Simple database setup for MALDI peaks - database

I have a very simple problem that I could come up with a crude solution to, but it seems to me that there is probably some off the shelf answer.
Problem: I have a list of discrete values (these are mass units) that I want to find within a database of discrete values (known mass units) and their identities, allowing for some inexact match. Example: If I am looking for 500.23 in the database then anything +/- 0.025 would be considered a match (50 ppm or 0.005%). This tolerance should be adjustable. So in this example, 500.23 may return the database text value, 500.25 which is Compound A.
I could also make this tool myself if someone would like to suggest the most straightforward approach. I am competent in Matlab, somewhat in R, good in excel, poor in access, and don't know anything about SQL. Best case would be for this tool to be used by non-coders.
Background: The real background of this problem is that I have MALDI TOF data where I have identified peaks of interest from an experiment (masses; m/z). These masses correspond to molecules that were released after enzymatic digestion. This class of molecule has reported masses with known identities, but unlike peptide mass fingerprinting, or metabolomic databases, these known masses are mostly unpublished and/or uncollated, so I would like to cross-reference them with a database of my own making. Each mass corresponds to one identity. The masses will not match exactly, and being able to search with a specified mass tolerance is key.

There are plenty of mass spectrometer data solutions you may want to look at. For example: http://www.ionsource.com/links/programs.htm

Related

How to make the database structure extensible for a turn based game?

I'm working on a fantasy turn base game.
I now have to create the database structure for my spells. The problem is that I don't really have a good idea on how to create it. Maybe the effects of those spells should not be stored in a database?
For instance, effects could be; increase attack, pull an enemy, heal, teleport, hide, put a mine and so on... Effects are pretty different and I would like the database structure to be extensible.
Edit:
It's a turn based game, time is the same as turns and distance represents the squares.
Some examples of what I mean below.
Let's say we have Incinerate:
it can target only 1 enemy (not ally)
it can be casted at a distance of 3 squares
it deals 5 damage per turn
it lasts 3 turns
Now we can take Shock Wave:
it travels in a line for 4 squares
it starts from a square near the caster
it damages the first target it hits (ally or enemy)
it deals 5 damage to the target and knocks it back 1 square
And the last one Rain Call:
it can be casted at any distance
it's a cloud the size of a 5x5 square
it can target both ally and enemies
only fire creatures take damage
while casting the caster is immobilized and it loses 5 mana/turn
As you can see there are a lot of possible columns: the distance it travels, turns, casting distance, type (damage, heal, armor, etc), value (+2), target (enemy, ally, both), size, etc.
I would not use a relational database for storing spells. Relational databases are good in cases when most of the following conditions apply:
you have very large amount of data,
the data can logically be organized as n-ary relations (tables, rows, columns),
you have many users that access to the data concurrently,
you need ACID properties,
et cetera
Databases are like trucks. They are big. They are difficult to use. They are expensive. (in terms of needed expertise, maintenance time, run time efficiency, etc. if not monetarily) They are very good at what they are good at, but not at anything else. Don't use a truck when a bicycle would suffice.
Let's come to your problem. The number of different types of spells is surely bounded and known at compile time, why don't you define an interface ISpell, and let each spell type be a class that implements ISpell? (You can also define an abstract class for common code) Then a SpellFactory may construct and provide access to all the spells when the program starts. Do you really need the spells be accessible from outside independent of your code?
If hard coding a SpellFactory is not flexible enough for your purposes, you can use xml configuration files. <spell type="blind" description="bla bla" picture="file.jpg"> <effects> <effect .. /> .. </effects> <range>5</range> etc. I don't know much about computer games, but this is what they did in sid meier civilization game, for example. Then, instead of hard coding the different spells in the SpellFactory, you can let it read them from the configuration file at the start up.
As far as I can see, using configuration files instead of a database has the following advantages:
It is a fast, easy, lightweight solution,
It is much more flexible than having all the spells having the same set of columns, (most of which will not make sense for a specific spell)
It is much easier to have more than one version of set of spells at the same time, for experiments, variations, etc,
You can let end users access and manipulate xml files for customizing the game without letting them access the database that would also contain sensitive data,
et cetera.
The disadvantages:
More people know about relational databases than xml format, so you might need a couple of hours to learn how to read and manipulate xml "elements".
Your question is pretty large. It depends on a lot of things, are you going to load the spell during runtime? Maybe you will load them at the beginning of the game? What database will you be using?
Amit Bhargava's suggestion is good and has the advantage of being user-understandable. However string are pretty slow, so what you could do is use flags in your spell table. Then, based on the flag you know which type of spell it is.

