Add Graph Classification tutorial (#568)

* Add GlobalPool * Add graph classification tutorial * Add `GlobalPool` pooling docs * Fix ref * Add `GlobalPool` test * Fix Co-authored-by: Carlo Lucibello <carlo.lucibello@gmail.com> * Fix text Co-authored-by: Carlo Lucibello <carlo.lucibello@gmail.com> * Add changes to the src file * Fix pooling layer --------- Co-authored-by: Carlo Lucibello <carlo.lucibello@gmail.com>
JuliaGraphs · Dec 25, 2024 · 1687abe · 1687abe
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diff --git a/GNNLux/docs/make.jl b/GNNLux/docs/make.jl
@@ -62,6 +62,7 @@ makedocs(;
             "Introductory tutorials" => [
                 "Hands on" => "tutorials/gnn_intro.md",
                 "Node Classification" => "tutorials/node_classification.md",
+                "Graph Classification" => "tutorials/graph_classification.md",
                 ],
             ],
 

diff --git a/GNNLux/docs/make_tutorials.jl b/GNNLux/docs/make_tutorials.jl
@@ -2,4 +2,6 @@ using Literate
 
 Literate.markdown("src_tutorials/gnn_intro.jl", "src/tutorials/"; execute = true)
 
-Literate.markdown("src_tutorials/node_classification.jl", "src/tutorials/"; execute = true)
+Literate.markdown("src_tutorials/graph_classification.jl", "src/tutorials/"; execute = true)
+
+Literate.markdown("src_tutorials/node_classification.jl", "src/tutorials/"; execute = true)
diff --git a/GNNLux/docs/src/api/pool.md b/GNNLux/docs/src/api/pool.md
@@ -0,0 +1,19 @@
+```@meta
+CurrentModule = GNNLux
+CollapsedDocStrings = true
+```
+
+# Pooling Layers
+
+## Index
+
+```@index
+Order = [:type, :function]
+Pages   = ["pool.md"]
+```
+
+```@autodocs
+Modules = [GNNLux]
+Pages   = ["layers/pool.jl"]
+Private = false
+```
diff --git a/GNNLux/docs/src/tutorials/graph_classification.md b/GNNLux/docs/src/tutorials/graph_classification.md
@@ -0,0 +1,304 @@
+# Graph Classification with Graph Neural Networks
+
+*This tutorial is a Julia adaptation of the Pytorch Geometric tutorial that can be found [here](https://pytorch-geometric.readthedocs.io/en/latest/notes/colabs.html).*
+
+In this tutorial session we will have a closer look at how to apply **Graph Neural Networks (GNNs) to the task of graph classification**.
+Graph classification refers to the problem of classifying entire graphs (in contrast to nodes), given a **dataset of graphs**, based on some structural graph properties and possibly on some input node features.
+Here, we want to embed entire graphs, and we want to embed those graphs in such a way so that they are linearly separable given a task at hand.
+
+A common graph classification task is **molecular property prediction**, in which molecules are represented as graphs, and the task may be to infer whether a molecule inhibits HIV virus replication or not.
+
+The TU Dortmund University has collected a wide range of different graph classification datasets, known as the [**TUDatasets**](https://chrsmrrs.github.io/datasets/), which are also accessible via MLDatasets.jl.
