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| • | riso.addons.* (1) | • | riso.approximation.* (8) | • | riso.apps.* (25) | • | riso.belief_nets.* (13) |
| • | riso.distributions.* (116) | • | riso.general.* (13) | • | riso.numerical.* (22) | • | riso.regression.* (6) |
| • | riso.remote_data.* (5) | • | riso.render.* (3) |
Package Samples:
• riso.distributions
• riso.distributions.computes_lambda_message
• riso.distributions.computes_pi_message
• riso.distributions.computes_pi
• riso.distributions.computes_lambda
• riso.distributions.computes_posterior
• riso.regression
• riso.belief_nets
• riso.remote_data
• riso.apps
• riso.render
• riso.approximation
• riso.addons.dbn
• riso.numerical
• riso.general
Classes:
• TopDownSplayTree: An implementation of top-down splaying D. Sleator http://www.cs.cmu.edu/afs/cs.cmu.edu/user/sleator/www/home.html March 1992 [Java translation of splay(), insert(), and delete() by Robert Dodier, July 1998; max() and min() added by Robert Dodier. Permission to redistribute under GPL given by Danny Sleator to Robert Dodier. Following comments are from the original C code.] "Splay trees", or "self-adjusting search trees" are a simple and efficient data structure for storing an ordered set. The data structure consists of a binary tree, without parent pointers, and no additional fields. It allows searching, ...
• AbstractConditionalDistribution_AbstractDistribution_AbstractDistribution: This class implements a lambda message helper for a variable x with one or more parents u1,...,un . Except for the parent to which we are sending the lambda message, each parent sends a pi message to x . Let us suppose that we are sending the lambda message to parent uk . The lambda message is defined as p( e \ e_u1(above) | uk ) = \int p( x, e \ e_uk(above) | uk ) dx = \int p( x, e_x(below) + e_x(above) \ e_uk(above) | uk ) dx = \int p( e_x(below) | x ) p( x | e_x(above) \ e_uk(above), uk ) p( e_x(above) \ e_uk(above) | uk ) dx = p( e_x(above) \ e_uk(above) ) \int p( e_x(below) | x ) \int ... ...
• LBFGS: This class contains code for the limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm for large-scale multidimensional unconstrained minimization problems. This file is a translation of Fortran code written by Jorge Nocedal. It is distributed as part of the RISO project. Following is a message from Jorge Nocedal: From: Jorge Nocedal [mailto:nocedal@dario.ece.nwu.edu] Sent: Friday, August 17, 2001 9:09 AM To: Robert Dodier Subject: Re: Commercial licensing terms for LBFGS? Robert: The code L-BFGS (for unconstrained problems) is in the public domain. It can be used in any commercial ...
• MainFrame: Run an Applet as an application. This class was written by Jef Poskanzer, and it is redistributed as part of the RISO project under the terms stated in the comments of the source file. Using this class you can add a trivial main program to any Applet and run it directly, as well as from a browser or the appletviewer. And unlike some versions of this concept, MainFrame implements both images and sound. Sample main program: public static void main( String[] args ) { new Acme.MainFrame( new ThisApplet(), args, 400, 400 ); } The only methods you need to know about are the constructors. You can specify ...
• ConditionalGaussian: An instance of this class represents a conditional Gaussian distribution. The dependence enters only through the mean, which is a linear combination the parents plus an offset. The variance is constant. Writing the marginal means of the child and parent variables, respectively, as mu(1) and mu(2) , and the respective marginal variances as Sigma(11) and Sigma(22) , and the covariance as Sigma(12) , then the conditional mean mu(1|2) and conditional variance Sigma(1|2) are as follows. mu(1|2) = mu(1) + Sigma(12) Sigma(22)^{-1} (X(2)-mu(2)) Sigma(1|2) = Sigma(11) - Sigma(12) Sigma(22)^{-1} Sigma(21) ...
• Semaphore: An instance of this class represents a counting semaphore. The file Semaphore.java was written by Stephen Hartley; see http://www.mcs.drexel.edu/~shartley/ConcProgJava/ . This file is released under the terms of the GNU GPL by permission of Stephen Hartley: Date: Sun, 27 Jan 2002 07:47:54 -0500 (EST) From: "Stephen J. Hartley" To: "Robert Dodier" Subject: Re: Permission to redistribute concurrent software? Robert, Yes, you have my permission. Please include a header comment on the files as to their origin. I am glad that my software was able to help you. I'd like to see the program sometime. Can ...
