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	<title>Healthy Algorithms</title>
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	<link>http://healthyalgorithms.com</link>
	<description>A blog about algorithms, combinatorics, and optimization applications in global health informatics.</description>
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		<title>Healthy Algorithms</title>
		<link>http://healthyalgorithms.com</link>
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		<item>
		<title>Journal Club: Improving the Measurement of Maternal Mortality</title>
		<link>http://healthyalgorithms.com/2013/05/09/journal-club-improving-the-measurement-of-maternal-mortality/</link>
		<comments>http://healthyalgorithms.com/2013/05/09/journal-club-improving-the-measurement-of-maternal-mortality/#comments</comments>
		<pubDate>Thu, 09 May 2013 18:08:22 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[global health]]></category>
		<category><![CDATA[journal club]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2169</guid>
		<description><![CDATA[This week in journal club we will read Improving the Measurement of Maternal Mortality: The Sisterhood Method Revisited by Merdad et al. A method I am quite fond of.<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2169&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>This week in journal club we will read <a href="http://www.plosone.org/article/info%253Adoi%252F10.1371%252Fjournal.pone.0059834">Improving the Measurement of Maternal Mortality: The Sisterhood Method Revisited</a> by Merdad et al.  A method I am quite fond of.</p>
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			<media:title type="html">Abraham Flaxman</media:title>
		</media:content>
	</item>
		<item>
		<title>Replication, replication</title>
		<link>http://healthyalgorithms.com/2013/05/03/replication-replication/</link>
		<comments>http://healthyalgorithms.com/2013/05/03/replication-replication/#comments</comments>
		<pubDate>Fri, 03 May 2013 20:34:09 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[global health]]></category>
		<category><![CDATA[my research]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2145</guid>
		<description><![CDATA[A colleague forwarded me this RFP specifically for replication of controversial impact evaluations. It includes a recent journal club article (by other IHME colleagues) on the candidate study list. Cool! I&#8217;ve also made it really easy for someone to replicate &#8230; <a href="http://healthyalgorithms.com/2013/05/03/replication-replication/">Continue reading <span class="meta-nav">&#8594;</span></a><img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2145&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>A colleague forwarded me this <a href="http://www.3ieimpact.org/media/filer/2013/03/21/replication_rfp_rw2_2.pdf">RFP specifically for replication of controversial impact evaluations</a>. It includes a recent journal club article (by other IHME colleagues) on <a href="http://www.3ieimpact.org/en/funding/replication-window/replication-candidate-studies/">the candidate study list</a>.  Cool!</p>
<p>I&#8217;ve also made it really easy for someone to <a href="http://ghdx.healthmetricsandevaluation.org/record/hepatitis-c-prevalence-1990-and-2005-all-gbd-regions">replicate the results in one recent paper I was involved in</a>, on <a href="http://www.ncbi.nlm.nih.gov/pubmed/23172780">hepatitis C virus seroprevalence</a>.  Well, easy if you manage to <a href="https://github.com/aflaxman/gbd">get dismod installed</a>&#8230;  making <em>that</em> really easy is still on my to-do list.</p>
<br />  <a rel="nofollow" href="http://feeds.wordpress.com/1.0/gocomments/healthyalgorithms.wordpress.com/2145/"><img alt="" border="0" src="http://feeds.wordpress.com/1.0/comments/healthyalgorithms.wordpress.com/2145/" /></a> <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2145&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></content:encoded>
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			<media:title type="html">Abraham Flaxman</media:title>
		</media:content>
	</item>
		<item>
		<title>Contest results</title>
		<link>http://healthyalgorithms.com/2013/05/03/contest-results/</link>
		<comments>http://healthyalgorithms.com/2013/05/03/contest-results/#comments</comments>
		<pubDate>Fri, 03 May 2013 08:00:02 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[machine learning]]></category>
		<category><![CDATA[contest]]></category>
		<category><![CDATA[whales]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2162</guid>
		<description><![CDATA[I mentioned in February a couple of contests that caught my eye, and the Whale Detection one turned out to be quite interesting. Now it has completed, and the prediction quality (AUC, if I recall correctly) has been raised from &#8230; <a href="http://healthyalgorithms.com/2013/05/03/contest-results/">Continue reading <span class="meta-nav">&#8594;</span></a><img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2162&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>I mentioned in February <a href="http://healthyalgorithms.com/2013/02/15/contests-and-links/">a couple of contests that caught my eye</a>, and the Whale Detection one turned out to be quite interesting.  Now it has completed, and the prediction quality (AUC, if I recall correctly) has been raised from .72 to .98.  Very cool.  </p>
<p>Some links: </p>
<ul>
<li><a href="https://www.kaggle.com/c/whale-detection-challenge/forums/t/4472/summary-of-the-competition">summary from kaggle</a>,
</li>
<li><a href="http://marinexplore.org/blog/the-kaggle-challenge-improves-cornells-whale-detection-model-to-98/">report from MarineExplore</a>,
</li>
<li><a href="https://github.com/nmkridler/moby">python code for winning entry</a>.
