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Book Review- Machine Learning for Hackers

This is review of the fashionably named book Machine Learning for Hackers by Drew Conway and John Myles White (O’Reilly ). The book is about hacking code in R.

 

The preface introduces the reader to the authors conception of what machine learning and hacking is all about. If the name of the book was machine learning for business analytsts or data miners, I am sure the content would have been unchanged though the popularity (and ambiguity) of the word hacker can often substitute for its usefulness. Indeed the many wise and learned Professors of statistics departments through out the civilized world would be mildly surprised and bemused by their day to day activities as hacking or teaching hackers. The book follows a case study and example based approach and uses the GGPLOT2 package within R programming almost to the point of ignoring any other native graphics system based in R. It can be quite useful for the aspiring reader who wishes to understand and join the booming market for skilled talent in statistical computing.

Chapter 1 has a very useful set of functions for data cleansing and formatting. It walks you through the basics of formatting based on dates and conditions, missing value and outlier treatment and using ggplot package in R for graphical analysis. The case study used is an Infochimps dataset with 60,000 recordings of UFO sightings. The case study is lucid, and done at a extremely helpful pace illustrating the powerful and flexible nature of R functions that can be used for data cleansing.The chapter mentions text editors and IDEs but fails to list them in a tabular format, while listing several other tables like Packages used in the book. It also jumps straight from installation instructions to functions in R without getting into the various kinds of data types within R or specifying where these can be referenced from. It thus assumes a higher level of basic programming understanding for the reader than the average R book.

Chapter 2 discusses data exploration, and has a very clear set of diagrams that explain the various data summary operations that are performed routinely. This is an innovative approach and will help students or newcomers to the field of data analysis. It introduces the reader to type determination functions, as well different kinds of encoding. The introduction to creating functions is quite elegant and simple , and numerical summary methods are explained adequately. While the chapter explains data exploration with the help of various histogram options in ggplot2 , it fails to create a more generic framework for data exploration or rules to assist the reader in visual data exploration in non standard data situations. While the examples are very helpful for a reader , there needs to be slightly more depth to step out of the example and into a framework for visual data exploration (or references for the same). A couple of case studies however elaborately explained cannot do justice to the vast field of data exploration and especially visual data exploration.

Chapter 3 discussed binary classification for the specific purpose for spam filtering using a dataset from SpamAssassin. It introduces the reader to the naïve Bayes classifier and the principles of text mining suing the tm package in R. Some of the example codes could have been better commented for easier readability in the book. Overall it is quite a easy tutorial for creating a naïve Bayes classifier even for beginners.

Chapter 4 discusses the issues in importance ranking and creating recommendation systems specifically in the case of ordering email messages into important and not important. It introduces the useful grepl, gsub, strsplit, strptime ,difftime and strtrim functions for parsing data. The chapter further introduces the reader to the concept of log (and affine) transformations in a lucid and clear way that can help even beginners learn this powerful transformation concept. Again the coding within this chapter is sparsely commented which can cause difficulties to people not used to learn reams of code. ( it may have been part of the code attached with the book, but I am reading an electronic book and I did not find an easy way to go back and forth between the code and the book). The readability of the chapters would be further enhanced by the use of flow charts explaining the path and process followed than overtly verbose textual descriptions running into multiple pages. The chapters are quite clearly written, but a helpful visual summary can help in both revising the concepts and elucidate the approach taken further.A suggestion for the authors could be to compile the list of useful functions they introduce in this book as a sort of reference card (or Ref Card) for R Hackers or atleast have a chapter wise summary of functions, datasets and packages used.

Chapter 5 discusses linear regression , and it is a surprising and not very good explanation of regression theory in the introduction to regression. However the chapter makes up in practical example what it oversimplifies in theory. The chapter on regression is not the finest chapter written in this otherwise excellent book. Part of this is because of relative lack of organization- correlation is explained after linear regression is explained. Once again the lack of a function summary and a process flow diagram hinders readability and a separate section on regression metrics that help make a regression result good or not so good could be a welcome addition. Functions introduced include lm.

