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--- assignments:assignment3 [2013/10/06 11:54]
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+++ assignments:assignment3 [2015/10/02 09:48]
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 ========= Assignment 3: Support Vector Machines ============
+Due:  October 20th at 6pm
 ===== Part 1:  SVM with no bias term =====
-Formulate a soft-margin SVM without the bias term, i.e. $f(\mathbf{x}) = \mathbf{w}^{T} \mathbf{x}$.
+Formulate a soft-margin SVM without the bias term, i.e. one where the discriminant function is equal to $\mathbf{w}^{T} \mathbf{x}$.
 Derive the saddle point conditions, KKT conditions and the dual.
 Compare it to the standard SVM formulation.
-What is the implication of the difference on the design of SMO-like algorithms?
+As we discussed in class, SMO-type algorithms for the dual optimize the smallest number of variables at a time, which is two variables.
-Recall that SMO algorithms work by iteratively optimizing two variables at a time.
+Is this still the case for the formulation you have derived?
 Hint:  consider the difference in the constraints.
-===== Part 2:  Closest Centroid Algorithm =====
+===== Part 2:  Soft-margin SVM for separable data =====
-Express the closest centroid algorithm in terms of kernels, i.e. determine how the coefficients $\alpha_i$ will be determined using a given labeled dataset.
+Consider training a soft-margin SVM
+with the soft margin constant $C$ set to some positive constant. Suppose the training data is linearly separable.
+Since increasing the $\xi_i$ can only increase the objective of the primal problem (which
+we are trying to minimize), at the optimal solution to the primal problem, all the
+training examples will have $\xi_i$ equal
+to zero. True or false?  Explain!
+Given a linearly separable dataset, is it necessarily better to use a
+a hard margin SVM over a soft-margin SVM?  Explain!
 ===== Part 3:  Using SVMs =====
@@ Line 22: / Line 31: @@
 problem
 of distinguishing a particular class of proteins from a selection of
-examples sampled from the rest of the SCOP database.
+examples sampled from the rest of the SCOP database
+using features derived from their sequence (note that a protein is an arbitrary length sequence over the alphabet of the 20 amino acids).
 I chose to represent the proteins in
 terms of their motif composition.  A sequence motif is a
-pattern of nucleotides/amino acids that is conserved in evolution.
+pattern of amino acids that is conserved in evolution.
 Motifs are usually associated with regions of the protein that are
 important for its function, and are therefore useful in differentiating between classes of proteins.
@@ Line 36: / Line 46: @@
   * A. Ben-Hur and D. Brutlag. [[http://bioinformatics.oxfordjournals.org/content/19/suppl_1/i26.abstract | Remote homology detection: a motif based approach]]. In: Proceedings, eleventh international conference on intelligent systems for molecular biology. Bioinformatics 19(Suppl. 1): i26-i33, 2003.
-Download the dataset associated with this assignment from the homework
+In this part of the assignment we will explore the dependence of classifier accuracy on
-page of the course.
+the kernel, kernel parameters, kernel normalization, and the SVM soft-margin parameter.
-In this assignment we will explore the dependence of classifier accuracy on
+In your implementation you can use the scikit-learn [[http://scikit-learn.org/stable/modules/generated/sklearn.svm.SVC.html | svm]] class.
-the kernel, kernel parameters, kernel normalization, and SVM parameter.
-The use of the SVM class is discussed in the PyML [[http://pyml.sourceforge.net/tutorial.html#svms|tutorial]].
-By default a dataset is instantiated with a linear kernel attached to it.
-To use a different kernel you need to attach a new kernel to the dataset:
-<code python>
->>> from PyML import ker
->>> data.attachKernel(ker.Gaussian(gamma = 0.1))
-</code>
-or
-<code python>
->>> from PyML import her
->>> data.attachKernel(ker.Polynomial(degree = 3))
-</code>
 In this question we will consider both the Gaussian and polynomial kernels:
 $$
-K_{gaus}(\mathbf{x}, \mathbf{x'}) = \exp(-\gamma || \mathbf{x} - \mathbf{x}' ||^2)
+K_{gauss}(\mathbf{x}, \mathbf{x'}) = \exp(-\gamma || \mathbf{x} - \mathbf{x}' ||^2)
 $$
 $$
-K_{poly}(\mathbf{x}, \mathbf{x'}) = (1 + \mathbf{x}^T \mathbf{x}') ^{p}
+K_{poly}(\mathbf{x}, \mathbf{x'}) = (\mathbf{x}^T \mathbf{x}' + 1) ^{p}
 $$
-Plot the accuracy of the classifier, measured using the success rate and the area under the ROC curve
-as a function of both the ridge parameter of the classifier, and the free parameter
+Plot the accuracy of the SVM, measured using the area under the ROC curve
+as a function of both the soft-margin parameter of the SVM, and the free parameter
 of the kernel function.
