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  • hierarchical clustering on correlations in Python scipy/numpy?

    - by user248237
    How can I run hierarchical clustering on a correlation matrix in scipy/numpy? I have a matrix of 100 rows by 9 columns, and I'd like to hierarchically clustering by correlations of each entry across the 9 conditions. I'd like to use 1-pearson correlation as the distances for clustering. Assuming I have a numpy array "X" that contains the 100 x 9 matrix, how can I do this? I tried using hcluster, based on this example: Y=pdist(X, 'seuclidean') Z=linkage(Y, 'single') dendrogram(Z, color_threshold=0) however, pdist is not what I want since that's euclidean distance. Any ideas? thanks.

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  • How Can I up my Street Cred in the coding world

    - by RedEye
    I know this isn't directly related to a specific coding problem. It's a more general programming question. I'm a n00b... Been coding for 1 year, and it's where I belong. I want to get hardcore and put everything I have into it. I started with C++ and now I'm into C#. I love it all. What can I do to up my game and up my respect in the programming world?

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  • Mahout Naive Bayes Classifier for Items

    - by Nimesh Parikh
    Team, I am working on a project where i need to classify Items into certain category. I have a single file as input; which contains target variable and space separated features. My training data will look like Category Name [Tab] DataString Plumbing [Tab] Pipe Tap Plastic Pipe PVC Pipe Cold Water Line Hot Water Line Tee outlet up Elbow turned up Elbow turned down Gate valve Globe valve Paint [Tab] Ivory Black Burnt Umber Caput Mortuum Violet Earth Red Yellow Ochre Titanium White Cadmium Yellow Light Cadmium Yellow Deep Cloths [Tab] Shirt T-Shirt Pent Jeans Tee Cargo Well, I have really big set of Category. I have couple of question here am i using correct data for Training? If no then what should i use? Once I train and Test my model, what is next step? How can i use output? Please help me with this Thanks, Nimesh

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  • Explaining training method for AdaBoost algorithm

    - by konzti8
    Hi, I'm trying to understand the Haar feature method used for the training step in the AdaBoost algorithm. I don't understand the math that well so I'd appreciate more of a conceptual answer (as much as possible, anyway). Basically, what does it do? How do you choose positive and negative sets for what you want to select? Can it be generalized? What I mean by that is, can you choose it to find any kind of feature that you want no matter what the background is? So, for example, if I want to find some kind of circular blob - can I do that? I've also read that it is used on small patches for the images around the possible feature - does that mean you have to manually select that image patch or can it be automated to process the entire image? Is there matlab code for the training step? Thanks for any help...

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  • What is the fastest, most efficient way to get up to speed on a new technology?

    - by SLC
    My current job involves working with a huge number of technologies, most of which are very niche and unheard of. In some cases I have to write something about the technology, or with the technology, such as some lessons, examples, or tutorials, on behalf of the developer of that technology or someone that is backing it. When I get told to learn about a new technology, my first port of call is to check our internal library, and then look on amazon for a book on the subject. Failing that, or if the project is too small to warrant a purchase, I hit up google and youtube. However the results of randomly googling what I want to learn are hit and miss. Some days, I can find everything I want to know in a series of lessons or videos, and it's no problem. Other times, I can find almost nothing, and I really have to piece together things from sites. The result is that there are various resources out there, videos, interactive lessons, tutorials, books etc. but when I need to learn something fast, I often don't know the best way to go about it. It's not about fun, because I don't always have the luxury of working my way through a 600 page textbook named "A Complete Guide To Technology X", I have to deliver results quickly. One of the examples I'd like to use is ASP.NET MVC 2 which is something I have been told to learn. I grabbed a book on MVC 1 to refresh my knowledge, but googling it does't produce much useful information. I've seen a ton of ScottGu's tutorials on it, but they are mostly feature presentations, and some date back almost a year. The same applies to channel 9 and there are no books out yet on amazon. My question therefore has two parts, the first asks, "Where are the best places to look to get the information needed to learn a new technology?" and the second asks "What is the most efficient way to use such resources to learn a new technology?"

