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	<title>Cornell CS 322 - Intro to Scientific Computing</title>
	<link>http://expertvoices.nsdl.org/cornell-cs322</link>
	<description>Student blog for Cornell CS 322 "Introduction to Scientific Computing" (Spring 2008, professor Doug James). http://www.cs.cornell.edu/courses/cs322/2008sp</description>
	<pubDate>Fri, 09 May 2008 20:11:21 +0000</pubDate>
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	<language>en</language>
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		<title>Think You&#8217;re Good at Go?</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/08/think-youre-good-at-go/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/08/think-youre-good-at-go/#comments</comments>
		<pubDate>Thu, 08 May 2008 18:39:37 +0000</pubDate>
		<dc:creator>berner6</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/08/think-youre-good-at-go/</guid>
		<description><![CDATA[Go is a traditional strategy-based board game originating from China circa 4th century BCE.  It involves two players placing  black and white playing pieces called stones on a 19&#215;19 grid. The relatively new field of Computer Go is a field of Artificial Intelligence that focuses on creating creating computer programs to autonomously play Go.

Monte Carlo [...]]]></description>
			<content:encoded><![CDATA[<p>Go is a traditional strategy-based board game originating from China circa 4th century BCE.  It involves two players placing  black and white playing pieces called stones on a 19&#215;19 grid. The relatively new field of Computer Go is a field of Artificial Intelligence that focuses on creating creating computer programs to autonomously play Go.<img src="http://en.wikipedia.org/wiki/Image:Go-Equipment-Narrow-Black.png" /><img src="http://en.wikipedia.org/wiki/Image:Go-Equipment-Narrow-Black.png" /></p>
<p><img src="http://upload.wikimedia.org/wikipedia/en/thumb/0/08/Go-Equipment-Narrow-Black.png/250px-Go-Equipment-Narrow-Black.png" height="192" width="250" /></p>
<p>Monte Carlo methods have been developed for these computer programs to more effectively choose the most appropriate next move. To do so, the program simulates literally thousands of games from the current state, in the end choosing the best move. This method requires little domain knowledge of Go (knowledge of how to play the game) and thus leads to strong strategy but poor tactics.</p>
<p>To remedy the problem a new search technique was developed, called Upper Confidence Bounds Applied to Trees (UCT) which is a natural extension of Monte-Carlo Go programs. UCT is essentially &#8220;player memory&#8221; in that it remembers states of previous games and the outcomes of those games based on the chosen moves. It then guides the program towards the randomly generated moves that would yield the most successful result based on past &#8220;experience&#8221;.</p>
<p>Now beating the computer at Go is harder than ever.</p>
<p>http://en.wikipedia.org/wiki/Computer_Go#Monte-Carlo_methods</p>
<p>http://senseis.xmp.net/?UCT</p>
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		<title>Rendering an Even Better Water-Bunny</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/08/rendering-an-even-better-water-bunny/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/08/rendering-an-even-better-water-bunny/#comments</comments>
		<pubDate>Thu, 08 May 2008 18:05:30 +0000</pubDate>
		<dc:creator>berner6</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/08/rendering-an-even-better-water-bunny/</guid>
		<description><![CDATA[In my first post I wrote about a team at Stanford University that created a raytracing algorithm called the Hybrid Particle Level Set Method for rendering images, treating the object when appropriate as either a liquid or as composed of tiny metaballs. Although this method was groundbreaking enough to win an Oscar, the bounds of [...]]]></description>
			<content:encoded><![CDATA[<p>In my first post I wrote about a team at Stanford University that created a raytracing algorithm called the Hybrid Particle Level Set Method for rendering images, treating the object when appropriate as either a liquid or as composed of tiny metaballs. Although this method was groundbreaking enough to win an Oscar, the bounds of creating realism had still not yet been reached.</p>
<p>Into the picture steps a team of computer scientists from UC San Diego with new raytracing algorithm that vastly cuts the computing costs for smoky and foggy images, thus allowing for much more realistic 3-D scenes. Traditional raytracing methods calculate the light at thousands of points, while the new method, called photon mapping, calculates the entire lightray in one shot. One of the co-authors explains, &#8220;Instead of computing the light at thousands of discrete points along the ray between the camera and the object, which is the conventional approach, we compute the lighting along the whole length of the ray all at once.&#8221;</p>
<p>Although the more costly raytracing methods may be adequate for scenarios such as movies, there simply isn&#8217;t enough computer power to effectively render images in near real-time as required in video games. However, the photon mapping method is much more apt for use in video games due to its much higher efficiency.</p>
<p>Below are two images of a lighthouse in fog, both rendered with the same computational resources. The top image, which is clearly more realistic, was rendered with the new photon mapping method.<img src="http://www.jacobsschool.ucsd.edu/uploads/news_release/2008/magick_lighthouseverticalcompare1.jpg" height="548" width="450" /></p>
<p>http://www.jacobsschool.ucsd.edu/news/news_releases/release.sfe?id=731</p>
