I'm having fmri dataset for the classification of Normal Controls and Alzheimer diseased patients. Now, as a newbie I'm unable to extract features from my dataset. I want to extract activation patterns, GM,WM, CSF, volumetric measures and hemo-dynamics in numerical form. Please guide me how and where to start from and please suggest some easy and efficient softwares for my work... I'll be obliged...
Take a look at the software packages called FSL (FMRIB Software Library) and SPM (Statistical Parametric Mapping).
Each of them can do the kind of analyses you're asking about. However, be warned that none of these analyses are trivial. You should probably read up a bit on the subject, first. The Handbook of Functional MRI Data Analysis is a great place to start for beginners.
Like #WeirdAlchemy says, these are many analyses you want to carry out, and all of them non-trivial. You typically learn to these over weeks at a relevant intensive course or months during a neuro Masters programme. To answer your question very explicitly:
GM, WM & CSF volumetric measures - You can do this with FSL SIENA, SPM VBM, AFNI 3Dclust, among others.
"Extract activation patterns" is too vague. In all probability, you likely have task-related BOLD fMRI data and want to perform a general linear model (GLM) analysis. FSL FEAT, SPM fMRI, AFNI and others support this. However, without knowing the experimental design, the nature of the data, and what you want to learn from it, it's hard to be more specific about which tool is appropriate.
"Haemodynamics in numerical form" This can mean a number of things, but if you are thinking about the amount of haemodynamic signal modulation (e.g. Condition led to a 2% change in BOLD signal), you get that out of the GLM analysis mentioned above.
Related
[I'm approaching this as an outsider to machine learning. It just seems like a classification problem which I should be able to solve with fairly good accuracy with Machine Larning.]
Training Dataset:
I have millions of URLs, each tagged with a particular category. There are limited number of categories (50-100).
Now given a fresh URL, I want to categorize it into one of those categories. The category can be determined from the URL using conventional methods, but would require a huge unmanageable mess of pattern matching.
So I want to build a box where INPUT is URL, OUTPUT is Category. How do I build this box driven by ML?
As much as I would love to understand the basic fundamentals of how this would work out mathematically, right now much much more focussed on getting it done, so a conceptual understanding of the systems and processes involved is what I'm looking to get. I suppose machine learning is at a point where you can approach reasonably straight forward problems in that manner.
If you feel I'm wrong and I need to understand the foundations deeply in order to get value out of ML, do let me know.
I'm building this inside an AWS ecosystem so I'm open to using Amazon ML if it makes things quicker and simpler.
I suppose machine learning is at a point where you can approach reasonably straight forward problems in that manner.
It is not. Building an effective ML solution requires both an understanding of problem scope/constraints (in your case, new categories over time? Runtime requirements? Execution frequency? Latency requirements? Cost of errors? and more!). These constraints will then impact what types of feature engineering / processing you may look at, and what types of models you will look at. Your particular problem may also have issues with non I.I.D. data, which is an assumption of most ML methods. This would impact how you evaluate the accuracy of your model.
If you want to learn enough ML to do this problem, you might want to start looking at work done in Malicious URL classification. An example of which can be found here. While you could "hack" your way to something without learning more about ML, I would not personally trust any solution built in that manner.
If you feel I'm wrong and I need to understand the foundations deeply in order to get value out of ML, do let me know.
Okay, I'll bite.
There are really two schools of thought currently related to prediction: "machine learners" versus statisticians. The former group focuses almost entirely on practical and applied prediction, using techniques like k-fold cross-validation, bagging, etc., while the latter group is focused more on statistical theory and research methods. You seem to fall into the machine-learning camp, which is fine, but then you say this:
As much as I would love to understand the basic fundamentals of how this would work out mathematically, right now much much more focussed on getting it done, so a conceptual understanding of the systems and processes involved is what I'm looking to get.
While a "conceptual understanding of the systems and processes involved" is a prerequisite for doing advanced analytics, it isn't sufficient if you're the one conducting the analysis (it would be sufficient for a manager, who's not as close to the modeling).
With just a general idea of what's going on, say, in a logistic regression model, you would likely throw all statistical assumptions (which are important) to the wind. Do you know whether certain features or groups shouldn't be included because there aren't enough observations in that group for the test statistic to be valid? What can happen to your predictions and hypotheses when you have high variance-inflation factors?
These are important considerations when doing statistics, and oftentimes people see how easy it is to do from sklearn.svm import SVC or somthing like that and run wild. That's how you get caught with your pants around your ankles.
How do I build this box driven by ML?
You don't seem to have even a rudimentary understanding of how to approach machine/statistical learning problems. I would highly recommend that you take an "Introduction to Statistical Learning"- or "Intro to Regression Modeling"-type course in order to think about how you translate the URLs you have into meaningful features that have significant power predicting URL class. Think about how you can decompose a URL into individual pieces that might give some information as to which class a certain URL pertains. If you're classifying espn.com domains by sport, it'd be pretty important to parse nba out of http://www.espn.com/nba/team/roster/_/name/cle, don't you think?
Good luck with your project.