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  • A simple explanation of Naive Bayes Classification

    - by Jaggerjack
    I am finding it hard to understand the process of Naive Bayes, and I was wondering if someone could explained it with a simple step by step process in English. I understand it takes comparisons by times occurred as a probability, but I have no idea how the training data is related to the actual dataset. Please give me an explanation of what role the training set plays. I am giving a very simple example for fruits here, like banana for example training set--- round-red round-orange oblong-yellow round-red dataset---- round-red round-orange round-red round-orange oblong-yellow round-red round-orange oblong-yellow oblong-yellow round-red

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  • How to figure out optimal C / Gamma parameters in libsvm?

    - by Cuga
    I'm using libsvm for multi-class classification of datasets with a large number of features/attributes (around 5,800 per each item). I'd like to choose better parameters for C and Gamma than the defaults I am currently using. I've already tried running easy.py, but for the datasets I'm using, the estimated time is near forever (ran easy.py at 20, 50, 100, and 200 data samples and got a super-linear regression which projected my necessary runtime to take years). Is there a way to more quickly arrive at better C and Gamma values than the defaults? I'm using the Java libraries, if that makes any difference.

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  • What should every programmer know?

    - by Matt Lacey
    Regardless of programming language(s) or operating system(s) used or the environment they develop for, what should every programmer know? Some background: I'm interested in becoming the best programmer I can. As part of this process I'm trying to understand what I don't know and would benefit me a lot if I did. While there are loads of lists around along the lines of "n things every [insert programming language] developer should know", I have yet to find anything similar which isn't limited to a specific language. I also expect this information to be of interest and benefit to others.

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  • Prolog: Not executing code as expected.

    - by Louis
    Basically I am attempting to have an AI agent navigate a world based on given percepts. My issue is handling how the agent moves. Basically, I have created find_action/4 such that we pass in the percepts, action, current cell, and the direction the agent is facing. As it stands the entire code looks like: http://wesnoth.pastebin.com/kdNvzZ6Y My issue is mainly with lines 102 to 106. Basically, in it's current form the code does not work and the find_action is skipped even when the agent is in fact facing right (I have verified this). This broken code is as follows: % If we are headed right, take a left turn find_action([_, _, _, _, _], Action, _, right) :- retractall(facing(_)), assert(facing(up)), Action = turnleft . However, after some experimentation I have concluded that the following works: % If we are headed right, take a left turn find_action([_, _, _, _, _], Action, _, _) :- facing(right), retractall(facing(_)), assert(facing(up)), Action = turnleft . I am not entire sure why this is. I've attempted to create several identical find_action's as well, each checking a different direction using the facing(_) format, however swipl does not like this and throws an error. Any help would be greatly appreciated.

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  • What do you do to keep current

    - by griegs
    I've noticed that as I progress in my career I my day to day activities require less and less actual hands on development. However, I feel that I need to stay current, both for my own personal desire as well as being able to guide a team to best practices etc. I'm finding it very hard to stay on top of the game because there are so many new frameworks, technologies and patterns coming out. Do I concentrate on a particular aspect or framework? Do I become a generalist or a specialist? What are others doing to maintain a certain level of proficiency and currentness (sic)?

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  • What is your favorite pastime to engage in while your project is buidling?

    - by ondesertverge
    As my average project grows in size the sum of build times throughout the day (and night) adds up to a substantial amount of time. Some of the things I or others do in this time include: Reading the news Thinking of ways to advance the project Looking at other projects Throwing darts Checking the unanswered list on stackoverflow.com Build times aren't constant making it hard to plan constructive use of them. I would like to hear of a method in use to make beneficial use of those few minutes that can add up to a few hours.

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  • java web development, what skills do I need?

