graph-tool January 2020

graph-tool@skewed.de

11 participants
28 discussions

How to control the orientation of the graph topology
by Xun Xiao 26 Feb '22

26 Feb '22

Hi Tiago, sometimes, when delete the graph and create a new one, then plot it, the plotted graph is shown upside down (in terms of the node text). So how could we control the orientation of the graph? Or which parameter we should use to always make node text shown in a correct orientation. Thanks a lot. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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Upside down labels
by charlie 26 Feb '22

26 Feb '22

Hi, I'm suffering from the same issue mentioned in this post: https://git.skewed.de/count0/graph-tool/issues/174 Namely, I'm trying to draw a graph that includes a lot of self-looping edges, and my labels are being printed upside down. If I remove the self-loops the labels are shown the right way up. Is there a fix for it? Thanks, Charlie -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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random graph
by JM 01 Sep '21

01 Sep '21

Dear Tiago, I have a directed graph of about half a million nodes and approximately a million edges following scale free behaviour and a power law degree distribution. To test some of my hypothesis, I would like to generate random smaller graphs (about 50 up to 200 nodes) representative of the big one. When I used a sample function that samples straight away from the real distribution of the big network, I have following problems: - I generate unconnected nodes with both 0 in AND out degree. - I generate small sub parts of a few nodes that are not connected to the main graph. - If only sampling from nodes with at least 1 degree, the generated graph is coherent, but not representative anymore as I need a big portion of nodes with either only one in or one out degree. Here is the part of my script I used for that, where samples are drawn from dictionaries of the degrees: def sample_in(): a=np.random.randint(num) k_in = in_degrees[a] return k_in def sample_out(): if sample_in()==0: b=np.random.randint(num_out) k_out=out_zero_zeros.values()[b] return k_out else: b=np.random.randint(num) k_out=out_degrees[b] return k_out N=200 g=gt.random_graph(N, lambda:(sample_in(), sample_out()), model="constrained-configuration", directed=True) I also tried sampling from a list of tuples as you have mentioned before in the forum, but I didn't receive any results, as the tuples randomly drawn from my list might not be combinable. degs=[(7,1),(4,3),(5,6),(2,4),(6,8),(2,0),(3,5),(0,3),(2,7),(2,1)] g = gt.random_graph(4, lambda i: degs[i], directed=True) - Is there any option I could active that would help me in those cases I described above? - Is there a better way how to create representative small networks? Any help on that issue will be much appreciated. Best wishes, Jana -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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What formula is used for std in vertex_average and edge_average?
by VaSa 16 Jul '20

16 Jul '20

I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average >>> t2=gt.Graph() >>> t2.add_vertex(2) >>> t2.add_edge(t2.vertex(0), t2.vertex(1)) >>> gt.vertex_average(t2, "in") (0.5, 0.35355339059327373) Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ? also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710 0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some relation to that. A little bigger graph. >>> t3=gt.Graph() >>> t3.add_vertex(5) >>> t3.add_edge(t3.vertex(0), t3.vertex(1)) >>> gt.vertex_average(t3, "in") (0.2, 0.17888543819998318) Now, we should have 0,1,0,0,0 series for vertex incoming degree. So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854 come from ? Reason, I am asking because, I have a large graph, where the average looks quite alright but the std makes no sense, as going by the histogram, degree values are quite a bit more distributed than the std would indicate. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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Analysing and visualising
by Ruffle, James 24 Apr '20

24 Apr '20

Dear Graph-Tool Community, I am interested in analysing the hierarchical partitions generated by the nested blockmodel. Specifically, after I have generated a nested SBM; I would then like to post-process this and calculate measures such as eigenvector centrality for a given hierarchical node; save this as a property, and then in visualisation apply either a size or colormap constraint to said node weighted by its centrality. Using the collection data; g = gt.collection.data["celegansneural”] state = gt.minimize_nested_blockmodel_dl(g) I can then ascertain what my levels are with; l1state = state.levels[1].g l2state = state.levels[2].g etc. I can then calculate eigenvector centrality of a given hierarchical partition as follows; ee1, x1 = gt.eigenvector(l1state) ee2, x2 = gt.eigenvector(l2state) 1) This presumably then needs to be saved as a hvprops(?!). But, I am unclear how to do this, not least in a way that I know for sure that the correct hierarchical vertices within l1state and l2state are aligning to the generated centrality measures of x1 and x2, respectively. 2) Furthermore, if/when that is achieved, how can I call upon this in drawing, for example to size the level 1 hierarchical vertices according to centrality, or level 2 vertices by another measure, etc.? Hugely grateful for any solutions! James

