. That would be a dramatic setback.

No Google = no Google search, no GMail, no YouTube, no Google maps, no Google Earth. Again, very significant impact for me personally. Not to mention the exciting research at Google in very different areas such as self-driving vehicles.

No Facebook = no problem (at least for me). I deactivated my own Facebook account months ago simply because it cost me a lot of time and I got very little value out of it. In fact, I got annoyed with compulsively looking at updates from mere acquaintances about mundane details of their lives. Why would I care? I finally got around to actually deleting my account, although Facebook makes that somewhat cumbersome (which probably inflates the account numbers somewhat).

I’m not saying Facebook isn’t valuable to some people. Having nearly 1B user accounts is very impressive. Hosting by far the largest photo collection on the planet is extraordinary. Facebook exploded because it satisfied our basic need of sharing, just like Google did with search, Amazon did with shopping or eBay did with selling. But the entry barrier to sharing is small (see LinkedIn, Twitter or Pinterest) and Facebook doesn’t seem to be particularly well positioned for mobile.

I strongly suspect that Facebook’s valuation is both initially inflated – the $50 per account estimate of early social networks doesn’t scale up with the demographics of the massive user base – as well as lately hyped up by greedy investors who sense an opportunity to make a quick buck. My hunch is that FB will trade below its IPO price within the first year, possibly well below. But then again, I have been surprised before…

I’m not buying the hype. What am I missing? Let me know what you think!

UPDATE 8/16/2012: Well, here we are after one quarter, and Facebook’s stock valuation hasn’t done so well. Look at the first 3 month chart of FB:

First 3 month of Facebook stock price (Screenshot of StockTouch on iPad)

What started as a $100b market valuation is now at $43b. One has to hand it to Mark Zuckerberg, he really extracted maximum value out of those shares. It turns out sitting on the sidelines was the right move for investors in this case.

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Posted by on May 16, 2012 in Financial, Socioeconomic


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Sankey Diagrams

Sankey Diagrams

Whenever you want to show the flow of a quantity (such as energy or money) through a network of nodes you can use Sankey diagrams:

“A Sankey diagram is a directional flow chart where the width of the streams is proportional to the quantity of flow, and where the flows can be combined, split and traced through a series of events or stages.”

One area where this can be applied very well is that of costing. By modeling the flow of cost through a company one can analyze the aggregated cost and thus determine the profitability of individual products, customers or channels. Using the principles of activity-based costing one can create a cost-assignment network linking cost pools or accounts (as tracked in the General Ledger) via the employees and their activities to the products and customers. Such a Cost Flow can then be visualized using a Sankey diagram:

Cost Flow from Accounts via Expenses and Activities to Products

The direction of flow (here from left to right) is indicated by the color assignment from nodes to its outflowing streams. Note also the intuitive notion of zero-loss assignment: For each node the sum of the in- and outflowing streams (= height of that node) remains the same. Hence all the cost is accounted for, nothing is lost. If you stacked all nodes on top of one another they would rise to the same height. (Random data for illustration purposes only.)

The above diagram was created in Mathematica using modified source code originally from Sam Calisch who had posted it in 2011 here. Sam also included a “SankeyNotes.pdf” document explaining the details of the algorithms encoded in the source, such as how to arrange the node lists and how to draw the streams.

I find these a perfect example of how a manual drawing can go a long ways to illustrate the ideas behind an algorithm, which makes it a lot easier to understand and reuse the source code. Thanks to Sam for this code and documentation. Sam by the way used the code to illustrate the efficiency of energy use (vs. waste) in Australia:

Energy Flow comparison between New South Wales and Australia (Sam Calisch)

Note the sub-flows within each stream to compare a part (New South Wales) against the whole (Australia).

Another interesting use of Sankey Diagrams has been published a few weeks ago on ProPublica about campaign finance flow. This is particularly useful as it is interactive (click on image to get to interactive version).

Tangled Web of Campaign Finance Flow

Note the campaigns in green and the Super-PACs in brown color. The data is sourced from FEC and the New York Times Campaign Finance API. Note that in the interactive version you can click on any source on the left or any destination on the right to see the outgoing and incoming streams.

Finance Flow From Obama-For-America

Finance Flow to American Express

Here are some more examples. Sankey diagrams are also used in Google Flow Analytics (called Event Flow, Goal Flow, Visitor Flow). I wouldn’t be surprised to see Sankey Diagrams make their way into modern data visualization tools such as Tableau or QlikView, perhaps even into Excel some day… Here are some Visio shapes and links to other resources.


Posted by on May 14, 2012 in Financial, Industrial


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Quarterly Comparison: Apple, Microsoft, Google, Amazon

Quarterly Comparison: Apple, Microsoft, Google, Amazon

Last quarter we looked at the financials and underlying product & service portfolios of four of the biggest technology companies in the post “Side by Side: Apple, Microsoft, Google, Amazon“. With the recent reporting of results for Q1 2012 it is a good time to revisit this subject.

Comparison of Financials Q4 2011 and Q1 2012 for Apple, Microsoft, Google, and Amazon.

Market cap has grown roughly by 25% for both Apple and Amazon, whereas Microsoft and Google only added 5% or less. A sequential quarter comparison can be misleading due to seasonal changes, which impact different industries and business models in a different way. For example, Google’s ad revenue is somewhat less impacted by seasonal shopping than the other companies.

Sequential quarter comparison of financials

Apple and Microsoft seem to be impacted in a similar way by seasonal changes. For Amazon, which already has by far the lowest margin of all four companies, operating income decreased by 40% while it increased its headcount by 17%. This leads to much lower income per employee and with increased stock price to a doubling of its already very high P/E ratio. I’m not a stock market analyst, but Amazon’s P/E ratio of now near 200 seems extraordinarily high. By comparison, the other companies look downright cheap: Apple 8.8, Microsoft 10.5, Google 14.5

Horace Dediu from has also revisited this topic in his post “Which is best: hardware, software, or services?“. What’s striking is that all three companies (except Amazon) now have operating margins between 30-40% – very high for such large businesses – with Apple taking the top near 40%. Over the last 5 years, Apple has doubled it’s margin (20% to 40%), whereas Microsoft (35-40%) and Google (30-35%) remained near their levels.


Long term the most important aspect of a business is not how big it has become, but how profitable it is. In that regard Amazon is the odd one out. Their operating income last quarter was about 1% of revenue. Amazon needs to move $100 worth of goods to earn $1. They employ 65,000 people and had revenue of $13.2b last quarter, yet only earned $130m during that time! Apple earns more money just with their iPad covers! Amazon’s strategy is to subsidize the initial Kindle Fire sale and hoping to make money on the additional purchases over the lifetime of the product. In light of these numbers, do you think Amazon has a future with it’s Kindle Fire tablet against the iPad?

But what really struck me about the extreme differences in profitability is this comparison of Apple and Microsoft product lines (source: @asymco twitter):

(source: @asymco twitter)

This shows what an impressive and sustained success the iPhone has been. And the iPad is on track to grow even faster. Horace Dediu guesses that Apple’s iPad will be a bigger profit generator than Windows in one quarter, and a bigger profit generator than Google (yes, all of Google) in three quarters. We will check on those predictions when the time comes…


Posted by on May 2, 2012 in Financial, Industrial


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