+Let's import the necessary packages. Then we'll load and inspect one of the smaller ones, the **MUTAG dataset**:
+
+````julia
+using Lux, GNNLux
+using MLDatasets, MLUtils
+using LinearAlgebra, Random, Statistics
+using Zygote, Optimisers, OneHotArrays
+
+ENV["DATADEPS_ALWAYS_ACCEPT"] = "true"  # don't ask for dataset download confirmation
+rng = Random.seed!(42); # for reproducibility
+
+dataset = TUDataset("MUTAG")
+````
+
+````
+dataset TUDataset:
+  name        =>    MUTAG
+  metadata    =>    Dict{String, Any} with 1 entry
+  graphs      =>    188-element Vector{MLDatasets.Graph}
+  graph_data  =>    (targets = "188-element Vector{Int64}",)
+  num_nodes   =>    3371
+  num_edges   =>    7442
+  num_graphs  =>    188
+````
+
+````julia
+dataset.graph_data.targets |> union
+````
+
+````
+2-element Vector{Int64}:
+  1
+ -1
+````
+
+````julia
+g1, y1 = dataset[1] # get the first graph and target
+````
+
+````
+(graphs = Graph(17, 38), targets = 1)
+````
+
+````julia
+reduce(vcat, g.node_data.targets for (g, _) in dataset) |> union
+````
+
+````
+7-element Vector{Int64}:
+ 0
+ 1
+ 2
+ 3
+ 4
+ 5
+ 6
+````
+
+````julia
+reduce(vcat, g.edge_data.targets for (g, _) in dataset) |> union
+````
+
+````
+4-element Vector{Int64}:
+ 0
+ 1
+ 2
+ 3
+````
+
+This dataset provides **188 different graphs**, and the task is to classify each graph into **one out of two classes**.
+
+By inspecting the first graph object of the dataset, we can see that it comes with **17 nodes** and **38 edges**.
+It also comes with exactly **one graph label**, and provides additional node labels (7 classes) and edge labels (4 classes).
+However, for the sake of simplicity, we will not make use of edge labels.
+
+We now convert the `MLDatasets.jl` graph types to our `GNNGraph`s and we also onehot encode both the node labels (which will be used as input features) and the graph labels (what we want to predict):
+
+````julia
+graphs = mldataset2gnngraph(dataset)
+graphs = [GNNGraph(g,
+                    ndata = Float32.(onehotbatch(g.ndata.targets, 0:6)),
+                    edata = nothing)
+            for g in graphs]
+y = onehotbatch(dataset.graph_data.targets, [-1, 1])
+````
+
+````
+2×188 OneHotMatrix(::Vector{UInt32}) with eltype Bool:
+ ⋅  1  1  ⋅  1  ⋅  1  ⋅  1  ⋅  ⋅  ⋅  ⋅  1  ⋅  ⋅  1  ⋅  1  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  1  ⋅  1  1  1  ⋅  1  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  ⋅  1  1  ⋅  ⋅  ⋅  1  ⋅  ⋅  1  ⋅  ⋅  1  1  1  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  ⋅  ⋅  1  1  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  1  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  1  1  ⋅  1  1  ⋅  1  ⋅  ⋅  1  1  ⋅  ⋅  1  1  ⋅  ⋅  ⋅  ⋅  1  1  1  1  1  ⋅  1  ⋅  ⋅  1  1  ⋅  1  1  1  1  ⋅  ⋅  1  ⋅  ⋅  1  ⋅  ⋅  ⋅  1  1  1  ⋅  ⋅  ⋅  1  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  ⋅  ⋅  1  ⋅  1  1  ⋅  ⋅  1  1  ⋅  1
+ 1  ⋅  ⋅  1  ⋅  1  ⋅  1  ⋅  1  1  1  1  ⋅  1  1  ⋅  1  ⋅  1  1  1  1  1  1  1  1  1  1  1  1  1  1  ⋅  1  ⋅  1  ⋅  ⋅  ⋅  1  ⋅  1  1  1  1  1  1  1  1  1  1  1  1  ⋅  1  1  1  1  1  1  ⋅  1  1  ⋅  ⋅  1  1  1  ⋅  1  1  ⋅  1  1  ⋅  ⋅  ⋅  1  1  1  1  1  ⋅  1  1  1  ⋅  ⋅  1  1  1  1  1  1  1  1  ⋅  1  ⋅  1  1  1  1  1  1  1  1  1  ⋅  ⋅  1  ⋅  ⋅  1  ⋅  1  1  ⋅  ⋅  1  1  ⋅  ⋅  1  1  1  1  ⋅  ⋅  ⋅  ⋅  ⋅  1  ⋅  1  1  ⋅  ⋅  1  ⋅  ⋅  ⋅  ⋅  1  1  ⋅  1  1  ⋅  1  1  1  ⋅  ⋅  ⋅  1  1  1  ⋅  1  1  1  1  1  1  1  ⋅  1  1  1  1  1  1  ⋅  1  1  1  ⋅  1  ⋅  ⋅  1  1  ⋅  ⋅  1  ⋅
+````
+
+We have some useful utilities for working with graph datasets, *e.g.*, we can shuffle the dataset and use the first 150 graphs as training graphs, while using the remaining ones for testing:
+
+````julia
+train_data, test_data = splitobs((graphs, y), at = 150, shuffle = true) |> getobs
+
+
+train_loader = DataLoader(train_data, batchsize = 32, shuffle = true)
