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• hierarchical clustering with gene expression matrix in python

  - by user248237

  how can I do a hierarchical clustering (in this case for gene expression data) in Python in a way that shows the matrix of gene expression values along with the dendrogram? What I mean is like the example here: http://www.mathworks.cn/access/helpdesk/help/toolbox/bioinfo/ug/a1060813239b1.html shown after bullet point 6 (Figure 1), where the dendrogram is plotted to the left of the gene expression matrix, where the rows have been reordered to reflect the clustering. How can I do this in Python using numpy/scipy or other tools? Also, is it computationally practical to do this with a matrix of about 11,000 genes, using euclidean distance as a metric? thanks.

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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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• Will be self-taught limit me?

  - by Isaiah

  I'm 21 and am pretty efficient in html/css, python, and javascript. I also know my way around lisp languages and enjoy programing in them. My problem is that I'm extremely self-taught and not quite confident that I could land a job programing, but I really need a job soon as I've just become a father. I haven't even created a resume yet because I'm not really sure what to put on it except my lone experience. So I wanted to ask, will being primarily self-taught with some experience on small projects I've done for a few clients limit me too much? I mean I know I need some kind of education so I've enrolled part time in a community college to work on a degree in computer science, but it's years till then. And if it will limit me a lot, what kind of skills would be good to work on to make my chances any better? Thank You

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• Going from a math career to a cs career: how to do it?

  - by Joseph

  Hey, I'm looking for some advice on how to successfully make the transition from mathematics to CS. My academic background is in mathematics (BS and MSc), and I've taken loads of math courses as well. You name it, and I took it: Measure Theory, Algebra, PDES, Manifolds, Complex Analysis, etc. I progressed quite far along this track, and at one point, I thought I would be a professional mathematician...But around the time I was finishing my MSc, I really got sick of it. Studying very abstract mathematics was fun, but it really lost it's appeal to me. Outside of a couple hundred people, I'm not sure if anybody would understand my research. I did not want to be 60 years old and say that my only contribution to the world consisted of published papers. Anyways, I've been an off and on hobbyist programmer since 2002. I've programmed in C and Java (just small projects), and I really started to be drawn to the area as time passed. There's a real appeal to CS work because, well, it actually means something to other people out there! I enjoy all parts of it: designing webpages (a real artistic appeal). On the other end, I do enjoy toying with compilers and more nitty-gritty stuff as well. Suffice to say, I have broad interests out there. Anyways, I know it's a bit late, but I was wondering if there were other folks out there who made the change, and if so, how I could do so. I know I have some fairly big gaps to fill in terms of data structures, lack of internship experience, etc. But I really would like to make this work. So my question is simply: How can I make the switch from math to CS? To pay the bills, I'll be doing financial analysis for a company, but I'd like to eventually transition into a developer type position. I've been reading "Algorithm Design" by Tardos and doing all the problems. It's not hard to make progress since the problems are far more concrete than the stuff I've been doing the past six years. I feel I can make fairly rapid progress in picking up all the materials from data structures, etc. but none of it can substitute the past several years I've lost. Anyways, I'm eager to learn but would love some advice/concrete direction. Thanks, Joseph

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• Recommended OpenGL / GLUT Reference

  - by TJB

  What OpenGL / GLUT reference is the best around? Ideally I'm looking for something with C++ sample code to help me learn OpenGL as well as details about the APIs similar to what MSDN provides for .net programming. If there isn't a one stop shop, then please list the set of references I should use and what the strengths of each one is. Thanx!

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• When to use Genetic Algorithms and when to use Neural Networks?

  - by Neil N

  Is there a rule of thumb or set of examples to determine when Genetic Algorithms versus when to use Neural Networks to solve a problem? I know there are cases in which you can have both methods mixed, but I am looking for a high level reasoning between the two methods. EDIT: XKCD has now touched on genetic algo's:

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• Object Orientated PHP books

  - by user275074

  Hi, I've realised just how rusty my knowledge of PHP 5 and advanced PHP programming is after completing some questions for a test. I seriously need to read a book or something. Any recommendations for PHP 5 books?

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• Books or resources for high-loaded sites.

  - by Alex

  Currently I'm developing high-loaded financial portal(we use LAMP to run our project). There are great number of incoming data to be processed and stored. So optimization tasks become very important for us. Could you suggest books, articles or resources, that discover optimization questions (especially bboks). NOTE: At the moment I'm reading great book High Performance MySQL, but besides I want to know other facilities of optimization.

