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liblinear-train(1) [debian man page]

LIBLINEAR-TRAIN(1)					      General Commands Manual						LIBLINEAR-TRAIN(1)

NAME
liblinear-train - train a linear classifier and produce a model SYNOPSIS
liblinear-train [options] training_set_file [model_file] DESCRIPTION
liblinear-train trains a linear classifier using liblinear and produces a model suitable for use with liblinear-predict(1). training_set_file is the file containing the data used for training. model_file is the file to which the model will be saved. If model_file is not provided, it defaults to training_set_file.model. To obtain good performances, sometimes one needs to scale the data. This can be done with svm-scale(1). OPTIONS
A summary of options is included below. -s type Set the type of the solver: 0 ... L2-regularized logistic regression 1 ... L2-regularized L2-loss support vector classification (dual) (default) 2 ... L2-regularized L2-loss support vector classification (primal) 3 ... L2-regularized L1-loss support vector classification (dual) 4 ... multi-class support vector classification 5 ... L1-regularized L2-loss support vector classification 6 ... L1-regularized logistic regression 7 ... L2-regularized logistic regression (dual) -c cost Set the parameter C (default: 1) -e epsilon Set the tolerance of the termination criterion For -s 0 and 2: |f'(w)|_2 <= epsilon*min(pos,neg)/l*|f'(w0)_2, where f is the primal function and pos/neg are the number of positive/negative data (default: 0.01) For -s 1, 3, 4 and 7: Dual maximal violation <= epsilon; similar to libsvm (default: 0.1) For -s 5 and 6: |f'(w)|_inf <= epsilon*min(pos,neg)/l*|f'(w0)|_inf, where f is the primal function (default: 0.01) -B bias If bias >= 0, then instance x becomes [x; bias]; if bias < 0, then no bias term is added (default: -1) -wi weight Weight-adjusts the parameter C of class i by the value weight -v n n-fold cross validation mode -q Quiet mode (no outputs). EXAMPLES
Train a linear SVM using L2-loss function: liblinear-train data_file Train a logistic regression model: liblinear-train -s 0 data_file Do five-fold cross-validation using L2-loss SVM, using a smaller stopping tolerance 0.001 instead of the default 0.1 for more accurate solutions: liblinear-train -v 5 -e 0.001 data_file Train four classifiers: positive negative Cp Cn class 1 class 2,3,4 20 10 class 2 class 1,3,4 50 10 class 3 class 1,2,4 20 10 class 4 class 1,2,3 10 10 liblinear-train -c 10 -w1 2 -w2 5 -w3 2 four_class_data_file If there are only two classes, we train ONE model. The C values for the two classes are 10 and 50: liblinear-train -c 10 -w3 1 -w2 5 two_class_data_file Output probability estimates (for logistic regression only) using liblinear-predict(1): liblinear-predict -b 1 test_file data_file.model output_file SEE ALSO
liblinear-predict(1), svm-predict(1), svm-train(1) AUTHORS
liblinear-train was written by the LIBLINEAR authors at National Taiwan university for the LIBLINEAR Project. This manual page was written by Christian Kastner <debian@kvr.at>, for the Debian project (and may be used by others). March 08, 2011 LIBLINEAR-TRAIN(1)

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TIGR-GLIMMER	 (1)   (1)				      General Commands Manual					TIGR-GLIMMER	 (1)   (1)

NAME
tigr-glimmer -- Ceates and outputs an interpolated Markov model(IMM) SYNOPSIS
tigr-build-icm DESCRIPTION
Program build-icm.c creates and outputs an interpolated Markov model (IMM) as described in the paper A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved Microbial Gene Identification with Glimmer. Nucleic Acids Research, 1999, in press. Please refer- ence this paper if you use the system as part of any published research. Input comes from the file named on the command-line. Format should be one string per line. Each line has an ID string followed by white space followed by the sequence itself. The script run-glimmer3 generates an input file in the correct format using the 'extract' program. The IMM is constructed as follows: For a given context, say acgtta, we want to estimate the probability distribution of the next character. We shall do this as a linear combination of the observed probability distributions for this context and all of its suffixes, i.e., cgtta, gtta, tta, ta, a and empty. By observed distributions I mean the counts of the number of occurrences of these strings in the training set. The linear combination is determined by a set of probabilities, lambda, one for each context string. For context acgtta the linear combi- nation coefficients are: lambda (acgtta) (1 - lambda (acgtta)) x lambda (cgtta) (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x lambda (gtta) (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta) (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x (1 - lambda (tta)) x (1 - lambda (ta)) x (1 - lambda (a)) We compute the lambda values for each context as follows: - If the number of observations in the training set is >= the constant SAM- PLE_SIZE_BOUND, the lambda for that context is 1.0 - Otherwise, do a chi-square test on the observations for this context compared to the distribution predicted for the one-character shorter suffix context. If the chi-square significance < 0.5, set the lambda for this context to 0.0 Otherwise set the lambda for this context to: (chi-square significance) x (# observations) / SAMPLE_WEIGHT To run the program: build-icm <train.seq > train.model This will use the training data in train.seq to produce the file train.model, containing your IMM. SEE ALSO
tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly (1), tigr-extract (1), tigr-check (1), tigr-codon-usage (1), tigr- compare-lists (1), tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1), http://www.tigr.org/software/glimmer/ Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR
This manual page was quickly copied from the glimmer web site and readme file by Steffen Moeller moeller@debian.org for the Debian system. TIGR-GLIMMER (1) (1)
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