Ejection fraction (EF) measurements from MRI: Data Science Bowl 2015

I was eagerly anticipating this next competition in the Booz Allen Hamilton Data Science Bowl series on Kaggle, in association with the NIH's National Heart, Lung and Blood Institute.

I have just finished a refresher course in statistics, and am now moving onto more serious analytics tools. I'm looking forward to this practical application of data science that utilizes my domain knowledge and experience in medicine, as well as my work in producing medical media.


Here's the task:

4-chamber Cine MRI

"The 2015 Data Science Bowl challenges you to create an algorithm to automatically measure end-systolic and end-diastolic volumes in cardiac MRIs."

The purpose of these measurements is to determine cardiac output (volume of blood pumped per minute) by way of the ejection fraction (EF). "EF is the percentage of blood ejected from the left ventricle with each heartbeat." The end-systolic and end-diastolic volumes are used to derive the EF, which quantifies the heart's ability to pump blood.

Cardiac Output and Ejection Fraction

When the competition was started yesterday morning, what immediately came to mind was my experience as a surgery resident. Patients were scheduled for elective procedures and it was my job to ensure that they were prep'ed and cleared for surgery.

A patient's primary care physician might note that he or she had a cardiac history that needed to be addressed given the stresses of general anesthesia. EF was necessary to be determined.

This required a cardiac consult, which would involve a MUGA (multigated acquistion) scan (now MRI video is used), for the cardiologist to determine the EF. It was the number the anesthesiologist would look for on the chart before the patient was brought to the OR.

The Cleveland Clinic Web site provides an excellent discussion of the role of ejection fraction in determining cardiac health.

Frank-Starling Mechanism and a rubber band (a closer look why cardiac output and ejection fraction are important)

I remember reading my physiology text in medical school seeing this rubber band analogy to explain the Frank-Starling mechanism for heart function.

The heart muscle, specifically the left ventricle that has the major task of pumping throughout the entire body, stretches as venous blood is returned to the heart. Think of this as a rubber band stretching. Then the muscle contracts. This is the rubber band being allowed to apply a force as it contracts.

In this way, the heart can produce more forceful contractions if more blood is being returned from its trip through the body's circulatory system.

Systole is when the heart chamber (in this case we're looking at the left ventricle) is completely contracted, and diastole is when the the chamber is stretched and about to apply the force of contraction. As you can see in the photos, diastole 1 is moderate filling of the chamber, and diastole 2 is a greater filling. With diastole 2 in this example, you see how the rubber band (representing the heart muscle fibers) is stretched more and will apply a greater force when it contracts then with diastole 1. In the heart, the more the filling, the greater to force of contraction and therefore greater cardiac output.

"It's the heart's intrinsic way of synchronizing cardiac output with an increased venous return," says the author of this YouTube video.

With a diseased heart, this mechanism breaks down and the blood returning to the heart is not being adequately pumped to supply the oxygen needs of the body.



Good luck to all those teams participating. I'll be participating under the team name "Heartland Data."

(#datascibowl on Twitter)

Make / Happen: A Conference for Doers in Omaha

I was attracted to this conference when I noticed the inclusion of Seth Godin as the keynoter. I've read a number of his books on marketing and personal branding strategy, and even spoke to him on the phone once about the mathematics of blackjack. (I think it was in the context of the book about the MIT students who were counting cards at the casinos around the country.)

He has a new book out "Poke the Box," and you can read and listen to it for free with Amazon's Kindle Unlimtied program.

This conference is hosted by the Greater Omaha Chamber of Commerce and will be held locally here in Omaha at the Holland Center on Oct. 8.

http://www.make-happen.com/

From their "About" page:

No offense to the "sit-back-and-watch-er," but we're really looking for doers

Business and community leaders ready to reach beyond the status quo, stir something up and create real plans of action to positively impact themselves, their business and the community. Together, we’ll explore new paths toward personal development, learn how to ignite innovation and practice taking intentional risks. 