Chapter 6 showcases Generalized Additive Model (GAM) and Polynomial Regression, including an introduction to singularity and of over-fitting. Functions included in this chapter are transform, and poly while the package glmnet is also used here. The chapter also introduces the reader formally to the concept of cross validation (though examples of cross validation had been introduced in earlier chapters) and regularization. Logistic regression is also introduced at the end in this chapter.

Chapter 7 is about optimization. It describes error metric in a very easy to understand way. It creates a grid by using nested loops for various values of intercept and slope of a regression equation and computing the sum of square of errors. It then describes the optim function in detail including how it works and it’s various parameters. It introduces the curve function. The chapter then describes ridge regression including definition and hyperparameter lamda. The use of optim function to optimize the error in regression is useful learning for the aspiring hacker. Lastly it describes a case study of breaking codes using the simplistic Caesar cipher, a lexical database and the Metropolis method. Functions introduced in this chapter include .Machine$double.eps .

Chapter 8 deals with Principal Component Analysis and unsupervised learning. It uses the ymd function from lubridate package to convert string to date objects, and the cast function from reshape package to further manipulate the structure of data. Using the princomp functions enables PCA in R.The case study creates a stock market index and compares the results with the Dow Jones index.

Chapter 9 deals with Multidimensional Scaling as well as clustering US senators on the basis of similarity in voting records on legislation .It showcases matrix multiplication using %*% and also the dist function to compute distance matrix.

Chapter 10 has the subject of K Nearest Neighbors for recommendation systems. Packages used include class ,reshape and and functions used include cor, function and log. It also demonstrates creating a custom kNN function for calculating Euclidean distance between center of centroids and data. The case study used is the R package recommendation contest on Kaggle. Overall a simplistic introduction to creating a recommendation system using K nearest neighbors, without getting into any of the prepackaged packages within R that deal with association analysis , clustering or recommendation systems.

Chapter 11 introduces the reader to social network analysis (and elements of graph theory) using the example of Erdos Number as an interesting example of social networks of mathematicians. The example of Social Graph API by Google for hacking are quite new and intriguing (though a bit obsolete by changes, and should be rectified in either the errata or next edition) . However there exists packages within R that should be atleast referenced or used within this chapter (like TwitteR package that use the Twitter API and ROauth package for other social networks). Packages used within this chapter include Rcurl, RJSONIO, and igraph packages of R and functions used include rbind and ifelse. It also introduces the reader to the advanced software Gephi. The last example is to build a recommendation engine for whom to follow in Twitter using R.

Chapter 12 is about model comparison and introduces the concept of Support Vector Machines. It uses the package e1071 and shows the svm function. It also introduces the concept of tuning hyper parameters within default algorithms . A small problem in understanding the concepts is the misalignment of diagram pages with the relevant code. It lastly concludes with using mean square error as a method for comparing models built with different algorithms.

 

Overall the book is a welcome addition in the library of books based on R programming language, and the refreshing nature of the flow of material and the practicality of it’s case studies make this a recommended addition to both academic and corporate business analysts trying to derive insights by hacking lots of heterogeneous data.

Have a look for yourself at-
http://shop.oreilly.com/product/0636920018483.do

How to learn to be a hacker easily

1) Are you sure. It is tough to be a hacker. And football players get all the attention.

2) Really? Read on

3) Read Hacker’s Code

http://muq.org/~cynbe/hackers-code.html

The Hacker’s Code

“A hacker of the Old Code.”

  • Hackers come and go, but a great hack is forever.
  • Public goods belong to the public.*
  • Software hoarding is evil.
    Software does the greatest good given to the greatest number.
  • Don’t be evil.
  • Sourceless software sucks.
  • People have rights.
    Organizations live on sufferance.
  • Governments are organizations.
  • If it is wrong when citizens do it,
    it is wrong when governments do it.
  • Information wants to be free.
    Information deserves to be free.
  • Being legal doesn’t make it right.
  • Being illegal doesn’t make it wrong.
  • Subverting tyranny is the highest duty.
  • Trust your technolust!