Is the HTM cortical learning algorithm defined by Numenta's paper restricted by Euclidean geometry?

Specifically, their most recent implementation.
http://www.numenta.com/htm-overview/htm-algorithms.php
Essentially, I'm asking whether non-euclidean relationships, or relationships in patterns that exceed the dimensionality of the inputs, can be effectively inferred by the algorithm in its present state?
HTM uses Euclidean geometry to determine "neighborship" when analyzing patterns. Consistently framed input causes the algorithm to exhibit predictive behavior, and sequence length is practically unlimited. This algorithm learns very well - but I'm wondering whether it has the capacity to infer nonlinear attributes from its input data.
For example, if you input the entire set of texts from Project Gutenberg, it's going to pick up on the set of probabilistic rules that comprise English spelling, grammar, and readily apparent features from the subject matter, such as gender associations with words, and so forth. These are first level "linear" relations, and can be easily defined with probabilities in a logical network.
A nonlinear relation would be an association of assumptions and implications, such as "Time flies like an arrow, fruit flies like a banana." If correctly framed, the ambiguity of the sentence causes a predictive interpretation of the sentence to generate many possible meanings.
If the algorithm is capable of "understanding" nonlinear relations, then it would be able to process the first phrase and correctly identify that "Time flies" is talking about time doing something, and "fruit flies" are a type of bug.
The answer to the question is probably a simple one to find, but I can't decide either way. Does mapping down the input into a uniform, 2d, Euclidean plane preclude the association of nonlinear attributes of the data?
If it doesn't prevent nonlinear associations, my assumption would then be that you could simply vary the resolution, repetition, and other input attributes to automate the discovery of nonlinear relations - in effect, adding a "think harder" process to the algorithm.
From what I understand of HTM's, the structure of layers and columns mimics the structure of the neocortex. See appendix B here: http://www.numenta.com/htm-overview/education/HTM_CorticalLearningAlgorithms.pdf
So the short answer would be that since the brain can understand non-linear phenomenon with this structure, so can an HTM.
Initial, instantaneous sensory input is indeed mapped to 2D regions within an HTM. This does not limit HTM's to dealing with 2D representations any more than a one dimensional string of bits is limited to representing only one dimensional things. It's just a way of encoding stuff so that sparse distributed representations can be formed and their efficiencies can be taken advantage of.
To answer your question about Project Gutenberg, I don't think an HTM will really understand language without first understanding the physical world on which language is based and creates symbols for. That said, this is a very interesting sequence for an HTM, since predictions are only made in one direction, and in a way the understanding of what's happening to the fruit goes backwards. i.e. I see the pattern 'flies like a' and assume the phrase applies to the fruit the same way it did to time. HTM's do group subsequent input (words in this case) together at higher levels, so if you used Fuzzy Grouping (perhaps) as Davide Maltoni has shown to be effective, the two halves of the sentence could be grouped together into the same high level representation and feedback could be sent down linking the two specific sentences. Numenta, to my knowledge has not done too much with feedback messages yet, but it's definitely part of the theory.
The software which runs the HTM is called NuPIC (Numenta Platform for Intelligent Computing). A NuPIC region (representing a region of neocortex) can be configured to either use topology or not, depending on the type of data it's receiving.
