De Rerum Natura

I am writing a Mathematica program to produce the precision error signal and reconstruction matrix for an arbitrary number of models. The maximum number I had tried before was ten models because it corresponded to the number of maps we have for the 29 Palms dataset.

My first try consisted of systematically creating all possible permutations of the precision error equations, squaring them, and then storing the coefficients. The program would then systematically look at the equations and augment an independent set every time it found an equation that could not be written as linear combinations of the previous ones in the set.

This worked okay for ten or so models, but I want to produce the full covariance matrix for twenty questions in a multiple-choice exam. No problem, I was making some grilled lamb for Easter dinner yesterday, so I put the computer to work and walked away. Three hours later, the computer was still trying to finish the list of all possible equation permutations! I confess that I have not worked out the combinatorics for the equations yet so perhaps it is of order $20!$. This would be 2,432,902,008,176,640,000 combinations. Compare this to $10!=3628800$ and you can see why the computation got hard quickly.

So my second incantation of the program was to do the computation randomly. Two integers $P$ and $Q$ are picked randomly such that $1\le P\le m$ and $1\le Q\le m$ where $m$ is the number of models. These random numbers are then used to randomly sample the model variables and construct a precision error difference equation. If the equation is independent from the set currently at hand, it is kept, otherwise discarded.

This second version is taking about ten minutes to produce a result. This made me think about how we perceive randomness as haphazardly: “Oh, you are just randomly trying to guess the right answer.” We perceive randomly as wasteful or misguided. The case presented here is just another example of how random is sometimes faster than systematic.

I picked up a copy of this month’s Discover magazine and found an interesting news item on the half-life of English irregular verbs. This piqued my interest since I have been doing some studying of Natural Language Processing to see how precision error could be used in the field.

A Student’s Introduction to English Grammar (co-written by one of the principals at the Language Log) defines irregular verbs as those that do not have a well-defined rule to generate their inflectional forms. The preterite form of “walk” is “walked”. “Walk” is a regular verb that uses the “-ed” rule for forming the preterite and past participle inflections. On the other hand, “fly” is an irregular verb since the preterite form is given by “flew” and the past participle by “flown”.

Erez Lieberman and co-authors did a quantitaive study of how often irregular verbs in English turn regular. From historical records (Old English -> Middle English -> Modern English) they were able to determine that the half-life of irregular verbs was proportional to the square root of their frequency. An irregular verb a 100 times less frequent in daily use than another verb will regularize 10 times faster than the frequently used one.

The idea of a half-life comes from nuclear physics. Given a sample of $n$ radioactive atoms, the half-life is the average time you have to wait for half the atoms to decay to another type. The half-life of the uranium isotope U-230 is about $4.5$ billion years. This, by the way, explains why we can still find U-238 on Earth (which is, itself, 4 billion years old). If the half life of U-238 was a million years or less, it would all have disappeared by the time we became clever enough to discover radioactivity (about a hundred years ago).

The half life for verbs with a frequency of $1/100$ to $1/1000$ is estimated to be $\mathrm{5,400}$ years. Examples of verbs in this frequency bin are: “begin” and “help”. “Begin” is still irregular (“began”) but “help” decayed from “holp” to “helped” sometime between Middle English and Modern English. Although the Oxford English Dictionary says “holp” is still used in obscure American dialects. The OED quotes Mark Twain in “The Prince and the Pauper” as saying: “Of a truth I was right — he hath holpen in a kitchen.”

The most common verbs — “be” and “have” — have not been observed to decay but extrapolating using the square root of the frequency rule allows the authors to estimate a half-life of $\mathrm{39,000}$ thousand years! In other words, English as a language will probably die before “be” becomes regular.

In previous posts I talked about precision error matrices as being tensors. Boy, was I wrong! This is another case of my intuition getting way ahead of my math and science. I know just enough math to shot myself in the foot with these speculations. I’ll explain.

Matrices are multi-dimensional arrays of numbers. A two-dimensional matrix $M$ needs two indices $i$ and $j$ to specify a component $M_{\mathrm{ij}}$. A three-dimensional matrix would need three indices and so on. Tensors can be thought of as matrices but the converse is not true. Not all matrices are tensors. That is where I went wrong.

Tensors are multi-dimensional geometrical objects. Yes, they can be represented by matrices but their true hallmark is that they transform correctly under coordinate transformations. The simplest example of the geometrical nature of tensors can be made with a vector. Take a vector drawn on a sheet of paper. No coordinate system has been drawn on the paper. The vector exists independent of any coordinate system. It has a length, for example, and we need no coordinate system to measure it — just a ruler. Two different coordinate systems can be put on the paper that would result in completely different components for the vector. What makes the vector a tensor is that given a coordinate transformation from one system to the next the vector transforms in such a way that both coordinate systems agree on the length of the vector.

This is the geometrical signature of tensors. Different coordinate systems (observers in the parlance of General Relativity) may have different components for the matrices they use to represent a tensor. But they agree on geometrical properties such as the length of a vector or the area of a polygon.

My claim that precision error matrices can be made into tensors may be correct, but I definitely have not proven it until I can show that the tensors I define transform properly under coordinate transformations.

