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Programming Languages for Machine Learning Implementations

Machine learning algorithms have a much better chance of being widely adopted if they are implemented in some easy-to-use code. There are several important concerns associated with machine learning which stress programming languages on the ease-of-use vs. speed frontier.

  1. Speed The rate at which data sources are growing seems to be outstripping the rate at which computational power is growing, so it is important that we be able to eak out every bit of computational power. Garbage collected languages (java, ocaml, perl and python) often have several issues here.
    1. Garbage collection often implies that floating point numbers are “boxed”: every float is represented by a pointer to a float. Boxing can cause an order of magnitude slowdown because an extra nonlocalized memory reference is made, and accesses to main memory can are many CPU cycles long.
    2. Garbage collection often implies that considerably more memory is used than is necessary. This has a variable effect. In some circumstances it results in no slowdown while in others it can cause a 4-order of magnitude slowdown. The basic rule here is that you never want to run out of physical memory and use swap.
    3. Some of these languages are interpreted rather than executed. As a rule of thumb, interpreted languages are an order of magnitude slower than an executed languages.
    4. Even when these languages are compiled, there are often issues with how well they are compiled. Compiling to a modern desktop processor is a tricky business, and only a few compilers do this well.
  2. Programming Ease Ease of use of a language is very subjective because it is always easiest to use the language you are most familiar with. Nevertheless, significant differences exist.
    1. Syntax Syntax is often overlooked, but it can make a huge difference in the ease of both learning to program and using the language. A good syntax allows you study and improve the algorithm rather than the program implementing it. (Algorithmic improvements often yield the greatest speedups while optimizing.) The syntax needs to be concise (so that you can view the entire algorithm) and simple (so that it can become second nature).
    2. Library Support Languages vary dramatically in terms of library support, and having the right linear algebre/graphics/IO library can make a task dramatically easier. Perl has a huge number of associated libraries which greatly ease use.
    3. Built in Functionality Languages differ in terms of the primitives that are available. Which of these primiitives are useful is a subject of significant debate.
      1. Some form of generic programming (templates, polymorphism, etc…) seems important.
      2. Functions as first class objects is often very convenient while programming.
      3. Builting lists and hash tables are often extremely useful primitives. One caveat here is that when you make a speed optimization pass, you often have to avoid these primitives.
      4. Support for modularity is important. Objects (as in object oriented programming) is one example of this, but there are many others. The essential quantity here seems to be an interface creation mechanism.
    4. Scalability Scalability is where otherwise higher level languages often break down. A simple example of this is a language with file I/O built in that fails to perform correctly when the file has size 231 or 232. I am particularly familiar with Ocaml which has the following scalability issues:
      1. List operations often end up consuming the stack and segfaulting. The Unison crew were annoyed enough by this that they created their own “safelist” library with all the same interfaces as the list type.
      2. Arrays on a 32 bit machine can have only 222-1 elements due to dynamic type information set aside for the garbage collector. As a substitute, there is a “big array” library. However, having big arrays, arrays, and strings, often becomes annoying because they have different interfaces for objects which are semantically the same.
    5. Familiarity This isn’t just your familiarity, but also the familiarity of other people who might use the code. At one extreme, you can invent your own language (as Yann LeCun has done with Lush). At the other extreme, you can use a language which many people are familiar with such as C or Java.

The existing significantly used machine learning code bases seem to favor lower level languages.

  1. Weka is one of the best known general purpose machine learning toolkits. It is implemented in Java and has far more algorithmic coverage than any other system I know of.
  2. LibSVM is implemented in C++ and Java.
  3. SVMlight is implemented in C.
  4. C4.5 is implemented in C.
  5. SNNS is written in C.

Both R and Matlab are also useful languages, although I have not used them.

None of the language choices seem anywhere near ideal. The higher level languages often can’t execute fast and the lower level ones which can are often quite clumsy. The approach I’ve taken is to first implement in a higher level language (my choice was ocaml) to test ideas and then reimplement in a lower level language (C or C++) for speed where the ideas work out. This reimplementation step is quite clumsy and I would love to find a way to avoid it.

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What is missing for online collaborative research?