If you use topology, the usual setup maps each column to a set of inputs which is centred on the corresponding position in the input space (the connections will be selected randomly according to a probability distribution which favours the centre). The spatial pattern recognising component of NuPIC, known as the Spatial Pooler (SP), will then learn to recognise and represent localised topological features in the data.
There is absolutely no restriction on the "linearity" of the input data which NuPIC can learn. NuPIC can learn sequences of spatial patterns in extremely high-dimensional spaces, and is limited only by the presence (or lack of) spatial and temporal structure in the data.
To answer the specific part of your question, yes, NuPIC can learn non-Euclidean and non-linear relationships, because NuPIC is not, and cannot be modelled by, a linear system. On the other hand, it seems logically impossible to infer relationships of a dimensionality which exceeds that of the data.
The best place to find out about HTM and NuPIC, its Open Source implementation, is at NuPIC's community website (and mailing list).
Yes, It can do non-linear. Basically it is multilayer. And all multilayer neural networks can infer non linear relationships. And I think the neighborship is calculated locally. If it is calcualted locally then globally it can be piece wise non linear for example look at Local Linear Embedding.
Yes HTM uses euclidean geometry to connect synapses, but this is only because it is mimicking a biological system that sends out dendrites and creates connections to other nearby cells that have strong activation at that point in time.
The Cortical Learning Algorithm (CLA) is very good at predicting sequences, so it would be good at determining "Time flies like an arrow, fruit flies like a" and predict "banana" if it has encountered this sequence before or something close to it. I don't think it could infer that a fruit fly is a type of insect unless you trained it on that sequence. Thus the T for Temporal. HTMs are sequence association compressors and retrievers (a form of memory). To get the pattern out of the HTM you play in a sequence and it will match the strongest representation it has encountered to date and predict the next bits of the sequence. It seems to be very good at this and the main application for HTMs right now are predicting sequences and anomalies out of streams of data.
To get more complex representations and more abstraction you would cascade a trained HTMs outputs to another HTMs inputs along with some other new sequence based input to correlate to. I suppose you could wire in some feedback and do some other tricks to combine multiple HTMs, but you would need lots of training on primitives first, just like a baby does, before you will ever get something as sophisticated as associating concepts based on syntax of the written word.
ok guys, dont get silly, htms just copy data into them, if you want a concept, its going to be a group of the data, and then you can have motor depend on the relation, and then it all works.
our cortex, is probably way better, and actually generates new images, but a computer cortex WONT, but as it happens, it doesnt matter, and its very very useful already.
but drawing concepts from a data pool, is tricky, the easiest way to do it is by recording an invarient combination of its senses, and when it comes up, associate everything else to it, this will give you organism or animal like intelligence.
drawing harder relations, is what humans do, and its ad hoc logic, imagine a set explaining the most ad hoc relation, and then it slowly gets more and more specific, until it gets to exact motor programs... and all knowledge you have is controlling your motor, and making relations that trigger pathways in the cortex, and tell it where to go, from the blast search that checks all motor, and finds the most successful trigger.
woah that was a mouthful, but watch out dummies, you wont get no concepts from a predictive assimilator, which is what htm is, unless you work out how people draw relations in the data pool, like a machine, and if you do that, its like a program thats programming itself.
no shit.

Is this data appropriate for keeping in a database?

