Xavier Bresson

Xiaoxin He, Bryan Hooi, Thomas Laurent et al.

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: \url{https://github.com/XiaoxinHe/Graph-ViT-MLPMixer}.

Burak Satar, Hongyuan Zhu, Xavier Bresson et al.

With the emergence of social media, voluminous video clips are uploaded every day, and retrieving the most relevant visual content with a language query becomes critical. Most approaches aim to learn a joint embedding space for plain textual and visual contents without adequately exploiting their intra-modality structures and inter-modality correlations. This paper proposes a novel transformer that explicitly disentangles the text and video into semantic roles of objects, spatial contexts and temporal contexts with an attention scheme to learn the intra- and inter-role correlations among the three roles to discover discriminative features for matching at different levels. The preliminary results on popular YouCook2 indicate that our approach surpasses a current state-of-the-art method, with a high margin in all metrics. It also overpasses two SOTA methods in terms of two metrics.

Yong Liang Goh, Wee Sun Lee, Xavier Bresson et al.

The traveling salesman problem is a fundamental combinatorial optimization problem with strong exact algorithms. However, as problems scale up, these exact algorithms fail to provide a solution in a reasonable time. To resolve this, current works look at utilizing deep learning to construct reasonable solutions. Such efforts have been very successful, but tend to be slow and compute intensive. This paper exemplifies the integration of entropic regularized optimal transport techniques as a layer in a deep reinforcement learning network. We show that we can construct a model capable of learning without supervision and inferences significantly faster than current autoregressive approaches. We also empirically evaluate the benefits of including optimal transport algorithms within deep learning models to enforce assignment constraints during end-to-end training.

Stephen G. Dale, Nikita Kazeev, Alastair J. A. Price et al.

Artificial intelligence and machine learning are reshaping how we approach scientific discovery, not by replacing established methods but by extending what researchers can probe, predict, and design. In this roadmap we provide a forward-looking view of AI-enabled science across biology, chemistry, climate science, mathematics, materials science, physics, self-driving laboratories and unconventional computing. Several shared themes emerge: the need for diverse and trustworthy data, transferable electronic-structure and interatomic models, AI systems integrated into end-to-end scientific workflows that connect simulations to experiments and generative systems grounded in synthesisability rather than purely idealised phases. Across domains, we highlight how large foundation models, active learning and self-driving laboratories can close loops between prediction and validation while maintaining reproducibility and physical interpretability. Taken together, these perspectives outline where AI-enabled science stands today, identify bottlenecks in data, methods and infrastructure, and chart concrete directions for building AI systems that are not only more powerful but also more transparent and capable of accelerating discovery in complex real-world environments.

Lovro Vrček, Xavier Bresson, Thomas Laurent et al.

A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered various tools and performed laborious manual inspection to achieve the first gapless genome sequence. However, such method can hardly be used as a general approach to assemble different genomes, especially when the assembly speed is critical given the large amount of data. In this work, we explore a different approach to the central part of the genome assembly task that consists of untangling a large assembly graph from which a genomic sequence needs to be reconstructed. Our main motivation is to reduce human-engineered heuristics and use deep learning to develop more generalizable reconstruction techniques. Precisely, we introduce a new learning framework to train a graph convolutional network to resolve assembly graphs by finding a correct path through them. The training is supervised with a dataset generated from the resolved CHM13 human sequence and tested on assembly graphs built using real human PacBio HiFi reads. Experimental results show that a model, trained on simulated graphs generated solely from a single chromosome, is able to remarkably resolve all other chromosomes. Moreover, the model outperforms hand-crafted heuristics from a state-of-the-art \textit{de novo} assembler on the same graphs. Reconstructed chromosomes with graph networks are more accurate on nucleotide level, report lower number of contigs, higher genome reconstructed fraction and NG50/NGA50 assessment metrics.

