graph-tool April 2021

graph-tool@skewed.de

8 participants
16 discussions

Layered block state with edge weights and/or different set of nodes across layers
by Malkamäki, Arttu J 20 Apr '21

20 Apr '21

Dear GT Community, I've been working on community detection for some time already (Louvain/Leiden algorithms), but I got started with graph-tool only recently. After spending some time reading the HOWTO, I still haven't found answers to two questions that are related to the applicability of SBM to my data. I'm analysing political coalitions by combining data from a survey, newspapers, and Twitter. To study coalitions across the three undirected and weighted networks (or more if I include temporal slices), I am using LayeredBlockState via NestedBlockState and sampling from the posterior distribution. Question 1: I haven't found an answer to whether it is possible to run SBM for layered networks with edge weights? I can get around this problem by extracting the noise-corrected 'backbone' of each network, which yields simple graphs, but ideally I wouldn't have to do too much violence to the data but be able to use the raw weighted networks as inputs. Is it possible to run LayeredBlockState with edge weights? Question 2: Even if the LayeredBlockState would not (yet) support weighted networks, I also have another, more fundamental question. As my three layers come from different data generation processes, they do not share the exact same set of nodes. For example, one organisation responded the survey but does not necessarily appear in the newspaper data. Is it possible to determine constraints for certain nodes in certain layers that would tell the LayeredBlockState to not consider layer-specific isolates? This is how I currently set up the LayeredBlockState, but I'm not sure if I can count on the results due to the potential issue outlined in Q2. g = binary multigraph with three layers stored in ep.layer state = gt.inference.nested_blockmodel.NestedBlockState(g, base_type=LayeredBlockState, state_args=dict(ec=g.ep.layer, layers=True)) All help is much appreciated, Arttu Malkamäki ----- Arttu Malkamäki, PhD Postdoctoral researcher Faculty of Social Sciences Helsinki Institute of Sustainability Science Unioninkatu 35, University of Helsinki Email: arttu.malkamaki(a)helsinki.fi Phone: +358503361645 Twitter<https://twitter.com/ArttuMalkamaki> ResearchGate<https://www.researchgate.net/profile/Arttu_Malkamaeki> GoogleScholar<https://scholar.google.fi/citations?user=75YLHGMAAAAJ&hl=fi>

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get_hierarchy_control_points return values
by Davide Cittaro 20 Apr '21

20 Apr '21

Hi again, I'm writing a small package that builds on graph-tool, but not on its graphics capabilities (also because I have to represent other things rather than the graph itself). Still I could use some of the functions "under the hood" for my purposes. I have a question about gt.draw.get_hierarchy_control_points(): the function returns the Bézier spline control points for edges in a given graph, but I'm having difficulties in understanding how this information is encoded. For a single edge in graph, I have dozens of values as control points (half dozens + 2), hence I suspect all splines going from node A to the root of a hierarchy and back to node B are encoded there, and control points should be taken 6 by 6 (3x2 by 3x2 coordinates?). How (x,y) for control points are encoded then: (x, x, x, y, y, y) or (x, y, x, y, x, y)? What are the 2 additiona values I have for each vector? Also, are values absolute or relative to one node in particular (A, B or root...)? Thanks d

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Re: Question about entropy
by Lietz, Haiko 19 Apr '21

19 Apr '21

> I am going to compare NestedBlockState.entropy() of the two run, but I am not sure this is correct. > How should I take into account the fact that the networks are slightly different? Would normalization make the two entropies comparable? I'd be interested to hear opinions about using, for normalization, the entropy of a NestedBlockState where each node is in its own group. Best Haiko

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Weird error when interfaced with joblib
by Davide Cittaro 14 Apr '21