In relation to my previous question where I was asking for some database suggestions; it just occured to me that I don't even know if what I'm trying to store there is appropriate for a database. Or should some other data storage method be used.
I have some physical models testing (let's say wind tunnel data; something similar) where for every model (M-1234) I have:
name (M-1234)
length L
breadth B
height H
L/B ratio
L/H ratio
...
lot of other ratios and dimensions ...
force versus speed curve given in the form of a lot of points for x-y plotting
...
few other similar curves (all of them of type x-y).
Now, what I'm trying to accomplish is store that in some reasonable way, so that the user who will be using the database can come and see what are the closest ten models to L/B=2.5 (or some similar demand). Then for that, somehow get all the data of those models, including the curve data (in a plain text file format).
Is a sql database (or any other, for that matter) an appropriate way of handling something like this ? Or should I take some other approach ?
I have about a month to finish this, and in that time I have to learn enough about databases as well, so ... give your suggestions, please, bearing that in mind. Assume no previous knowledge on the subject, whatsoever.
I think what you're looking for is possible. I'm using Postgresql here, but any database should work. This is my test database
CREATE TABLE test (
id serial primary key,
ratio double precision
);
COPY test (id, ratio) FROM stdin;
1 0.29999999999999999
2 0.40000000000000002
3 0.59999999999999998
4 0.69999999999999996
.
Then, to find the nearest values to a particular ratio
select id,ratio,abs(ratio-0.5) as score from test order by score asc limit 2;
In this case, I'm looking for the 2 nearest to 0.5
I'd probably do a datamodel where you have one table for the main data, the ratios and so on, and then a second table which holds the curve points, as I'm assuming that the curves aren't always the same size.
Yes, a database is probably the best approach for this.
A relational database (which usually uses SQL for data access) is suitable for data that is more or less structured as tables.
To give you an idea:
You could have a main table model with fields name, width etc. . Then subtable(s) for any values which can appear more than once, which refers back to model (look up "foreign key").
Then a subtable for your actual curves, again refering back to model.
How to actually model the curves in the DB I don't know, as I don't know how you model them. But if its lots of numbers, it can go into the DB.
It seems you know little about relational DBMS. Consider reading something on WIkipedia, or doing a few simple DBMS tutorials (PostgreSQL has some: http://www.postgresql.org/docs/8.4/interactive/tutorial.html , but there are many others). Then pick a DBMS for trying out (PostgreSQL is probably not a bad choice, but again there are many others).
Then try implementing a simple table schema, and get back to us with any detail questions (which you'll probably have).
One more thing: Those questions are probably more appropriate to serverfault.com.
This is arguably scientific data: you might find libraries/formats intended for arbitrary scientific data useful: HDF5 http://www.hdfgroup.org/ (note I am not an expert)

