GNN | Graph neural networks | Machine Learning library

 by   john-bradshaw Python Version: Current License: GPL-3.0

kandi X-RAY | GNN Summary

kandi X-RAY | GNN Summary

GNN is a Python library typically used in Artificial Intelligence, Machine Learning, Deep Learning, Pytorch applications. GNN has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However GNN build file is not available. You can download it from GitHub.

Playground for me to explore different patterns of doing Gated Graph Neural Networks (Li et al., 2015; Gilmer et al., 2017). So far the code in this library is mostly just an incomplete PyTorch port of some of the methods in We are only interested in running these networks on small graphs (eg representing organic chemical molecules), for which we expect to be able to fit multiple graphs in each minibatch. If you're looking for a full featured GNN libary in PyTorch you may want to check out PyTorch Gometric.
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            kandi-support Support

              GNN has a low active ecosystem.
              It has 8 star(s) with 2 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              GNN has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of GNN is current.

            kandi-Quality Quality

              GNN has no bugs reported.

            kandi-Security Security

              GNN has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              GNN is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              GNN releases are not available. You will need to build from source code and install.
              GNN has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are available. Examples and code snippets are not available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed GNN and discovered the below as its top functions. This is intended to give you an instant insight into GNN implemented functionality, and help decide if they suit your requirements.
            • Run the experiment
            • Validate and evaluate the model
            • Update the statistics
            • Train the model
            • Collate graph
            • Convert from NumPy to torch
            • Map all properties to the graph
            • Convert graph to graph
            • Return a tuple of edge names and projection
            • Convert a numpy array to a numpy array
            • Returns a torch Tensor object
            • Split data into two graphs
            • Map a function to inplace
            • Pad variable with padding
            • Concatenate a tensor
            • Pad a variable with padding
            • Bincount function
            Get all kandi verified functions for this library.

            GNN Key Features

            No Key Features are available at this moment for GNN.

            GNN Examples and Code Snippets

            No Code Snippets are available at this moment for GNN.

            Community Discussions

            QUESTION

            How to implement Flatten layer with batch size > 1 in Pytorch (Pytorch_Geometric)
            Asked 2021-May-11 at 14:39

            I am new to Pytorch and am trying to transfer my previous code from Tensorflow to Pytorch due to memory issues. However, when trying to reproduce Flatten layer, some issues kept coming out.

            In my DataLoader object, batch_size is mixed with the first dimension of input (in my GNN, the input unpacked from DataLoader object is of size [batch_size*node_num, attribute_num], e.g. [4*896, 32] after the GCNConv layers). Basically, if I implement torch.flatten() after GCNConv, samples are mixed together (to [4*896*32]) and there would be only 1 output from this network, while I expect #batch_size outputs. And if I use nn.Flatten() instead, nothing seems to happen (still [4*896, 32]). Should I set batch_size as the first dim of the input at the very beginning, or should I directly use view() function? I tried directly using view() and it (seemed to have) worked, although I am not sure if this is the same as Flatten. Please refer to my code below. I am currently using global_max_pool because it works (it can separate batch_size directly).

            By the way, I am not sure why training is so slow in Pytorch... When node_num is raised to 13000, I need an hour to go through an epoch, and I have 100 epoch per test fold and 10 test folds. In tensorflow the whole training process only takes several hours. Same network architecture and raw input data, as shown here in another post of mine, which also described the memory issues I met when using TF.

            Have been quite frustrated for a while. I checked this and this post, but it seems their problems somewhat differ from mine. Would greatly appreciate any help!

            Code:

            ...

            ANSWER

            Answered 2021-May-11 at 14:39

            The way you want the shape to be batch_size*node_num, attribute_num is kinda weird.

            Usually it should be batch_size, node_num*attribute_num as you need to match the input to the output. And Flatten in Pytorch does exactly that.

            If what you want is really batch_size*node_num, attribute_num then you left with only reshaping the tensor using view or reshape. And actually Flatten itself just calls .reshape.

            tensor.view: This will reshape the existing tensor to a new shape, if you edit this new tensor the old one will change too.

            tensor.reshape: This will create a new tensor using the data from old tensor but with new shape.

            Source https://stackoverflow.com/questions/67469355

            QUESTION

            Annotated bubble chart from a dataframe
            Asked 2021-Apr-08 at 10:09

            I have the following data frame

            ...