+Accuracy should be measured in five-fold cross-validation.
 Show a couple of representative cross sections of this plot for a given value
-of the ridge parameter, and for a given value of the kernel parameter.
+of the soft margin parameter, and for a given value of the kernel parameter.
 Comment on the results.  When exploring the values of a continuous
 classifier/kernel parameter it is
-useful use values that are distributed on an exponential grid,
+useful to use values that are distributed on an exponential grid,
 i.e. something like 0.01, 0.1, 1, 10, 100 (note that the degree of the
 polynomial kernel is not such a parameter).
+Next, we will compare the accuracy of an SVM with a Gaussian kernel on the raw data with accuracy obtained when the data is normalized to be unit vectors (the values of the features of each example are divided by its norm).
+This is different than standardization which operates at the level of individual features.  Normalizing to unit vectors is more appropriate for this dataset as it is sparse, i.e. most of the features are zero.
+Perform your comparison by comparing the accuracy measured by the area under the ROC curve in five-fold cross validation.
+The optimal values of kernel parameters should be measured by cross-validation, where the optimal SVM/kernel parameters are chosen using grid search on the training set of each fold.
+Use the scikit-learn [[http://scikit-learn.org/stable/tutorial/statistical_inference/model_selection.html
+ | grid-search]] class for model selection.
-For this type of sparse dataset it is useful to normalize the input features before
-training and testing your classifier.
-One way to do so is to divide each input example by its norm.  This is
-accomplished in PyML by:
-<code python>
->>> data.normalize()
-</code>
-Compare the results under this normalization with what you obtain
-without normalization.
-You can visualize the whole kernel matrix associated with the data using the following commands:
+Finally, visualize the kernel matrix associated with the dataset.
-<code python>
->>> from PyML import ker
->>> ker.showKernel(data)
-</code>
 Explain the structure that you are seeing in the plot (it is more
 interesting when the data is normalized).
+===== Submission =====
+Submit your report via Canvas.  Python code can be displayed in your report if it is succinct (not more than a page or two at the most) or submitted separately.  The latex sample document shows how to display Python code in a latex document.  Code needs to be there so we can make sure that you implemented the algorithms and data analysis methodology correctly.  Canvas allows you to submit multiple files for an assignment, so DO NOT submit an archive file (tar, zip, etc).
+===== Grading =====
+A few general guidelines for this and future assignments in the course:
+  * Always provide a description of the method you used to produce a given result in sufficient detail such that the reader can reproduce your results on the basis of the description (UNLESS the method has been provided in class or is there in the book).  Your code needs to be provided in sufficient detail so we can make sure that your implementation is correct.  The saying that "the devil is in the details" holds true for machine learning, and is sometimes the makes the difference between correct and incorrect results.  If your code is more than a few lines, you can include it as an appendix to your report, or submit it as a separate file.  Make sure your code is readable!
+  * You can provide results in the form of tables, figures or text - whatever form is most appropriate for a given problem.
+  * In any machine learning paper there is a discussion of the results.  There is a similar expectation from your assignments that you reason about your results.  For example, for the learning curve problem, what can you say on the basis of the observed learning curve?
+  * Write succinct answers.  We will take off points for rambling answers that are not to the point, and and similarly, if we have to wade through a lot of data/results that are not to the point.
+<code>
+Grading sheet for assignment 2
+Part 1:  45 points.
+(10 points):  Primal SVM formulation is correct
+(10 points):  Lagrangian found correctly
+(10 points):  Derivation of saddle point equations
+(10 points):  Derivation of the dual
+( 5 points):  Discussion of the implication of the form of the dual for SMO-like algorithms
+Part 2:  15 points.
+Part 3:  40 points.
+(20 points):  Accuracy as a function of parameters and discussion of the results
+(15 points):  Comparison of normalized and non-normalized kernels and correct model selection
+( 5 points):  Visualization of the kernel matrix and observations made about it
+Report structure, grammar and spelling:  10 points
+(10 points):  Heading and subheading structure easy to follow and clearly divides report into logical sections.
+              Code, math, figure captions, and all other aspects of the report are well-written and formatted.
+              Grammar, spelling, and punctuation.
+</code>

CS545 fall 2016

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