Make / Happen is an unanswered question, an incomplete phrase, a _____ that you must fill in for yourself. Make "what" happen? That’s entirely up to you.

 Speaker list:

KEYNOTE: Seth Godin
Best-Selling Author and Entrepreneur

• GO – Make Something Happen!

Nicole M. Bianchi
Founder & President, Resolution Partners

• Big Problems = Big Opportunities
  Issues need courageous and inspired business leaders to build scalable solutions...build something you are passionate about! 

Fergus Hoban
CEO, Think Whole Person Healthcare

Kim Hoogeveen, Ph.D. 
CEO and Psychologist, MindSet LLC

• It's the Culture, Stupid!

Steve Martin
CEO, Blue Cross Blue Shield of Nebraska

Othello Meadows
Executive Director, Seventy Five North Revitalization Corp.

• Risking Comfort for Excellence

Doug Lipp
CEO & President, G. Douglas Lipp & Associates, International Consultant and Best-Selling Author

• Creating Cultures of Significance – The Magic of Imagine: Unleashing Your Creativity. Innovation lessons from Disney U.
   
• Budgets are Tight, Creativity is Free. Prescription for a No Excuses Culture

Jorge M. Zuniga, Ph.D.
Creighton University

• Giving a Hand to Innovation and Creativity: The 3D Printing Prosthetics Revolution

Joseph Plumeri
Vice Chairman, First Data Board of Directors

• The Power of Being Yourself: A game plan for success by putting passion into your life and work.

W. Todd  Johnson
Global Channel Leader, Entrepreneurship and Job Creation, Gallup

• Intrapreneurship: Finding the Right Intrapreneurs to Execute Ideas

The Gartner Hype Cycle for Emerging Tech in now over 20 years old

 http://www.gartner.com/newsroom/id/2819918

 Here's their update from last year (click to enlarge):

The more reports that I write, the more I come back to this curve. But there's a dimension missing here, namely geographic location. Maybe you could include the level of disruption tolerance.

Of all new technologies, the cell phone probably had the easiest path to acceptance because folks could grok that "it's a phone." Even as calls were dropped, expectations never seemed to run high.

Now it's used less like a phone (who likes receiving the random disruption of their day? Texting, social media and even video streaming has taken over, ensuring the cell phone never dropped into the trough of disillusionment.

What lessons are to be learned from this for streamlining the acceptance of new tech?

CNBC ranks Nebraska 7th in best for business poll

Nebraska scored high marks in friendliness and cost of living.

Nebraska's Internet Speed Metrics - Bingeing on Bits

Especially important for viewing a binge-watchable series (Netflix's Bloodline being worthy of the famous quote by Tolstoy about families) is adequate and reliable Internet bandwidth.

I picked this up from Gizmodo:

See How Fast Your State's Broadband Is With This Interactive Map

On this interactive map, it looks like Nebraska is below the national average for Internet speed as measured by Speedtest.net. (27.2 vs. 33.9). This makes Nebraska 34th out of 50 States and Wash. DC. (Reported in Mbps = megabits per second)

(Click on all graphics for a larger view. Then click "X" in the upper righthand corner to return to blog.)

A more nuanced view is seen in the Net Index Explorer Web page. Here you see Omaha (32.6 Mbps) as being just below the national average. The town of Bennington tops it at 46.8 Mbps. This merits some investigation. I can't vouch for these numbers, so I'll have to take them as a starting point to find the meaning of this and other reports. I'm skeptical by nature, and don't accept numbers at face value, especially at 4 significant digits. Time to start digging.

This prompted me to check my own connection. A download speed of 9 Mbps is quite a drop from when I last tested it. Have to look into this.

Come Meerkat

Got bit again. Someone new, something to try out. I'm like a crow finding a shiny bauble glinting in the grass. I can't resist. Neophile.

