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I have seen MICE implemented with different types of algorithms e.g. RandomForest or Stochastic Regression etc.
My question is that does it matter which type of algorithm i.e. does one perform the best? Is there any empirical evidence?
I am struggling to find any info on the web
Thank you
Yes, (depending on your task) it can matter quite a lot, which algorithm you choose.
You also can be sure, the mice developers wouldn't out effort into providing different algorithms, if there was one algorithm that anyway always performs best. Because, of course like in machine learning the "No free lunch theorem" is also relevant for imputation.
In general you can say, that the default settings of mice are often a good choice.
Look at this example from the miceRanger Vignette to see, how far imputations can differ for different algorithms. (the real distribution is marked in red, the respective multiple imputations in black)
The Predictive Mean Matching (pmm) algorithm e.g. makes sure that only imputed values appear, that were really in the dataset. This is for example useful, where only integer values like 0,1,2,3 appear in the data (and no values in between). Other algorithms won't do this, so while doing their regression they will also provide interpolated values like on the picture to the right ( so they will provide imputations that are e.g. 1.1, 1.3, ...) Both solutions can come with certain drawbacks.
That is why it is important to actually assess imputation performance afterwards. There are several diagnostic plots in mice to do this.
Recently, I was asked about how to pre-train a deep neural network with unlabeled data, meaning, instead of initializing the model weight with small random numbers, we set initial weight from a pretrained model (with unlabeled data).
Well, intuitively, I kinda get it, it probably helps with the vanishing gradient issue and shorten the training time when there are not too much labeled data available. But still, I don't really know how it is done, how can you train a neural network with unlabeled data? Is it something like SOM or Boltzmann machine?
Has anybody heard about this? If yes, can you provide some links to sources or papers. I am curious. Greatly appreciate!
There are lots of ways to deep-learn from unlabeled data. Layerwise pre-training was developed back in the 2000s by Geoff Hinton's group, though that's generally fallen out of favor.
More modern unsupervised deep learning methods include Auto-Encoders, Variational Auto-Encoders, and Generative Adversarial Networks. I won't dive into the details of all of them, but the simplest of these, auto-encoders, work by compressing an unlabeled input into a low dimensional real-valued representation, and using this compressed representation to reconstruct the original input. Intuitively, a compressed code that can effectively be used to recreate an input is likely to capture some useful features of said input. See here for an illustration and more detailed description. There are also plenty of examples implemented in your deep learning library of choice.
I guess in some sense any of the listed methods could be used as pre-training, e.g for preparing a network for a discriminative task like classification, though I'm not aware of that being a particularly common practice. Initialization methods, activation functions, and other optimization tricks are generally advanced enough to do well without more complicated initialization procedures.
I recently started learning neural networks, and I thought that creating a sudoku solver would be a nice application for NN. I started learning them with backward propagation neural network, but later I figured that there are tens of neural networks. At this point, I find it hard to learn all of them and then pick an appropriate one for my purpose. Hence, I am asking what would be a good choice for creating this solver. Can back propagation NN work here? If not, can you explain why and tell me which one can work.
Thanks!
Neural networks don't really seem to be the best way to solve sudoku, as others have already pointed out. I think a better (but also not really good/efficient) way would be to use an genetic algorithm. Genetic algorithms don't directly relate to NNs but its very useful to know how they work.
Better (with better i mean more likely to be sussessful and probably better for you to learn something new) ideas would include:
If you use a library:
Play around with the networks, try to train them to different datasets, maybe random numbers and see what you get and how you have to tune the parameters to get better results.
Try to write an image generator. I wrote a few of them and they are stil my favourite projects, with one of them i used backprop to teach a NN what x/y coordinate of the image has which color, and the other aproach combines random generated images with ine another (GAN/NEAT).
Try to use create a movie (series of images) of the network learning to create a picture. It will show you very well how backprop works and what parameter tuning does to the results and how it changes how the network gets to the result.
If you are not using a library:
Try to solve easy problems, one after the other. Use backprop or a genetic algorithm for training (whatever you have implemented).
Try to improove your implementation and change some things that nobody else cares about and see how it changes the results.
