Hi,
I am trying to solve a problem from bioinformatics area, in which the prediction is based on history sequence of Amino Acids, assigning different constraints and properties.
Was anyone trying to use the MaxEnt package to solve this type of problems?
thanks
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Hi,
I know there has been some work on applying NLP techniques and formalisms to predicting protein folding but don't know any specifics. The answer is probably yes, but I don't know for sure...Tom
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Sounds like you want to do something akin to part-of-speech tagging, in which a maxent model is used to estimate the parameters for classification at each stage of a Markov process. Look at Adwait Ratnarparkhi's dissertation and papers on POS-tagging, and look at the implementation in OpenNLP.
Hi,
I am trying to solve a problem from bioinformatics area, in which the prediction is based on history sequence of Amino Acids, assigning different constraints and properties.
Was anyone trying to use the MaxEnt package to solve this type of problems?
thanks
Hi,
I know there has been some work on applying NLP techniques and formalisms to predicting protein folding but don't know any specifics. The answer is probably yes, but I don't know for sure...Tom
Sounds like you want to do something akin to part-of-speech tagging, in which a maxent model is used to estimate the parameters for classification at each stage of a Markov process. Look at Adwait Ratnarparkhi's dissertation and papers on POS-tagging, and look at the implementation in OpenNLP.
http://opennlp.sourceforge.net/
You should download the latest release and look at the opennlp.tools.postag package, but as a direct pointer you can look at this:
http://cvs.sourceforge.net/viewcvs.py/opennlp/opennlp/src/java/opennlp/tools/postag/POSTaggerME.java?rev=1.9&view=auto
Cheers,
Jason