Thomas Laurent, James H. von Brecht, Xavier Bresson

We propose a simple data model inspired from natural data such as text or images, and use it to study the importance of learning features in order to achieve good generalization. Our data model follows a long-tailed distribution in the sense that some rare subcategories have few representatives in the training set. In this context we provide evidence that a learner succeeds if and only if it identifies the correct features, and moreover derive non-asymptotic generalization error bounds that precisely quantify the penalty that one must pay for not learning features.

Xiaoxin He, Yijun Tian, Yifei Sun et al.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~\footnote{Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}}

Yuchen Zhang, Tianle Zhang, Kai Wang et al. · pku

Graph condensation aims to reduce the size of a large-scale graph dataset by synthesizing a compact counterpart without sacrificing the performance of Graph Neural Networks (GNNs) trained on it, which has shed light on reducing the computational cost for training GNNs. Nevertheless, existing methods often fall short of accurately replicating the original graph for certain datasets, thereby failing to achieve the objective of lossless condensation. To understand this phenomenon, we investigate the potential reasons and reveal that the previous state-of-the-art trajectory matching method provides biased and restricted supervision signals from the original graph when optimizing the condensed one. This significantly limits both the scale and efficacy of the condensed graph. In this paper, we make the first attempt toward \textit{lossless graph condensation} by bridging the previously neglected supervision signals. Specifically, we employ a curriculum learning strategy to train expert trajectories with more diverse supervision signals from the original graph, and then effectively transfer the information into the condensed graph with expanding window matching. Moreover, we design a loss function to further extract knowledge from the expert trajectories. Theoretical analysis justifies the design of our method and extensive experiments verify its superiority across different datasets. Code is released at https://github.com/NUS-HPC-AI-Lab/GEOM.

Nian Liu, Xiaoxin He, Thomas Laurent et al.

Spectral graph convolution, an important tool of data filtering on graphs, relies on two essential decisions: selecting spectral bases for signal transformation and parameterizing the kernel for frequency analysis. While recent techniques mainly focus on standard Fourier transform and vector-valued spectral functions, they fall short in flexibility to model signal distributions over large spatial ranges, and capacity of spectral function. In this paper, we present a novel wavelet-based graph convolution network, namely WaveGC, which integrates multi-resolution spectral bases and a matrix-valued filter kernel. Theoretically, we establish that WaveGC can effectively capture and decouple short-range and long-range information, providing superior filtering flexibility, surpassing existing graph wavelet neural networks. To instantiate WaveGC, we introduce a novel technique for learning general graph wavelets by separately combining odd and even terms of Chebyshev polynomials. This approach strictly satisfies wavelet admissibility criteria. Our numerical experiments showcase the consistent improvements in both short-range and long-range tasks. This underscores the effectiveness of the proposed model in handling different scenarios. Our code is available at https://github.com/liun-online/WaveGC.

Nian Liu, Nikita Kazeev, Stephen Gregory Dale et al.

De novo crystal generation seeks to discover materials that are not merely realistic, but also stable and novel. However, most existing generative models are trained to maximize the likelihood of observed crystals, which encourages samples to stay close to known materials yet not necessarily align with the criteria that matter in discovery. Through an empirical investigation, we show that current crystal generative models are caught in a pronounced stability--novelty trade-off: moving toward the observed distribution preserves stability but limits novelty, whereas moving away from it quickly destroys stability. This suggests that the useful region for discovering crystals that are both stable and novel is extremely narrow. To escape the trade-off, we introduce Crys-JEPA, a joint embedding predictive architecture for crystals that learns an energy-aware latent space preserving formation-energy differences. In this space, stability assessment can be reformulated as an embedding-based comparison against accessible training crystals, reducing the reliance on expensive energy evaluation and task-specific external references. Building on Crys-JEPA, we further develop a screening-and-refinement pipeline that identifies promising generated crystals and reintroduces them to refine the generative model. On MP-20 and Alex-MP-20 datasets, we achieve improvements over baselines up to 81.4% and 82.6% on V.S.U.N metric, respectively.

Nian Liu, Yuwei Zeng, Ryoji Kubo et al.