4) Read How to be a hacker by

Eric Steven Raymond

http://www.catb.org/~esr/faqs/hacker-howto.html

or just get the Hacker Attitude

The Hacker Attitude

1. The world is full of fascinating problems waiting to be solved.
2. No problem should ever have to be solved twice.
3. Boredom and drudgery are evil.
4. Freedom is good.
5. Attitude is no substitute for competence.
5) If you are tired of reading English, maybe I should move on to technical stuff
6) Create your hacking space, a virtual disk on your machine.
You will need to learn a bit of Linux. If you are a Windows user, I recommend creating a VMWare partition with Ubuntu
If you like Mac, I recommend the more aesthetic Linux Mint.
How to create your virtual disk-
read here-
Download VM Player here
http://www.vmware.com/support/product-support/player/
Down iso image of operating system here
http://ubuntu.com
Downloading is the longest thing in this exercise
Now just do what is written here
http://www.vmware.com/pdf/vmware_player40.pdf
or if you want to try and experiment with other ways to use Windows and Linux just read this
http://www.decisionstats.com/ways-to-use-both-windows-and-linux-together/
Moving data back and forth between your new virtual disk and your old real disk
http://www.decisionstats.com/moving-data-between-windows-and-ubuntu-vmware-partition/
7) Get Tor to hide your IP address when on internet
https://www.torproject.org/docs/tor-doc-windows.html.en
8a ) Block Ads using Ad-block plugin when surfing the internet (like 14.95 million other users)
https://addons.mozilla.org/en-US/firefox/addon/adblock-plus/
 8b) and use Mafiafire to get elusive websites
https://addons.mozilla.org/en-US/firefox/addon/mafiaafire-redirector/
9) Get a  Bit Torrent Client at http://www.utorrent.com/
This will help you download stuff
10) Hacker Culture Alert-
This instruction is purely for sharing the culture but not the techie work of being a hacker
The website Pirate bay acts like a search engine for Bit torrents 
http://thepiratebay.se/
Visiting it is considered bad since you can get lots of music, videos, movies etc for free, without paying copyright fees.
The website 4chan is considered a meeting place to meet other hackers. The site can be visually shocking
http://boards.4chan.org/b/
You need to do atleast set up these systems, read the websites and come back in N month time for second part in this series on how to learn to be a hacker. That will be the coding part.
END OF PART  1
Updated – sorry been a bit delayed on next part. Will post soon.

Use R for Business- Competition worth $ 20,000 #rstats

All you contest junkies, R lovers and general change the world people, here’s a new contest to use R in a business application

http://www.revolutionanalytics.com/news-events/news-room/2011/revolution-analytics-launches-applications-of-r-in-business-contest.php

REVOLUTION ANALYTICS LAUNCHES “APPLICATIONS OF R IN BUSINESS” CONTEST

$20,000 in Prizes for Users Solving Business Problems with R

 

PALO ALTO, Calif. – September 1, 2011 – Revolution Analytics, the leading commercial provider of R software, services and support, today announced the launch of its “Applications of R in Business” contest to demonstrate real-world uses of applying R to business problems. The competition is open to all R users worldwide and submissions will be accepted through October 31. The Grand Prize winner for the best application using R or Revolution R will receive $10,000.

The bonus-prize winner for the best application using features unique to Revolution R Enterprise – such as itsbig-data analytics capabilities or its Web Services API for R – will receive $5,000. A panel of independent judges drawn from the R and business community will select the grand and bonus prize winners. Revolution Analytics will present five honorable mention prize winners each with $1,000.

“We’ve designed this contest to highlight the most interesting use cases of applying R and Revolution R to solving key business problems, such as Big Data,” said Jeff Erhardt, COO of Revolution Analytics. “The ability to process higher-volume datasets will continue to be a critical need and we encourage the submission of applications using large datasets. Our goal is to grow the collection of online materials describing how to use R for business applications so our customers can better leverage Big Analytics to meet their analytical and organizational needs.”