Edit:
To nudge you along, though: every ML problem boils down to some function mapping input to output. Your outputs are URL classes. Your inputs are URLs. However, machines only understand numbers, right? URLs aren't numbers (AFAIK). So you'll need to find a way to translate information contained in the URLs to what we call "features" or "variables." One place to start, there, would be one-hot encoding different parts of each URL. Think of why I mentioned the ESPN example above, and why I extracted info like nba from the URL. I did that because, if I'm trying to predict to which sport a given URL pertains, nba is a dead giveaway (i.e. it would very likely be highly predictive of sport).
Dear all I am working on a project in which I have to categories research papers into their appropriate fields using titles of papers. For example if a phrase "computer network" occurs somewhere in then title then this paper should be tagged as related to the concept "computer network". I have 3 million titles of research papers. So I want to know how I should start. I have tried to use tf-idf but could not get actual results. Does someone know about a library to do this task easily? Kindly suggest one. I shall be thankful.
If you don't know categories in advance, than it's not classification, but instead clustering. Basically, you need to do following:
Select algorithm.
Select and extract features.
Apply algorithm to features.
Quite simple. You only need to choose combination of algorithm and features that fits your case best.
When talking about clustering, there are several popular choices. K-means is considered one of the best and has enormous number of implementations, even in libraries not specialized in ML. Another popular choice is Expectation-Maximization (EM) algorithm. Both of them, however, require initial guess about number of classes. If you can't predict number of classes even approximately, other algorithms - such as hierarchical clustering or DBSCAN - may work for you better (see discussion here).
As for features, words themselves normally work fine for clustering by topic. Just tokenize your text, normalize and vectorize words (see this if you don't know what it all means).
Some useful links:
Clustering text documents using k-means
NLTK clustering package
Statistical Machine Learning for Text Classification with scikit-learn and NLTK
Note: all links in this answer are about Python, since it has really powerful and convenient tools for this kind of tasks, but if you have another language of preference, you most probably will be able to find similar libraries for it too.
For Python, I would recommend NLTK (Natural Language Toolkit), as it has some great tools for converting your raw documents into features you can feed to a machine learning algorithm. For starting out, you can maybe try a simple word frequency model (bag of words) and later on move to more complex feature extraction methods (string kernels). You can start by using SVM's (Support Vector Machines) to classify the data using LibSVM (the best SVM package).
The fact, that you do not know the number of categories in advance, you could use a tool called OntoGen. The tool basically takes a set of texts, does some text mining, and tries to discover the clusters of documents. It is a semi-supervised tool, so you must guide the process a little, but it does wonders. The final product of the process is an ontology of topics.
I encourage you, to give it a try.
I'd like to take a shot at characterizing incoming documents in my app as either "well" or "poorly" written. I realize this is no easy task, but even a rough idea would be useful. I feel like the way to do this would be via naïve Bayes classifier with two classes, but am open to suggestions. So two questions:
is this method the optimal (taking into account simplicity) way to do this
assuming a large enough training db?
are there libraries in ruby
(or any integratable JRuby or
whatever) that i can plug into my
rails app to make this happen with little fuss?
Thanks!
You might try using vocabulary vector analysis. Covered some here:
http://en.wikipedia.org/wiki/Semantic_similarity
Basically you build up a corpus of texts that you deem "well-written" or "poorly-written" and count the frequency of certain words. Make a normalized vector for each, and then compute the distance between those to the vectors of each incoming document. I am not a statistician, but I'm told it's similar to Bayesian filtering, but seems to deal with misspellings and outliers better.
This is not perfect, by any means. Depending on how accurate you need it to be, you will probably still need humans to make the final judgement. But we've had good luck using it as a pre-filter to reduce number of reviewers.
Another simple algorithm to check out is the Flesch-Kincaid readability metric. It is quite widely used and should be easy to implement. I assume one of the Ruby NLP libraries has syllable methods.
You may find interesting this Burstein, Chodorow, and Leacock on the Criterion essay evaluation system for a pretty interesting very high-level overview of how one particular system did essay evaluation as well as style correction.
I want to teach myself enough machine learning so that I can, to begin with, understand enough to put to use available open source ML frameworks that will allow me to do things like:
Go through the HTML source of pages
from a certain site and "understand"
which sections form the content,
which the advertisements and which
form the metadata ( neither the
content, nor the ads - for eg. -
TOC, author bio etc )
Go through the HTML source of pages
from disparate sites and "classify"
whether the site belongs to a
predefined category or not ( list of
categories will be supplied
beforhand )1.
... similar classification tasks on
text and pages.
As you can see, my immediate requirements are to do with classification on disparate data sources and large amounts of data.
As far as my limited understanding goes, taking the neural net approach will take a lot of training and maintainance than putting SVMs to use?
I understand that SVMs are well suited to ( binary ) classification tasks like mine, and open source framworks like libSVM are fairly mature?
In that case, what subjects and topics
does a computer science graduate need
to learn right now, so that the above
requirements can be solved, putting
these frameworks to use?