+test_loader = DataLoader(test_data, batchsize = 32, shuffle = false)
+````
+
+````
+2-element DataLoader(::Tuple{Vector{GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}}, OneHotArrays.OneHotMatrix{UInt32, Vector{UInt32}}}, batchsize=32)
+  with first element:
+  (32-element Vector{GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}}, 2×32 OneHotMatrix(::Vector{UInt32}) with eltype Bool,)
+````
+
+Here, we opt for a `batch_size` of 32, leading to 5 (randomly shuffled) mini-batches, containing all $4 \cdot 32+22 = 150$ graphs.
+
+## Mini-batching of graphs
+
+Since graphs in graph classification datasets are usually small, a good idea is to **batch the graphs** before inputting them into a Graph Neural Network to guarantee full GPU utilization.
+In the image or language domain, this procedure is typically achieved by **rescaling** or **padding** each example into a set of equally-sized shapes, and examples are then grouped in an additional dimension.
+The length of this dimension is then equal to the number of examples grouped in a mini-batch and is typically referred to as the `batchsize`.
+
+However, for GNNs the two approaches described above are either not feasible or may result in a lot of unnecessary memory consumption.
+Therefore, GNNLux.jl opts for another approach to achieve parallelization across a number of examples. Here, adjacency matrices are stacked in a diagonal fashion (creating a giant graph that holds multiple isolated subgraphs), and node and target features are simply concatenated in the node dimension (the last dimension).
+
+This procedure has some crucial advantages over other batching procedures:
+
+1. GNN operators that rely on a message passing scheme do not need to be modified since messages are not exchanged between two nodes that belong to different graphs.
+
+2. There is no computational or memory overhead since adjacency matrices are saved in a sparse fashion holding only non-zero entries, *i.e.*, the edges.
+
+GNNLux.jl can **batch multiple graphs into a single giant graph**:
+
+````julia
+vec_gs, _ = first(train_loader)
+````
+
+````
+(GNNGraphs.GNNGraph{Tuple{Vector{Int64}, Vector{Int64}, Nothing}}[GNNGraph(11, 22) with x: 7×11 data, GNNGraph(22, 50) with x: 7×22 data, GNNGraph(19, 44) with x: 7×19 data, GNNGraph(22, 50) with x: 7×22 data, GNNGraph(16, 36) with x: 7×16 data, GNNGraph(20, 44) with x: 7×20 data, GNNGraph(19, 42) with x: 7×19 data, GNNGraph(20, 44) with x: 7×20 data, GNNGraph(13, 26) with x: 7×13 data, GNNGraph(19, 40) with x: 7×19 data, GNNGraph(25, 56) with x: 7×25 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(28, 66) with x: 7×28 data, GNNGraph(19, 40) with x: 7×19 data, GNNGraph(19, 44) with x: 7×19 data, GNNGraph(17, 36) with x: 7×17 data, GNNGraph(12, 24) with x: 7×12 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(27, 66) with x: 7×27 data, GNNGraph(17, 38) with x: 7×17 data, GNNGraph(19, 42) with x: 7×19 data, GNNGraph(17, 36) with x: 7×17 data, GNNGraph(12, 26) with x: 7×12 data, GNNGraph(24, 50) with x: 7×24 data, GNNGraph(20, 46) with x: 7×20 data, GNNGraph(19, 42) with x: 7×19 data, GNNGraph(11, 22) with x: 7×11 data, GNNGraph(16, 34) with x: 7×16 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(13, 28) with x: 7×13 data, GNNGraph(16, 36) with x: 7×16 data], Bool[1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 1 1 1 1 0; 0 1 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 0 0 0 0 0 1])
+````
+
+````julia
+MLUtils.batch(vec_gs)
+````
+
+````
+GNNGraph:
+  num_nodes: 570
+  num_edges: 1254
+  num_graphs: 32
+  ndata:
+    x = 7×570 Matrix{Float32}
+````
+
+Each batched graph object is equipped with a **`graph_indicator` vector**, which maps each node to its respective graph in the batch:
+
+```math
+\textrm{graph\_indicator} = [1, \ldots, 1, 2, \ldots, 2, 3, \ldots ]
+```
+
+## Training a Graph Neural Network (GNN)