To enter Revolution Analytics’ “Applications of R in Business” competition (more…)

Machine Addictions

in the middle of essential and inevitable tasks
restless inner conscience wakens and asks
stuck again today to the computer are we now
please remind me this state we reached how

oh we had bills to pay student loans to repay
once we got hooked t’was easy to be carried away
just a matter of time before inevitable voices query
this is my machine that I want to marry

I spend more time with him/her as it is
the Machinery is devoted with focused loyalties
meanwhile the non machine world goes round
strives forth on things less profound

as we stroke the keys and click the mouse
machine addictions will only add to human grouse

The White Man's Burden-Poem

Rudyard Kipling, The White Man’s Burden

Take up the White Man’s burden–Send forth the best ye breed–

Go bind your sons to exile To serve your captives’ need;

To wait in heavy harness, On fluttered folk and wild–

Your new-caught, sullen peoples, Half-devil and half-child.

Take up the White Man’s burden–In patience to abide,

To veil the threat of terror And check the show of pride;

By open speech and simple, An hundred times made plain

To seek another’s profit, And work another’s gain.

Take up the White Man’s burden– The savage wars of peace–

Fill full the mouth of Famine And bid the sickness cease;

And when your goal is nearest The end for others sought,

Watch sloth and heathen Folly Bring all your hopes to nought.

Take up the White Man’s burden–No tawdry rule of kings,

But toil of serf and sweeper–The tale of common things.

The ports ye shall not enter,The roads ye shall not tread,

Go mark them with your living,And mark them with your dead.

Take up the White Man’s burden–And reap his old reward:

The blame of those ye better,The hate of those ye guard–

The cry of hosts ye humour (Ah, slowly!) toward the light:–

“Why brought he us from bondage, Our loved Egyptian night?”

Take up the White Man’s burden–Ye dare not stoop to less–

Nor call too loud on Freedom To cloke your weariness;

By all ye cry or whisper, By all ye leave or do,

The silent, sullen peoples Shall weigh your gods and you.

Take up the White Man’s burden– Have done with childish days–

The lightly proferred laurel, The easy, ungrudged praise.

Comes now, to search your manhood Through all the thankless years

Cold, edged with dear-bought wisdom, The judgment of your peers!

This famous poem, written by Britain‘s imperial poet, was a response to the American take over of the Phillipines after the Spanish-American War.(published in 1899)

source

http://www.fordham.edu/halsall/mod/kipling.html

Making NeW R

Tal G in his excellent blog piece talks of “Why R Developers  should not be paid” http://www.r-statistics.com/2010/09/open-source-and-money-why-r-developers-shouldnt-be-paid/

His argument of love is not very original though it was first made by these four guys

I am going to argue that “some” R developers should be paid, while the main focus should be volunteers code. These R developers should be paid as per usage of their packages.

Let me expand.

Imagine the following conversation between Ross Ihaka, Norman Nie and Peter Dalgaard.

Norman- Hey Guys, Can you give me some code- I got this new startup.

Ross Ihaka and Peter Dalgaard- Sure dude. Here is 100,000 lines of code, 2000 packages and 2 decades of effort.

Norman- Thanks guys.

Ross Ihaka- Hey, What you gonna do with this code.

Norman- I will better it. Sell it. Finally beat Jim Goodnight and his **** Proc GLM and **** Proc Reg.

Ross- Okay, but what will you give us? Will you give us some code back of what you improve?

Norman – Uh, let me explain this open core …

Peter D- Well how about some royalty?

Norman- Sure, we will throw parties at all conferences, snacks you know at user groups.

Ross – Hmm. That does not sound fair. (walks away in a huff muttering)-He takes our code, sells it and wont share the code

Peter D- Doesnt sound fair. I am back to reading Hamlet, the great Dane, and writing the next edition of my book. I am glad I wrote a book- Ross didnt even write that.

Norman-Uh Oh. (picks his phone)- Hey David Smith, We need to write some blog articles pronto – these open source guys ,man…

———–I think that sums what has been going on in the dynamics of R recently. If Ross Ihaka and R Gentleman had adopted an open core strategy- meaning you can create packages to R but not share the original where would we all be?

At this point if he is reading this, David Smith , long suffering veteran of open source  flameouts is rolling his eyes while Tal G is wondering if he will publish this on R Bloggers and if so when or something.

Lets bring in another R veteran-  Hadley Wickham who wrote a book on R and also created ggplot. Thats the best quality, most often used graphics package.