I would like to stay away from Java, is possible, and I have no language preferences otherwise. I am willing to learn and put in as much effort as I possibly can.
My intent is not to write code from scratch, but, to begin with putting the various frameworks available to use ( I do not know enough to decide which though ), and I should be able to fix things should they go wrong.
Recommendations from you on learning specific portions of statistics and probability theory is nothing unexpected from my side, so say that if required!
I will modify this question if needed, depending on all your suggestions and feedback.
"Understanding" in machine learn is the equivalent of having a model. The model can be for example a collection of support vectors, the layout and weights of a neural network, a decision tree, or more. Which of these methods work best really depends on the subject you're learning from and on the quality of your training data.
In your case, learning from a collection of HTML sites, you will like to preprocess the data first, this step is also called "feature extraction". That is, you extract information out of the page you're looking at. This is a difficult step, because it requires domain knowledge and you'll have to extract useful information, or otherwise your classifiers will not be able to make good distinctions. Feature extraction will give you a dataset (a matrix with features for each row) from which you'll be able to create your model.
Generally in machine learning it is advised to also keep a "test set" that you do not train your models with, but that you will use at the end to decide on what is the best method. It is of extreme importance that you keep the test set hidden until the very end of your modeling step! The test data basically gives you a hint on the "generalization error" that your model is making. Any model with enough complexity and learning time tends to learn exactly the information that you train it with. Machine learners say that the model "overfits" the training data. Such overfitted models seem to appear good, but this is just memorization.
While software support for preprocessing data is very sparse and highly domain dependent, as adam mentioned Weka is a good free tool for applying different methods once you have your dataset. I would recommend reading several books. Vladimir Vapnik wrote "The Nature of Statistical Learning Theory", he is the inventor of SVMs. You should get familiar with the process of modeling, so a book on machine learning is definitely very useful. I also hope that some of the terminology might be helpful to you in finding your way around.
Seems like a pretty complicated task to me; step 2, classification, is "easy" but step 1 seems like a structure learning task. You might want to simplify it to classification on parts of HTML trees, maybe preselected by some heuristic.
The most widely used general machine learning library (freely) available is probably WEKA. They have a book that introduces some ML concepts and covers how to use their software. Unfortunately for you, it is written entirely in Java.
I am not really a Python person, but it would surprise me if there aren't also a lot of tools available for it as well.
For text-based classification right now Naive Bayes, Decision Trees (J48 in particular I think), and SVM approaches are giving the best results. However they are each more suited for slightly different applications. Off the top of my head I'm not sure which would suit you the best. With a tool like WEKA you could try all three approaches with some example data without writing a line of code and see for yourself.
I tend to shy away from Neural Networks simply because they can get very very complicated quickly. Then again, I haven't tried a large project with them mostly because they have that reputation in academia.
Probability and statistics knowledge is only required if you are using probabilistic algorithms (like Naive Bayes). SVMs are generally not used in a probabilistic manner.
From the sound of it, you may want to invest in an actual pattern classification textbook or take a class on it in order to find exactly what you are looking for. For custom/non-standard data sets it can be tricky to get good results without having a survey of existing techniques.
It seems to me that you are now entering machine learning field, so I'd really like to suggest to have a look at this book: not only it provides a deep and vast overview on the most common machine learning approaches and algorithms (and their variations) but it also provides a very good set of exercises and scientific paper links. All of this is wrapped in an insightful language starred with a minimal and yet useful compendium about statistics and probability
I am working on testing several Machine Learning algorithm implementations, checking whether they can work as efficient as described in the papers and making sure they could offer a great power to our statistic NLP (Natural Language Processing) platform.
Could u guys show me some methods for testing an algorithm implementation?
1)What aspects?
2)How?
3)Do I have to follow some basic steps?
4)Do I have to consider diversity specific situations when using different programming languages?
5)Do I have to understand the algorithm? I mean, does it offer any help if I really know what the algorithm is and how it works?
Basically, we r using C or C++ to implement the algorithm and our working env is Linux/Unix. Our testing methods only focus on black box testing and testing input/output of functions. I am eager to improve them but I dont have any better idea now...
Great Thx!! LOL
For many machine learning and statistical classification tasks, the standard metric for measuring quality is Precision and Recall. Most published algorithms will make some kind of claim about these metrics, or you could implement them and run these tests yourself. This should provide a good indicative measure of the quality you can expect.
When you talk about efficiency of an algorithm, this is usually some statement about the time or space performance of an algorithm in terms of the size or complexity of its input (often expressed in Big O notation). Most published algorithms will report an upper bound on the time and space characteristics of the algorithm. You can use that as a comparative indicator, although you need to know a little bit about computational complexity in order to make sure you're not fooling yourself. You could also possibly derive this information from manual inspection of program code, but it's probably not necessary, because this information is almost always published along with the algorithm.
Finally, understanding the algorithm is always a good idea. It makes it easier to know what you need to do as a user of that algorithm to ensure you're getting the best possible results (and indeed to know whether the results you are getting are sensible or not), and it will allow you to apply quality measures such as those I suggested in the first paragraph of this answer.