</li>
</ul>
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		<slash:comments>0</slash:comments>
	
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			<media:title type="html">Abraham Flaxman</media:title>
		</media:content>
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		<item>
		<title>Journal Club: Incorporating Loss to Follow-up in Estimates of Survival</title>
		<link>http://healthyalgorithms.com/2013/05/02/journal-club-incorporating-loss-to-follow-up-in-estimates-of-survival/</link>
		<comments>http://healthyalgorithms.com/2013/05/02/journal-club-incorporating-loss-to-follow-up-in-estimates-of-survival/#comments</comments>
		<pubDate>Thu, 02 May 2013 17:54:06 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[global health]]></category>
		<category><![CDATA[journal club]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2163</guid>
		<description><![CDATA[The week journal club will read Incorporating Loss to Follow-up in Estimates of Survival Among HIV-Infected Individuals in Sub-Saharan Africa Enrolled in Antiretroviral Therapy Programs by Vergut et al.<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2163&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>The week journal club will read <a href="http://www.ncbi.nlm.nih.gov/pubmed/23100567">Incorporating Loss to Follow-up in Estimates of Survival Among HIV-Infected Individuals in Sub-Saharan Africa Enrolled in Antiretroviral Therapy Programs</a> by Vergut et al.</p>
<br />  <a rel="nofollow" href="http://feeds.wordpress.com/1.0/gocomments/healthyalgorithms.wordpress.com/2163/"><img alt="" border="0" src="http://feeds.wordpress.com/1.0/comments/healthyalgorithms.wordpress.com/2163/" /></a> <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2163&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></content:encoded>
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			<media:title type="html">Abraham Flaxman</media:title>
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	</item>
		<item>
		<title>Journal club: Effects of Newhints home-visits intervention</title>
		<link>http://healthyalgorithms.com/2013/04/24/journal-club-effects-of-newhints-home-visits-intervention/</link>
		<comments>http://healthyalgorithms.com/2013/04/24/journal-club-effects-of-newhints-home-visits-intervention/#comments</comments>
		<pubDate>Wed, 24 Apr 2013 17:44:47 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[global health]]></category>
		<category><![CDATA[journal club]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2159</guid>
		<description><![CDATA[This week&#8217;s paper Effect of the Newhints home-visits intervention on neonatal mortality rate and care practices in Ghana: a cluster randomised controlled trial, by Kirkwood et al. Cluster randomized trials and meta-analysis, a good combination to put new results in &#8230; <a href="http://healthyalgorithms.com/2013/04/24/journal-club-effects-of-newhints-home-visits-intervention/">Continue reading <span class="meta-nav">&#8594;</span></a><img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2159&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>This week&#8217;s paper <a href="http://www.ncbi.nlm.nih.gov/pubmed/23578528">Effect of the Newhints home-visits intervention on neonatal mortality rate and care practices in Ghana: a cluster randomised controlled trial</a>, by Kirkwood et al.  Cluster randomized trials and meta-analysis, a good combination to put new results in the context of the old.</p>
<p><a href="http://healthyalgorithms.files.wordpress.com/2013/04/meta-analysis.png"><img src="http://healthyalgorithms.files.wordpress.com/2013/04/meta-analysis.png?w=500&#038;h=313" alt="meta-analysis" width="500" height="313" class="aligncenter size-full wp-image-2160" /></a></p>
<br />  <a rel="nofollow" href="http://feeds.wordpress.com/1.0/gocomments/healthyalgorithms.wordpress.com/2159/"><img alt="" border="0" src="http://feeds.wordpress.com/1.0/comments/healthyalgorithms.wordpress.com/2159/" /></a> <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2159&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></content:encoded>
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			<media:title type="html">Abraham Flaxman</media:title>
		</media:content>

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			<media:title type="html">meta-analysis</media:title>
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		<title>hello, world of statistical graphics in IPython notebook</title>
		<link>http://healthyalgorithms.com/2013/04/22/hello-world-of-statistical-graphics-in-ipython-notebook/</link>
		<comments>http://healthyalgorithms.com/2013/04/22/hello-world-of-statistical-graphics-in-ipython-notebook/#comments</comments>