+
+Training a GNN for graph classification usually follows a simple recipe:
+
+1. Embed each node by performing multiple rounds of message passing
+2. Aggregate node embeddings into a unified graph embedding (**readout layer**)
+3. Train a final classifier on the graph embedding
+
+There exists multiple **readout layers** in literature, but the most common one is to simply take the average of node embeddings:
+
+```math
+\mathbf{x}_{\mathcal{G}} = \frac{1}{|\mathcal{V}|} \sum_{v \in \mathcal{V}} \mathcal{x}^{(L)}_v
+```
+
+GNNLux.jl provides this functionality via `GlobalPool(mean)`, which takes in the node embeddings of all nodes in the mini-batch and the assignment vector `graph_indicator` to compute a graph embedding of size `[hidden_channels, batchsize]`.
+
+The final architecture for applying GNNs to the task of graph classification then looks as follows and allows for complete end-to-end training:
+
+````julia
+function create_model(nin, nh, nout)
+    GNNChain(GCNConv(nin => nh, relu),
+             GCNConv(nh => nh, relu),
+             GCNConv(nh => nh),
+             GlobalPool(mean),
+             Dropout(0.5),
+             Dense(nh, nout))
+end;
+
+nin = 7
+nh = 64
+nout = 2
+model = create_model(nin, nh, nout)
+
+ps, st = LuxCore.initialparameters(rng, model), LuxCore.initialstates(rng, model);
+````
+
+````
+┌ Warning: `replicate` doesn't work for `TaskLocalRNG`. Returning the same `TaskLocalRNG`.
+└ @ LuxCore ~/.julia/packages/LuxCore/GlbG3/src/LuxCore.jl:18
+
+````
+
+Here, we again make use of the `GCNConv` with $\mathrm{ReLU}(x) = \max(x, 0)$ activation for obtaining localized node embeddings, before we apply our final classifier on top of a graph readout layer.
+
+Let's train our network for a few epochs to see how well it performs on the training as well as test set:
+
+````julia
+function custom_loss(model, ps, st, tuple)
+    g, x, y = tuple
+    logitcrossentropy = CrossEntropyLoss(; logits=Val(true))
+    st = Lux.trainmode(st)
+    ŷ, st = model(g, x, ps, st)
+    return  logitcrossentropy(ŷ, y), (; layers = st), 0
+end
+
+function eval_loss_accuracy(model, ps, st, data_loader)
+    loss = 0.0
+    acc = 0.0
+    ntot = 0
+    logitcrossentropy = CrossEntropyLoss(; logits=Val(true))
+    for (g, y) in data_loader
+        g = MLUtils.batch(g)
+        n = length(y)
+        ŷ, _ = model(g, g.ndata.x, ps, st)
+        loss += logitcrossentropy(ŷ, y) * n
+        acc += mean((ŷ .> 0) .== y) * n
+        ntot += n
+    end
+    return (loss = round(loss / ntot, digits = 4),
+            acc = round(acc * 100 / ntot, digits = 2))
+end
+
+function train_model!(model, ps, st; epochs = 500, infotime = 100)
+    train_state = Lux.Training.TrainState(model, ps, st, Adam(1e-2))
+
+    function report(epoch)
+        train = eval_loss_accuracy(model, ps, st, train_loader)
+        st = Lux.testmode(st)
+        test = eval_loss_accuracy(model, ps, st, test_loader)
+        st = Lux.trainmode(st)
+        @info (; epoch, train, test)
+    end
+    report(0)
+    for iter in 1:epochs
+        for (g, y) in train_loader
+            g = MLUtils.batch(g)
+            _, loss, _, train_state = Lux.Training.single_train_step!(AutoZygote(), custom_loss,(g, g.ndata.x, y), train_state)
+        end
+
+        iter % infotime == 0 && report(iter)
+    end
+    return model, ps, st
+end
+
+model, ps, st = train_model!(model, ps, st);
+````
+
+````
+┌ Warning: `training` is set to `Val{true}()` but is not being used within an autodiff call (gradient, jacobian, etc...). This will be slow. If you are using a `Lux.jl` model, set it to inference (test) mode using `LuxCore.testmode`. Reliance on this behavior is discouraged, and is not guaranteed by Semantic Versioning, and might be removed without a deprecation cycle. It is recommended to fix this issue in your code.