De novo crystal generation, a central task in materials discovery, aims to generate crystals that are simultaneously valid, stable, unique, and novel. Existing methods mainly rely on black-box stochastic sampling, providing limited control over how generated structures move beyond the observed distribution. In this paper, we introduce a concept-based compositional framework for crystal generation. We train a vector-quantized variational autoencoder to automatically discover a shared set of reusable crystal concepts, which serve as building blocks for guided generation. These learned concepts naturally exhibit interpretability from both local atomic environments and global symmetry patterns, and generalize to crystals from different distributions. By recombining such concepts, our framework enables controllable exploration of novel crystals beyond the training distribution, rather than relying solely on unconstrained random sampling. To further improve composition efficiency, we introduce a composition generator and iteratively refine it using high-quality samples generated by the model itself. The resulting concept compositions are then used to condition downstream crystal generation. Numerical experiments on MP-20 and Alex-MP-20 show that compositing concepts separately increase base model up to 53.2% and 51.7% on V.S.U.N metric, with particular gains in novelty.

Xiaoxin He, Xavier Bresson, Thomas Laurent et al.

Representation learning on text-attributed graphs (TAGs) has become a critical research problem in recent years. A typical example of a TAG is a paper citation graph, where the text of each paper serves as node attributes. Initial graph neural network (GNN) pipelines handled these text attributes by transforming them into shallow or hand-crafted features, such as skip-gram or bag-of-words features. Recent efforts have focused on enhancing these pipelines with language models (LMs), which typically demand intricate designs and substantial computational resources. With the advent of powerful large language models (LLMs) such as GPT or Llama2, which demonstrate an ability to reason and to utilize general knowledge, there is a growing need for techniques which combine the textual modelling abilities of LLMs with the structural learning capabilities of GNNs. Hence, in this work, we focus on leveraging LLMs to capture textual information as features, which can be used to boost GNN performance on downstream tasks. A key innovation is our use of explanations as features: we prompt an LLM to perform zero-shot classification, request textual explanations for its decision-making process, and design an LLM-to-LM interpreter to translate these explanations into informative features for downstream GNNs. Our experiments demonstrate that our method achieves state-of-the-art results on well-established TAG datasets, including Cora, PubMed, ogbn-arxiv, as well as our newly introduced dataset, tape-arxiv23. Furthermore, our method significantly speeds up training, achieving a 2.88 times improvement over the closest baseline on ogbn-arxiv. Lastly, we believe the versatility of the proposed method extends beyond TAGs and holds the potential to enhance other tasks involving graph-text data. Our codes and datasets are available at: https://github.com/XiaoxinHe/TAPE.

Vijay Prakash Dwivedi, Chaitanya K. Joshi, Anh Tuan Luu et al.

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

Peng Xu, Chaitanya K. Joshi, Xavier Bresson

Learning meaningful representations of free-hand sketches remains a challenging task given the signal sparsity and the high-level abstraction of sketches. Existing techniques have focused on exploiting either the static nature of sketches with Convolutional Neural Networks (CNNs) or the temporal sequential property with Recurrent Neural Networks (RNNs). In this work, we propose a new representation of sketches as multiple sparsely connected graphs. We design a novel Graph Neural Network (GNN), the Multi-Graph Transformer (MGT), for learning representations of sketches from multiple graphs which simultaneously capture global and local geometric stroke structures, as well as temporal information. We report extensive numerical experiments on a sketch recognition task to demonstrate the performance of the proposed approach. Particularly, MGT applied on 414k sketches from Google QuickDraw: (i) achieves small recognition gap to the CNN-based performance upper bound (72.80% vs. 74.22%), and (ii) outperforms all RNN-based models by a significant margin. To the best of our knowledge, this is the first work proposing to represent sketches as graphs and apply GNNs for sketch recognition. Code and trained models are available at https://github.com/PengBoXiangShang/multigraph_transformer.

Michaël Defferrard, Kirell Benzi, Pierre Vandergheynst et al.