            ANSWER

            Answered 2021-Apr-08 at 10:09

            The marker size s of scatter is set in units of points. So, if your markers are too small, scale the argument you are passing to s.

            Here is an example:

            Source https://stackoverflow.com/questions/67000823

            QUESTION

            Stack bar-chart intersected between each other
            Asked 2021-Mar-12 at 18:50

            I have the following code for the stack bar chart

            ...

            ANSWER

            Answered 2021-Mar-12 at 18:50

            The specific problem is that b_AE is calculated wrong. (Also, there is a list called count_AM for which there is no label).

            The more general problem, is that calculating all these values "by hand" is very prone to errors and difficult to adapt when there are changes. It helps to write things in a loop.

            The magic of numpy's broadcasting and vectorization lets you initialize bottom as a single zero, and then use numpy's adding to add the counts.

            To have a bit neater x-axis, you can put the individual words on separate lines. Also, plt.tight_layout() tries to make sure all text fits nicely into the plot.

            Source https://stackoverflow.com/questions/66600017

            QUESTION

            Using self in init part of a class in Python
            Asked 2021-Feb-06 at 13:48

            Is there any difference between the following two codes related to initializing a class in Python?

            ...

            ANSWER

            Answered 2021-Feb-02 at 18:45

            No. there is no difference between these two approaches in your case with this level of information. but could they? Yes. they could. if they have some modifications in their setters or getters. later in my answer I'll show you how.

            First of all, I prefer using this one:

            Source https://stackoverflow.com/questions/66012667

            QUESTION

            How to implement randomised log space search of learning rate in PyTorch?
            Asked 2021-Feb-05 at 05:27

            I am looking to fine tune a GNN and my supervisor suggested exploring different learning rates. I came across this tutorial video where he mentions that a randomised log space search of hyper parameters is typically done in practice. For sake of the introductory tutorial this was not covered.

            Any help or pointers on how to achieve this in PyTorch is greatly appreciated. Thank you!

            ...

            ANSWER

            Answered 2021-Feb-05 at 05:27

            Setting the scale in logarithm terms let you take into account more desirable values of the learning rate, usually values lower than 0.1

            Imagine you want to take learning rate values between 0.1 (1e-1) and 0.001 (1e-4). Then you can set this lower and upper bound on a logarithm scale by applying a logarithm base 10 on it, log10(0.1) = -1 and log10(0.001) = -4. Andrew Ng provides a clearer explanation in this video.

            In Python you can use np.random.uniform() for this

            Source https://stackoverflow.com/questions/66055798

            QUESTION

            Create Network from dictionary of Text and Numerical data - to train GNN
            Asked 2020-Oct-07 at 02:55

            I have been using the FUNSD dataset to predict sequence labeling in unstructured documents per this paper: LayoutLM: Pre-training of Text and Layout for Document Image Understanding . The data after cleaning and moving from a dict to a dataframe, looks like this: The dataset is laid out as follows:

            • The column id is the unique identifier for each word group inside a document, shown in column text (like Nodes)
            • The columnlabel identifies whether the word group are classified as a 'question' or an 'answer'
            • The column linking denoting the WordGroups which are 'linked' (like Edges), linking corresponding 'questions' to 'answers'
            • The column 'box' denoting the location coordinates (x,y top left, x,ybottom right) of the word group relative to the top left corner (0.0).
            • The Column 'words' holds each individual word inside the wordgroup, and its location (box).

            I aim to train a classifier to identify words inside the column 'words' that are linked together by using a Graph Neural Net, and the first step is to be able to transform my current dataset into a Network. My questions are as follows:

            1. Is there a way to break each row in the column 'words' into a two columns [box_word, text_word], each only for one word, while replicating the other columns which remain the same: [id, label, text, box], resulting in a final dataframe with these columns: [box,text,label,box_word, text_word]

            2. I can Tokenize the columns 'text' and text_word, one hot encode column label, split columns with more than one numeric box and box_word into individual columns , but How do I split up/rearrange the colum 'linking' to define the edges of my Network Graph?

            3. Am I taking the correct route in Using the dataframe to generate a Network, and use it to train a GNN?

            Any and all help/tips is appreciated.

            ...

            ANSWER

            Answered 2020-Oct-07 at 02:55

            Edit: process multiple entries in the column words.

            Your questions 1 and 2 are answered in the code. Actually quite simple (assuming the data format is correctly represented by what shown in the screenshot). Digest:

            Q1: apply the splitting function on the column and unpack by .tolist() such that separate columns can be created. See this post also.