<p>http://graphics.ucsd.edu/~wjarosz/publications/jarosz08beam.pdf</p>
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		<title>Automatic Music Transcription</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/07/automatic-music-transcription/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/07/automatic-music-transcription/#comments</comments>
		<pubDate>Thu, 08 May 2008 04:17:48 +0000</pubDate>
		<dc:creator>xpaperplane</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/07/automatic-music-transcription/</guid>
		<description><![CDATA[Automatic music transcription is a unique problem to which Monte Carlo methods can be applied. It is sometimes desirable to extract human-readable music scores from a performance by musicians, but it is not a simple task. The basic difficulties of extracting the information are, perhaps, somewhat obvious, but there also lie more subtle issues. For [...]]]></description>
			<content:encoded><![CDATA[<p><strong>Automatic music transcription</strong> is a unique problem to which <strong>Monte Carlo methods</strong> can be applied. It is sometimes desirable to extract human-readable music scores from a performance by musicians, but it is not a simple task. The basic difficulties of extracting the information are, perhaps, somewhat obvious, but there also lie more subtle issues. For example, music is usually performed in such a manner that the tempo is not constant throughout the piece. Even more troublesome are the instances where only one or two notes are drawn out for musical impact.</p>
<p>This process of extracting all this information starts with a probabilistic model for timing deviations and uses tempo tracking algorithms for quantization. Then, the Monte Carlo methods are used to approximate the probabilities of note placement. The paper cited followed a Bayesian modeling approach for the tempo tracking and transcription. This paper then goes on to specifically explore the <strong>Markov Chain Monte Carlo (MCMC)</strong> and the <strong>sequential Monte Carlo (SMC)</strong> methods using both fake data and real data. It was found that the SMC method outperformed the MCMC method in terms of the quality of the results. This is reasonable, as SMC is well suited for applications in which observations arrive sequentially.  </p>
<p><a href="http://www.iro.umontreal.ca/~pift6080/documents/papers/cemgil_tempo.pdf">Monte Carlo Methods for Tempo Tracking<br />
and Rhythm Quantization</a></p>
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		<title>Monte Carlo - Medical Application</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/07/monte-carlo-medical-application/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/07/monte-carlo-medical-application/#comments</comments>
		<pubDate>Thu, 08 May 2008 03:13:17 +0000</pubDate>
		<dc:creator>ace5678</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/07/monte-carlo-medical-application/</guid>
		<description><![CDATA[Monte Carlo methods are used in many areas including random number generations, nuclear reactor designs, traffic flows, oil-well explorations, economics etc.
PEREGRINE is a software/hardware system that implements the Monte Carlo method for the specific purpose of simulating medical radiation delivery. The major goals in its development have been to design a system specifically tailored to [...]]]></description>
			<content:encoded><![CDATA[<p>Monte Carlo methods are used in many areas including random number generations, nuclear reactor designs, traffic flows, oil-well explorations, economics etc.<br />
PEREGRINE is a software/hardware system that implements the Monte Carlo method for the specific purpose of simulating medical radiation delivery. The major goals in its development have been to design a system specifically tailored to radiation therapy applications and make Monte Carlo transport fast enough to be practical for day-to-day treatment planning.<br />
It simulates the transport of neutrons, photons, electrons and protons through a patient using a geometry derived from a computed tomography (CT) scan.<br />
This will help doctors to choose a treatment that maximizes the radiation dose to the tumor and minimizes the dose to normal tissues. Monte Carlo method is used here because it is the most accurate way to simulate radiation transport on a computer.<br />
Further advantages are accurate dose calculations for all materials, all geometries, simultaneous determination of dose deposition and image formation and detailed information of how dose is deposited in matter.</p>
<p><a href="http://expertvoices.nsdl.org/cornell-cs322/files/2008/05/picture2.jpg" title="picture2.jpg"><img src="http://expertvoices.nsdl.org/cornell-cs322/files/2008/05/picture2.thumbnail.jpg" alt="picture2.jpg" /></a></p>
<p>www.nuc.berkeley.edu/courses/classes/NE39/Vujic-cancer.ppt</p>
<p>www.mgnet.org/~douglas/Classes/cs521-s01/<strong>monte</strong>-<strong>carlo</strong>/<strong>application</strong>.ppt</p>
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		<title>Runge Kutta Video Game</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/runge-kutta-video-game/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/runge-kutta-video-game/#comments</comments>
		<pubDate>Wed, 07 May 2008 03:36:37 +0000</pubDate>
		<dc:creator>cmny21</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/runge-kutta-video-game/</guid>
		<description><![CDATA[http://www.youtube.com/watch?v=qaPuPouEfbM
Browsing on youtube, I found a game named after the two German mathematicians Carl Runge and Martin Kutta.  The author of the game says he used the Runge Kutta method to simulate the spring in the game.