We introduce the Free Music Archive (FMA), an open and easily accessible dataset suitable for evaluating several tasks in MIR, a field concerned with browsing, searching, and organizing large music collections. The community's growing interest in feature and end-to-end learning is however restrained by the limited availability of large audio datasets. The FMA aims to overcome this hurdle by providing 917 GiB and 343 days of Creative Commons-licensed audio from 106,574 tracks from 16,341 artists and 14,854 albums, arranged in a hierarchical taxonomy of 161 genres. It provides full-length and high-quality audio, pre-computed features, together with track- and user-level metadata, tags, and free-form text such as biographies. We here describe the dataset and how it was created, propose a train/validation/test split and three subsets, discuss some suitable MIR tasks, and evaluate some baselines for genre recognition. Code, data, and usage examples are available at https://github.com/mdeff/fma

Vijay Prakash Dwivedi, Yozen Liu, Anh Tuan Luu et al.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

Mufei Li, Dongqi Fu, Limei Wang et al. · gatech

Modern long-context large language models (LLMs) perform well on synthetic "needle-in-a-haystack" (NIAH) benchmarks, but such tests overlook how noisy contexts arise from biased retrieval and agentic workflows. We argue that haystack engineering is necessary to construct noisy long contexts that faithfully capture key real-world factors -- distraction from heterogeneous biased retrievers and cascading errors in agentic workflows -- to test models' long-context robustness. We instantiate it through HaystackCraft, a new NIAH benchmark built on the full English Wikipedia hyperlink network with multi-hop questions. HaystackCraft evaluates how heterogeneous retrieval strategies (e.g., sparse, dense, hybrid, and graph-based) affect distractor composition, haystack ordering, and downstream LLM performance. HaystackCraft further extends NIAH to dynamic, LLM-dependent settings that simulate agentic operations, where models refine queries, reflect on their past reasonings, and decide when to stop. Experiments with 15 long-context models show that (1) while stronger dense retrievers can introduce more challenging distractors, graph-based reranking simultaneously improves retrieval effectiveness and mitigates more harmful distractors; (2) in agentic tests, even advanced models like Gemini 2.5 Pro and GPT-5 suffer cascading failures from self-generated distractors or struggle to perform early stops. These results highlight persistent challenges in agentic long-context reasoning and establish HaystackCraft as a valuable testbed for future progress.

Yutong Xia, Runpeng Yu, Yuxuan Liang et al.

Graph Neural Networks have become the preferred tool to process graph data, with their efficacy being boosted through graph data augmentation techniques. Despite the evolution of augmentation methods, issues like graph property distortions and restricted structural changes persist. This leads to the question: Is it possible to develop more property-conserving and structure-sensitive augmentation methods? Through a spectral lens, we investigate the interplay between graph properties, their augmentation, and their spectral behavior, and observe that keeping the low-frequency eigenvalues unchanged can preserve the critical properties at a large scale when generating augmented graphs. These observations inform our introduction of the Dual-Prism (DP) augmentation methods, including DP-Noise and DP-Mask, which retain essential graph properties while diversifying augmented graphs. Extensive experiments validate the efficiency of our approach, providing a new and promising direction for graph data augmentation.

Thomas Laurent, James H. von Brecht, Xavier Bresson

We formalize and study a phenomenon called feature collapse that makes precise the intuitive idea that entities playing a similar role in a learning task receive similar representations. As feature collapse requires a notion of task, we leverage a simple but prototypical NLP task to study it. We start by showing experimentally that feature collapse goes hand in hand with generalization. We then prove that, in the large sample limit, distinct words that play identical roles in this NLP task receive identical local feature representations in a neural network. This analysis reveals the crucial role that normalization mechanisms, such as LayerNorm, play in feature collapse and in generalization.

Vijay Prakash Dwivedi, Anh Tuan Luu, Thomas Laurent et al.