List of 'tasks' for your Network:
XOR (basically the hello world of NN)
Pole balancing problem
Simple games like pong
More complex games like flappy bird, agar.io etc.
Choose more problems that you find interesting, maybe you are into image recognition, maybe text, audio, who knows. Think of something you can/would like to be able to do and find a way to make you computer do it for you.
It's not advisable to only use your own NN implemetation, since it will probably not work properly the first few times and you'll get frustratet. Experiment with librarys and your own implementation.
Good way to find almost endless resources:
Use google search and add 'filetype:pdf' in the end in order to only show pdf files. Search for neural network, genetic algorithm, evolutional neural network.
Neither neural nets not GAs are close to ideal solutions for Sudoku. I would advise to look into Constraint Programming (eg. the Choco or Gecode solver). See https://gist.github.com/marioosh/9188179 for example. Should solve any 9x9 sudoku in a matter of milliseconds (the daily Sudokus of "Le monde" journal are created using this type of technology BTW).
There is also a famous "Dancing links" algorithm for this problem by Knuth that works very well https://en.wikipedia.org/wiki/Dancing_Links
Just like was mentioned in the comments, you probably want to take a look at convolutional networks. You basically input the sudoku bord as an two dimensional 'image'. I think using a receptive field of 3x3 would be quite interesting, and I don't really think you need more than one filter.
The harder thing is normalization: the numbers 1-9 don't have an underlying relation in sudoku, you could easily replace them by A-I for example. So they are categories, not numbers. However, one-hot encoding every output would mean a lot of inputs, so i'd stick to numerical normalization (1=0.1, 2 = 0.2, etc.)
The output of your network should be a softmax with of some kind: if you don't use softmax, and instead outupt just an x and y coordinate, then you can't assure that the outputedd square has not been filled in yet.
A numerical value should be passed along with the output, to show what number the network wants to fill in.
As PLEXATIC mentionned, neural-nets aren't really well suited for these kind of task. Genetic algorithm sounds good indeed.
However, if you still want to stick with neural-nets you could have a look at https://github.com/Kyubyong/sudoku. As answered Thomas W, 3x3 looks nice.
If you don't want to deal with CNN, you could find some answers here as well. https://www.kaggle.com/dithyrambe/neural-nets-as-sudoku-solvers
I'm handling a Deep Learning classification task to distinguish whether an image/video is boring or interesting.
Based on ten-thousand labeled data(1. interesting 2. a little interesting 3. normal 4. boring), I used some pre-trained imagenet model(resnet / inception / VGG etc) to fine-tune my classification task.
My training error is very small, means it has been converged already. But test error is very high, accuracy is only around 35%, very similar with a random result.
I found the difficult parts are:
Same object has different label, for example, a dog on grass, maybe a very cute dog can be labeled as an interesting image. But an ugly dog may be labeled as a boring image.
Factors to define interesting or boring is so many, image quality, image color, the object, the environment... If we just detect good image quality image or we just detect good environment image, it may be possible, but how we can combine all these factors.
Every one's interesting point is different, I may be interested with pets, but some other one may think it is boring, but there are some common sense that everyone think the same. But how can I detect it?
At last, do you think it is a possible problem that can be solved using deep learning? If so, what will you do with this task?
This is a very broad question. I'll try and give some pointers:
"My training error is very small... But test error is very high" means you overfit your training set: your model learns specific training examples instead of learning general "classification rules" applicable to unseen examples.
This usually means you have too many trainable parameters relative to the number of training samples.
Your problem is not exactly a "classification" problem: classifying a "little interesting" image as "boring" is worse than classifying it as "interesting". Your label set has order. Consider using a loss function that takes that into account. Maybe "InfogainLoss" (if you want to maintain discrete labels), or "EuclideanLoss" (if you are willing to accept a continuous score).
If you have enough training examples, I think it is not too much to ask from a deep model to distinguish between an "interesting" dog image and a "boring" one. Even though the semantic difference is not large, there is a difference between the images, and a deep model should be able to capture it.
However, you might want to start your finetuning from a net that is trained for "aesthetic" tasks (e.g., MemNet, flickr style etc.) and not a "semantic" net like VGG/GoogLeNet etc.
