endif
endif
-HEADERS=$(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/x2x.h $(INC)/exceptions.h
+HEADERS=$(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/exceptions.h
TARGETS=tests utils $(LIB)/libdai$(LE) example$(EE) testregression doc
ifdef WITH_MATLAB
matlabs : matlab/dai.$(ME) matlab/dai_readfg.$(ME) matlab/dai_writefg.$(ME) matlab/dai_potstrength.$(ME)
-$(LIB)/libdai$(LE) : bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)
- ar rcus $(LIB)/libdai$(LE) bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)
+$(LIB)/libdai$(LE) : bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) exceptions$(OE) $(OBJECTS)
+ ar rcus $(LIB)/libdai$(LE) bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) exceptions$(OE) $(OBJECTS)
tests : tests/test$(EE)
alldai$(OE) : $(SRC)/alldai.cpp $(HEADERS)
$(CC) $(CCFLAGS) -c $(SRC)/alldai.cpp
-x2x$(OE) : $(SRC)/x2x.cpp $(HEADERS)
- $(CC) $(CCFLAGS) -c $(SRC)/x2x.cpp
-
# EXAMPLE
##########
!ENDIF\r
!ENDIF\r
\r
-HEADERS=$(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/x2x.h $(INC)/exceptions.h\r
+HEADERS=$(INC)/bipgraph.h $(INC)/diffs.h $(INC)/index.h $(INC)/var.h $(INC)/factor.h $(INC)/varset.h $(INC)/prob.h $(INC)/daialg.h $(INC)/properties.h $(INC)/alldai.h $(INC)/enum.h $(INC)/exceptions.h\r
\r
TARGETS=tests utils $(LIB)/libdai$(LE) example$(EE)\r
# testregression disabled, it uses diff\r
\r
matlabs : matlab/dai.$(ME) matlab/dai_readfg.$(ME) matlab/dai_writefg.$(ME) matlab/dai_potstrength.$(ME)\r
\r
-$(LIB)/libdai$(LE) : bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)\r
- lib /out:$(LIB)/libdai$(LE) bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) x2x$(OE) exceptions$(OE) $(OBJECTS)\r
+$(LIB)/libdai$(LE) : bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) exceptions$(OE) $(OBJECTS)\r
+ lib /out:$(LIB)/libdai$(LE) bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) exceptions$(OE) $(OBJECTS)\r
\r
tests : tests/test$(EE)\r
\r
alldai$(OE) : $(SRC)/alldai.cpp $(HEADERS)\r
$(CC) $(CCFLAGS) -c $(SRC)/alldai.cpp\r
\r
-x2x$(OE) : $(SRC)/x2x.cpp $(HEADERS)\r
- $(CC) $(CCFLAGS) -c $(SRC)/x2x.cpp\r
-\r
\r
# EXAMPLE\r
##########\r
+OPTIMIZATION:
- BipartiteGraph::isConnected should be optimized using boost::graph
-- http://www.boost.org/development/requirements.html#Design_and_Programming
-- Would it be a good idea to cache second-order neighborhoods (delta's) in BipGraph?
-- Would it be a good idea to add the variable label -> index hashmap in FactorGraph,
- to replace the linear searches that are performed every time for findVar()?
- No, a better idea is to avoid calls to findVar() as much as possible.
+- Can the FactorGraph constructors be optimized further?
+- Cache second-order neighborhoods (delta's) in BipGraph?
- Would it be a good idea to remove the states() caching from VarSet?
Then, we could turn a VarSet into an IndexSet (set of integers).
-- Can the FactorGraph constructors be optimized further?
+ This may restrict the use of findVar().
+
- Idea: use a PropertySet as output of a DAIAlg, instead of functions like maxDiff and Iterations().
- A DAIAlg<T> should not inherit from a FactorGraph/RegionGraph, but should store a reference to it
- Add max-product to BP
-- Remove x2x?
-- Remove MR?