Graph neural networks (GNNs) have become the standard learning architectures for graphs. GNNs have been applied to numerous domains ranging from quantum chemistry, recommender systems to knowledge graphs and natural language processing. A major issue with arbitrary graphs is the absence of canonical positional information of nodes, which decreases the representation power of GNNs to distinguish e.g. isomorphic nodes and other graph symmetries. An approach to tackle this issue is to introduce Positional Encoding (PE) of nodes, and inject it into the input layer, like in Transformers. Possible graph PE are Laplacian eigenvectors. In this work, we propose to decouple structural and positional representations to make easy for the network to learn these two essential properties. We introduce a novel generic architecture which we call LSPE (Learnable Structural and Positional Encodings). We investigate several sparse and fully-connected (Transformer-like) GNNs, and observe a performance increase for molecular datasets, from 1.79% up to 64.14% when considering learnable PE for both GNN classes.

Xavier Bresson, Thomas Laurent

The Traveling Salesman Problem (TSP) is the most popular and most studied combinatorial problem, starting with von Neumann in 1951. It has driven the discovery of several optimization techniques such as cutting planes, branch-and-bound, local search, Lagrangian relaxation, and simulated annealing. The last five years have seen the emergence of promising techniques where (graph) neural networks have been capable to learn new combinatorial algorithms. The main question is whether deep learning can learn better heuristics from data, i.e. replacing human-engineered heuristics? This is appealing because developing algorithms to tackle efficiently NP-hard problems may require years of research, and many industry problems are combinatorial by nature. In this work, we propose to adapt the recent successful Transformer architecture originally developed for natural language processing to the combinatorial TSP. Training is done by reinforcement learning, hence without TSP training solutions, and decoding uses beam search. We report improved performances over recent learned heuristics with an optimal gap of 0.004% for TSP50 and 0.39% for TSP100.

Axel Nilsson, Xavier Bresson

Spectral graph convolutional networks are generalizations of standard convolutional networks for graph-structured data using the Laplacian operator. A common misconception is the instability of spectral filters, i.e. the impossibility to transfer spectral filters between graphs of variable size and topology. This misbelief has limited the development of spectral networks for multi-graph tasks in favor of spatial graph networks. However, recent works have proved the stability of spectral filters under graph perturbation. Our work complements and emphasizes further the high quality of spectral transferability by benchmarking spectral graph networks on tasks involving graphs of different size and connectivity. Numerical experiments exhibit favorable performance on graph regression, graph classification, and node classification problems on two graph benchmarks. The implementation of our experiments is available on GitHub for reproducibility.

Vijay Prakash Dwivedi, Xavier Bresson

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

Chaitanya K. Joshi, Thomas Laurent, Xavier Bresson

We explore the impact of learning paradigms on training deep neural networks for the Travelling Salesman Problem. We design controlled experiments to train supervised learning (SL) and reinforcement learning (RL) models on fixed graph sizes up to 100 nodes, and evaluate them on variable sized graphs up to 500 nodes. Beyond not needing labelled data, our results reveal favorable properties of RL over SL: RL training leads to better emergent generalization to variable graph sizes and is a key component for learning scale-invariant solvers for novel combinatorial problems.

Xavier Bresson, Thomas Laurent

We propose a simple auto-encoder framework for molecule generation. The molecular graph is first encoded into a continuous latent representation $z$, which is then decoded back to a molecule. The encoding process is easy, but the decoding process remains challenging. In this work, we introduce a simple two-step decoding process. In a first step, a fully connected neural network uses the latent vector $z$ to produce a molecular formula, for example CO$_2$ (one carbon and two oxygen atoms). In a second step, a graph convolutional neural network uses the same latent vector $z$ to place bonds between the atoms that were produced in the first step (for example a double bond will be placed between the carbon and each of the oxygens). This two-step process, in which a bag of atoms is first generated, and then assembled, provides a simple framework that allows us to develop an efficient molecule auto-encoder. Numerical experiments on basic tasks such as novelty, uniqueness, validity and optimized chemical property for the 250k ZINC molecules demonstrate the performances of the proposed system. Particularly, we achieve the highest reconstruction rate of 90.5\%, improving the previous rate of 76.7\%. We also report the best property improvement results when optimization is constrained by the molecular distance between the original and generated molecules.