Meerkat is an iOS app which allows you to stream live video that viewers can watch on Twitter.

It turned out to be the hot app at SXSW, when Twitter decided to prevent access to its social graph, which didn't stave off burgeoning interest.

Mashable reports the early numbers:

"Cooley would not specify how many Meerkat users there currently are, but the app reportedly had 120,000 users when the Twitter crackdown occurred. That means at least another 36,000 people have signed up for Meerkat since then, based on back-of-the-envelope math — an impressive stat, however you look at it."

Hype leads to buzz leads to news leads to noise. The it gets picked up by CNN Money. They all generate numbers: users, faves, retweets, followers, etc., but to what lasting effect? What can be learned, it anything at all?

I was watching Jeremy, a UNO Professor whom I've met in the past at a local seminar, demo'ing Meerkat at an airport (perhaps it was Eppley Airfield, Omaha's almost-an-airport), when I decided to see if he had posted any thoughts about this on the Web. He did:

Social Media Lessons Learned from Meerkat

The takeaway...

Meerkat is barely three weeks old now, but there are some key lessons:

• Think mobile and social first because these devices are ubiquitous and always with us.

• Start with influencers, thought leaders and celebrities to gain traction.

• Engagement happens around events because social media is about being social and interesting. Audience size is no longer as important as social network structure and long-term relationships. [my emphasis]

• Entertainment drives interest. Music, comedy and engaging conversation all may attract audiences, but watch for video privacy and ethics issues.

• Social media works best in real-time with unique personalities and content. Interactive micro-broadcasting video has a future in building engagement. [my em]

So how do you measure engagement and how it translates into long-term relationships? This is a quant blog after all.

Influencer Vaynerchuk emphasizes the need for a narrative. You can jab, jab with blinky, tweety stuff to attract eyeballs, but you have to finish with memorable knockout blow. It has to be a coherent story, must be remarkable, must be worth engaging. It can't be like watching yet another Liam Neeson Taken movie when you know that he's just trying to extend his franchise as much as possible until he's stuck with the only other offer being a role in the next Expendables sequel.

He's pitching micro-content, but how do you know how well it works? But before that, what are the qualities that make this content really interesting?

The trouble I see with Meerkat is that it's too spontaneous. Could even say gratuitous, in the boring sense.

I jumped on a Meerkat stream by Jim Gaffigan. And he was serving his phone over something that look liked jelly shmeared on bread, chanting "carbs." I'm going to get to his latest audiobook when I have the chance, which I'm sure is more engaging than his Meerkats (meeks?)

Good and engaging content has to be scripted to some extent, and could be career ending if you're not careful. It's open season on journalists who try to be edgy impromptu, seeking attention with a jaded audience who has too many screens to watch.

Even catching trout requires some effort in advance. Tying flies. Trying to fool fish.

What numbers reflect the media that do engage? Data can be structured, can social networks also? Cathedral vs. the bazaar? Hierarchies or the open market?

Anyone up for PowerPoint karaoke? Maybe just once.

Google Web Designer: One idea. Any screen.

Google Web Designer:



Create engaging, interactive HTML5-based designs and motion graphics that can run on any device.



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DoubleClick Digital Marketing enables advertisers to more easily develop and run cross-screen campaigns for March Madness

DoubleClick Advertiser: Turner Sports reaches fans across screens for March Madness: "DoubleClick Digital Marketing platform that enable advertisers to more easily develop and run cross-screen campaigns."

Initial results from our beta show that converting Flash assets to HTML5 increases mobile reach by 400% and drives a 2-3x increase in average click-through rate (CTR).