In terms of economic utilty to end user- the ggplot package may be as useful if not more as the foreach package developed by Revolution Computing/Analytics.

Now http://cran.r-project.org/web/packages/foreach/index.html says that foreach is licensed under http://www.apache.org/licenses/LICENSE-2.0

However lets come to open core licensing ( read it here http://alampitt.typepad.com/lampitt_or_leave_it/2008/08/open-core-licen.html ) which is where the debate is- Revolution takes code- enhances it (in my opinion) substantially with new formats XDF for better efficieny, web services API, and soon coming next year a GUI (thanks in advance , Dr Nie and guys)

and sells this advanced R code to businesses happy to pay ( they are currently paying much more to DR Goodnight and HIS guys)

Why would any sane customer buy it from Revolution- if he could download exactly the same thing from http://r-project.org

Hence the business need for Revolution Analytics to have an enhanced R- as they are using a product based software model not software as a service model.

If Revolution gives away source code of these new enhanced codes to R core team- how will R core team protect the above mentioned intelectual property- given they have 2 decades experience of giving away free code , and back and forth on just code.

Now Revolution also has a marketing budget- and thats how they sponsor some R Core events, conferences, after conference snacks.

How would people decide if they are being too generous or too stingy in their contribution (compared to the formidable generosity of SAS Institute to its employees, stakeholders and even third party analysts).

Would it not be better- IF Revolution can shift that aspect of relationship to its Research and Development budget than it’s marketing budget- come with some sort of incentive for “SOME” developers – even researchers need grants and assistantships, scholarships, make a transparent royalty formula say 17.5 % of the NEW R sales goes to R PACKAGE Developers pool, which in turn examines usage rate of packages and need/merit before allocation- that would require Revolution to evolve from a startup to a more sophisticated corporate and R Core can use this the same way as John M Chambers software award/scholarship

Dont pay all developers- it would be an insult to many of them – say Prof Harrell creator of HMisc to accept – but can Revolution expand its dev base (and prospect for future employees) by even sponsoring some R Scholarships.

And I am sure that if Revolution opens up some more code to the community- they would the rest of the world and it’s help useful. If it cant trust people like R Gentleman with some source code – well he is a board member.

——————————————————————————————–

Now to sum up some technical discussions on NeW R

1)  An accepted way of benchmarking efficiencies.

2) Code review and incorporation of efficiencies.

3) Multi threading- Multi core usage are trends to be incorporated.

4) GUIs like R Commander E Plugins for other packages, and Rattle for Data Mining to have focussed (or Deducer). This may involve hiring User Interface Designers (like from Apple ;)  who will work for love AND money ( Even the Beatles charge royalty for that song)

5) More support to cloud computing initiatives like Biocep and Elastic R – or Amazon AMI for using cloud computers- note efficiency arguements dont matter if you just use a Chrome Browser and pay 2 cents a hour for an Amazon Instance. Probably R core needs more direct involvement of Google (Cloud OS makers) and Amazon as well as even Salesforce.com (for creating Force.com Apps). Note even more corporates here need to be involved as cloud computing doesnot have any free and open source infrastructure (YET)

_______________________________________________________

Debates will come and go. This is an interesting intellectual debate and someday the liitle guys will win the Revolution-

From Hugh M of Gaping Void-

http://www.gapingvoid.com/Moveable_Type/archives/cat_microsoft_blue_monster_series.html

HOW DOES A SOFTWARE COMPANY MAKE MONEY, IF ALL

SOFTWARE IS FREE?

“If something goes wrong with Microsoft, I can phone Microsoft up and have it fixed. With Open Source, I have to rely on the community.”

And the community, as much as we may love it, is unpredictable. It might care about your problem and want to fix it, then again, it may not. Anyone who has ever witnessed something online go “viral”, good or bad, will know what I’m talking about.

and especially-

http://gapingvoid.com/2007/04/16/how-well-does-open-source-currently-meet-the-needs-of-shareholders-and-ceos/

Source-http://gapingvoidgallery.com/

Kind of sums up why the open core licensing is all about.

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