Chaitanya K. Joshi, Thomas Laurent, Xavier Bresson

This paper introduces a new learning-based approach for approximately solving the Travelling Salesman Problem on 2D Euclidean graphs. We use deep Graph Convolutional Networks to build efficient TSP graph representations and output tours in a non-autoregressive manner via highly parallelized beam search. Our approach outperforms all recently proposed autoregressive deep learning techniques in terms of solution quality, inference speed and sample efficiency for problem instances of fixed graph sizes. In particular, we reduce the average optimality gap from 0.52% to 0.01% for 50 nodes, and from 2.26% to 1.39% for 100 nodes. Finally, despite improving upon other learning-based approaches for TSP, our approach falls short of standard Operations Research solvers.

Yao Yang Leow, Thomas Laurent, Xavier Bresson

We present GraphTSNE, a novel visualization technique for graph-structured data based on t-SNE. The growing interest in graph-structured data increases the importance of gaining human insight into such datasets by means of visualization. Among the most popular visualization techniques, classical t-SNE is not suitable on such datasets because it has no mechanism to make use of information from the graph structure. On the other hand, visualization techniques which operate on graphs, such as Laplacian Eigenmaps and tsNET, have no mechanism to make use of information from node features. Our proposed method GraphTSNE produces visualizations which account for both graph structure and node features. It is based on scalable and unsupervised training of a graph convolutional network on a modified t-SNE loss. By assembling a suite of evaluation metrics, we demonstrate that our method produces desirable visualizations on three benchmark datasets.

Xavier Bresson, Thomas Laurent

Graph-structured data such as social networks, functional brain networks, gene regulatory networks, communications networks have brought the interest in generalizing deep learning techniques to graph domains. In this paper, we are interested to design neural networks for graphs with variable length in order to solve learning problems such as vertex classification, graph classification, graph regression, and graph generative tasks. Most existing works have focused on recurrent neural networks (RNNs) to learn meaningful representations of graphs, and more recently new convolutional neural networks (ConvNets) have been introduced. In this work, we want to compare rigorously these two fundamental families of architectures to solve graph learning tasks. We review existing graph RNN and ConvNet architectures, and propose natural extension of LSTM and ConvNet to graphs with arbitrary size. Then, we design a set of analytically controlled experiments on two basic graph problems, i.e. subgraph matching and graph clustering, to test the different architectures. Numerical results show that the proposed graph ConvNets are 3-17% more accurate and 1.5-4x faster than graph RNNs. Graph ConvNets are also 36% more accurate than variational (non-learning) techniques. Finally, the most effective graph ConvNet architecture uses gated edges and residuality. Residuality plays an essential role to learn multi-layer architectures as they provide a 10% gain of performance.

Ron Levie, Federico Monti, Xavier Bresson et al.

The rise of graph-structured data such as social networks, regulatory networks, citation graphs, and functional brain networks, in combination with resounding success of deep learning in various applications, has brought the interest in generalizing deep learning models to non-Euclidean domains. In this paper, we introduce a new spectral domain convolutional architecture for deep learning on graphs. The core ingredient of our model is a new class of parametric rational complex functions (Cayley polynomials) allowing to efficiently compute spectral filters on graphs that specialize on frequency bands of interest. Our model generates rich spectral filters that are localized in space, scales linearly with the size of the input data for sparsely-connected graphs, and can handle different constructions of Laplacian operators. Extensive experimental results show the superior performance of our approach, in comparison to other spectral domain convolutional architectures, on spectral image classification, community detection, vertex classification and matrix completion tasks.