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Problem extracting hierarchical blocks
by James Ruffle 23 Mar '20

23 Mar '20

Dear community / Tiago I have a hierarchical partition of a nested block state. The original network contained 4453 vertices and 50051 edges. state.print_summary() l: 0, N: 4453, B: 126 l: 1, N: 126, B: 46 l: 2, N: 46, B: 20 l: 3, N: 20, B: 9 l: 4, N: 9, B: 3 l: 5, N: 3, B: 1 I want to extract the community label of each vertex of each possible hierarchical level. To do this I wrote a loop based upon the guide at https://graph-tool.skewed.de/static/doc/demos/inference/inference.html Where vertexblocksdf is simply a df populated with the vertex numbers 0-4452. for idx in range(len(vertexblocksdf)): r = levels[0].get_blocks()[idx] # group membership of node idx in level 0 vertexblocksdf.ix[idx, 'level0'] = r r = levels[0].get_blocks()[r] # group membership of node idx in level 1 vertexblocksdf.ix[idx, 'level1'] = r r = levels[0].get_blocks()[r] # group membership of node idx in level 2 vertexblocksdf.ix[idx, 'level2'] = r r = levels[0].get_blocks()[r] # group membership of node idx in level 3 vertexblocksdf.ix[idx, 'level3'] = r r = levels[0].get_blocks()[r] # group membership of node idx in level 4 vertexblocksdf.ix[idx, 'level4'] = r r = levels[0].get_blocks()[r] # group membership of node idx in level 5 vertexblocksdf.ix[idx, 'level5'] = r But, I am getting strange results. My level0 column variables make sense, with 126 possibilities (as per l0 above). But my level1 column is a number between 0 and 13; of which none of my levels have 14 blocks. My level2 output is either 0 or 1, again doesn’t make sense! Level3-5 are all simply 0. *this also reproduces the same behaviour if done manually without loop. Any ideas?? James

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assigning vertex properties when adding edges
by m jadidi 04 Mar '20

04 Mar '20

Hi, I was wondering if there is any way to assign vertex properties while adding edges to the graph. for example using "add_edge_list" I can assign edge properties but later I have to iterate through all vertices again to assign their properties. I know this is not a problem when the vertex property is of the type "int" or "float" because then one can use "vprop.a = values", but in case of "string" and "object" this method doesn't work What would be the best/fastest way to handle this situation. I guess it would be very helpful to extend the "add_edge_list" function to accept vertex property in some way. cheers, -- Mohsen

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Installation on MacOS
by lenarpooo 02 Mar '20

02 Mar '20

Dear Tiago, Thanks for building this wonderful package! As a novice in Python I'm struggling to install this package- My operating system is MacOS and I installed graph-tool via Homebrew. It seems the installation was successful. When compiling, the command './configure' doesn't work, could you please give the further instructions? Many thanks, Yingjie -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Installation issue on AWS
by redBlackTree 01 Mar '20

01 Mar '20

Hi all, I wanted to install graph-tool to my AWS sagemaker notebook. I have tried all installers available on anaconda.org, but none worked... Please see one examples below: Example: conda install -n python3 -c ostrokach-forge/label/dev graph-tool Solving environment: failed PackagesNotFoundError: The following packages are not available from current channels: - graph-tool - cairomm - graph-tool - cgal=4.11 - graph-tool - sparsehash Current channels: - https://conda.anaconda.org/ostrokach-forge/label/dev/linux-64 - https://conda.anaconda.org/ostrokach-forge/label/dev/noarch - https://repo.anaconda.com/pkgs/main/linux-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/free/linux-64 - https://repo.anaconda.com/pkgs/free/noarch - https://repo.anaconda.com/pkgs/r/linux-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/pro/linux-64 - https://repo.anaconda.com/pkgs/pro/noarch Which channels do I need to add to solve this issue? Thank you! -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Re: [graph-tool] Speeding up graph copy?
by Zouhair 22 Jan '20