14 Apr '21

Hi all, I'm using graph-tool a lot and I usually perform multiple random initializations only to choose, in the end, the solution with lowest entropy. As each init is a separate and independent process, I was thinking to use joblib to parallelize the process. However I noticed something weird. Here we go: >>> from joblib import delayed, Parallel >>> import graph_tool.all as gt # choose a graph >>> g = gt.collection.data['football'] # set some variables, as the number of inits >>> n_init = 3 >>> fast_tol = 1e-3 >>> beta = 1000 >>> n_sweep = 10 # define a function for sweep, this is essentially what is found in official docs >>> def fast_min(state, beta, n_sweep, fast_tol): >>> dS = 1 >>> while np.abs(dS) > fast_tol: >>> dS, _, _ = state.multiflip_mcmc_sweep(beta=beta, niter=n_sweep) >>> return state # test with standard python list comprehension, this works >>> pstates = [gt.PPBlockState(g) for x in range(n_init)] >>> pstates = [fast_min(state, beta, n_sweep, fast_tol) for state in pstates] >>> selected = pstates[np.argmin([x.entropy() for x in pstates])] >>> print(gt.modularity(g, selected.get_blocks())) 0.5986403881107808 # test with 'threading' backend in joblib >>> pstates = [gt.PPBlockState(g) for x in range(n_init)] >>> pstates = Parallel(n_jobs=3, prefer='threads')(delayed(fast_min)(state, beta, n_sweep, fast_tol) for state in pstates) >>> selected = pstates[np.argmin([x.entropy() for x in pstates])] >>> print(gt.modularity(g, selected.get_blocks())) 0.5926606505592532 # test with default backend in joblib >>> pstates = [gt.PPBlockState(g) for x in range(n_init)] >>> pstates = Parallel(n_jobs=3)(delayed(fast_min)(state, beta, n_sweep, fast_tol) for state in pstates) >>> selected = pstates[np.argmin([x.entropy() for x in pstates])] >>> print(gt.modularity(g, selected.get_blocks())) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-8-733a38606e1a> in <module> 3 4 selected = pstates[np.argmin([x.entropy() for x in pstates])] ----> 5 print(gt.modularity(g, selected.get_blocks())) ~/anaconda3/envs/experimental/lib/python3.8/site-packages/graph_tool/inference/modularity.py in modularity(g, b, gamma, weight) 84 Q = libinference.modularity(g._Graph__graph, gamma, 85 _prop("e", g, weight), ---> 86 _prop("v", g, b)) 87 return Q 88 ~/anaconda3/envs/experimental/lib/python3.8/site-packages/graph_tool/__init__.py in _prop(t, g, prop) 177 raise ValueError("Received orphaned property map") 178 if g.base is not u.base: --> 179 raise ValueError("Received property map for graph %s (base: %s), expected: %s (base: %s)" % 180 (str(g), str(g.base), str(u), str(u.base))) 181 return pmap._get_any() ValueError: Received property map for graph <Graph object, undirected, with 115 vertices and 613 edges, 4 internal vertex properties, 2 internal graph properties, at 0x7fd7032982e0> (base: <Graph object, undirected, with 115 vertices and 613 edges, 4 internal vertex properties, 2 internal graph properties, at 0x7fd7032982e0>), expected: <GraphView object, undirected, with 115 vertices and 613 edges, 4 internal vertex properties, 2 internal graph properties, at 0x7fd707c650d0> (base: <Graph object, undirected, with 115 vertices and 613 edges, 4 internal vertex properties, 2 internal graph properties, at 0x7fd7067e3700>) I cannot figure out why I get this error, as the g.base and selected.g.state are the same. I understand this is not directly a graph-tool issue, rather a joblib one, still I'd like to understand why I'm getting this error Thanks d

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Description length of consensus partition
by Lietz, Haiko 10 Apr '21

10 Apr '21

Dear Tiago, all, I'm happy to have discovered the new partition overlap functionality. It works very nicely. But is it possible to obtain the description length of a nested consensus state? Getting the description length of the consensus state works fine for an unnested model: from graph_tool.all import * h = collection.data['polbooks'] num_models = 2 states = [minimize_blockmodel_dl(h) for i in range(num_models)] bs = [states[i].get_blocks().a for i in range(num_models)] c, r = partition_overlap_center(bs) h_blocks = h.new_vp('int') h_blocks.a = c BlockState(h, h_blocks).entropy() For nested partitions, getting the consensus state is a bit more complicated: states_nested = [minimize_nested_blockmodel_dl(h) for i in range(num_models)] bs_nested = [] for j in range(num_models): l = [] for k in range(len(states_nested[j].get_levels())): l.append(states_nested[j].get_bstack()[k].vp.b.a) bs_nested.append(l) c_nested, r_nested = nested_partition_overlap_center(bs_nested) But how can I get its description length? Many thanks for your attention Haiko GESIS, Cologne

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numpy not found when run ./configure
by Kasper 08 Apr '21

08 Apr '21

when I run ./configure this is the output I get: checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... (cached) yes checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... gcc3 checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking whether g++ supports C++17 features by default... no checking whether g++ supports C++17 features with -std=gnu++17... yes configure: WARNING: C++17 is not yet standardized, so the checks may change in incompatible ways anytime checking whether to enable debug info... no checking whether to enable parallel algorithms with openmp... checking for OpenMP flag of C++ compiler... -fopenmp checking whether to enable cairo drawing... yes checking for EXPAT... yes checking for a Python interpreter with version >= 2.7... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for python2.7... (cached) /usr/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.17'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/dist-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for boostlib >= 1.55.0 (105500)... yes checking whether the Boost::Python library is available... yes checking whether boost_python27 is the correct library... no checking whether boost_python-py27 is the correct library... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking whether the Boost::Context library is available... yes checking for exit in -lboost_context... yes checking whether the Boost::Coroutine library is available... yes checking for exit in -lboost_coroutine... yes checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... yes checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes checking for __gmpz_init in -lgmp... yes checking for __gmpz_init in -lgmp... (cached) yes checking whether CGAL is available in /usr... yes checking whether to enable debbuging with valgrind... no checking python module: numpy... no configure: error: failed to find required module numpy I have numpy istalled in the right place (Ibelieve) To check this I've run : pip install numpy and got: numpy in /home/kaspersegers/.local/lib/python3.6/site-packages (1.17.3) What can I do to remedy this? -- Sent from: https://nabble.skewed.de/

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graph-tool April 2021