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A professor asked me to help making a specification for a college project.
By the time the students should know the basics of programming.
The professor is a mathematician and has little experience in other programming languages, so it should really be in MATLAB.
I would like some projects ideas. The project should
last about 1 to 2 months
be done individually
have web interface would be great
doesn't necessary have to go deep in maths, but some would be great
use a database (or store data in files)
What kind of project would make the students excited?
If you have any other tips I'll appreciate.
UPDATE: The students are sophomores and have already studied vector calculus. This project is for an one year Discrete Mathematics course.
UPDATE 2: The topics covered in the course are
Formal Logic
Proofs, Recursion, and Analysis of Algorithms
Sets and Combinatorics
Relations, Functions, and Matrices
Graphs and Trees
Graph Algorithms
Boolean Algebra and Computer Logic
Modeling Arithmetic, Computation, and Languages
And it'll be based on this book Mathematical Structures for Computer Science: A Modern Approach to Discrete Mathematics by Judith L. Gersting
General Suggestions:
There are many teaching resources at The MathWorks that may give you some ideas for course projects. Some sample links:
The MATLAB Central blogs, specifically some posts by Loren that include using LEGO Mindstorms in teaching and a webinar about MATLAB for teaching (note: you will have to sign up to see the webinar)
The Curriculum Exchange: a repository of course materials
Teaching with MATLAB and Simulink: a number of other links you may find useful
Specific Suggestions:
One of my grad school projects in non-linear dynamics that I found interesting dealt with Lorenz oscillators. A Lorenz oscillator is a non-linear system of three variables that can exhibit chaotic behavior. Such a system would provide an opportunity to introduce the students to numerical computation (iterative methods for simulating systems of differential equations, stability and convergence, etc.).
The most interesting thing about this project was that we were using Lorenz oscillators to encode and decode signals. This "encrypted communication" aspect was really cool, and was based on the following journal article:
Kevin M. Cuomo and Alan V. Oppenheim,
Circuit Implementation of Synchronized Chaos with Applications
to Communications, Physical Review
Letters 71(1), 65-68 (1993)
The article addresses hardware implementations of a chaotic communication system, but the equivalent software implementation should be simple enough to derive (and much easier for the students to implement!).
Some other useful aspects of such a project:
The behavior of the system can be visualized in 2-D and 3-D plots, thus exposing the students to a number of graphing utilities in MATLAB (PLOT, PLOT3, COMET, COMET3, etc.).
Audio signals can be read from files, encrypted using the Lorenz equations, written out to a new file, and then decrypted once again. You could even have the students each encrypt a signal with their Lorenz oscillator code and give it to another student to decrypt. This would introduce them to various file operations (FREAD, FWRITE, SAVE, LOAD, etc.), and you could even introduce them to working with audio data file formats.
You can introduce the students to the use of the PUBLISH command in MATLAB, which allows you to format M-files and publish them to various output types (like HTML or Word documents). This will teach them techniques for making useful help documentation for their MATLAB code.
I have found that implementing and visualizing Dynamical systems is great
for giving an introduction to programming and to an interesting branch of
applied mathematics. Because one can see the 'life' in these systems,
our students really enjoy this practical module.
We usually start off by visualizing a 1D attractor, so that we can
overlay the evolution rule/rate of change with the current state of
the system. That way you can teach computational aspects (integrating the system) and
visualization, and the separation of both in implementation (on a simple level, refreshing
graphics at every n-th computation step, but in C++ leading to threads, unsure about MATLAB capabilities here).
Next we add noise, and then add a sigmoidal nonlinearity to the linear attractor. We combine this extension with an introduction to version control (we use a sandbox SVN repository for this): The
students first have to create branches, modify the evolution rule and then merge
it back into HEAD.
When going 2D you can simply start with a rotation and modify it to become a Hopf oscillator, and visualize either by morphing a grid over time or by going 3D when starting with a distinct point. You can also visualize the bifurcation diagram in 3D. So you again combine generic MATLAB skills like 3D plotting with the maths.