TODO FOR RELEASE:
+- http://www.boost.org/development/requirements.html#Design_and_Programming
- Test {Visual C++, cygwin, gcc various version} compatibility; state tested compilers/build environments in README
- Figure out which libraries are required and document in README
boost headers, boost::program_options library, boost::graph library,
boost::math library (under Windows)
- Change email address
-FILES IN SVN HEAD THAT ARE NO LONGER RELEVANT FOR GIT MASTER:
-diffs.h
-index.h
-util.h
-util.cpp
-bipgraph.h
-weightedgraph.h
-weightedgraph.cpp
-clustergraph.h
-clustergraph.cpp
-varset.h
-var.h
-utils/createfg.cpp
-exceptions.h
-exceptions.cpp
-enum.h
-doxygen.conf
-example.cpp
-FILEFORMAT
-Makefile
-exact.h
-exact.cpp
-alldai.h
-alldai.cpp
-properties.h
-properties.cpp
-factor.h
-prob.h
-factorgraph.h
-factorgraph.cpp
-regiongraph.h
-regiongraph.cpp
-daialg.h
-daialg.cpp
-matlab/
- dai.cpp
- dai.m
- dai_potstrength.cpp
- dai_potstrength.m
- dai_readfg.cpp
- dai_readfg.m
- dai_writefg.cpp
- dai_writefg.m
- matlab.cpp
- matlab.h
-utils/
- fg2dot.cpp
- fginfo.cpp
- createfg.cpp
- viewfg
-tests/
- alarm.fg
- hoi1.fg
- hoi2.fg
- hoi3.fg
- hoi4.fg
- testfast.fg
- aliases.conf
- testall
- testregression
- test.cpp
-mf.h
-mf.cpp
-bp.h
-bp.cpp
-jtree.h
-jtree.cpp
-hak.h
-hak.cpp
-lc.h
-lc.cpp
-treeep.h
-treeep.cpp
-mr.h
-mr.cpp
-TODO
-ChangeLog
-README
-
FILES IN SVN HEAD RELEVANT FOR A LATER RELEASE:
matlab/dai_potstrength.*
matlab/dai_bpconvbound.*
+++ /dev/null
-/* Copyright (C) 2006-2008 Joris Mooij [j dot mooij at science dot ru dot nl]
- Radboud University Nijmegen, The Netherlands
-
- This file is part of libDAI.
-
- libDAI is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- libDAI is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with libDAI; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-*/
-
-
-#ifndef __defined_libdai_x2x_h
-#define __defined_libdai_x2x_h
-
-
-#include <cmath>
-#include <cstring>
-
-
-namespace x2x {
-
- // Probability tables store -1 first, then +1
-
- /// Convert moments to cumulants upto order k
- void m2c (int N, double *x, int k);
-
- /// Convert cumulants to moments upto order k
- void c2m (int N, double *x, int k);
-
- /// Convert (generalized) weights to log probability or energy
- void w2logp (int N, double *x);
-
- /// Convert log probability or energy to (generalized) weights
- void logp2w (int N, double *x);
-
- /// Convert probability to moments
- void p2m (int N, double *x);
-
- /// Convert moments to probability
- void m2p (int N, double *x);
-
- /// Convert log probability to probability
- void logp2p (int N, double *x);
-
- /// Convert probability to log probability
- void p2logp (int N, double *x);
-
- /// Normalize a log probability table
- void logpnorm (int N, double *x);
-
- /// Normalize a probability table, use logpnorm whenever possible
- void pnorm (int N, double *x);
-
- /// Fills table with v for all entries with more than k indices
- /// used for example when cumulants or moments are converted upto some order
- void fill (int N, double *x, int k, double v);
-
-} // end of namespace x2x
-
-
-#endif
+++ /dev/null
-/*
-Copyright (C) 2005 Martijn Leisink m.leisink at science.ru.nl
-
-This program is free software; you can redistribute it and/or
-modify it under the terms of the GNU General Public License
-as published by the Free Software Foundation; either version 2
-of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-CHANGES:
- 2006-11-20 Joris Mooij
- * removed MATLAB interface
- * put into namespace "x2x"
-*/
-
-
-#include <cmath>
-#include <cstring>
-#include <dai/util.h>
-
-
-namespace x2x {
-
- // helper functions to compute the sum over all partitions
- double psum (double *x, long s, int n=0);
