My first UniKernel image for sequence prediction

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Introduction

Predicting the next item of a sequence over a finite alphabet has important applications in many domains. Since I always wanted to implemented something like that, while I was looking for an interesting approach I found this interesting idea based on tree. And you don’t deal with trees since a lot, be prepared because as usual it seams simple, but it not. Moreover, since I like Golang and I always wanted to try UniK, I decided to implement my version of the CPT using Golang and use this exercise as a source to build my first unikernel image.

golang sequenceprediction unik

The entire code is available in the Github repo here.

Too much all together

I knew just a little bit of Golang, almost anything about the algorithm and nothing at all about unik. Let’s start from the algorithm.

Compact Prediction Tree

A CPT (*C*ompact *P*rediction *T*ree) losslessly compress the training data so that all relevant information is available for each prediction. Nice. The approach originally proposed1 by the T. Gueniche and P. F. Viger is incremental, offers a low time complexity for its training phase and it is easily adaptable for different applications and contexts. The performance of CPT with state of the art techniques, namely PPM (*P*rediction by *P*artial *M*atching), DG (*D*ependency *G*raph) and *all-K-th-order Markov chain. The results show that CPT yield higher accuracy on most datasets (up to 12% more than the second best approach), has better training time than DG and PPM, and is considerably smaller than all-K-th-Order Markov.

The structure

The entire code is based on two foundamental structure: a trie2 or PredictionTree (code of the package) and n InvertedIndexTable (code).

Prediction Tree

A Prediction Tree is a struct composed by 3 element: - Item – the actual item stored in the tree, that in our case represent a 32bit int; - Children – the children of the tree, a slice of PredictionTree (see the code); - Parent – A reference to the Parent tree of the tree

This is the reason a Prediction Tree is basically a trie data structure which compresses the entire training data into the form of a tree. Let’s say you have 4 difference sequence that contains a set of symbol predefined, like the one below:

Then, the respective Prediction Tree will be like the one below:

Inverted Index Table

The Inverted Index Table maintain a reference for each symbol to respective sequences it belongs to. Let’s say you have 4 difference sequence that contains a set of symbol predefined, like the one below:

Then, the respective Inverted Index Table will be like the one below:

seq_1 seq_2 seq_3 seq_4
A 1 1 0 0
B 0 1 0 0
C 1 1 0 1
D 0 0 1 1
E 1 0 0 1
F 1 0 1 1

In the code a list of sequence references is maintained instead of a table.

#### Training (build the structs) The training step consists in fullfill the structs by scanning a list of training sequences (list of list of symbols).

Testing (prediction)

The prediction step involves making predictions for each testing sequence in an iterative manner. For a single row, the sequences similar to that row are found thanks to the Inverted Index Table. The consequent of the similar sequences are isolated and maintained in a dictionary with their scores. In the end, this dictionary is used to return the item with the highest score as the final prediction.

[A, C, F, E]: the subsequence after last occurence of C is [F, E]. Both of them are not present in [A,C], thus the consequent of this similar sequence is [F, E]. If you encountered in this set element part of the original target sequence, remove them; [A, C, B]: the subsequence after last occurence of C is [B]. Again, B is not present in [A,C], thus the consequent of this similar sequence is [B];

So for element E, i.e. the first item in the consequent of the first similar sentence, the score will be score[F] = 1 + (13) + 1/(0+1) * 0.001 = 1.3343 score[E] = 1 + (13) + 1/(1+1) * 0.001 = 1.3338 score[B] = 1 + (13) + 1/(2+1) * 0.001 = 1.3336

Finally, [A,C] the key is returned with the greatest value in the dictionary of scores as the prediction. In the case of the above example, F is returned as a sequence prediction.

UniKImage

True, linux is monolithic, and I agree that microkernels are nicer… As has been noted (not only by me), the linux kernel is a minuscule part of a complete system: Full sources for linux currently runs to about 200kB compressed. And all of that source is portable, except for this tiny kernel that you can (probably: I did it) re-write totally from scratch in less than a year without having /any/ prior knowledge.

Linus Torvalds, 1992

UniK is a tool for compiling application sources into unikernels (lightweight bootable disk images) and MicroVM rather than binaries. UniK runs and manages instances of compiled images across a variety of cloud providers as well as locally: you can utilize it with a simple docker-like command line interface, that let you make and build unikernels and MicroVM as easy as building containers. UniK is built to be easily extensible, allowing (and encouraging) adding support for unikernel/MicroVM compilers and cloud providers. here more details about the architecture.

Steps to build image

To have the sequence prediction engine available as a bootable image, I used as said in the beginning. You can have a look at the repository on how to install everything is required. In the next paragraph I will provide someinsight you can find the original repository.

Install and configure UniK

Install unik by following instruction in official repository from here.

git clone https://github.com/solo-io/unik.git
cd unik
make

then follow configuration step here.

Golang server

Again, taken from unik repository. You have to ensure the project is cloned in $GOPATH, then:

This will create a Godeps/Godeps.json file as well as place all dependencies of your project in the ./vendor directory. This will allow UniK to compile your application entirely using only the root directory of your project.

Open a shell and run the daemon - then keep it running:

unik daemon --debug

To build and run the image - remember to use godep to let unik include dependencies first!! - run:

unik build --name go-cpt-image --path ./ --base rump --language go --provider virtualbox --force
unik run --instanceName go-cpt-instance --imageName go-cpt-image

To retrieve the running instances:

unik instances

You should get something like this:

golang

You can see IP assigned to instances in the last column of the output. To see the logs of the running instances run:

unik logs --instance go-cpt-instance

What this image does is actually expose the different endpoint to initialize training and make prediction by rest api - it's only a draft:

A sample file are already uploaded into the upload folder: you can modify the main.go root of the project to avoid cutting the training and testing set. Otherwise, to see the run you can both execute the code locally or

curl http://<YOUR_RUNNING_INSTANCES>:8080/initcpt

You should see predictions for the first 10 sequences :-)

golang

Conclusion

Many thanks to UniK contributors for sure, to NeerajSarwan for his work over CPT and all who want to contribute

Thank you everybody for reading!


  1. The original paper is available at here. [return]
  2. Trie (Wikipedia). [return]

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