Clustering in Bayesian Network Analysis (bnlearn) - cluster-analysis

everyone! I am new to this site, so please grant me patience if I'm doing this wrong or I incorrectly searched for this question and missed it in another forum. I'm currently a PhD student and trying to broaden my statistical toolkit. I'm trying to learn Bayesian networks and, at this moment, Bayesian Network Analysis specifically. I'm using the R package "bnlearn" and have no issues with the structure learning step. However, I have theoretical reasoning to believe my data may be clustered (by site the sample was taken) and I have no idea how to account for this in my analysis (or if I even need to account for it in BNA?) In the bnlearn manual, it talks about using the R package parallel, but I'm unclear if that is the actual answer to my question or if it's something different.
Has anyone done something similar or have any ideas how this is accomplished, if needed, in bnlearn?

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AS/RS simulation in Anylogic Simulation Software

I need to simulate a fully functional AS/RS in warehousing. Moreover, I am a complete beginner in this field. Can some please let me know if I could get readymade simulation file? Or if not, please let me know how to learn to do it.
I have checked out the Anylogic website and it's tutorials (They are too lengthy).
fortunately for you, i have developed an AS/RS example that is a ready-made downloadable model for you, available at https://cloud.anylogic.com/model/1f5c7d1f-8782-40ac-957d-d3ba97bf6bf0?mode=SETTINGS
In general, when you want a model example, the first thing you should do is check the anylogic cloud, and if you are lucky the model is downloadable. Unfortunately, most people don't share
It really depends on what type of ASRS you are modeling (shuttle versus unit load) and level of detail you need. Do you need specific slotting and inventory tracking, or simplier black box delays with the assumption inventory is always available? The level of detail you need depends on questions you are asking, and should be addressed prior to starting development. If results from the model are critical and urgent, and you need anything more than simple black box delays, you should consider outsourcing to an experienced professional until you can get your AnyLogic skills up to speed.

Scentific approach to evaluting software

I'm currently in school and have been tasked with objectively evaluating a software (atlassians Jira platform). I'm currently having issues in staying objective. For example, saying that the platform is "easy to use" is according to my opinion of the platform and not so much based on evidence. So I'm curious to hear from you guys if you know if any scientific method to evaluate software or services? I've currently done a survey asking users how they use Jira and what they think about the platform. But I feel that this is not enough I would like to have some numbers that can point to how good or bad the software is.
The fist thing to mention is that a scientific work is always a collective work. Keep in mind that others might already have done such an scientific work you might use. So you have to create a small team or look for well-founded scientific work throu the internet or contacts in universities if you have such contacts.
If there are no results that fits you have to create knowledge. In this case a mathematical based decision will help. The Decisiontable might be the source for a scientifc decisions. The Decisiontable requires a couple of possible decisions, a couple of factors to respect in a specific weight. It contains the analysis and synthesis. After you have created the Decisiontable you should discus it in a critical team until the team agrees the results (and might offer them to the public).

Simple examples/applications of Bayesian Networks

Thanks for reading.
I want to implement a Baysian Network using the Matlab's BNT toolbox.The thing is, I can't find "easy" examples, since it's the first time I have to deal with BN.
Can you propose some possible applications, (with not many nodes) please ^^ ?
Have a look at Tom Mitchell's "Machine Learning" book, which covers the subject starting with small, simple examples. I suspect there are many course slides you could access online which also give simple examples.
I think it helps to start with higher level tools to get a feel for how to construct networks before constructing them in code. Having a UI also allows you to play with the network and get a feel for the way the networks behave (propagation, explaining away, etc).
For example have a look at the free Genie (http://genie.sis.pitt.edu) and its samples, and/or the 50 node limited Hugin-Lite (http://www.hugin.com/productsservices/demo/hugin-lite) with it's sample networks. You can then check your BNT implementations to make sure they verify against the software packages.
Edit: I forgot to mention Netica which is another BN/Influence diagram software package which I think has the biggest selection of examples http://www.norsys.com/netlibrary/index.htm.