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The Data Science Venn Diagram — skills needed to be a fully competent data scientist

The Data Science Venn Diagram — Drew Conway: "skills needed to be a fully competent data scientist"

Finally, a word on the hacking skills plus substantive expertise danger zone. This is where I place people who, "know enough to be dangerous," and is the most problematic area of the diagram. In this area people who are perfectly capable of extracting and structuring data, likely related to a field they know quite a bit about, and probably even know enough R to run a linear regression and report the coefficients; but they lack any understanding of what those coefficients mean. It is from this part of the diagram that the phrase "lies, damned lies, and statistics" emanates, because either through ignorance or malice this overlap of skills gives people the ability to create what appears to be a legitimate analysis without any understanding of how they got there or what they have created. [my emphasis]

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NodeXL - Network Overview Discovery and Exploration in Excel - Microsoft Research

NodeXL - Network Overview Discovery and Exploration in Excel - Microsoft Research:

NodeXL is a powerful and easy-to-use interactive network visualisation and analysis tool that leverages the widely available MS Excel application as the platform for representing generic graph data, performing advanced network analysis and visual exploration of networks. The tool supports multiple social network data providers that import graph data (nodes and edge lists) into the Excel spreadsheet.

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New York Times Shifts Resources to Mobile (Mobile Monetization Problem)

New York Times Shifts Resources to Mobile | Media - Advertising Age: "50% of its traffic coming from mobile, yet mobile contributes just 10% of digital ad revenue."



Interview with Cliff Levy, Editor of NYT Now:

Mr. Levy: We obviously look at analytics and we let the analytics to some extent inform our story selection, but it doesn't dictate or even strongly guide our story selection.

There are a limited number of stories available:

NYT Now subscribers have unlimited access to the most important stories of the day. These stories are hand-selected by NYT Now editors and typically include the top articles on the homepage as well as our most noteworthy blog posts, slide shows and multimedia features.

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DAP: Digital Analytics Program | DigitalGov

DAP: Digital Analytics Program | DigitalGov:

The Digital Analytics Program offers advanced, easy Web analytics to federal agencies. The program is a hosted shared service provided by the Digital Services Innovation Center in GSA’s Office of Citizen Services and Innovative Technologies.

Here's a listing of the Top 20 visited Gov't Web sites at https://analytics.usa.gov/. It's no wonder that "Where's My Refund" is number one:

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Learn Python the Hard Way 3rd Edition - Books on Google Play

Learn Python the Hard Way 3rd Edition - Books on Google Play:

Highly recommended for the beginner. Will be listing other resources on the Web.

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Big Data Discovery | SmartData Collective

Big Data Discovery | SmartData Collective:

The next trend in analytics: "big data discovery." While we have seen the acceptance and use of big data, data discovery and data science, there are advantages and disadvantages to each.

For example, Data Discovery excels in ease of use, but allows only limited depth of exploration, while Data Science provides powerful analysis but is slow, complex, and difficult to implement.

It's proposed by Gartner Strategic Planning to evolve into a distinct market category:

According to Gartner Analyst Joao Tapadinhas, these tools will be used by new “Citizen Data Scientists” who marry the skills of traditional business analysts with some of the expertise of expert statisticians.

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Omaha March Madness

Once again, Omaha is in the national spotlight for a national sporting event. (The Olympic Swim trials held here merit even worldwide exposure. They will return next year.). Last year Warren Buffett offered a $1 billion prize for a perfect bracket, but not this year.

You can watch the various NCAA 2015 Basketball Championship teams practice today at the CenturyLink Center, and even get free parking.

Nate Silver at his fivethirtyeight.com blog gives you a statistical advantage with his 2015 March Madness Predictions interactive bracket.

Just mouse over each time and receive his statistical analysis of each team's performance. Kentucky is his favorite (no big surprise):

The Wall Street Journal has produced their NCAA Tournament Round of 64: Live Blog.

CNBC get have Buffett on enough, and their live-wire financial journalist(?) Jim Cramer makes his picks.

12 best meat cities in America - CNN.com

12 best meat cities in America - CNN.com:



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Google Launches New Gaming Analytics and Native Ads Tools

Google Launches New Gaming Analytics and Native Ads Tools:



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