    - by mrblah
    I want to learn, at least at a basic level, how to build java web applications (coming from a .net background). Meaning, I would like to be able to build, deploy a simple cms type application from the ground up. What exactly do I need to learn? Tomcat seems to be a good web server for Java. What options are there for the web? I know there is hibernate for an ORM. Does java have MVC? what about JSP? can MVC and JSP be together? beans? Maybe a book that covers all of these?

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  • What Level of Education Is Most Useful?

    - by Steve Rowe
    If you were going to hire a programmer to work for/with you, what level of CS education would you prefer them to have and why? This assumes all other things are equal which, of course, they never are in real life. Self taught? Bachelor's? Masters? PHD? The important part of the answer is why, not the level. I'm looking for how important people think a Computer Science education really is and if one can go too far. A little clarification: To make things a little more even, assume you're hiring them without a lot of work experience. Obviously having a higher education is of less value the farther you are from graduation.

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  • How to learn flex?

    - by Zenzen
    So I'm starting an internship as a Flex developer in ~2weeks thanks to a friend of mine. The thing is I know squat about Flex - it is an internship after all so I'm supposed to learn there, but nonetheless I want to have some basic understanding of Flex before I start (eventually I want to become a JEE/Flex dev). So my question is simple, which book(s) would you recommend me to start with? Are there any "must have" books, like let's say "Thinking in C++" for C++ etc.? I already heard about a few video tutorials and I will surely check them out but I'd also want to get some decent books.

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  • Understanding Smarty and MVC Frameworks

    - by Korrupzion
    Hello there, I just created this thread to discuss with people who have adopted the smarty system, and how many time it took to you to understand it, because i just can't get the idea, instead of making every easier as everybody says i think it just make more complex to code. More than a problem with only smarty is with the whole MVC model, with CakePHP or KohanaPHP i experience the same problems, u need to do 3x lines of code and files for something that u can do with a few lines of simple php. Maybe u can tell how did u learned to code using MVC model :)

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  • Multiple levels of 'collection.defaultdict' in Python

    - by Morlock
    Thanks to some great folks on SO, I discovered the possibilities offered by collections.defaultdict, notably in readability and speed. I have put them to use with success. Now I would like to implement three levels of dictionaries, the two top ones being defaultdict and the lowest one being int. I don't find the appropriate way to do this. Here is my attempt: from collections import defaultdict d = defaultdict(defaultdict) a = [("key1", {"a1":22, "a2":33}), ("key2", {"a1":32, "a2":55}), ("key3", {"a1":43, "a2":44})] for i in a: d[i[0]] = i[1] Now this works, but the following, which is the desired behavior, doesn't: d["key4"]["a1"] + 1 I suspect that I should have declared somewhere that the second level defaultdict is of type int, but I didn't find where or how to do so. The reason I am using defaultdict in the first place is to avoid having to initialize the dictionary for each new key. Any more elegant suggestion? Thanks pythoneers!

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  • Classification: Dealing with Abstain/Rejected Class

    - by abner.ayala
    I am asking for your input and/help on a classification problem. If anyone have any references that I can read to help me solve my problem even better. I have a classification problem of four discrete and very well separated classes. However my input is continuous and has a high frequency (50Hz), since its a real-time problem. The circles represent the clusters of the classes, the blue line the decision boundary and Class 5 equals the (neutral/resting do nothing class). This class is the rejected class. However the problem is that when I move from one class to the other I activate a lot of false positives in the transition movements, since the movement is clearly non-linear. For example, every time I move from class 5 (neutral class) to 1 I first see a lot of 3's before getting to the 1 class. Ideally, I will want my decision boundary to look like the one in the picture below where the rejected class is Class =5. Has a higher decision boundary than the others classes to avoid misclassification during transition. I am currently implementing my algorithm in Matlab using naive bayes, kNN, and SVMs optimized algorithms using Matlab. Question: What is the best/common way to handle abstain/rejected classes classes? Should I use (fuzzy logic, loss function, should I include resting cluster in the training)?

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  • How about the "Certified Secure Software Lifecycle Professional"?

