Friday, August 28, 2009

Shazam, A Case Study in Memory Based Reasoning (MBR)

Many users are probably aware of Shazam, one of the few mobile applications that really seems to live up to the notion "Wow! It's Magic." When you are listening to music, you can run the application (presumably on your phone), click "tag it", and after a few tens of seconds of listening and processing, Shazam will tell you what you are listening to, the artist and other details.

Recently, I found an interesting article describing how it works. A presentation, with more pictures and less text, is available here. Kudos to the company and to the author, Avery Wang, for providing technical detail.

The paper does a very good job explaining the details of the algorithm. My goal here is to describe the algorithm from a higher perspective, because it is an interesting example of a memory-based reasoning algorithm. That is, an algorithm that combines information from "nearest neighbors" to arrive at a prediction.

Assume that we have a database of songs and an excerpt that we want to find in a database of millions of songs. A first approach might be to do an exhaustive search of the database to find a match. This would take a long time.

Alternatively, we can frame the problem as follows: for all songs in the database, what is the longest period of time where the excerpt overlaps part of a song. The nearest neighbors are the ones with the longest period, and, in general, we would choose the single one with the longest overlap.

Simple problem to describe. However, the real world hits quickly. The songs are probably quite clean acoustically. However, the excerpt is subject to numerous problems: background noise, loss of fidelity due to compression as the excerpt is transmitted, poor (or at least different) equipment for recording the excerpt, and so on.

Fortunately, the world of acoustics has something of a solution for this, called the "frequency domain". This is a map of all the sound frequencies, taken at a periodic interval -- say, one second. If "frequency domain" conjures up memories of things like Fourier Transforms, then you really do understand the subject.

However, for our purposes, it is enough to say that the frequency domain for a song produces a very, very bumpy curve for each second of the song -- each point is the strength of a particular acoustic frequency at that point in the song. The song can be thought of as a collection of all these curves. Taken together, these curves might resemble a map of a very hilly area. This would be a three-dimensional map of the song.

This map has peaks anologous to the tops of hills (or perhaps the tops of buildings in a city). These peaks are called a constellations, and they pretty much uniquely identify the song, regardless of all the problems mentioned above. That is, the constellations are resilitient to background noise, loss of fidelity, and so on.

Of course, we can do this for the songs in the database in advance. And, we can do this processing for a single excerpt pretty quickly.

So, the problem of finding the song with the longest overlap in seconds with the excerpt is now handled by finding consecutive seconds in a song where the frequency domain peaks match the frequency domain peaks from the excerpt. This is still a daunting problem, because there are so many peaks available. In other word, comparing one excerpt to millions of songs requires comparing hundreds of peaks in the excerpts to the many, many billions in the database -- very time consuming.

Shazam takes a very clever approach to this problem. The algorithm treats each peak as an anchor, and creates peak-pairs with other peaks "close" to the anchor. Here, "close" means that the other peaks are within a few seconds of the first and not too different in frequency. These peak-pairs are then calculated for both the song and the excerpt. The pairs are used to find sets of anchors that match between each song and the excerpt. Because the algorithm is looking for exact matches, it can use some programming tricks to make things even faster (these are described in the paper).

In the end, there is a set of anchors for each song matched by a given excerpt. For each song, these are scanned to find consecutive seconds where the anchors in each second overlap. The longest period of overlap is the distance between the excerpt and the song.

The algorithm is quite clever on several different levels. I do think that understanding it at a high level is valuable, especially since it can provide guidance to other very difficult recognition problems. On the other hand, when I use Shazam and it identifies a song, I still think it's magic.

Tuesday, August 25, 2009

Neural Networks, Predicting Continuous Values

Very good blog...
I'm doing some stuff with Clementine... and I have an issue...
My target for NN train dataset is a continuos value between 0 and 100... the problem is that is a normal/gaussian distribution and makes the NN predict bad...

How can I resolve the unbalancing data? split into classe with same frequency!?