- double psumx (double *x, long a, long s, int n) {
- // recursively process all one bits remaining after psum
- // put some of them into the same subset and call psum again for the rest
- if((s>>n)>1) {
- while(!((s>>++n)&1))
- {};
- return(psumx(x,a,s,n)+psumx(x,a^(1l<<n),s,n));
- } else {
- return(x[a]*psum(x,s^a,0));
- };
- }
- double psum (double *x, long s, int n) {
- // take the first one bit and put it in the first subset, then call psumx
- if(s>>n) {
- while(!((s>>n)&1)) ++n;
- return(psumx(x,1l<<n,s,n));
- } else return(1);
- }
-
- // convert moments to cumulants upto order k
- void m2c (int N, double *x, int k) {
- int *c=new int[k+1];
- long s;
- int z;
- x[0]=log(x[0]); // to get the correct answer if not normalized
- for(int b=1;b<=k;++b) {
- // start with marginals, then two-point correlations and so on
- c[z=b]=-1;
- s=0; // index into x
- do {
- while(--z>=0) s^=(1l<<(c[z]=c[z+1]+1));
- // c_ijk = m_ijk - c_i*c_jk - c_j*c_ik - c_k*c_ij - c_i*c_j*c_k
- x[s]=2*x[s]-psum(x,s);
- // increment b indices
- for(z=0;z<b&&(s^=3l<<c[z],++c[z]==N-z);++z) s^=1l<<c[z];
- } while(z<b);
- };
- delete[] c;
- }
-
- // convert cumulants to moments upto order k
- void c2m (int N, double *x, int k) {
- int *c=new int[k+1];
- long s;
- int z;
- for(int b=k;b>=1;--b) {
- // start with k-point cumulants, then k-1-point cumulants and so on
- c[z=b]=-1;
- s=0; // index into x
- do {
- while(--z>=0) s^=(1l<<(c[z]=c[z+1]+1));
- // m_ijk = c_ijk + c_i*c_jk + c_j*c_ik + c_k*c_ij + c_i*c_j*c_k
- x[s]=psum(x,s);
- // increment b indices
- for(z=0;z<b&&(s^=3l<<c[z],++c[z]==N-z);++z) s^=1l<<c[z];
- } while(z<b);
- };
- x[0]=exp(x[0]); // to get the correct answer if not normalized
- delete[] c;
- }
-
- // convert (generalized) weights to log probability or energy
- void w2logp (int N, double *x) {
- for(long s=1l<<N;s>>=1;) for(long j=1l<<N;(j-=(s<<1))>=0;)
- for(long k=j+s;--k>=j;) { x[k+s]+=x[k]; x[k]=2*x[k]-x[k+s]; };
- }
-
- // convert log probability or energy to (generalized) weights
- void logp2w (int N, double *x) {
- for(long s=1l<<N;s>>=1;) for(long j=1l<<N;(j-=(s<<1))>=0;)
- for(long k=j+s;--k>=j;) { x[k]=(x[k]+x[k+s])/2; x[k+s]-=x[k]; };
- }
-
- // convert probability to moments
- void p2m (int N, double *x) {
- for(long s=1l<<N;s>>=1;) for(long j=1l<<N;(j-=(s<<1))>=0;)
- for(long k=j+s;--k>=j;) { x[k+s]-=x[k]; x[k]=2*x[k]+x[k+s]; };
- }
-
- // convert moments to probability
- void m2p (int N, double *x) {
- for(long s=1l<<N;s>>=1;) for(long j=1l<<N;(j-=(s<<1))>=0;)
- for(long k=j+s;--k>=j;) { x[k]=(x[k]-x[k+s])/2; x[k+s]+=x[k]; };
- }
-
- // convert log probability to probability
- void logp2p (int N, double *x) {
- for(long s=1l<<N;s--;) x[s]=exp(x[s]);
- }
-
- // convert probability to log probability
- void p2logp (int N, double *x) {
- for(long s=1l<<N;s--;) x[s]=log(x[s]);
- }
-
- // normalize a log probability table
- void logpnorm (int N, double *x) {
- double f=x[0];
- for(long s=1l<<N;--s;)
- if(f>x[s]) f+=log1p(exp(x[s]-f));
- else f=x[s]+log1p(exp(f-x[s]));
- for(long s=1l<<N;s--;) x[s]-=f;
- }
-
- // normalize a probability table, use logpnorm whenever possible
- void pnorm (int N, double *x) {
- double z=0;
- for(long s=1l<<N;s--;) z+=x[s];
- for(long s=1l<<N;s--;) x[s]/=z;
- }
-
- // fills table with v for all entries with more than k indices
- // used for example when cumulants or moments are converted upto some order
- void fill (int N, double *x, int k, double v) {
- if(k>N) return;
- long ss=0,s;
- int n=0;
- for(long i=1l<<N;i--;) { // make use of gray code to count number of bits
- if(n>k) x[ss]=v;
- s=i^(i>>1);
- if(s>ss) ++n; else --n;
- ss=s;
- };
- }
-
-} // end of namespace x2x
projects / libdai.git / commitdiff