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Title: A Fair Comparison of Graph Neural Networks for Graph Classification

Paper content:
Experimental reproducibility and replicability are critical topics in machine learning.
Authors have often raised concerns about their lack in scientific publications to improve the quality of the field.
Recently, the graph representation learning field has attracted the attention of a wide research community, which resulted in a large stream of works.
As such, several Graph Neural Network models have been developed to effectively tackle graph classification.
However, experimental procedures often lack rigorousness and are hardly reproducible.
Motivated by this, we provide an overview of common practices that should be avoided to fairly compare with the state of the art.
To counter this troubling trend, we ran more than 47000 experiments in a controlled and uniform framework to re-evaluate five popular models across nine common benchmarks.
Moreover, by comparing GNNs with structure-agnostic baselines we provide convincing evidence that, on some datasets, structural information has not been exploited yet.
We believe that this work can contribute to the development of the graph learning field, by providing a much needed grounding for rigorous evaluations of graph classification models.
Over the years, researchers have raised concerns about several flaws in scholarship, such as experimental reproducibility and replicability in machine learning (McDermott, 1976; Lipton & Steinhardt, 2018) and science in general (National Academies of Sciences & Medicine, 2019) .
These issues are not easy to address, as a collective effort is required to avoid bad practices.
Examples include the ambiguity of experimental procedures, the impossibility of reproducing results and the improper comparison of machine learning models.
As a result, it can be difficult to uniformly assess the effectiveness of one method against another.
This work investigates these issues for the graph representation learning field, by providing a uniform and rigorous benchmarking of state-of-the-art models.
Graph Neural Networks (GNNs) (Micheli, 2009; Scarselli et al., 2008) have recently become the standard tool for machine learning on graphs.
These architectures effectively combine node features and graph topology to build distributed node representations.
GNNs can be used to solve node classification (Kipf & Welling, 2017) and link prediction tasks, or they can be applied to downstream graph classification (Bacciu et al., 2018) .
In literature, such models are usually evaluated on chemical and social domains (Xu et al., 2019) .
Given their appeal, an ever increasing number of GNNs is being developed (Gilmer et al., 2017) .
However, despite the theoretical advancements reached by the latest contributions in the field, we find that the experimental settings are in many cases ambiguous or not reproducible.
Some of the most common reproducibility problems we encounter in this field concern hyperparameters selection and the correct usage of data splits for model selection versus model assessment.
Moreover, the evaluation code is sometimes missing or incomplete, and experiments are not standardized across different works in terms of node and edge features.
These issues easily generate doubts and confusion among practitioners that need a fully transparent and reproducible experimental setting.
As a matter of fact, the evaluation of a model goes through two different phases, namely model selection on the validation set and model assessment on the test set.
Clearly, to fail in keeping these phases well separated could lead to over-optimistic and biased estimates of the true performance of a model, making it hard for other researchers to present competitive results without following the same ambiguous evaluation procedures.
With this premise, our primary contribution is to provide the graph learning community with a fair performance comparison among GNN architectures, using a standardized and reproducible experimental environment.
More in detail, we performed a large number of experiments within a rigorous model selection and assessment framework, in which all models were compared using the same features and the same data splits.
Secondly, we investigate if and to what extent current GNN models can effectively exploit graph structure.
To this end, we add two domain-specific and structure-agnostic baselines, whose purpose is to disentangle the contribution of structural information from node features.
Much to our surprise, we found out that these baselines can even perform better than GNNs on some datasets; this calls for moderation when reporting improvements that do not clearly outperform structure-agnostic competitors.
Our last contribution is a study on the effect of node degrees as features in social datasets.
Indeed, we show that providing the degree can be beneficial in terms of performances, and it has also implications in the number of GNN layers needed to reach good results.
We publicly release code and dataset splits to reproduce our results, in order to allow other researchers to carry out rigorous evaluations with minimum additional effort 1 .
Disclaimer Before delving into the work, we would like to clarify that this work does not aim at pinpointing the best (or worst) performing GNN, nor it disavows the effort researchers have put in the development of these models.
Rather, it is intended to be an attempt to set up a standardized and uniform evaluation framework for GNNs, such that future contributions can be compared fairly and objectively with existing architectures.
In this paper, we wanted to show how a rigorous empirical evaluation of GNNs can help design future experiments and better reason about the effectiveness of different architectural choices.
To this aim, we highlighted ambiguities in the experimental settings of different papers, and we proposed a clear and reproducible procedure for future comparisons.
We then provided a complete re-evaluation of five GNNs on nine datasets, which required a significant amount of time and computational resources.
This uniform environment helped us reason about the role of structure, as we found that structure-agnostic baselines outperform GNNs on some chemical datasets, thus suggesting that structural properties have not been exploited yet.
Moreover, we objectively analyzed the effect of the degree feature on performances and model selection in social datasets, unveiling an effect on the depth of GNNs.
Finally, we provide the graph learning community with reliable and reproducible results to which GNN practitioners can compare their architectures.
We hope that this work, along with the library we release, will prove useful to researchers and practitioners that want to compare GNNs in a more rigorous way.

assistant: text: We provide a rigorous comparison of different Graph Neural Networks for graph classification.