    - by Ekkapop
    I have invited to join Certified Secure Software Lifecycle Professional training course, however I have no idea about this course. Course's details give me only an overview of information, for example, this course is about how to gathering requirement about security, how to doing something in more secure ways etc. Did anyone have experience about Certified Secure Software Lifecycle Professional? Is it worth to attend this course?

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  • Proper way to assert type of variable in Python

    - by Morlock
    In using a function, I wish to ensure that the type of the variables are as expected. How to do it right? Here is an example fake function trying to do just this before going on with its role: def my_print(text, begin, end): """Print text in UPPER between 'begin' and 'end' in lower """ for i in (text, begin, end): assert type(i) == type("") out = begin.lower() + text.upper() + end.lower() print out Is this approach valid? Should I use something else than type(i) == type("") ? Should I use try/except instead? Thanks pythoneers

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  • NoSql Crash Course/Tutorial

    - by Chris Thompson
    Hi all, I've seen NoSQL pop up quite a bit on SO and I have a solid understanding of why you would use it (from here, Wikipedia, etc). This could be due to the lack of concrete and uniform definition of what it is (more of a paradigm than concrete implementation), but I'm struggling to wrap my head around how I would go about designing a system that would use it or how I would implement it in my system. I'm really stuck in a relational-db mindset thinking of things in terms of tables and joins... At any rate, does anybody know of a crash course/tutorial on a system that would use it (kind of a "hello world" for a NoSQL-based system) or a tutorial that takes an existing "Hello World" app based on SQL and converts it to NoSQL (not necessarily in code, but just a high-level explanation). I see this having one solid answer, but if you guys feel like it should be community wiki, I'll be happy to change it. Thanks! Chris

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  • how much time does grid.py take to run ?

    - by trinity
    Hello all , I am using libsvm for binary classification.. I wanted to try grid.py , as it is said to improve results.. I ran this script for five files in separate terminals , and the script has been running for more than 12 hours.. this is the state of my 5 terminals now : [root@localhost tools]# python grid.py sarts_nonarts_feat.txt>grid_arts.txt Warning: empty z range [61.3997:61.3997], adjusting to [60.7857:62.0137] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [61.3997:61.3997], adjusting to [60.7857:62.0137] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py sgames_nongames_feat.txt>grid_games.txt Warning: empty z range [64.5867:64.5867], adjusting to [63.9408:65.2326] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [64.5867:64.5867], adjusting to [63.9408:65.2326] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py sref_nonref_feat.txt>grid_ref.txt Warning: empty z range [62.4602:62.4602], adjusting to [61.8356:63.0848] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [62.4602:62.4602], adjusting to [61.8356:63.0848] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py sbiz_nonbiz_feat.txt>grid_biz.txt Warning: empty z range [67.9762:67.9762], adjusting to [67.2964:68.656] line 2: warning: Cannot contour non grid data. Please use "set dgrid3d". Warning: empty z range [67.9762:67.9762], adjusting to [67.2964:68.656] line 4: warning: Cannot contour non grid data. Please use "set dgrid3d". [root@localhost tools]# python grid.py snews_nonnews_feat.txt>grid_news.txt Wrong input format at line 494 Traceback (most recent call last): File "grid.py", line 223, in run if rate is None: raise "get no rate" TypeError: exceptions must be classes or instances, not str I had redirected the outputs to files , but those files for now contain nothing.. And , the following files were created : sbiz_nonbiz_feat.txt.out sbiz_nonbiz_feat.txt.png sarts_nonarts_feat.txt.out sarts_nonarts_feat.txt.png sgames_nongames_feat.txt.out sgames_nongames_feat.txt.png sref_nonref_feat.txt.out sref_nonref_feat.txt.png snews_nonnews_feat.txt.out (-- is empty ) There's just one line of information in .out files.. the ".png" files are some GNU PLOTS . But i dont understand what the above GNUplots / warnings convey .. Should i re-run them ? Can anyone please tell me on how much time this script might take if each input file contains about 144000 lines.. Thanks and regards

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