He says he uses RK4 with a frame timestep of t = t + 0.1, when running at 60fps.  [...]]]></description>
			<content:encoded><![CDATA[<p><a href="http://www.youtube.com/watch?v=qaPuPouEfbM">http://www.youtube.com/watch?v=qaPuPouEfbM</a></p>
<p>Browsing on youtube, I found a game named after the two German mathematicians Carl Runge and Martin Kutta.  The author of the game says he used the Runge Kutta method to simulate the spring in the game.</p>
<p>He says he uses RK4 with a frame timestep of t = t + 0.1, when running at 60fps.  He says he used the Runge Kutta method because RK4 appeared accurate and fast compared to the other methods out there.</p>
<p>By clicking on the link, you will see a quick demo to the game.</p>
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		<title>Brief Monte Carlo History</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/brief-monte-carlo-history/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/brief-monte-carlo-history/#comments</comments>
		<pubDate>Wed, 07 May 2008 02:39:58 +0000</pubDate>
		<dc:creator>cmny21</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/brief-monte-carlo-history/</guid>
		<description><![CDATA[Enrico Fermi in the 1930&#8217;s used Monte Carlo in the calculation of neutron diffusion.  He would later design a Monte Carlo mechanical device used in calculating criticality in nuclear reactors.  That device was called the Fermiac.John Louis von Neumann in the 1940&#8217;s established the mathematical basis for PDF&#8217;s, CDF&#8217;s, and pseudorandom number generators. [...]]]></description>
			<content:encoded><![CDATA[<p>Enrico Fermi in the 1930&#8217;s used Monte Carlo in the calculation of neutron diffusion.  He would later design a Monte Carlo mechanical device used in calculating criticality in nuclear reactors.  That device was called the Fermiac.John Louis von Neumann in the 1940&#8217;s established the mathematical basis for PDF&#8217;s, CDF&#8217;s, and pseudorandom number generators.  The Monte Carlo method was used for these establishments.</p>
<p>Currently, Monte Carlo methods are used in cancer therapy, traffic flow, Dow-Jones forecasting, oil well exploration, and several physics applications.  Examples of those applications include stellar evolution, reactor design, and quantum chromo-dynamics.  In addition, Monte Carlo is used widely in modeling materials and chemicals.<br />
Expanding on using Monte Carlo in cancer treatment, the U.S. Department of Energy&#8217;s Brookhaven National Laboratory has been conducting a trial of an experimental treatment called boron neutron capture therapy (BNCT).  Studies have concluded that a BNCT neutron source engineering input deck could complete its calculation in 19.35 minutes using the ORNL Intel Paragon XPS-150 computer.  On the other hand, this identical calculation required 4.7 days to execute on a DEC Alpha workstation at INEEL.  Overall, the speed-up ratio was 350.  This conclusion could prove to be significant in the use of MCNP code.  Having the calculations finished in under an hour will be an important factor in cancer treatment, especially for the brain cancer glioblastoma multiforme.<br />
http://www.csm.ornl.gov/ssi-expo/MChist.html</p>
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		<title>B-splines</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/b-splines/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/b-splines/#comments</comments>
		<pubDate>Tue, 06 May 2008 17:32:37 +0000</pubDate>
		<dc:creator>pvd87</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/06/b-splines/</guid>
		<description><![CDATA[Although we have never covered this in class, splines are a very important component in numerical analysis and computer graphics.  A spline is a special piecewise defined function.  To go along with what we have learned in class, polynomial interpolation can be executed by spline interpolation.  In more specific areas of computer graphics, spline functions [...]]]></description>
			<content:encoded><![CDATA[<p>Although we have never covered this in class, splines are a very important component in numerical analysis and computer graphics.  A spline is a special piecewise defined function.  To go along with what we have learned in class, polynomial interpolation can be executed by spline interpolation.  In more specific areas of computer graphics, spline functions usually mean piecewise polynomial curves. A neat application of splines is modeling irregularly shaped objects.  A specific type of splines are triangular B-splines.  They help smooth surfaces of an object with the lowest degree polynomial.  They are a tool for modeling complex objects with nonrectangular surfaces.   There are many useful features from this B-spline technique for modeling irregularly shaped objects over random triangulations.  This technique can be applied to design problems such as filling polygonal holes or designing smooth blends. http://en.wikipedia.org/wiki/Spline_(mathematics)http://ieeexplore.ieee.org/iel1/38/6686/00267471.pdf</p>
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		<title>Numerical Relativity</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/04/numerical-relativity/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/04/numerical-relativity/#comments</comments>
		<pubDate>Sun, 04 May 2008 17:37:56 +0000</pubDate>
		<dc:creator>xpaperplane</dc:creator>
		
		<category><![CDATA[General]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/04/numerical-relativity/</guid>
		<description><![CDATA[Computational physics is one branch of physics that solves problems in physics by implementing computational algorithms. Especially in theoretical physics, the study of numerical physics is significantly useful and often used for simulations. 