• PlotDistribution: This class implements an applet to display a plot of a density. The applet tag specifies the name of the variable and the belief network which contains it. Here is an example: If the variable and belief network are not specified, nothing is drawn. The variable in question can be discrete, in which case the plot is a bar graph, or continuous, in which case the plot is a line graph. The applet shows a panel on which the plot is drawn. There is also a text box in which the user can enter the name of a variable, like this: host/beliefnetwork-name.variable-name result-type#result-index The result-type ...
• Matrix: Linear algebra computations. All the methods of this class are static and operate on double[][] objects. This works for ordinary matrices; however, it would be nice to (eventually) define special kinds of matrices, e.g. IdentityMatrix or BlockDiagonalMatrix, and have these be interchangeable with ordinary matrices -- but this scheme won't allow that. Objects of types derived from Matrix aren't anything like double[][]. This code ( Matrix.java ) is derived in large part, via translation from C to Java, from gauss_el.c and gauss_so.c from the NUMLIBC web site . The above web site states only "These ...
• ShellSort: This class contains a static method to sort a list of objects using Shell's algorithm. This code is a translation of a C program, shl.txt , by Thomas Niemann, available at http://epaperpress.com/sortsearch . This program is distributed with RISO under the terms of the GPL by permission of Thomas Niemann. In response to my question: > Do I have your permission to redistribute the shell > sort code (which I've translated into Java) under > the GPL? Thomas Niemann wrote: From: "Thomas Niemann" To: "Robert Dodier" Subject: Re: Permission to redistribute shell sort code? Date: Tue, 1 Jan 2002 13:19:24 ...
• SpecialMath: The special function math library. This is copied from JSci version 0.876, and redistributed under GPL by permission of Mark Hale. See the JSci project home page . See also Mark Hale's home page . In response to my question, > Do I have your permission to redistribute the > SpecialMath.java file under the GPL? Mark Hale wrote: Date: Fri, 04 Jan 1980 12:44:25 +0000 From: "Mark" Reply-to: mark.hale@physics.org To: "Robert Dodier" Subject: Re: Permission to redistribute SpecialMath code? Yes, sure. I will probably unbundle xml4j at some stage so I can explicitly include a GPL license with JSci. M ...
• qagse: qagse.java, qags.java, qelg.java, qk21.java, and qpsrt.java are derivative works (translations) of Fortran code by Robert Piessens and Elise de Doncker. These five files are released under GPL by permission of Robert Piessens. In response to my question, >I would like to have your permission to distribute my >Java translation of your QUADPACK routines under the >terms of the GPL. Do I have your permission to do so? Robert Piessens writes: Date: Mon, 28 Jan 2002 14:41:58 +0100 To: "Robert Dodier" From: "Robert Piessens" Subject: Re: Permission to redistribute QUADPACK translation? OK, You have my ...
• qags: qagse.java, qags.java, qelg.java, qk21.java, and qpsrt.java are derivative works (translations) of Fortran code by Robert Piessens and Elise de Doncker. These five files are released under GPL by permission of Robert Piessens. In response to my question, >I would like to have your permission to distribute my >Java translation of your QUADPACK routines under the >terms of the GPL. Do I have your permission to do so? Robert Piessens writes: Date: Mon, 28 Jan 2002 14:41:58 +0100 To: "Robert Dodier" From: "Robert Piessens" Subject: Re: Permission to redistribute QUADPACK translation? OK, You have my ...
• qelg: qagse.java, qags.java, qelg.java, qk21.java, and qpsrt.java are derivative works (translations) of Fortran code by Robert Piessens and Elise de Doncker. These five files are released under GPL by permission of Robert Piessens. In response to my question, >I would like to have your permission to distribute my >Java translation of your QUADPACK routines under the >terms of the GPL. Do I have your permission to do so? Robert Piessens writes: Date: Mon, 28 Jan 2002 14:41:58 +0100 To: "Robert Dodier" From: "Robert Piessens" Subject: Re: Permission to redistribute QUADPACK translation? OK, You have my ...