+└ @ LuxLib.Utils ~/.julia/packages/LuxLib/ru5RQ/src/utils.jl:314
+┌ Warning: `replicate` doesn't work for `TaskLocalRNG`. Returning the same `TaskLocalRNG`.
+└ @ LuxCore ~/.julia/packages/LuxCore/GlbG3/src/LuxCore.jl:18
+[ Info: (epoch = 0, train = (loss = 0.6934, acc = 51.67), test = (loss = 0.6902, acc = 50.0))
+[ Info: (epoch = 100, train = (loss = 0.3979, acc = 81.33), test = (loss = 0.5769, acc = 69.74))
+[ Info: (epoch = 200, train = (loss = 0.3904, acc = 84.0), test = (loss = 0.6402, acc = 65.79))
+[ Info: (epoch = 300, train = (loss = 0.3813, acc = 85.33), test = (loss = 0.6331, acc = 69.74))
+[ Info: (epoch = 400, train = (loss = 0.3682, acc = 85.0), test = (loss = 0.7273, acc = 69.74))
+[ Info: (epoch = 500, train = (loss = 0.3561, acc = 86.67), test = (loss = 0.6825, acc = 73.68))
+
+````
+
+As one can see, our model reaches around **74% test accuracy**.
+Reasons for the fluctuations in accuracy can be explained by the rather small dataset (only 38 test graphs), and usually disappear once one applies GNNs to larger datasets.
+
+## (Optional) Exercise
+
+Can we do better than this?
+As multiple papers pointed out ([Xu et al. (2018)](https://arxiv.org/abs/1810.00826), [Morris et al. (2018)](https://arxiv.org/abs/1810.02244)), applying **neighborhood normalization decreases the expressivity of GNNs in distinguishing certain graph structures**.
+An alternative formulation ([Morris et al. (2018)](https://arxiv.org/abs/1810.02244)) omits neighborhood normalization completely and adds a simple skip-connection to the GNN layer in order to preserve central node information:
+
+```math
+\mathbf{x}_i^{(\ell+1)} = \mathbf{W}^{(\ell + 1)}_1 \mathbf{x}_i^{(\ell)} + \mathbf{W}^{(\ell + 1)}_2 \sum_{j \in \mathcal{N}(i)} \mathbf{x}_j^{(\ell)}
+```
+
+This layer is implemented under the name `GraphConv` in GraphNeuralNetworks.jl.
+
+As an exercise, you are invited to complete the following code to the extent that it makes use of `GraphConv` rather than `GCNConv`.
+This should bring you close to **82% test accuracy**.
+
+## Conclusion
+
+In this chapter, you have learned how to apply GNNs to the task of graph classification.
+You have learned how graphs can be batched together for better GPU utilization, and how to apply readout layers for obtaining graph embeddings rather than node embeddings.
+
+---
+
+*This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
+