            Q2: Use list comprehension to unpack the extra list layer and retain only non-empty edges.

            Q3: Yes and no. Yes because pandas is good at organizing data with heterogeneous types. For example, lists, dict, int and float can be present at different columns. Several I/O functions, such as pd.read_csv() or pd.read_json(), are also very handy.

            However, there is overhead in data access, and that is especially costly for iterating over rows (records). Therefore, the transformed data that feeds directly into your model is usually converted into numpy.array or more efficient formats. Such a format conversion task is the data scientist's sole responsibility.

            Code and Output

            I make up my own sample dataset. Irrelevant columns were ignored (as I am not obliged to and shouldn't do).

            Source https://stackoverflow.com/questions/64218247

            QUESTION

            Textview not displaying in the card view of Recycler View
            Asked 2020-Aug-26 at 15:49

            I want to display a String of names in the text view of recycler view. the .xml of this step is below

            ...

            ANSWER

            Answered 2020-Aug-26 at 15:06

            You are applying differente adapters to the same recyclerview, which means the last one that will be visible will be the last one.

            You can see it here:

            Source https://stackoverflow.com/questions/63594851

            QUESTION

            How to read fields without numeric index in JSON
            Asked 2020-Jul-10 at 17:05

            I have a json file where I need to read it in a structured way to insert in a database each value in its respective column, but in the tag "customFields" the fields change index, example: "Tribe / Customer" can be index 0 (row['customFields'][0]) in a json block, and in the other one be index 3 (row['customFields'][3]), so I tried to read the data using the name of the row field ['customFields'] ['Tribe / Customer'], but I got the error below:

            TypeError: list indices must be integers or slices, not str

            Script:

            ...

            ANSWER

            Answered 2020-Jul-10 at 17:05

            You'll have to parse the list of custom fields into something you can access by name. Since you're accessing multiple entries from the same list, a dictionary is the most appropriate choice.

            Source https://stackoverflow.com/questions/62838931

            QUESTION

            How can I run a .py file with its options in Python console?
            Asked 2020-Feb-24 at 18:16

            I am trying to run this GitHub project in python, but I could only run it using the Terminal of Pycharm IDE.

            According to the guide from the GitHub repository, I removed the $ sign from the beginning of $ python train.py RGCN PPI and could run it there. What does $ mean here and how can I run a file like this in Python Console (for example after >>> sign)?

            ...

            ANSWER

            Answered 2020-Feb-24 at 18:16

            The '$' isn't part of Python's syntax, it's a visual cue in the documentation representing the command prompt.

            To answer the question from the title of this post, I'll provide some instructions first on how to load scripts into the Python console. However, for your specific case, you don't need this. Scroll down to the part about debugging in PyCharm.

            There's two ways you can get your script into the console. One is to simply load it using the right version of the two lines I give right below, or you can load it as a module - even if it wasn't intended to be one.

            In general, to execute a script in the Python shell on Python 2 you can do

            Source https://stackoverflow.com/questions/60359375

            QUESTION

            an array in python displayed using elements in qml
            Asked 2019-Oct-22 at 11:48

            I should display some rects with qml. These Rectangle{} the positiopn of those depend on x=array[i][0] and y=array[i][1], and the quantity of those depend on array.lenght().

            array in qml should be equal to self.__rectanglePos in Python

            So I need a way to draw Rectangle in a different position and in different amount that depends array.

            how can I do that?

            _____.py

            ...

            ANSWER

            Answered 2019-Oct-22 at 11:48

            Your code has many errors, for example you want to access an attribute of the class: self.__rectanglePos) which only makes sense when creating an object from a part of the code that is executed before creating the class: rectanglePosChanged = Signal(type(self.__rectanglePos)), so I will avoid pointing out what your errors are except those necessary for my solution.

            If you want to send information as a list where you add, replace or remove items then it is better to use a model as it will notify you in view of the changes. In this case for simplicity I use a QStandardItemModel, so each part of the element as "x" and "y" will be accessed through roles.

            In the case of QML, as you want to place Rectangles in any position, using ListView is not the right option since this view restricts the position, instead you must use a Repeater.

            main.py

            Source https://stackoverflow.com/questions/58433444

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install GNN

            PyTorch: We're now using Version 1.3
            pytest for testing
            Pytorch Scatter https://github.com/rusty1s/pytorch_scatter -- added this to be able to do sparse attention.

            Support

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