I am not aware that neural networks have a problem with predicting values with normal distributions. In fact, if you randomize the weights in a neural network whose output layer has a linear transfer function, then the output is likely to follow a normal distribution -- just from the Central Limit Theorem of statistics.

So, you have a neural network that is not producing good results. There can be several causes.

The first thing to look for is too many inputs. Clementine has options to prune the input variables on a neural network. Be sure that you do not have too many inputs. I would recommend a variable reduction technique such as principal components, and advise you to avoid categorical variables that have many levels.

A similar problem can occur if your hidden layer is too large.

Whatever the network, it is worthwhile looking at the number of weights in the network (or a related measure called the degrees of freedom). Remember, you want to have lots of training data for each weight.

Another problem may be that the target is continuous, but bounded between 0 and 100. This could result in a neural network where the output layer uses a linear transfer function. Although not generally a bad idea, it may not work in this case because the range of a linear function is from minus infinity to positive infinity, which far exceeds the range of the data.

One simple solution would be to divide the output by 100 and treat it as a probability. The neural network should then be set up with a logistic function in the target layer.

Your idea of binning the results might also work, assuming that bins work for solving the business problem. Equal sized bins are reasonable, since they are readily understandable as quantiles.

Good luck.

Sunday, August 9, 2009

Pharmaceutical Data and Privacy

Today's New York Times has another misguided article on privacy in the medical world. This article seems to be designed to scare Americans into believing that health care privacy is endangered, and that such data is regularly and wantonly traded among companies.

My perspective is different, since I am coming from the side of analyzing data.

First, the pharmaceutical industry is different from virually every other industry in the United States. For the most part, it is illegal for pharmaceutical manufacturers to identify the users of their products. This is based originated with the Health Information Portability and Privacy Act (HIPAA), explained in more detail at this government site.

What is absurd about this situation is that pharmaceutical companies are, in theory, responsible for the health of the millions of people who use their products. To give an example of the dangers, imagine that you have a popular product that causes cardiac damage after several months of use. The cardiac damage, in turn, is sometimes fatal. How does the manufacturer connect the use of the product to death registries? The simple answer. They cannot.

This is not a made-up example. Millions of people used Cox-2 inhibitors, which were on the market until 2004, when Merck voluntarily took Vioxx off the market. This issue here is whether the industry could have known earlier that such dangers lurked in the use of the drug. My contention is that the manufactureres do not have a chance, because they could not do something that virutally every other company can do -- match their customer records to publicly available mortality records.

To be clear about the laws related to drugs. If someone has an adverse reaction while on a drug, then that must be reported to the pharmaceutical company. However, if the adverse reaction is detected a certain amount of time after the patient stops therapy (I believe two weeks), then there is not reporting requirement. Guess what. Cardiac damage caused by Cox-2 inhibitors does not necessarily kill patients right away. Nor is the damage necessarily detected while the patient is still on the therapy.

I have used deidentified records at pharmaceutical clients for various analyses that have ranged from the amusing (anniversary effects in the scripts for ED therapies) to the socially useful (do poor patients have less adherence due to copayments) to the actionable (what messages to give to prescribers). In all cases, we have had to do more work than necessary because of the de-identification requirements, and to make assumptions and work-arounds that may have hurt the analyses. And, contrary to what the New York Times article may lead you to believe, both IMS and Verispan take privacy very seriously. Were I inclined to try to identify particular records, it would be virtually impossible.

Every time a drug is used, there is perhaps an opportunity to learn about its effectiveness and interactions with other therapies. In many cases, these are questions that scientists do not even know to ask, and such exploratory data mining can be critical in establishing hypotheses. Questions such as:
  • Are the therapies equally effective, regardless of gender, age, race, and geography?
  • Do demographics affect adherence?
  • What interactions does a given therapy have with other therapies?
  • Does the use of a particular therapy have an effect on mortality?
Everytime patients purchase scripts and the data is shielded from the manufacturers, opportunities to better understand and improve health care outcomes are lost. Even worse, asa the New York Times article points out, HIPAA does not protect consumers from the actions of nefarious employees and adroit criminals. There has to be a better way.