The internet has recently made the research process much smoother: papers are easy to obtain, citations are easy to follow, and unpublished “tutorials” are often available. Yet, new research fields can look very complicated to outsiders or newcomers. Every paper is like a small piece of an unfinished jigsaw puzzle: to understand just one publication, a researcher without experience in the field will typically have to follow several layers of citations, and many of the papers he encounters have a great deal of repeated information. Furthermore, from one publication to the next, notation and terminology may not be consistent which can further confuse the reader.

But the internet is now proving to be an extremely useful medium for collaboration and knowledge aggregation. Online forums allow users to ask and answer questions and to share ideas. The recent phenomenon of Wikipedia provides a proof-of-concept for the “anyone can edit” system. Can such models be used to facilitate research and collaboration? This could potentially be extremely useful for newcomers and experts alike. On the other hand, entities of this sort already exist to some extent: Wikipedia::Machine Learning, MLpedia, the discussion boards on kernel-machines.org, Rexa, and the gradual online-ification of paper proceedings to name a few.

None of these have yet achieved takeoff velocity. You’ll know that takeoff velocity has been achieved when these become a necessary part of daily life rather than a frill.

Each of these efforts seems to be missing critical pieces, such as:

  1. A framework for organizing and summarizing information. Wikipedia and MLpedia are good examples, yet this is not as well solved as you might hope as mathematics on the web is still more awkward than it should be.
  2. A framework for discussion. Kernel-machines.org handles this, but is too area-specific. There does exist a discussion framework on Wikipedia/MLpedia, but the presentation format marginalizes discussion, placed on a separate page and generally not viewed by most observers. The discussion, in fact, should be an integral part of the presentation.
  3. Researchers have incentives to contribute. Wikipedia intentionally anonymizes contributors in the presentation, because recognizing them might invite the wrong sort of contributor. Incentives done well, however, are one of the things creating (6). One of the existing constraints within academia is that the basic unit of credit is coauthorship on a peer-reviewed paper. Given this constraint, it would be very handy if a system could automatically translate a subset of an online site into a paper, with authorship automatically summarized. The site itself might also track and display who has contributed how much and who has contributed recently.
  4. Explicit mechanisms for handling disagreements. If you get 3 good researchers on a topic in a room, you might have about 5 distinct opinions. Much of research has to do with thinking carefully about what is important and why, the sorts of topics likely to provoke disagreement. Given that disagreement is a part of the process of research, there needs to be a way to facilitate, and even spotlight, disagreements for a healthy online research mechanism. One crude system for handling disagreements is illustrated by the linux kernel “anyone can download and start their own kernel tree”. A more fine-grained version of this may be effective “anyone can clone a webpage and start their own version of it”. Perhaps this can be coupled with a version voting system, although that is tricky. A fundamental point is: a majority vote does not determine the correctness of a theorem. Integrating a peer review system may work well. None of the existing systems handle this problem effectively.
  5. Low entry costs. Many systems handle this well, but it must be emphasized because small changes in the barrier to entry can have a large effect on (6).
  6. Community buy-in. Wikipedia is the big success story here, but Wikipedia::MachineLearning has more limited success. There are many techniques which might aid community buy in, but they may not be enough.

Can a site be created that simultaneously handles all of the necessary pieces for online research?

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Incentive Compatible Reviewing

Reviewing is a fairly formal process which is integral to the way academia is run. Given this integral nature, the quality of reviewing is often frustrating. I’ve seen plenty of examples of false statements, misbeliefs, reading what isn’t written, etc…, and I’m sure many other people have as well.

Recently, mechanisms like double blind review and author feedback have been introduced to try to make the process more fair and accurate in many machine learning (and related) conferences. My personal experience is that these mechanisms help, especially the author feedback. Nevertheless, some problems remain.

The game theory take on reviewing is that the incentive for truthful reviewing isn’t there. Since reviewers are also authors, there are sometimes perverse incentives created and acted upon. (Incidentially, these incentives can be both positive and negative.)

Setting up a truthful reviewing system is tricky because their is no final reference truth available in any acceptable (say: subyear) timespan. There are several ways we could try to get around this.