One of the most exiting branches of computational physics is numerical relativity. It is the astrophysical study to simulate objects in space-time [...]]]></description>
			<content:encoded><![CDATA[<p>Computational physics is one branch of physics that solves problems in physics by implementing computational algorithms. Especially in theoretical physics, the study of numerical physics is significantly useful and often used for simulations. </p>
<p>One of the most exiting branches of computational physics is <strong>numerical relativity</strong>. It is the astrophysical study to simulate objects in space-time universe like stars, black holes, and gravitational waves, based on Einstein&#8217;s Theory of General Relativity. </p>
<p>The physical law in space-time can basically be represented by one equation: the Einstein Equation. Therefore, <strong>numerical relativity</strong> is primarily the study of numerical solution of the Einstein equations:</p>
<p><font size="4"><strong>Gij = 8&pi;Tij</strong>.</font></p>
<p>These are16 coupled hyperbolic-elliptic nonlinear partial differential equations (which reduce to 10 by symmetry). They equate the curvature of space-time (Einstein tensor G) with the energy and momentum in the space-time (stress-energy tensor T). As the result, the differential equations evolve time and space derivatives. Simulating the movements of objects in space-time on computer requires the methods to take spatial derivatives and time derivative. I introduce some of the practical methods we learned in class to deal with these problems. </p>
<p><font size="+1"><u>Special derivatives</u></font><br />
Einstein equations by themselves cannot be differentiated exactly. Therefore, we need to change them to the forms so that they can be differentiated exactly. <strong>Fourier series expansion</strong>, expansion in terms of <strong>Chebyshev polynomials</strong> are used for this purpose. These methods are effective because they have high convergence rates.</p>
<p><font size="+1"><u>Time derivatives</u></font><br />
<strong>Runge-Kutta equations</strong> of fourth-order are often used in this step. As we increase the order of <strong>Runge-Kutta equations</strong>, we can acquire arbitrary convergence rate.</p>
<p>Numerical Relativity group at the Albert Einstein Institute is expert in these simulations, and I site their resulted images.</p>
<p><a href="http://en.wikipedia.org/wiki/Numerical_relativity"><br />
General information of Numerical Relativity</a><br />
<a href="http://numrel.aei.mpg.de/Visualisations/index.html"><br />
Image and Movie Archive of the AEI Numerical Relativity Group</a></p>
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		<title>Robust Monte Carlo Methods for Light Transport Simulation</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/01/robust-monte-carlo-methods-for-light-transport-simulation/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/01/robust-monte-carlo-methods-for-light-transport-simulation/#comments</comments>
		<pubDate>Fri, 02 May 2008 00:14:26 +0000</pubDate>
		<dc:creator>nick</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/01/robust-monte-carlo-methods-for-light-transport-simulation/</guid>
		<description><![CDATA[      In Eric Veach of Stanford University’s dissertation Robust Monte Carlo Methods for Light Transport Simulation, he describes how newly developed Monte Carlo techniques can extend the range of input models for which light transport simulations are practical. This includes brand spanking new theoretical models, statistical methods and rendering algorithms. For the theoretical basis for [...]]]></description>
			<content:encoded><![CDATA[<p class="MsoNormal"><font face="Times New Roman">      In Eric Veach of Stanford University’s dissertation <em>Robust Monte Carlo Methods for Light Transport Simulation</em>, he describes how newly developed Monte Carlo techniques can extend the range of input models for which light transport simulations are practical. This includes brand spanking new theoretical models, statistical methods and rendering algorithms. For the theoretical basis for bi-directional light transport Veach proposes a linear operator formulation, which does not assume anything about the physical validity of the input. Using bi-directional techniques, he shows how to get correct mathematical results. He then uses a different formulation, this time for any physically valid input such that the transport operators are symmetric. He finally shows how light transport can be formulated as and integral over a space of paths. This allows the new sampling and integration techniques to be applied and uses this model to look at the limitations of unbiased Monte Carlo methods and show that various kinds of paths cannot be sampled. </font></p>