		<pubDate>Mon, 22 Apr 2013 17:33:11 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[software engineering]]></category>
		<category><![CDATA[data viz]]></category>
		<category><![CDATA[ipython]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2152</guid>
		<description><![CDATA[A few months ago, I had great success invoking the internet to come up with the &#8220;hello, world&#8221; of statistical graphics. There are some exciting new developments in javascript-based plotting, and this graphic is just the thing to compare them. &#8230; <a href="http://healthyalgorithms.com/2013/04/22/hello-world-of-statistical-graphics-in-ipython-notebook/">Continue reading <span class="meta-nav">&#8594;</span></a><img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2152&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>A few months ago, I had great success invoking the internet <a href="http://healthyalgorithms.com/2013/01/03/what-is-hello-world-for-statistical-graphics/">to come up with the &#8220;hello, world&#8221; of statistical graphics</a>.</p>
<p>There are some exciting new developments in javascript-based plotting, and this graphic is just the thing to compare them.  <a href="http://d3js.org/">D3js</a> has conquered the world in recent years, and is something that my colleagues are starting to think they need to know. Meanwhile, one of the d3js instigators has unveiled the next in his series of revolutions in data visualization, <a href="http://trifacta.github.io/vega/">Vega</a>.  This is still in development, but may be <a href="https://github.com/trifacta/vega/wiki/Vega-and-D3">more appropriate than d3js for routine plots</a>.  And it was very soon after the Vega specification and runtime appeared that a python package for it was also released.</p>
<p><a href="http://nbviewer.ipython.org/5436794">Here is an IPython notebook comparing all of these options</a>.  The notebook doesn&#8217;t save javascript in a way that redisplays, but if you put it in your own notebook server and execute all the cells you should see something like this:</p>
<p><a href="http://healthyalgorithms.files.wordpress.com/2013/04/vincent_vega.png"><img src="http://healthyalgorithms.files.wordpress.com/2013/04/vincent_vega.png?w=500&#038;h=388" alt="vincent_vega" width="500" height="388" class="aligncenter size-full wp-image-2153" /></a></p>
<p>p.s. google <a href="https://www.google.com/search?q=vincent+vega&amp;tbm=isch">vincent vega</a> to learn the pop culture joke behind this strangely named python package.</p>
<br />  <a rel="nofollow" href="http://feeds.wordpress.com/1.0/gocomments/healthyalgorithms.wordpress.com/2152/"><img alt="" border="0" src="http://feeds.wordpress.com/1.0/comments/healthyalgorithms.wordpress.com/2152/" /></a> <img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2152&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></content:encoded>
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			<media:title type="html">Abraham Flaxman</media:title>
		</media:content>

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			<media:title type="html">vincent_vega</media:title>
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	</item>
		<item>
		<title>Journal Club: Secret Paper</title>
		<link>http://healthyalgorithms.com/2013/04/17/journal-club-secret-paper/</link>
		<comments>http://healthyalgorithms.com/2013/04/17/journal-club-secret-paper/#comments</comments>
		<pubDate>Wed, 17 Apr 2013 08:00:44 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[global health]]></category>
		<category><![CDATA[journal club]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2147</guid>
		<description><![CDATA[This week in journal club we are reading something that I&#8217;m not going to name, because it says &#8220;do not cite or distribute without permission&#8221; on the top of the paper. This secret paper sounds interesting, maybe I can tell &#8230; <a href="http://healthyalgorithms.com/2013/04/17/journal-club-secret-paper/">Continue reading <span class="meta-nav">&#8594;</span></a><img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2147&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>This week in journal club we are reading something that I&#8217;m not going to name, because it says &#8220;do not cite or distribute without permission&#8221; on the top of the paper.  This secret paper sounds interesting, maybe I can tell you about it some day.</p>
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			<media:title type="html">Abraham Flaxman</media:title>
		</media:content>
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		<title>Methods debates</title>
		<link>http://healthyalgorithms.com/2013/04/15/methods-debates/</link>
		<comments>http://healthyalgorithms.com/2013/04/15/methods-debates/#comments</comments>