What are some good resources for learning about Artificial Neural Networks? [closed]

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I'm really interested in Artificial Neural Networks, but I'm looking for a place to start.
What resources are out there and what is a good starting project?
First of all, give up any notions that artificial neural networks have anything to do with the brain but for a passing similarity to networks of biological neurons. Learning biology won't help you effectively apply neural networks; learning linear algebra, calculus, and probability theory will. You should at the very least make yourself familiar with the idea of basic differentiation of functions, the chain rule, partial derivatives (the gradient, the Jacobian and the Hessian), and understanding matrix multiplication and diagonalization.
Really what you are doing when you train a network is optimizing a large, multidimensional function (minimizing your error measure with respect to each of the weights in the network), and so an investigation of techniques for nonlinear numerical optimization may prove instructive. This is a widely studied problem with a large base of literature outside of neural networks, and there are plenty of lecture notes in numerical optimization available on the web. To start, most people use simple gradient descent, but this can be much slower and less effective than more nuanced methods like
Once you've got the basic ideas down you can start to experiment with different "squashing" functions in your hidden layer, adding various kinds of regularization, and various tweaks to make learning go faster. See this paper for a comprehensive list of "best practices".
One of the best books on the subject is Chris Bishop's Neural Networks for Pattern Recognition. It's fairly old by this stage but is still an excellent resource, and you can often find used copies online for about $30. The neural network chapter in his newer book, Pattern Recognition and Machine Learning, is also quite comprehensive. For a particularly good implementation-centric tutorial, see this one on CodeProject.com which implements a clever sort of network called a convolutional network, which constrains connectivity in such a way as to make it very good at learning to classify visual patterns.
Support vector machines and other kernel methods have become quite popular because you can apply them without knowing what the hell you're doing and often get acceptable results. Neural networks, on the other hand, are huge optimization problems which require careful tuning, although they're still preferable for lots of problems, particularly large scale problems in domains like computer vision.
I'd highly recommend this excellent series by Anoop Madhusudanan on Code Project.
He takes you through the fundamentals to understanding how they work in an easy to understand way and shows you how to use his brainnet library to create your own.
Here are some example of Neural Net programming.
http://www.codeproject.com/KB/recipes/neural_dot_net.aspx
you can start reading here:
http://web.archive.org/web/20071025010456/http://www.geocities.com/CapeCanaveral/Lab/3765/neural.html
I for my part have visited a course about it and worked through some literature.
Neural Networks are kind of declasse these days. Support vector machines and kernel methods are better for more classes of problems then backpropagation. Neural networks and genetic algorithms capture the imagination of people who don't know much about modern machine learning but they are not state of the art.
If you want to learn more about AI and machine learning, I recommend reading Peter Norvig's Artificial Intelligence: A Modern Approach. It's a broad survey of AI and lots of modern technology. It goes over the history and older techniques too, and will give you a more complete grounding in the basics of AI and machine Learning.
Neural networks are pretty easy, though. Especially if you use a genetic algorithm to determine the weights, rather then proper backpropagation.
I second dwf's recommendation of Neural Networks for Pattern Recognition by Chris Bishop. Although, it's perhaps not a starter text. Norvig or an online tutorial (with code in Matlab!) would probably be a gentler introduction.
A good starter project would be OCR (Optical Character Recognition). You can scan in pages of text and feed each character through the network in order to perform classification. (You would have to train the network first of course!).
Raul Rojas' book is a a very good start (it's also free). Also, Haykin's book 3rd edition, although of large volume, is very well explained.