<p class="MsoNormal"><font face="Times New Roman">A new technique called multiple importance sampling greatly increases the robustness of Monte Carlo integration. To evaluate an integral, it uses more than one sampling technique and combines these samples in a way that is very close to optimal. Veach finally links all of these ideas together to get new Monte Carlo light transport algorithms. Once of these is the bi-directional path tracing that uses a family of different path sampling techniques and creates some path vertices starting from a from either a light source or a sensor. The algorithm is unbiased, handles arbitrary geometry and materials, and most importantly, it is simple to implement. The second algorithm is called metropolis light transport. This algorithm generates paths by following a random walk through path space so the probability of visiting each path is in proportion to the contribution it makes to the optimal image. This algorithm is also unbiased, it handles arbitrary geometry and materials, and more importantly it requires little storage and can be orders of magnititude more efficient than its predecessors. </font></p>
<p class="MsoNormal"><font face="Times New Roman">This dissertation by Eric Veach of Stanford University has a little relationship with one of the techniques that we have been learning about in CS 322 Scientific Computing. We have learned the basic Monte Carlo integration technique and we see that here it is applied to a model that is used for light transportation simulation and used to create light transport algorithms that generate realistic images by simulating the emission and scattering of light in an artificial environment. There are many applications for which these algorithms are good for that include lighting design, architecture, and computer animation. Related engineering applications include neutron transport and radiative heat transfer. As we can see, the things that we learn in CS 322 are not a waste of our time but have useful applications in this world. </font></p>
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		<title>Topology testing of phylogenies using least squares methods</title>
		<link>http://expertvoices.nsdl.org/cornell-cs322/2008/05/01/topology-testing-of-phylogenies-using-least-squares-methods/</link>
		<comments>http://expertvoices.nsdl.org/cornell-cs322/2008/05/01/topology-testing-of-phylogenies-using-least-squares-methods/#comments</comments>
		<pubDate>Thu, 01 May 2008 19:02:57 +0000</pubDate>
		<dc:creator>nick</dc:creator>
		
		<category><![CDATA[Uncategorized]]></category>

		<guid isPermaLink="false">http://expertvoices.nsdl.org/cornell-cs322/2008/05/01/topology-testing-of-phylogenies-using-least-squares-methods/</guid>
		<description><![CDATA[In the article Topology Testing of Phylogenies Using Least Squares methods, Aleksandra Czarna et al. use the least squares method to analyze data from a variety of biology topics including mammalian mitochondrial protein sequences, nucleotides, Hepatitis C, and DNA hybridization. The researchers found that the weighted least squares method provides a computationally efficient approximation to [...]]]></description>
			<content:encoded><![CDATA[<p class="MsoNormal"><font face="Times New Roman">In the article <em>Topology Testing of Phylogenies Using Least Squares methods</em>, Aleksandra Czarna et al. use the least squares method to analyze data from a variety of biology topics including mammalian mitochondrial protein sequences, nucleotides, Hepatitis C, and DNA hybridization. The researchers found that the weighted least squares method provides a computationally efficient approximation to the generalized least squares method. This was particularly useful when analyzing sets of trees, and when assessing the phylogenetic signal in the data when other methods are not available. </font></p>
<p class="MsoNormal"><font face="Times New Roman">            It is easy to see that this topic ties into the topics of the CS 322 course Scientific Computing. In the course, we learn about a lot of methods and one of these happens to be the least squares method. However, we do not get to see much of the methods we learn in practice. This article shows how the use of the least squares method can be very beneficial for the analysis of Biomedical data. The authors point out that they used the weighted least squares method because it was both computationally efficient and it gave a great approximation to the generalized least squares method. That is exactly what this course is about, methods to guarantee computations that a extremely close to optimal if not optimal, while still taking in consideration computational efficiency. There seems to be a trade-off in the amount of error a method has and its efficiency. </font></p>
<p class="MsoNormal"><font face="Times New Roman">            This article may not be the most exciting read, but it shows that there is a use for the Least Squares method out there. In one of the author’s studies, they analyzed a set of mammalian mitochondrial protein data that included 3414 aligned amino acids from the cow, harbor seal, human, mouse, opossum, and rabit. They used generalized least squares in a program to construct a confidence set of trees to analyze this data. They used similar techniques for studying Hepatitis C, and DNA hybridization data. So in conclusion, there are uses for the least squares method out there and scientific computing is cool.  </font></p>
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