		<pubDate>Mon, 15 Apr 2013 08:00:56 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[global health]]></category>
		<category><![CDATA[health metrics]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2149</guid>
		<description><![CDATA[An interesting exchange has been going on regarding the GBD 2010 estimates of deaths due to HIV, published as part of our GBD work last December, along with mortality estimates for 234 other causes of death. The UNAIDS reference group &#8230; <a href="http://healthyalgorithms.com/2013/04/15/methods-debates/">Continue reading <span class="meta-nav">&#8594;</span></a><img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2149&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>An interesting exchange has been going on regarding the GBD 2010 estimates of deaths due to HIV, <a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)61728-0/abstract">published as part of our GBD work</a> last December, along with mortality estimates for 234 other causes of death.  The <a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(13)60703-5/fulltext">UNAIDS reference group comment</a>, and <a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(13)60703-5/fulltext">my colleagues respond</a>.</p>
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		<slash:comments>0</slash:comments>
	
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			<media:title type="html">Abraham Flaxman</media:title>
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		<title>ML in Python: Naive Bayes the hard way</title>
		<link>http://healthyalgorithms.com/2013/04/13/ml-in-python-naive-bayes-the-hard-way/</link>
		<comments>http://healthyalgorithms.com/2013/04/13/ml-in-python-naive-bayes-the-hard-way/#comments</comments>
		<pubDate>Sat, 13 Apr 2013 23:42:38 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[machine learning]]></category>
		<category><![CDATA[MCMC]]></category>
		<category><![CDATA[pymc]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2141</guid>
		<description><![CDATA[A recent question on the PyMC mailing list inspired me to make a really inefficient version of the Naive Bayes classifier. Enjoy.<img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2141&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>A <a href="https://groups.google.com/d/msg/pymc/MOkDnX1NrMA/uE4ZxXysUJYJ">recent question on the PyMC mailing list</a> inspired me to make  <a href="http://nbviewer.ipython.org/5380476">a really inefficient version of the Naive Bayes classifier</a>. Enjoy.</p>
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			<media:title type="html">Abraham Flaxman</media:title>
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		<item>
		<title>The Mastery Table for Planning Classes</title>
		<link>http://healthyalgorithms.com/2013/04/11/the-mastery-table-for-planning-classes/</link>
		<comments>http://healthyalgorithms.com/2013/04/11/the-mastery-table-for-planning-classes/#comments</comments>
		<pubDate>Thu, 11 Apr 2013 08:00:55 +0000</pubDate>
		<dc:creator>Abraham Flaxman</dc:creator>
				<category><![CDATA[education]]></category>
		<category><![CDATA[software carpentry]]></category>

		<guid isPermaLink="false">http://healthyalgorithms.com/?p=2130</guid>
		<description><![CDATA[I&#8217;m quite taken with the Software Carpentry approach to teaching scientists computer skills, especially since I saw it in action in UW a few months ago. One aspect that I&#8217;ve been trying out for my own course is the &#8220;mastery &#8230; <a href="http://healthyalgorithms.com/2013/04/11/the-mastery-table-for-planning-classes/">Continue reading <span class="meta-nav">&#8594;</span></a><img alt="" border="0" src="http://stats.wordpress.com/b.gif?host=healthyalgorithms.com&#038;blog=4781973&#038;post=2130&#038;subd=healthyalgorithms&#038;ref=&#038;feed=1" width="1" height="1" />]]></description>
				<content:encoded><![CDATA[<p>I&#8217;m quite taken with the <a href="http://software-carpentry.org/">Software Carpentry approach</a> to teaching scientists computer skills, especially since <a href="http://healthyalgorithms.com/2013/02/26/software-carpentry-at-uw/">I saw it in action in UW a few months ago</a>.  One aspect that I&#8217;ve been trying out for my own course is the &#8220;mastery table&#8221; approach that the Software Carpentry Instructor Study Groups use. Here is <a href="http://teaching.software-carpentry.org/2013/02/25/mastery-table-version-control/">a mastery table for teaching version control</a>.  I have made a few of my own, but I don&#8217;t think I said enough for any novice to leave competent, according to my ambitions.  I will keep trying.</p>
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			<media:title type="html">Abraham Flaxman</media:title>
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