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• How to start recognizing design patterns as you are programming?

  - by Jon Erickson

  I have general academic knowledge of the various design patterns that are discussed in GoF and Head First Design Patterns, but I have a difficult time applying them to the code that I am writing. A goal for me this year is to be able to recognize design patterns that are emerging from the code that I write. Obviously this comes with experience (I have about 2 years in the field), but my question is how can I jumpstart my ability to recognize design patterns as I am coding, maybe a suggestion as to what patterns are easiest to start applying in client-server applications (in my case mainly c# webforms with ms sql db's, but this could definitely be language agnostic).

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• Shortest way of determining a name ends with an `s`, `x` or `z`, and then use the `I18n.t` method wi

  - by Koning Baard XIV

  I'm creating a Rails application where users can have a first and last name. Since I'm a perfectionist, the application may not show something like Dennis's profile or Xianx's profile, but rather Dennis' profile and Xianx' profile. I use L18n, so I wanted to ask what is the shortest way of implementing this? This grammar is the same for both English and Dutch, where the application will be translated to. Oh, some important things: I am not afraid of using helpers and the application controller My language files are in Ruby, not YAML Thanks!

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• Source code of books made with TeX/LaTeX to learn

  - by Diego Sevilla

  Some time ago, reading this entry I found a nice image and a pointer to a better book entitled "Thinking Forth". To my surprise, the LaTeX sources of the book were ready to download, with pearls like: %% There's no bold typewriter in Computer Modern. %% Emulate with printing several times, slightly moving \newdimen\poormove \poormove0.0666pt \newcommand{\poorbf}[1]{% \llap{\hbox to \poormove{#1\hss}}% \raise\poormove\rlap{#1\hss}% \lower\poormove\rlap{#1\hss}% \rlap{\hbox to \poormove{\hss}\hbox{#1}}% #1} %\let\poorbf=\textbf \renewcommand{\poorbf}[1]{{\fontencoding{OT1}\fontfamily{cmtt}\fontseries{b}\selectfont#1}} in which it can simulate the bold stroking of a font that doesn't have it. Since reading that, I was unaware of \llap and such, but now I can use them to define boxes, etc. So, my question is twofold: Do you know of sites that show that relatively advanced use of TeX/LaTeX in terms of useful recipes, and Do you know any books that offer their TeX/LaTeX source to inspect and learn (and that are worth doing so.)?

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• Infix to Postfix and unary/binary operators

  - by Jaapjan

  I have a piece of code that converts an infix expression to an expression tree in memory. This works just fine. There's just one small trouble. I just connect work out how to involve the unary operators correctly (the right associative ones). With the following infix expression : +1 + +2 - -3 - -4 I would expect an RPN of: 1+2++3-4-- Yet, none of the online infix-post converters I can find handle this example in the way I would expect. Does anyone have a clear explanation of handling right associative operators, specifically the binary ones that can be mistaken for the unary ones?

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• How to compute the probability of a multi-class prediction using libsvm?

  - by Cuga

  I'm using libsvm and the documentation leads me to believe that there's a way to output the believed probability of an output classification's accuracy. Is this so? And if so, can anyone provide a clear example of how to do it in code? Currently, I'm using the Java libraries in the following manner SvmModel model = Svm.svm_train(problem, parameters); SvmNode x[] = getAnArrayOfSvmNodesForProblem(); double predictedValue = Svm.svm_predict(model, x);

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• How to convince someone, that reading programming related books(blogs, so..) is important? [closed]

  - by hgulyan

  Dear all, please, help me to convince, that no matter what you're doing, you need to read some stuff, try to learn something new. They say, that they don't want to sit in front of computer in the end of a day and they don't have opportunity to read in working hours, or they're too tired for doing something. Have you faced this kind of situation? What did you do? What if you want to help them? What methodology you'd suggest? How to open their eyes? EDIT I'm really concerned about this people. EDIT 2 Just to be clear, I'm not talking about one person or two. Some of them, just do their job good. Company doesn't motivate them to learn something. They're not bad people, not bad developers, they just need something or someone to help, show another view, but you can't just describe this new view or say smth like "You need to learn!" and that's it, you'll start to learn or you're not a good programmer. I started to learn OOP, DB structure 6 years ago and I had someone who had guided me. He told me to learn Java and MySQL, gave me some manuals and API's. That's how I started. What if they don't have that kind person or something else?