22 Jan '20

> > > How are you doing steps 3.a and 3.e exactly? > > Are you calling g.add_vertex() and g.remove_vertex() repeatedly? > Yes I am. I assumed that's not the best thing but compared to copying the graph, adding then removing the vertices was performing better. I investigated a different approach whereas I allow additional vertices to exist as long as I keep track of the original number of vertices (n_orig): For a set of candidate vertices of size m - if graph size is not large enough, add new vertices - create a graph view that only keeps (n_orig + m) - add edges as needed (this relies on vertex properties) - do graph computation - when done, remove edges (but not vertices) When finished with all candidate sets, remove the extra vertices. Now I am only spending ~25% of the time in resizing the graph (around 20% in remove_edges, despite having set_fast_edge_removal(True)). That's still more than I'd like, but it's an improvement from the 80% I had with adding / removing vertices. If you have other suggestions on how to tackle this that'd be great (for example, I tried without remove_edges, but the edges that get added to the graphview end up showing up in the original graph. Is there a way to avoid that or to filter such that only the original edges are kept in the graphview?) as a minimal working example: ``` import graph_tool.all as gt import numpy as np g = gt.Graph(directed=False) g.add_vertex(10) original_edges = [[0, 1], [0, 4]] g.add_edge_list(original_edges) g.set_fast_edge_removal(True) n_orig = g.num_vertices() def foo(g, m, skipEdgeRemoval = False): n_act = g.num_vertices() n_extra = n_act - (n_orig+m) if n_extra < 0: print(f'adding {-n_extra} vertices ...') g.add_vertex(-n_extra) n_extra = 0 n_act = g.num_vertices() filt = np.ones(n_act) if n_extra > 0: filt[(-n_extra):] = 0 gv = gt.GraphView(g, filt) #print(f'filt = {filt}') new_vtx_ids = np.arange(n, n+m) print(f'indices of new vertices = {new_vtx_ids}') #Check that all edges are expected for e in list(gv.edges()): if [e.source(), e.target()] not in original_edges: raise Exception(f'{e.source()} -> {e.target()} was not in original graph') #Add a bunch of random edges connecting to new candidates edge_list = [] for s, t in zip(np.random.choice(range(n_orig), m), np.random.choice(new_vtx_ids, m)): edge_list.append([s,t]) #also updates some vertex properties, but that's easy/fast to undo, not done in this MWE gv.add_edge_list(edge_list) print('Current edges:') for e in list(gv.edges()): print(f'{e.source()} -> {e.target()}') #computation on new graph goes here ... pass #print('Cleanup ...') #If cleanup is not done, this fails as the edges that were added to the graphview #end up being added to the original graph as well :s if not skipEdgeRemoval: for e in edge_list: gv.remove_edge(gv.edge(e[0], e[1])) foo(g, 1) foo(g, 4) foo(g, 3) foo(g, 5) #above is all good foo(g, 3, True) #skip cleanup foo(g, 4) #fails ``` > Message: 3 > Date: Tue, 21 Jan 2020 15:01:53 +0100 > From: Tiago de Paula Peixoto <tiago(a)skewed.de> > To: Main discussion list for the graph-tool project > <graph-tool(a)skewed.de> > Subject: Re: [graph-tool] Speeding up graph copy? > Message-ID: <1eb5aeab-0a3d-d3fa-84e3-60734afdd360(a)skewed.de> > Content-Type: text/plain; charset="utf-8" > > Am 20.01.20 um 19:43 schrieb Zouhair: > > Hi, > > > > I'm using graph-tool in my project, and my use case is as follows: > > 1) build an undirected graph with vertices and edges (~1e5 vtx and ~5e6 > > edges) > > 2) attach some properties to the vertices > > 3) for about ~5000 sets of *new* candidate vertices (each set has about > > 2-30 vertices) > > ? 3.a - add new vertices to graph > > ? 3.b - add edges as necessary between new vertices and old ones > > ? 3.c - update the properties > > ? 3.d - run an algorithm which depends on properties and edges, save > > result to a list > > ? 3.e - remove new vertices from graph and restore properties (i.e. undo > > 3.a-c) > > > > Steps 1) and 2) are going well. For step 3), the algorithm in step 3.d > > runs fast, 3.b and 3.c are also fast, however, the bottleneck I'm facing > > is 3.a and 3.e (about 80% of runtime is spent there) > > > > iii- use GraphView but only filter on the original vertices in the > > graph: this avoids having to delete the vertices, but making GraphView > > with a filter function is still slow (doing `gt.GraphView(g, lambda v: v > > < n_nodes_orig)` takes 75% of runtime, and the number of vertices in the > > original graph keeps growing... > > This can be improved by passing a boolean-valued vertex property map > instead of a lambda function. In this way the GraphView creation becomes > O(1) instead of O(N). > > Best, > Tiago > > -- > Tiago de Paula Peixoto <tiago(a)skewed.de> > >

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graph-tool January 2020