I can recommend where not to start. I bought An Introduction to Neural Networks by Kevin Gurney which has good reviews on Amazon and claims to be a "highly accessible introduction to one of the most important topics in cognitive and computer science". Personally, I would not recommend this book as a start. I can comprehend only about 10% of it, but maybe it's just me (English is not my native language). I'm going to look into other options from this thread.
http://www.ai-junkie.com/ann/evolved/nnt1.html is a clear introduction to multi-layers perceptron, although it does not describe the backpropagation algorithm
you can also have a look at generation5.org which provides a lot of articles about AI in general and has some great texts about neural network
If you don't mind spending money, The Handbook of Brain Theory and Neural Networks is very good. It contains 287 articles covering research in many disciplines. It starts with an introduction and theory and then highlights paths through the articles to best cover your interests.
As for a first project, Kohonen maps are interesting for categorization: find hidden relationships in your music collection, build a smart robot, or solve the Netflix prize.
I think a good starting point would always be Wikipedia. There you'll find some usefull links to documentations and projects which use neural nets, too.
Two books that where used during my study:
Introductional course: An introduction to Neural Computing by Igor Aleksander and Helen Morton.
Advanced course: Neurocomputing by Robert Hecht-Nielsen
I found Fausett's Fundamentals of Neural Networks a straightforward and easy-to-get-into introductory textbook.
I found the textbook "Computational Intelligence" to be incredibly helpful.
Programming Collective Intelligence discusses this in the context of Search and Ranking algorithms. Also, in the code available here (in ch.4), the concepts discussed in the book are illustrated in a Python example.
I agree with the other people who said that studying biology is not a good starting point... because theres a lot of irrelevant info in biology. You do not need to understand how a neuron works to recreate its functionality - you only need to simulate its actions. I recomend "How To Create A Mind" by Ray Kurzweil - it goes into the aspect of biology that is relevant for computational models, (creating a simualted neuron by combining several inputs and firing once a threshhold is reached) but ignores the irrelvant stuff like how the neuron actually adds thouse inputs togeather. (You will just use + and an inequality to compare to a threshold, for example)
I should also point out that the book isn't really about 'creating a mind' - it only focuses on heirarchical pattern recognition / the neocortex. The general theme has been talked about since the 1980s I beleive, so there are plenty of older books that probably contain slightly dated forms of the same information. I have read older documents stating that the vision system, for example, is a multi layered pattern recognizer. He contends that this applies to the entire neocortex. Also, take his 'predictions' with a grain of salt - his hardware estimates are probably pretty accurate, but i think he underestimates how complicated simple tasks can be (ex: driving a car). Granted, he has seen a lot of progress (and been part of some of it) but i still think he is over optimistic. There is a big difference between an AI car being able to drive a mile successfully 90% of the time, when compared to the 99.9+% that a human can do. I don't expect any AI to be truly out driving me for atleast 20 years... (I don't count BMWs track cars that need to be 'trained' on the actual course, as they aren't really playing the same game)
If you already have a basic idea of what AI is and how it can be modeled, you may be better off skipping to something more technical.
If you want to do quickly learn about applications of some neural network concepts on a real simulator, there is a great online book (now wiki) called 'Computational Cognitive Neuroscience' at http://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Main
The book is used at schools as a textbook, and takes you through lots of different brain areas, from individual neurons all the way to higher-order executive functioning.
In addition, each section is augmented with homework 'projects' that are already down for you. Just download, follow the steps, and simulate everything that the chapter talked about. The software they use, Emergent, is a little finnicky but incredibly robust: its the product of more than 10 years of work I believe.
I went through it in an undergrad class this past semester, and it was great. Walks you through everything step by step

