Searching for tools to do bayesian network "structure" learning - structure

There are a lot of programs that do parameter learning for Bayes nets. I am having a hard time finding libraries or tools that do (or try to do) structure learning. Specifically, one that uses an information theoretic approach, by looking at the information gain from adding an edge, or analyzing the cross entropy across Random Variables to determine if they have any relationships or are independent. This is not the core problem I am trying to work on, but learning structure is an important part of it. So finding an existing tool/library would help immensely.

Try the bnlearn library. It contains structure learning, parameter learning, inference and various well-known example datasets such as Sprinkler, Asia, Alarm.
Github documentation pages
Examples can be found here
Blog about detecting causal relationships can be found here.

Related

How are customized heuristics implemented to optimization problems (in IDE) and solvers?

I have read up on several papers that described the use of heuristics in various routing problems that results in a faster run time for the solvers used (e.g. Gecode, CBC). For e.g., in the CPLEX/MiniZinc IDE, we have a constraint problem for the Vehicle Routing Problem (VRP), and a data file with contains the locations which the vehicle needs to go to (.dzn file in MiniZinc). Then, the authors in these papers implemented various kinds of routing heuristics to obtain a solution (may not be optimal) for each constraint model.
Thus my question is, how are the heuristics (can be customized to one that you designed, that is not built-in with he solver) implemented? Are the heuristics done in another IDE?
I have been looking around online literature but have yet to find out how this is actually done, especially for the case of MiniZinc and Cplex with the Gecode solver for example. It will be great if some insight can be shared on this issue! :)

IPA (International Phonetic Alphabet) Transcription with Tensorflow

I'm looking into designing a software platform that will aid linguists and anthropologists in their study of previously unstudied languages. Statistics show that around 1,000 languages exist that have never been studied by a person outside of their respective speaker groups.
My goal is to utilize TensorFlow to make a platform that will allow linguists to study and document these languages more efficiently, and to help them create written systems for the ones that don't have a written system already. One of their current methods of accomplishing such a task is three-fold: 1) Record a native speaker conversing in the language, 2) Listening to that recording and trying to transcribe it into the IPA, 3) From the phonetics, analyzing the phonemics and phonotactics of the language to eventually create a written system for the speaker.
My proposed platform would cut that research time down from a minimum of a year to a maximum of six months. Before I start, I have some questions...
What would be required to train TensorFlow to transcribe live audio into the IPA? Has this already been done? and if so, how would I utilize a previous solution for this project? Is a project like this even possible with TensorFlow? if not, what would you recommend using instead?
My apologies for the magnitude of this question. I don't have much experience in the realm of machine learning, as I am just beginning the research process for this project. Any help is appreciated!
I guess I will take a first shot at answering this. Since the question is pretty general, my answer will have to be pretty general as well.
What would be required. At the very least you would have to have a large dataset of pre-transcribed data. Ideally a large amount of spoken language audio mapped to characters in the phonetic alphabet, so the system could learn the sound of individual characters rather than whole transcribed words. If such a dataset doesn't exist, a less granular dataset could be used, mapping single words to their transcriptions. Then you would need a model, that is the actual neural network architecture implemented in code. And lastly you would need some computing resources. This is not something you can train casually, you would either have to buy some time in a cloud based machine learning framework (like Google Cloud ML) or build a fairly expensive machine to train at home.
Has this been done? I don't know. I don't think so. There have been published papers reporting various degrees of success at training systems to transcribe speech. Here is one, for example, http://deeplearning.stanford.edu/lexfree/lexfree.pdf It seems that since the alphabet you want to transcribe to is specifically designed to capture the way words sound rather than just write down the words you might have more success at training such a model.
Is it possible with TensorFlow. Yes, most likely. TensorFlow is well suited for implementing most modern deep learning architectures. Unless you end up designing some really weird and very original model for this purpose, TensorFlow should work just fine.
Edit: after some thought in part 1, you would have to use a dataset mapping spoken words to their transcriptions, since I expect that the same sound pronounced separately would be different from when the same sound is used in a word.
This has actually been done, albeit in PyTorch, by a group at CMU: https://github.com/xinjli/allosaurus