I’ve been nibbling on a bunch of books for the past week. They are, in no particular order:

Mirage: Napoleon’s Scientists and the Unveiling of Egypt deals with the scientific side of Napoleon’s famous imperialistic debacle — the 1798 invasion of Egypt. We tend to think of historical knowledge as continuous in time. If we know something now, everyone in the past must have known it. This book shatters that illusion. Ancient Egypt had been lost to humanity for centuries. The savants in the expedition started the recovery of this lost civilization. One young scientist that participated in the expedition was Joseph Fourier. I have read many biographical sketches of Fourier but I do not recall ever reading that he was part of Napoleon’s Egypt “expedition”. One of the categories in this blog, “Fourier analysis”, is named after him. We can thank Fourier for many things but one that comes immediately to mind is the MP3 music file standard.

The World Without Us has been getting a lot of press. It clearly deserves it. The premise — what would happen to the world if we just disappeared overnight — forms a great hook on which to hang all sorts of scientific observations about biology, the durability of materials, the relentless march of entropy, human evolution, and much more. I highly recommend this book.

Questions in an exam are detectors of student competency. Students are detectors of the correct answers in a test. What is the variation in the student’s model of the correct exam? The precision error equations can be used to construct a covariance matrix for the students instead of the questions. What makes the difference is what is being averaged. When you want to use a test to tell you something about the questions, you average over the students. The covariance matrix is then indexed by the questions. When you want the test to tell you about the students, you average over the questions. The covariance matrix is indexed by students.

All of this suggests that it would be possible to build a completely parameter-less approach to detecting latent groups in students. This would be a different approach from that involved in topic models which use a specific probability distribution — the Dirichlet distribution. In this approach, you would assume a number of groups and arbitrarily assign students to these groups in a probabilistic fashion (60% group 1, 30% group 2, etc.). One can then see how well this group distribution predicts the observed covariance matrix by use of non-commutative harmonic analysis. Group assignment is thereby completely determined by the data — no parameters are needed.

I have started the update of MediaWiki 1.11.2 to incorporate Blahtex functionality. My goal is to have pages that validate as correct XHTML+MathML. The work is being detailed here.

The update is not trivial. The current hacked version of MediaWiki at BerliOS that incorporates blahtex is based on version 1.7. The MediaWiki installation I am playing with is at the latest version: 1.11.2. To figure out how to concentrate on the relevant parts, I am using Unix utilities diff and wc. Basically, I start by counting lines and try to figure out how many new lines are accounted for by new classes or functions added.

I have started the painful process of enabling MathML support on MediaWiki. This is crucial for my use of wiki technology in my workflow. Check out the first step I have taken: enabling texvc (which produces either HTML or .png output).

The next step is to connect it with blahtex so I produce true MathML and correct XHTML headers with MathML. This is not trivial since the blahtex hacked distribution over at BerliOS is at version 1.7 for MediaWiki but the current version is at number 1.11.2. This means that I have to go thru the list of blahtex modified files in the current version.

I have done something similar for MathML on this blog (using itex2MML). It clearly is the case that the math enabled web is still far from being the default. When I have time, and if I succeed in creating a strict XHTML+MathML MediaWiki version, I’ll document my steps somewhat similarly to the steps I took with WordPress .

One possible application of the precision error tensors framework is to use it as a criterion for selecting the number of clusters needed to describe a dataset. The number of clusters problem refers to the generic problem of deciding how many clusters describe a dataset. Many clustering algorithms exist. Deciding which one is appropriate in a particular task is up to the investigator. Suppose that one has settled on a clustering algorithm. An algorithm like k-clusters has no natural stopping criterion. You dial in how many clusters you want, i.e. you manually set the value of $k$, and the algorithm gives you the data clustered into $k$ groups.

Putting aside the correctness of using a particular algorithm for clustering a specific dataset, we can ask: what number of clusters gives me the smallest precision error? This provides an automatic algorithm for deciding on the optimal number of clusters given the chosen algorithm and the dataset to which it is applied.

Author Stewart Mader makes a convincing case in his wikipatterns book that wikis are a powerful collaboration tool. I have dabbled briefly with wikis. I’ve come to rely more and more on wikipedia to understand technical terms quickly. I just don’t practice collaboration with them.

This may change if a grant that we currently have pending with the NSF is approved. We proposed a collaboration with New Mexico scientists at the Jornada Experimental Range to develop a photogrammetric system for UAV images. Collaboration management was a mandated section of the proposal and we included a slew of tools that we currently use — revision control, emails, issue tracking — as well as the MediaWiki software in a list of tools we intend to use to facilitate managing the work related to the collaboration.

The more tools like Wikis become part of our scientific practice, the more I wondered how anybody got things done in the past. How did scientists communicate before emails? I know letters were written. I wrote a few of them back in graduate school. But it seems so strange now to think of writing a letter to someone instead of sending an email.

My previous post on precision error tensors was misleading. We tend to think of tensors as complicated mathematical structures. Vectors are rank 1 tensors. Driving home from work today, I realized that I had already shown that precision error vectors can be calculated in our horizontal decorrelation estimation paper. So mathematically speaking, I have already shown that precision error should be treated as tensors. The precision error vector is the rank 1 tensor example. The precision error covariance matrix is the rank-2 tensor. Two examples in the usual tensor progression. At some future time I should calculate the rank-3 tensor. How would one induce representations of the Symmetric group in rank-3 tensors?