  1. We could try to engineer new mechanisms for finding a reference truth into a conference and then use a ‘proper scoring rule’ which is incentive compatible. For example, we could have a survey where conference participants short list the papers which interested them. There are significant problems here:
    1. Conference presentations mostly function as announcements of results. Consequently, the understanding of the paper at the conference is not nearly as deep as, say, after reading through it carefully in a reading group.
    2. This is inherently useless for judging reviews of rejected papers and it is highly biased for judging reviews of papers presented in two different formats (say, a poster versus an oral presentation).
  2. We could ignore the time issue and try to measure reviewer performance based upon (say) long term citation count. Aside from the bias problems above, there is also a huge problem associated with turnover. Who the reviewers are and how an individual reviewer reviews may change drastically in just a 5 year timespan. A system which can provide track records for only a small subset of current reviewers isn’t very capable.
  3. We could try to manufacture an incentive compatible system even when the truth is never known. This paper by Nolan Miller, Paul Resnick, and Richard Zeckhauser discusses the feasibility of this approach. Essentially, the scheme works by rewarding reviewer i according to a proper scoring rule applied to P(reviewer j’s score | reviewer i’s score). (A simple example of a proper scoring rule is log[P()].) This is approach is pretty fresh, so there are lots of problems, some of which may or may not be fundamental difficulties for application in practice. The significant problem I see is that this mechanism may reward joint agreement instead of a good contribution towards good joint decision making.

None of these mechanisms are perfect, but they may each yield a little bit of information about what was or was not a good decision over time. Combining these sources of information to create some reviewer judgement system may yield another small improvement in the reviewing process.

The important thing to remember is that we are the reviewers as well as the authors. Are we interested in tracking our reviewing performance over time in order to make better judgements? Such tracking often happens on an anecdotal or personal basis, but shifting to an automated incentive compatible system would be a big change in scope.

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How to solve an NP hard problem in quadratic time

This title is a lie, but it is a special lie which has a bit of truth.

If n players each play each other, you have a tournament. How do you order the players from weakest to strongest?

The standard first attempt is “find the ordering which agrees with the tournament on as many player pairs as possible”. This is called the “minimum feedback arcset” problem in the CS theory literature and it is a well known NP-hard problem. A basic guarantee holds for the solution to this problem: if there is some “true” intrinsic ordering, and the outcome of the tournament disagrees k times (due to noise for instance), then the output ordering will disagree with the original ordering on at most 2k edges (and no solution can be better).

One standard approach to tractably solving an NP-hard problem is to find another algorithm with an approximation guarantee. For example, Don Coppersmith, Lisa Fleischer and Atri Rudra proved that ordering players according to the number of wins is a 5-approximation to the NP-hard problem.

An even better approach is to realize that the NP hard problem may not be the real problem. The real problem may be finding a good approximation to the “true” intrinsic ordering given noisy tournament information.

In a learning setting, the simplest form of ranking problem is “bipartite ranking” where every element has a value of either 0 or 1 and we want to order 0s before 1s. A common way to measure the performance of bipartite ranking is according to “area under the ROC curve” (AUC) = 1 – the fraction of out-of-order pairs. Nina, Alina, Greg and I proved that if we learn a comparison function which errs on k dissimilar pairs, then ordering according to the number of wins yields an order within 4k edge reversals of the original ordering. As a reduction statement(*), this shows that an error rate of e for a learned pairwise binary classifier produces an ordering with an expected AUC of 1 – 4e. The same inequality even holds for a (stronger) regret transform. If r = e – emin is the regret of the binary pairwise classifier, then the AUC regret is bounded by 4r. (Here emin is the error rate of the best possible classifier which predicts knowing the most likely outcome.) The regret result extends to more general measures of ordering than simply AUC.

We were unable to find any examples where ordering according to the degree produced more than a 2r AUC regret. Nikhil Bansal, Don, and Greg have worked out a tightened proof which gives exactly this upper bound. At the end of the day, we have an algorithm with satisfies precisely the same guarantee as the NP hard solution.

There are two lessons here. The learning lesson is that a good pairwise comparator implies the ability to rank well according to AUC. The general research lesson is that an NP hard problem for an approximate solution is not an intrinsic obstacle. Sometimes there exist simple tractable algorithms which satisfy the same guarantees as the NP hard solution.

(*) To prove the reduction, you must make sure that your form pairwise examples in the right way. Your source of pairwise ordering examples must be uniform over the dissimilar pairs containing one example with label 1 and one example with label 0.