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• Domain Driven Design And The Entity Framework

  - by Hossein

  hi, I'm new to DDD and i want to use entity framework v4.0 (shipped with .net 4.0) in my new project. since i have few time to learn DDD and entity framework, which books are good for me to read first?! i'm going to first read Domain-Driven Design Tackling Complexity in the Heart of Software by Eric Evan and next Pro Entity Framework 4.0 (Apress Scott Klein)... the problem here is Eric Evan's book is too abstract,I want to know if the Pro Entity framework 4.0 is complete enough i just skip the first book! in the end recommend me some good books in DDD and Entity Framework Thanks

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• What programming hack from your past are you most ashamed of?

  - by LeopardSkinPillBoxHat

  We've all been there (usually when we are young and inexperienced). Fixing it properly is too difficult, too risky or too time-consuming. So you go down the hack path. Which hack from your past are you most ashamed of, and why? I'm talking about the ones where you would be really embarrassed if someone could attribute the hack to you (quite easily if you are using revision control software). One hack per answer please. Mine was shortly after I started in my first job. I was working on a legacy C system, and there was this strange defect where a screen view failed to update properly under certain circumstances. I wasn't familiar with how to use the debugger at this time, so I added traces into the code to figure out what was going on. Then I realised that the defect didn't occur anymore with the traces in the code. I slowly backed out the traces one-by-one, until I realised that only a single trace was required to make the problem go away. My logic now would tell me that I was dealing with some sort of race-condition or timing related issue that the trace just "hid under the rug". But I checked in the code with the following line, and all was well: printf(""); Which hacks are you ashamed of?

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• Training sets for AdaBoost algorithm

  - by palau1

  How do you find the negative and positive training data sets of Haar features for the AdaBoost algorithm? So say you have a certain type of blob that you want to locate in an image and there are several of them in your entire array - how do you go about training it? I'd appreciate a nontechnical explanation as much as possible. I'm new to this. Thanks.

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• Detecting syllables in a word

  - by user50705

  I need to find a fairly efficient way to detect syllables in a word. E.g., invisible - in-vi-sib-le There are some syllabification rules that could be used: V CV VC CVC CCV CCCV CVCC *where V is a vowel and C is a consonant. e.g., pronunciation (5 Pro-nun-ci-a-tion; CV-CVC-CV-V-CVC) I've tried few methods, among which were using regex (which helps only if you want to count syllables) or hard coded rule definition (a brute force approach which proves to be very inefficient) and finally using a finite state automata (which did not result with anything useful). The purpose of my application is to create a dictionary of all syllables in a given language. This dictionary will later be used for spell checking applications (using Bayesian classifiers) and text to speech synthesis. I would appreciate if one could give me tips on an alternate way to solve this problem besides my previous approaches. I work in Java, but any tip in C/C++, C#, Python, Perl... would work for me.

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• When do you learn from your mistakes?

  - by smayers81

  When are you supposed to learn from your mistakes in coding / design? Is it something you take with you to the next project or do you learn in the middle of your current one, sacrificing consistency for cleaner, more well-informed code? For example, my application can be distinctly demarcated down two lines of business -- say one side is for sales and the other is for marketing. Both are somewhat tied together, but as far as the team structure, use cases, developers, etc. the app consists of the Sales code and the Marketing Code. Now, say the Sales code went in first and while good-intentioned, made some bad mistakes. Should the Marketing Code follow suit and make the same mistakes for the sake of consistency or should Marketing architects and designers instead learn from the mistakes that Sales made and developer a cleaner codebase, even though Sales and Marketing are in the exact same system? Basically, do you learn from your mistakes while in a project or do you continue to pile crap on top of crap?

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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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• What's the reason for leaving an extra blank line at the end of a code file?

  - by Lord Torgamus

  Eclipse and MyEclipse create new Java files with an extra blank line after the last closing brace by default. I think CodeWarrior did the same thing a few years back, and that some people leave such blank lines in their code either by intention or laziness. So, this seems to be at least a moderately widespread behavior. As a former human language editor -- copy editing newspapers, mostly -- I find that those lines look like sloppiness or accidents, and I can't think of a reason to leave them in source files. I know they don't affect compilation in C-style languages, including Java. Are there benefits to having those lines, and if so, what are they?