Generating 'neighbours' for users based on rating

I'm looking for techniques to generate 'neighbours' (people with similar taste) for users on a site I am working on; something similar to the way last.fm works.
Currently, I have a compatibilty function for users which could come into play. It ranks users on having 1) rated similar items 2) rated the item similarly. The function weighs point 2 heigher and this would be the most important if I had to use only one of these factors when generating 'neighbours'.
One idea I had would be to just calculate the compatibilty of every combination of users and selecting the highest rated users to be the neighbours for the user. The downside of this is that as the number of users go up then this process couls take a very long time. For just a 1000 users, it needs 1000C2 (0.5 * 1000 * 999 = = 499 500) calls to the compatibility function which could be very heavy on the server also.
So I am looking for any advice, links to articles etc on how best to achieve a system like this.
In the book Programming Collective Intelligence
http://oreilly.com/catalog/9780596529321
Chapter 2 "Making Recommendations" does a really good job of outlining methods of recommending items to people based on similarities between users. You could use the similarity algorithms to find the 'neighbours' you are looking for. The chapter is available on google book search here:
http://books.google.com/books?id=fEsZ3Ey-Hq4C&printsec=frontcover
Be sure to look at Collaborative Filtering. Many recommendation systems use collaborative filtering to suggest items to users. They do it by finding 'neighbors' and then suggesting items your neighbors rated highly but you haven't rated. You could go as far as finding neighbors, and who knows, maybe you'll want recommendations in the future.
GroupLens is a research lab at the University of Minnesota that studies collaborative filtering techniques. They have a ton of published research as well as a few sample datasets.
The Netflix Prize is a competition to determine who can most effectively solve this sort of problem. Follow the links off their LeaderBoard. A few of the competitors share their solutions.
As far as a computationally inexpensive solution, you could try this:
Create categories for your items. If we're talking about music, they might be classical, rock, jazz, hip-hop... or go further: Grindcore, Math Rock, Riot Grrrl...
Now, every time a user rates an item, roll up their ratings at the category level. So you know 'User A' likes Honky Tonk and Acid House because they give those items high ratings frequently. Frequency and strength is probably important for your category aggregate score.
When it's time to find neighbors, instead of cruising through all ratings, just look for similar scores in the categories.
This method wouldn't be as accurate but it's fast.
Cheers.
What you need is a clustering algorithm, which would automatically group similar users together. The first difficulty that you are facing is that most clustering algorithms expect the items they cluster to be represented as points in a Euclidean space. In your case, you don't have the coordinates of the points. Instead, you can compute the value of the "similarity" function between pairs of them.
One good possibility here is to use spectral clustering, which needs precisely what you have: a similarity matrix. The downside is that you still need to compute your compatibility function for every pair of points, i. e. the algorithm is O(n^2).
If you absolutely need an algorithm faster than O(n^2), then you can try an approach called dissimilarity spaces. The idea is very simple. You invert your compatibility function (e. g. by taking its reciprocal) to turn it into a measure of dissimilarity or distance. Then you compare every item (user, in your case) to a set of prototype items, and treat the resulting distances as coordinates in a space. For instance, if you have 100 prototypes, then each user would be represented by a vector of 100 elements, i. e. by a point in 100-dimensional space. Then you can use any standard clustering algorithm, such as K-means.
The question now is how do you choose the prototypes, and how many do you need. Various heuristics have been tried, however, here is a dissertation which argues that choosing prototypes randomly may be sufficient. It shows experiments in which using 100 or 200 randomly selected prototypes produced good results. In your case if you have 1000 users, and you choose 200 of them to be prototypes, then you would need to evaluate your compatibility function 200,000 times, which is an improvement of a factor of 2.5 over comparing every pair. The real advantage, though, is that for 1,000,000 users 200 prototypes would still be sufficient, and you would need to make 200,000,000 comparisons, rather than 500,000,000,000 an improvement of a factor of 2500. What you get is O(n) algorithm, which is better than O(n^2), despite a potentially large constant factor.
The problem seems like to be 'classification problems'. Yes there are so many solutions and approaches.
To start exploration check this:
http://en.wikipedia.org/wiki/Statistical_classification
Have you heard of kohonen networks?
Its a self organing learning algorithm that clusters similar variables into similar slots. Although most sites like the one I link you to displays the net as bidimensional there is little involved in extending the algorithm into a multiple dimension hypercube.
With such a data structure finding and storing neighbours with similar tastes is trivial as similar users should be stores into similar locations (almost like a reverse hash code).
This reduces your problem into one of finding the variables that will define similarity and establishing distances between possible enumerate values ,like for example classical and acoustic are close toghether while death metal and reggae are quite distant (at least in my oppinion)
By the way in order to find good dividing variables the best algorithm is a decision tree. The nodes closer to the root will be the most important variables to establish 'closeness'.
It looks like you need to read about clustering algorithms. The general idea is that instead of comparing every point with every other point each time you divide them in clusters of similar points. Then the neighborhood may be all the points in the same cluster. The number/size of the clusters is usually a parameter of the clustering algorithm.
Yo can find a video about clustering in Google's series about cluster computing and mapreduce.
Concerns over performance can be greatly mitigated if you consider this as a build/batch problem rather than a realtime query.
The graph can be statically computed then latently updated e.g. hourly, daily etc. to then generate edges and storage optimized for runtime query e.g. top 10 similar users for each user.
+1 for Programming Collective Intelligence too - it is very informative - wish it wasn't (or I was!) as Python-oriented, but still good.

Clustering Lat/Longs in a Database

I'm trying to see if anyone knows how to cluster some Lat/Long results, using a database, to reduce the number of results sent over the wire to the application.
There are a number of resources about how to cluster, either on the client side OR in the server (application) side .. but not in the database side :(
This is a similar question, asked by a fellow S.O. member. The solutions are server side based (ie. C# code behind).
Has anyone had any luck or experience with solving this, but in a database? Are there any database guru's out there who are after a hawt and sexy DB challenge?
please help :)
EDIT 1: Clarification - by clustering, i'm hoping to group x number of points into a single point, for an area. So, if i say cluster everything in a 1 mile / 1 km square, then all the results in that 'square' are GROUP'D into a single result (say ... the middle of the square).
EDIT 2: I'm using MS Sql 2008, but i'm open to hearing if there are other solutions in other DB's.
I'd probably use a modified* version of k-means clustering using the cartesian (e.g. WGS-84 ECF) coordinates for your points. It's easy to implement & converges quickly, and adapts to your data no matter what it looks like. Plus, you can pick k to suit your bandwidth requirements, and each cluster will have the same number of associated points (mod k).
I'd make a table of cluster centroids, and add a field to the original data table to indicate what cluster it belonged too. You'd obviously want to update the clustering periodically if your data is at all dynamic. I don't know if you could do that with a stored procedure & trigger, but perhaps.
*The "modification" would be to adjust the length of the computed centroid vectors so they'd be on the surface of the earth. Otherwise you'd end up with a bunch of points with negative altitude (when converted back to LLH).
If you're clustering on geographic location, and I can't imagine it being anything else :-), you could store the "cluster ID" in the database along with the lat/long co-ordinates.
What I mean by that is to divide the world map into (for example) a 100x100 matrix (10,000 clusters) and each co-ordinate gets assigned to one of those clusters.
Then, you can detect very close coordinates by selecting those in the same square and moderately close ones by selecting those in adjacent squares.
The size of your squares (and therefore the number of them) will be decided by how accurate you need the clustering to be. Obviously, if you only have a 2x2 matrix, you could get some clustering of co-ordinates that are a long way apart.
You will always have the edge cases such as two points close together but in different clusters (one northernmost in one cluster, the other southernmost in another) but you could adjust the cluster size OR post-process the results on the client side.
I did a similar thing for a geographic application where I wanted to ensure I could cache point sets easily. My geohashing code looks like this:
def compute_chunk(latitude, longitude)
(floor_lon(longitude) * 0x1000) | floor_lat(latitude)
end
def floor_lon(longitude)
((longitude + 180) * 10).to_i
end
def floor_lat(latitude)
((latitude + 90) * 10).to_i
end
Everything got really easy from there. I had some code for grabbing all of the chunks from a given point to a given radius that would translate into a single memcache multiget (and some code to backfill that when it was missing).
For movielandmarks.com I used the clustering code from Mike Purvis, one of the authors of Beginning Google Maps Applications with PHP and AJAX. It builds trees of clusters/points for different zoom levels using PHP and MySQL, storing it in the database so that recall is very fast. Some of it may be useful to you even if you are using a different database.
Why not testing multiple approaches?
translate the weka library in .NET CLI with IKVM.NET
add an assembly resulted from your code and weka.dll (use ilmerge) into your database
Make some tests, that is. No specific clustering works better than anyone else.
I believe you can use MSSQL's spatial data types. If they are similar to other spatial data types I know, they will store your points in a tree of rectangles, and then you can go to the lower-resolution rectangles to get implicit clusters.
If you end up wanting to explore Geohash's (which were invented at exactly the same time you posted this question), here's a more fleshed-out implementation of Geohash related functions for SQL Server's TSQL in which you might be interested.
QalGeohash-TSQL
I have used the Integer version of the Geohash extensively to cluster results to reduce data sent to a client for a limited viewport.

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