Neural Networks or Human-computer interaction

I will be entering my third year of university in my next academic year, once I've finished my placement year as a web developer, and I would like to hear some opinions on the two modules in the Title.
I'm interested in both, however I want to pick one that will be relevant to my career and that I can apply to systems I develop.
I'm doing an Internet Computing degree, it covers web development, networking, database work and programming. Though I have had myself set on becoming a web developer I'm not so sure about that any more so am trying not to limit myself to that area of development.
I know HCI would help me as a web developer, but do you think it's worth it? Do you think Neural Network knowledge could help me realistically in a system I write in the future?
Thanks.
EDIT:
I thought it would be useful to follow-up with what I decided to do and how it's worked out.
I picked Artificial Neural Networks over HCI, and I've really enjoyed it. Having a peek into cognitive science and machine learning has ignited my interest for the subject area, and I will be hoping to take on a postgraduate project a few years from now when I can afford it.
I have got a job which I am starting after my final exams (which are in a few days) and I was indeed asked if I had done a module in HCI or similar. It didn't seem to matter, as it isn't a front-end developer position!
I would recommend taking the module if you have it as an option, as well as any module consisting of biological computation, it will open up more doors should you want to go onto postgraduate research in the future.
The worthiness depends on three factors:
How familiar are you with the topic already?
How good is the course/class you want to take?
What are your interested in more?
Especially for HCI, there is a broad range of "common sense" information you would also easily obtain from reading a good book or a wider range of articles about it also published on the internet. On the other hand, there indeed exist many deeper insights mostly obtained by Psychology studies. If the course is done right, you can indeed learn a lot about the topic and the real considerations to use for developing an interface.
For Neural Networks, one has to say that this is a typical hype topic. It would be mainly interesting in what application domain the course wants to deal with neural networks. You can be quite sure that you won't program or use any neural networks for web development. On the other hand, if the course is done right, this could be a good opportunity for you to broaden your knowledge. Especially, deepening your understanding about the theory of computer science. This highly depends on how the course is laid out, though.
HCI is a topic which helps your career as a web developer, but only if you feel incompetent in that topic (then it is a must) or it is done very well. Neural Networks is a topic which has more potential of being really interesting hardcore computer science stuff, where you indeed learn a better understanding about something. If you are interested in NN, you should not pass the opportunity to get an education which is not narrowly concentrated on the domain of web development -- and, after all, perhaps find more interest in other stuff (it is always good to know other directions you would perhaps like to go into for the future).
Neural networks sound cool until you read the fine print:
In modern software implementations of
artificial neural networks the
approach inspired by biology has more
or less been abandoned for a more
practical approach based on statistics
and signal processing.
This is something that has mystified me for years. Here you have an amazingly complex and powerful control system (real-world biological neural networks), and an academic discipline that appears to be about modeling these systems in software but that has in reality abandoned that activity.
If you're doing web development, your time is probably better spent in the HCI course.
Go with what interests you the most. The HCI stuff will be much easier to pick up later as needed, you'll likely never get another chance to learn about neural networks!
For prospective employers (at least the good ones!) you need to show a passion and excitement about what you do. I'd sooner hire someone who can enthusiastically talk about neural networks than someone who has an extra credit in HCI.
Unless you want to do the research end of the world, ie, get a Masters/PhD, go HCI.
I studied Neural Computation at University when I studied AI. I now run my own company. The number of times since I studied that I have used my NN skills equals zero. I'm glad I did it, as it was quite fascinating, but I would have found HCI much more useful from the position I'm at now. I think that you'd pick up a lot more insight from an HCI course relevant to the software industry, but if you think you experience should be more on the esoteric/almost arty side of development, go for NN.
Which sounds like more fun? Or, equivalently, which will you work harder at? Pick that one.
Did two courses in NN and some other AI-courses - its fun to poke round with that stuff and I actually managed to implement the stuff in some of the things I've done like face-recognition, and it's useful in some other areas to if you wanna plot your lab data etc. I have never used the NN:s in my web development career though I am sure it could be used for something however what it all really boils down to is to find a client or employee willing pay for it when you can just take the straight path. So I would rather read book about it if I wasn't that hardcore about it.
Fundamental Neural Networks doesn't take to much knowledge in math, and was what I used in my first course.
as a programmer to be you need the knowledge of neural network. if parallel processing is the way to go in hardware then future programmers must be knowledgable in neural network. don't forget that NN works better with noise or imprecise data but other systems may not. Note that most data we use for analysis are sample data which is a fraction of the whole and you could imagine if some in the sample are way off. so you need knowledge of NN if you want to last in computer programming field.