• qk21: qagse.java, qags.java, qelg.java, qk21.java, and qpsrt.java are derivative works (translations) of Fortran code by Robert Piessens and Elise de Doncker. These five files are released under GPL by permission of Robert Piessens. In response to my question, >I would like to have your permission to distribute my >Java translation of your QUADPACK routines under the >terms of the GPL. Do I have your permission to do so? Robert Piessens writes: Date: Mon, 28 Jan 2002 14:41:58 +0100 To: "Robert Dodier" From: "Robert Piessens" Subject: Re: Permission to redistribute QUADPACK translation? OK, You have my ...
• qpsrt: qagse.java, qags.java, qelg.java, qk21.java, and qpsrt.java are derivative works (translations) of Fortran code by Robert Piessens and Elise de Doncker. These five files are released under GPL by permission of Robert Piessens. In response to my question, >I would like to have your permission to distribute my >Java translation of your QUADPACK routines under the >terms of the GPL. Do I have your permission to do so? Robert Piessens writes: Date: Mon, 28 Jan 2002 14:41:58 +0100 To: "Robert Dodier" From: "Robert Piessens" Subject: Re: Permission to redistribute QUADPACK translation? OK, You have my ...
• ConditionalMixture: An instance of this class represents a conditional mixture model. This is similar to an unconditional mixture (represented by the Mixture class), but the mixing coefficients can vary with the context (i.e., the parent variables). In the Mixture class, mixing coefficients are stored in an array, since they don't change; here, each mixing coefficient is returned by a function that takes the context as an argument. In addition, the mixture components are conditional distributions, not unconditional. This class is declared abstract (i.e., it cannot be instantiated) because there is no generic way to ...
• BorderPanel: A panel that adds a border around the contents. This class was written by Jef Poskanzer, and it is redistributed as part of the RISO project under the terms stated in the comments of the source file. Sample usage: BorderPanel p = new BorderPanel( BorderPanel.IN ); Fetch the software. Fetch the entire Acme package.
• LowDiscrepency: Translated from http://www.netlib.org/toms/659 , an implementation of Sobol's low-discrepency sequence generator, by P Bratley and B L Fox. Described in ACM Trans. on Mathematical Software , vol. 14, no. 1, pp 88--100. Note that this scheme works only in 2 or more dimensions -- it cannot generate a 1-dimensional sequence. This file is distributed under the terms of the ACM Software Copyright and License Agreement. A copy of the license agreement, ACM-LICENSE.html , is included with the RISO distribution.
• DistributionProduct: An instance of this class represents a pointwise product of distributions. Given densities p_1, p_2, p_3,... the density of the product is p_1(x) p_2(x) p_3(x)... . Such products arise in the computation of the likelihood and posterior for a variable, since the posterior is proportional to the pointwise product of the likelihood and the prior, and the likelihood is proportional to the pointwise product of the likelihood messages.
• ComputeDeltaH: An instance of this class is a helper to compute the difference in entropy from first argument of the constructor (some distribution) to the second (some other distribution). Typically the first distribution is a prior distribution and the second is the posterior over the same variable as the prior; the entropy of the first is generally greater than the second, and so the value returned by do_compute_delta_h is generally positive.
• AbstractDistribution: Abstract base class for unconditional distributions. Since Distribution is derived from ConditionalDistribution, any unconditional distribution must implement all of the functions defined for conditional distributions. Some of these have trivial implementations, which are given here. It would be cleaner, perhaps, to put these in the definition of Distribution, but Java doesn't allow code in an interface... . So here they are.
• AbstractConditionalDistribution: Abstract base class for conditional distributions. This class implements only a few methods; most of the methods from the ConditionalDistribution interface are not implemented, and so must be provided by subclasses. This classs is helpful in part because message-passing algorithms can be formulated as generic for all conditional distributions -- handlers are named only by classes, not by interfaces.
• Gaussian: A Gaussian (normal) distribution. The descriptive data which can be changed without causing the interface functions to break down is public. The other data is protected. Included in the public data are the regularization parameters. If not otherwise specified, the prior mean, prior covariance, and other regularization parameters are given neutral values, so that they have no effect on parameter estimation.
• MixGaussians: This class represents an additive mixture of Gaussian densities. There is little added functionality; the main thing is the name guarantees that all mixture components are Gaussian . The descriptive data which can be changed without causing the interface functions to break down is public. The other data is protected. Included in the public data are the regularization parameters.
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