To link in other topics, browse around in wikipedia: you can bring in hunter/predator models, chaotic systems, physical systems, etc.etc.
We usually do not teach object-oriented-programming from within MATLAB, although it is possible and you can easily make up your own use cases in the dynamical systems setting.
When introducing inheritance, we will already have moved on to C++, and I'm again unaware of MATLAB's capabilities here.
Coming back to your five points:
Duration is easily adjusted, because the simple 1D attractor can be
done quickly and from then on, extensions are ample and modular.
We assign this as an individual task, but allow and encourage discussion among students.
About the web interface I'm at a loss: what exactly do you have in mind, why is it
important, what would it add to the assignment, how does it relate to learning MATLAB.
I would recommend dropping this.
Complexity: A simple attractor is easily understood, but the sky's the limit :)
Using a database really is a lot different from config files. As to the first, there
is a database toolbox for accessing databases from MATLAB. Few institutes have the license though, and apart from that: this IMHO does not belong into such a course. I suggest introducing to the concept of config files, e.g. for the location and strength of the attractor, and later for the system's respective properties.
All this said, I would at least also tell your professor (and your students!) that Python is rising up against MATLAB. We are in the progress of going Python with our tutorials, but I understand if someone wants to stick with what's familiar.
Also, we actually need the scientific content later on, so the usefulness for you will probably depend on which department your course will be related to.
A lot of things are possible.
The first example that comes in mind is to model a public transportation network (the network of your city, with underground, buses, tramways, ...). It is represented by a weighted directed graph (you can use sparse matrix to represent it, for example).
You may, for example, ask them to compute the shortest path from one station to another one (Moore-dijkistra algorithm, for example) and display it.
So, for the students, the several steps to do are:
choose an appropriate representation for the network (it could be some objects to represent the properties of the stations and the lines, and a sparse matrix for the network)
load all the data (you can provide them the data in an XML file)
be able to draw the network (since you will put the coordinates of the stations)
calculate the shortest path from one point to another and display it in a pretty way
create a fronted (with GUI)
Of course, this could be complicated by adding connection times (when you change from one line to another), asking for several options (shortest path with minimum connections, take in considerations the time you loose by waiting for a train/bus, ...)
The level of details will depend on the level of the students and the time they could spend on it (it could be very simple, or very realist)
You want to do a project with a web interface and a database, but not any serious math... and you're doing it in MATLAB? Do you understand that MATLAB is especially designed to be used for "deep math", and not for web interfaces or databases?
I think if this is an intro to a Discrete Mathematics course, you should probably do something involving Discrete Mathematics, and not waste the students' time as they learn a bunch of things in that language that they'll never actually use.
Why not do something involving audio? I did an undergraduate project in which we used MATLAB to automatically beat-match different tunes and DJ mix between them. The full program took all semester, but you could do a subset of it. wavread() and the like are built in and easy to use.
Or do some simple image processing like finding Waldo using cross-correlation.
Maybe do something involving cryptography, have them crack a simple encryption scheme and feel like hackers.
MATLAB started life as a MATrix LAB, so maybe concentrating on problems in linear algebra would be a natural fit.
Discrete math problems using matricies include:
Spanning trees and shortest paths
The marriage problem (bipartite graphs)
Matching algorithms
Maximal flow in a network
The transportation problem
See Gil Strang's "Intro to Applied Math" or Knuth's "Concrete Math" for ideas.
You might look here: http://www.mathworks.com/academia/student_center/tutorials/launchpad.html
on the MathWorks website. The interactive tutorial (second link) is quite popular.
--Loren
I always thought the one I was assigned in grad school was a good choice-a magnetic lens simulator. The math isn't completely overwhelming so you can focus more on learning the language, and it's a good intro to the graphical capabilities (e.g., animating the path of an off-axis electron going through the lens).
db I/O and fancy interfaces are out of place in a discrete math course.
my matlab labs were typically algorithm implementations, with charts as output, and simple file input.
how hard is the material? image processing is really easy in matlab, can you do some discrete 2D filtering? blurs and stuff. http://homepages.inf.ed.ac.uk/rbf/HIPR2/filtops.htm