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• Semantic Diff Utilities

  - by rubancache

  I'm trying to find some good examples of semantic diff/merge utilities. The traditional paradigm of comparing source code files works by comparing lines and characters.. but are there any utilities out there (for any language) that actually consider the structure of code when comparing files? For example, existing diff programs will report "difference found at character 2 of line 125. File x contains v-o-i-d, where file y contains b-o-o-l". A specialized tool should be able to report "Return type of method doSomething() changed from void to bool". I would argue that this type of semantic information is actually what the user is looking for when comparing code, and should be the goal of next-generation progamming tools. Are there any examples of this in available tools?

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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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• 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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• Blackberry - application settings save/load

  - by Max Gontar

  Hi! I know two ways to save/load application settings: use PersistentStore use filesystem (store, since SDCard is optional) I'd like to know what are you're practicies of working with application settings? Using PersistentStore to save/load application settings The persistent store provides a means for objects to persist across device resets. A persistent object consists of a key-value pair. When a persistent object is committed to the persistent store, that object's value is stored in flash memory via a deep copy. The value can then be retrieved at a later point in time via the key. Example of helper class for storing and retrieving settings: class PSOptions { private PersistentObject mStore; private LongHashtableCollection mSettings; private long KEY_URL = 0; private long KEY_ENCRYPT = 1; private long KEY_REFRESH_PERIOD = 2; public PSOptions() { // "AppSettings" = 0x71f1f00b95850cfeL mStore = PersistentStore.getPersistentObject(0x71f1f00b95850cfeL); } public String getUrl() { Object result = get(KEY_URL); return (null != result) ? (String) result : null; } public void setUrl(String url) { set(KEY_URL, url); } public boolean getEncrypt() { Object result = get(KEY_ENCRYPT); return (null != result) ? ((Boolean) result).booleanValue() : false; } public void setEncrypt(boolean encrypt) { set(KEY_ENCRYPT, new Boolean(encrypt)); } public int getRefreshPeriod() { Object result = get(KEY_REFRESH_PERIOD); return (null != result) ? ((Integer) result).intValue() : -1; } public void setRefreshRate(int refreshRate) { set(KEY_REFRESH_PERIOD, new Integer(refreshRate)); } private void set(long key, Object value) { synchronized (mStore) { mSettings = (LongHashtableCollection) mStore.getContents(); if (null == mSettings) { mSettings = new LongHashtableCollection(); } mSettings.put(key, value); mStore.setContents(mSettings); mStore.commit(); } } private Object get(long key) { synchronized (mStore) { mSettings = (LongHashtableCollection) mStore.getContents(); if (null != mSettings && mSettings.size() != 0) { return mSettings.get(key); } else { return null; } } } } Example of use: class Scr extends MainScreen implements FieldChangeListener { PSOptions mOptions = new PSOptions(); BasicEditField mUrl = new BasicEditField("Url:", "http://stackoverflow.com/"); CheckboxField mEncrypt = new CheckboxField("Enable encrypt", false); GaugeField mRefresh = new GaugeField("Refresh period", 1, 60 * 10, 10, GaugeField.EDITABLE|FOCUSABLE); ButtonField mLoad = new ButtonField("Load settings", ButtonField.CONSUME_CLICK); ButtonField mSave = new ButtonField("Save settings", ButtonField.CONSUME_CLICK); public Scr() { add(mUrl); mUrl.setChangeListener(this); add(mEncrypt); mEncrypt.setChangeListener(this); add(mRefresh); mRefresh.setChangeListener(this); HorizontalFieldManager hfm = new HorizontalFieldManager(USE_ALL_WIDTH); add(hfm); hfm.add(mLoad); mLoad.setChangeListener(this); hfm.add(mSave); mSave.setChangeListener(this); loadSettings(); } public void fieldChanged(Field field, int context) { if (field == mLoad) { loadSettings(); } else if (field == mSave) { saveSettings(); } } private void saveSettings() { mOptions.setUrl(mUrl.getText()); mOptions.setEncrypt(mEncrypt.getChecked()); mOptions.setRefreshRate(mRefresh.getValue()); } private void loadSettings() { mUrl.setText(mOptions.getUrl()); mEncrypt.setChecked(mOptions.getEncrypt()); mRefresh.setValue(mOptions.getRefreshPeriod()); } }

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