Federico Monti, Michael M. Bronstein, Xavier Bresson

Matrix completion models are among the most common formulations of recommender systems. Recent works have showed a boost of performance of these techniques when introducing the pairwise relationships between users/items in the form of graphs, and imposing smoothness priors on these graphs. However, such techniques do not fully exploit the local stationarity structures of user/item graphs, and the number of parameters to learn is linear w.r.t. the number of users and items. We propose a novel approach to overcome these limitations by using geometric deep learning on graphs. Our matrix completion architecture combines graph convolutional neural networks and recurrent neural networks to learn meaningful statistical graph-structured patterns and the non-linear diffusion process that generates the known ratings. This neural network system requires a constant number of parameters independent of the matrix size. We apply our method on both synthetic and real datasets, showing that it outperforms state-of-the-art techniques.

Youngjoo Seo, Michaël Defferrard, Pierre Vandergheynst et al.

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed.

Michaël Defferrard, Xavier Bresson, Pierre Vandergheynst

In this work, we are interested in generalizing convolutional neural networks (CNNs) from low-dimensional regular grids, where image, video and speech are represented, to high-dimensional irregular domains, such as social networks, brain connectomes or words' embedding, represented by graphs. We present a formulation of CNNs in the context of spectral graph theory, which provides the necessary mathematical background and efficient numerical schemes to design fast localized convolutional filters on graphs. Importantly, the proposed technique offers the same linear computational complexity and constant learning complexity as classical CNNs, while being universal to any graph structure. Experiments on MNIST and 20NEWS demonstrate the ability of this novel deep learning system to learn local, stationary, and compositional features on graphs.

Rodrigo Pena, Xavier Bresson, Pierre Vandergheynst

We cast the problem of source localization on graphs as the simultaneous problem of sparse recovery and diffusion kernel learning. An l1 regularization term enforces the sparsity constraint while we recover the sources of diffusion from a single snapshot of the diffusion process. The diffusion kernel is estimated by assuming the process to be as generic as the standard heat diffusion. We show with synthetic data that we can concomitantly learn the diffusion kernel and the sources, given an estimated initialization. We validate our model with cholera mortality and atmospheric tracer diffusion data, showing also that the accuracy of the solution depends on the construction of the graph from the data points.

Kirell Benzi, Vassilis Kalofolias, Xavier Bresson et al.

This work formulates a novel song recommender system as a matrix completion problem that benefits from collaborative filtering through Non-negative Matrix Factorization (NMF) and content-based filtering via total variation (TV) on graphs. The graphs encode both playlist proximity information and song similarity, using a rich combination of audio, meta-data and social features. As we demonstrate, our hybrid recommendation system is very versatile and incorporates several well-known methods while outperforming them. Particularly, we show on real-world data that our model overcomes w.r.t. two evaluation metrics the recommendation of models solely based on low-rank information, graph-based information or a combination of both.

Xavier Bresson, Thomas Laurent, James von Brecht

This work aims at recovering signals that are sparse on graphs. Compressed sensing offers techniques for signal recovery from a few linear measurements and graph Fourier analysis provides a signal representation on graph. In this paper, we leverage these two frameworks to introduce a new Lasso recovery algorithm on graphs. More precisely, we present a non-convex, non-smooth algorithm that outperforms the standard convex Lasso technique. We carry out numerical experiments on three benchmark graph datasets.

Nauman Shahid, Vassilis Kalofolias, Xavier Bresson et al.

Principal Component Analysis (PCA) is the most widely used tool for linear dimensionality reduction and clustering. Still it is highly sensitive to outliers and does not scale well with respect to the number of data samples. Robust PCA solves the first issue with a sparse penalty term. The second issue can be handled with the matrix factorization model, which is however non-convex. Besides, PCA based clustering can also be enhanced by using a graph of data similarity. In this article, we introduce a new model called "Robust PCA on Graphs" which incorporates spectral graph regularization into the Robust PCA framework. Our proposed model benefits from 1) the robustness of principal components to occlusions and missing values, 2) enhanced low-rank recovery, 3) improved clustering property due to the graph smoothness assumption on the low-rank matrix, and 4) convexity of the resulting optimization problem. Extensive experiments on 8 benchmark, 3 video and 2 artificial datasets with corruptions clearly reveal that our model outperforms 10 other state-of-the-art models in its clustering and low-rank recovery tasks.

Artiom Kovnatsky, