I have a bunch of PDB files containing the structures of novel peptides, and I want to see if any of them will bind to LPS via computational prediction. I could do molecular dynamics, but that requires a lot of computing power unfortunately. Any other good options?
Thanks :)
One easy idea is to take the PDB of a peptide you are confident binds to LPS and then claim that peptides that look structurally similar also have a shot of binding LPS. This is a semi-qualitative argument.
As an example, I found w/ a quick search this peptide sequence which binds LPS: KNYSSSISSIHAC
(source: https://www.ncbi.nlm.nih.gov/pubmed/20816904)
Then to get the predicted structure of that sequence I used PEP-Fold which is an online tool
(source: http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3)
I think you can download from the job I submitted
(http://mobyle.rpbs.univ-paris-diderot.fr/data/jobs/PEP-FOLD3/C24081178740978)
After you download the PDB, you want to find the RMSD of each of your peptide structures to this PDB, and low RMSDs could represent LPS binding, but its definitely not definitive and unclear where to draw the line of "close enough".
This is all very wishy-washy, and as you say, molecular dynamics is a better option. You might also consider just sequence alignments w/ peptides that do bind LPS w/out worrying about 3D.
You might get better responses at Biostars or some other forum since your question is not coding based
Related
I was wondering if there are any algorithms or techniques that can be used to determine (make an educated guess, really) what type of data are represented by an unknown binary segment.
For example, I recently came this post on Steve Lamb's blog and I found the concept of the DiskScape tool interesting. I was wondering exactly what they might be analyzing, and how they were analyzing it, in order to make their determinations (and graphs).
I was also curious as to whether a similar technique could be expanded to analyze the format/contents of data as well.
I have to manually go through a long list of terms (~3500) which have been entered by users through the years. Beside other things, I want to reduce the list by looking for synonyms, typos and alternate spellings.
My work will be much easier if I can group the list into clusters of possible typos before starting. I was imagining to use some metric which can calculate the similarity to a term, e.g. in percent, and then cluster everything which has a similarity higher than some threshold. As I am going through it manually anyway, I don't mind a high failure rate, if it can keep the whole thing simple.
Ideally, there exists some easily available library to do this for me, implemented by people who know what they are doing. If there is no such, then at least one calculating a similarity metric for a pair of strings would be great, I can manage the clustering myself.
If this is not available either, do you know of a good algorithm which is simple to implement? I was first thinking a Hamming distance divided by word length will be a good metric, but noticed that while it will catch swapped letters, it won't handle deletions and insertions well (ptgs-1 will be caught as very similar to ptgs/1, but hematopoiesis won't be caught as very similar to haematopoiesis).
As for the requirements on the library/algorithm: it has to rely completely on spelling. I know that the usual NLP libraries don't work this way, but
there is no full text available for it to consider context.
it can't use a dictionary corpus of words, because the terms are far outside of any everyday language, frequently abbreviations of highly specialized terms.
Finally, I am most familiar with C# as a programming language, and I already have a C# pseudoscript which does some preliminary cleanup. If there is no one-step solution (feed list in, get grouped list out), I will prefer a library I can call from within a .NET program.
The whole thing should be relatively quick to learn for somebody with almost no previous knowledge in information retrieval. This will save me maybe 5-6 hours of manual work, and I don't want to spend more time than that in setting up an automated solution. OK, maybe up to 50% longer if I get the chance to learn something awesome :)
The question: What should I use, a library, or an algorithm? Which ones should I consider? If what I need is a library, how do I recognize one which is capable of delivering results based on spelling alone, as opposed to relying on context or dictionary use?
edit To clarify, I am not looking for actual semantic relatedness the way search or recommendation engines need it. I need to catch typos. So, I am looking for a metric by which mouse and rodent have zero similarity, but mouse and house have a very high similarity. And I am afraid that tools like Lucene use a metric which gets these two examples wrong (for my purposes).
Basically you are looking to cluster terms according to Semantic Relatedness.
One (hard) way to do it is following Markovitch and Gabrilovitch approach.
A quicker way will be consisting of the following steps:
download wikipedia dump and an open source Information Retrieval library such as Lucene (or Lucene.NET).
Index the files.
Search each term in the index - and get a vector - denoting how relevant the term (the query) is for each document. Note that this will be a vector of size |D|, where |D| is the total number of documents in the collection.
Cluster your vectors in any clustering algorithm. Each vector represents one term from your initial list.
If you are interested only in "visual" similarity (words are written similar to each other) then you can settle for levenshtein distance, but it won't be able to give you semantic relatedness of terms.For example, you won't be able to relate between "fall" and "autumn".
I'm writing up a Smart Home software for my bachelor's degree, that will only simulate the actual house, but I'm stuck at the NLP part of the project. The idea is to have the client listen to voice inputs (already done), transform it into text (done) and send it to the server, which does all the heavy lifting / decision making.
So all my inputs will be fairly short (like "please turn on the porch light"). Based on this, I want to take the decision on which object to act, and how to act. So I came up with a few things to do, in order to write up something somewhat efficient.
Get rid of unnecessary words (in the previous example "please" and "the" are words that don't change the meaning of what needs to be done; but if I say "turn off my lights", "my" does have a fairly important meaning).
Deal with synonyms ("turn on lights" should do the same as "enable lights" -- I know it's a stupid example). I'm guessing the only option is to have some kind of a dictionary (XML maybe), and just have a list of possible words for one particular object in the house.
Detecting the verb and subject. "turn on" is the verb, and "lights" is the subject. I need a good way to detect this.
General implementation. How are these things usually developed in terms of algorithms? I only managed to find one article about NLP in Smart Homes, which was very vague (and had bad English). Any links welcome.
I hope the question is unique enough (I've seen NLP questions on SO, none really helped), that it won't get closed.
If you don't have a lot of time to spend with the NLP problem, you may use the Wit API (http://wit.ai) which maps natural language sentences to JSON:
It's based on machine learning, so you need to provide examples of sentences + JSON output to configure it to your needs. It should be much more robust than grammar-based approaches, especially because the voice-to-speech engine might make mistakes that will break your grammar (but the machine learning module can still get the meaning of the sentence).
I am no way a pioneer in NLP(I love it though) but let me try my hand on this one. For your project I would suggest you to go through Stanford Parser
From your problem definition I guess you don't need anything other then verbs and nouns. SP generates POS(Part of speech tags) That you can use to prune the words that you don't require.
For this I can't think of any better option then what you have in mind right now.
For this again you can use grammatical dependency structure from SP and I am pretty much sure that it is good enough to tackle this problem.
This is where your research part lies. I guess you can find enough patterns using GD and POS tags to come up with an algorithm for your problem. I hardly doubt that any algorithm would be efficient enough to handle every set of input sentence(Structured+unstructured) but something that is more that 85% accurate should be good enough for you.
First, I would construct a list of all possible commands (not every possible way to say a command, just the actual function itself: "kitchen light on" and "turn on the light in the kitchen" are the same command) based on the actual functionality the smart house has available. I assume there is a discrete number of these in the order of no more than hundreds. Assign each some sort of identifier code.
Your job then becomes to map an input of:
a sentence of english text
location of speaker
time of day, day of week
any other input data
to an output of a confidence level (0.0 to 1.0) for each command.
The system will then execute the best match command if the confidence is over some tunable threshold (say over 0.70).
From here it becomes a machine learning application. There are a number of different approaches (and furthermore, approaches can be combined together by having them compete based on features of the input).
To start with I would work through the NLP book from Jurafsky/Manning from Stanford. It is a good survey of current NLP algorithms.
From there you will get some ideas about how the mapping can be machine learned. More importantly how natural language can be broken down into a mathematical structure for machine learning.
Once the text is semantically analyzed, the simplest ML algorithm to try first would be of the supervised ones. To generate training data have a normal GUI, speak your command, then press the corresponding command manually. This forms a single supervised training case. Make some large number of these. Set some aside for testing. It is also unskilled work so other people can help. You can then use these as your training set for your ML algorithm.
I was wondering if anyone knew of a source which provides 2D model search spaces to test a GA against. I believe i read a while ago that there are a bunch of standard search spaces which are typically used when evaluating these type of algorithms.
If not, is it just a case of randomly generating this data yourself each time?
Edit: View from above and from the side.
The search space is completely dependent on your problem. The idea of a genetic algorithm being that modify the "genome" of a population of individuals to create the next generation, measure the fitness of the new generation and modify the genomes again with some randomness thrown is to try to prevent getting stuck in local minima. The search space however is completely determined by what you have in your genome, which in turn in completely determined by what the problem is.
There might be standard search spaces (i.e. genomes) that have been found to work well for particular problems (I haven't heard of any) but usually the hardest part in using GAs is defining what you have in your genome and how it is allowed to mutate. The usefulness comes from the fact that you don't have to explicitly declare all the values for the different variables for the model, but you can find good values (not necessarily the best ones though) using a more or less blind search.
EXAMPLE
One example used quite heavily is the evolved radio antenna (Wikipedia). The aim is to find a configuration for a radio antenna such that the antenna itself is as small and lightweight as possible, with the restriction that is has to respond to certain frequencies and have low noise and so on.
So you would build your genome specifying
the number of wires to use
the number of bends in each wire
the angle of each bend
maybe the distance of each bend from the base
(something else, I don't know what)
run your GA, see what comes out the other end, analyse why it didn't work. GAs have a habit of producing results you didn't expect because of bugs in the simulation. Anyhow, you discover that maybe the genome has to encode the number of bends individually for each of the wires in the antenna, meaning that the antenna isn't going to be symmetric. So you put that in your genome and run the thing again. Simulating stuff that needs to work in the physical world is usually the most expensive because at some point you have to test the indivudal(s) in the real world.
There's a reasonable tutorial of genetic algorithms here with some useful examples about different encoding schemes for the genome.
One final point, when people say that GAs are simple and easy to implement, they mean that the framework around the GA (generating a new population, evaluating fitness etc.) is simple. What usually is not said is that setting up a GA for a real problem is very difficult and usually requires a lot of trial and error because coming up with an encoding scheme that works well is not simple for complex problems. The best way to start is to start simple and make things more complex as you go along. You can of course make another GA to come with the encoding for first GA :).
There are several standard benchmark problems out there.
BBOB (Black Box Optimization Benchmarks) -- have been used in recent years as part of a continuous optimization competition
DeJong functions -- pretty old, and really too easy for most practical purposes these days. Useful for debugging perhaps.
ZDT/DTLZ multiobjective functions -- multi-objective optimization problems, but you could scalarize them yourself I suppose.
Many others
I have a database, consisting of a whole bunch of records (around 600,000) where some of the records have certain fields missing. My goal is to find a way to predict what the missing data values should be (so I can fill them in) based on the existing data.
One option I am looking at is clustering - i.e. representing the records that are all complete as points in some space, looking for clusters of points, and then when given a record with missing data values try to find out if there are any clusters that could belong in that are consistent with the existing data values. However this may not be possible because some of the data fields are on a nominal scale (e.g. color) and thus can't be put in order.
Another idea I had is to create some sort of probabilistic model that would predict the data, train it on the existing data, and then use it to extrapolate.
What algorithms are available for doing the above, and is there any freely available software that implements those algorithms (This software is going to be in c# by the way).
This is less of an algorithmic and more of a philosophical and methodological question. There are a few different techniques available to tackle this kind of question. Acock (2005) gives a good introduction to some of the methods. Although it may seem that there is a lot of math/statistics involved (and may seem like a lot of effort), it's worth thinking what would happen if you messed up.
Andrew Gelman's blog is also a good resource, although the search functionality on his blog leaves something to be desired...
Hope this helps.
Acock (2005)
http://oregonstate.edu/~acock/growth-curves/working%20with%20missing%20values.pdf
Andrew Gelman's blog
http://www.stat.columbia.edu/~cook/movabletype/mlm/
Dealing with missing values is a methodical question that has to do with the actual meaning of the data.
Several methods you can use (detailed post on my blog):
Ignore the data row. This is usually done when the class label is missing (assuming you data mining goal is classification), or many attributes are missing from the row (not just one). However you'll obviously get poor performance if the percentage of such rows is high
Use a global constant to fill in for missing values. Like "unknown", "N/A" or minus infinity. This is used because sometimes is just doesnt make sense to try and predict the missing value. For example if you have a DB if, say, college candidates and state of residence is missing for some, filling it in doesn't make much sense...
Use attribute mean. For example if the average income of a US family is X you can use that value to replace missing income values.
Use attribute mean for all samples belonging to the same class. Lets say you have a cars pricing DB that, among other things, classifies cars to "Luxury" and "Low budget" and you're dealing with missing values in the cost field. Replacing missing cost of a luxury car with the average cost of all luxury cars is probably more accurate then the value you'd get if you factor in the low budget cars
Use data mining algorithm to predict the value. The value can be determined using regression, inference based tools using Baysian formalism , decision trees, clustering algorithms used to generate input for step method #4 (K-Mean\Median etc.)
I'd suggest looking into regression and decision trees first (ID3 tree generation) as they're relatively easy and there are plenty of examples on the net.
As for packages, if you can afford it and you're in the Microsoft world look at SQL Server Analysis Services (SSAS for short) that implement most of the mentioned above.
Here are some links to free data minning software packages:
WEKA - http://www.cs.waikato.ac.nz/ml/weka/index.html
ORANGE - http://www.ailab.si/orange
TANAGRA - http://eric.univ-lyon2.fr/~ricco/tanagra/en/tanagra.html
Although not C# he's a pretty good intro to decision trees and baysian learning (using Ruby):
http://www.igvita.com/2007/04/16/decision-tree-learning-in-ruby/
http://www.igvita.com/2007/05/23/bayes-classification-in-ruby/
There's also this Ruby library that I find very useful (also for learning purposes):
http://ai4r.rubyforge.org/machineLearning.html
There should be plenty of samples for these algorithms online in any language so I'm sure you'll easily find C# stuff too...
Edited:
Forgot this in my original post. This is a definately MUST HAVE if you're playing with data mining...
Download Microsoft SQL Server 2008 Data Mining Add-ins for Microsoft Office 2007 (It requires SQL Server Analysis Services - SSAS - which isn't free but you can download a trial).
This will allow you to easily play and try out the different techniques in Excel before you go and implement this stuff yourself. Then again, since you're in the Microsoft ecosystem, you might even decide to go for an SSAS based solution and count on the SQL Server guys to do it for ya :)
Predicting missing values is generally considered to be part of data cleansing phase which needs to be done before the data is mined or analyzed further. This is quite prominent in real world data.
Please have a look at this algorithm http://arxiv.org/abs/math/0701152
Currently Microsoft SQL Server Analysis Services 2008 also comes with algorithms like these http://technet.microsoft.com/en-us/library/ms175312.aspx which help in predictive modelling of attributes.
cheers