Converting a deep learning model from GPU powered framework, such as Theano, to a common, easily handled one, such as Numpy

I have been playing around with building some deep learning models in Python and now I have a couple of outcomes I would like to be able to show friends and family.
Unfortunately(?), most of my friends and family aren't really up to the task of installing any of the advanced frameworks that are more or less necessary to have when creating these networks, so I can't just send them my scripts in the present state and hope to have them run.
But then again, I have already created the nets, and just using the finished product is considerably less demanding than making it. We don't need advanced graph compilers or GPU compute powers for the show and tell. We just need the ability to make a few matrix multiplications.
"Just" being a weasel word, regrettably. What I would like to do is convert the the whole model (connectivity,functions and parameters) to a model expressed in e.g. regular Numpy (which, though not part of standard library, is both much easier to install and easier to bundle reliably with a script)
I fail to find any ready solutions to do this. (I find it difficult to pick specific keywords on it for a search engine). But it seems to me that I can't be the first guy who wants to use a ready-made deep learning model on a lower-spec machine operated by people who aren't necessarily inclined to spend months learning how to set the parameters in an artificial neural network.
Are there established ways of transferring a model from e.g. Theano to Numpy?
I'm not necessarily requesting those specific libraries. The main point is I want to go from a GPU-capable framework in the creation phase to one that is trivial to install or bundle in the usage phase, to alleviate or eliminate the threshold the dependencies create for users without extensive technical experience.
An interesting option for you would be to deploy your project to heroku, like explained on this page:
https://github.com/sugyan/tensorflow-mnist

Suitability of Naive Bayes classifier in Mahout to classifying websites

I'm currently working on a project that requires a database categorising websites (e.g. cnn.com = news). We only require broad classifications - we don't need every single URL classified individually. We're talking to the usual vendors of such databases, but most quotes we've had back are quite expensive and often they impose annoying requirements - like having to use their SDKs to query the database.
In the meantime, I've also been exploring the possibility of building such a database myself. I realise that this is not a 5 minute job, so I'm doing plenty of research.
From reading various papers on the subject, it seems a Naive Bayes classifier is generally the standard approach for doing this. However, many of the papers suggest enhancements to improve its accuracy in web classification - typically by making use of other contextual information, such as hyperlinks, header tags, multi-word phrases, the URL, word frequency and so on.
I've been experimenting with Mahout's Naive Bayes classifier against the 20 Newsgroup test dataset, and I can see its applicability to website classification, but I'm concerned about its accuracy for my use case.
Is anyone aware of the feasibility of extending the Bayes classifier in Mahout to take into account additional attributes? Any pointers as to where to start would be much appreciated.
Alternatively, if I'm barking up entirely the wrong tree please let me know!
You can control the input about as much as you'd like. In the end the input is just a feature vector. The feature vector's features can be words, or bigrams -- but they can also be whatever you want. So, yes, you can inject new features by modifying the input as you like.
How best to weave in those features is another topic entirely -- there's not one best way to convert them to numbers. Mahout in Action covers this reasonably well FWIW.

How do you find the most discriminant terms in binary document classification?

I want to use feature selection to find the terms in a document that are most useful for a binary classification task.
I've been looking around:
This mentions Mutual Information and the chi-squared test metric
http://nlp.stanford.edu/IR-book/html/htmledition/feature-selection-1.html
MATLAB has a number of functions as well:
http://www.mathworks.com/help/toolbox/stats/brj0qbu.html
Feature Selection in MATLAB
Of the above, relieff and rankfeatures look promising.
I do not know if my data follows a normal distribution. Any thoughts on which technique performs the best? Are there any newer methods you would suggest? The focus is to increase classification accuracy.
Thank you!
Since the answer is highly dependent on the nature of your data, I'd suggest playing with several options, possibly using a hold-out set for verification.
The easiest path would probably be to use Weka or RapidMiner for experimenting. Choosing from the plethora of options provided by them, you'll probably get acquainted with several other methods.
Having said that, I have found Mutual Information/Infogain to be useful on a large variety of problems.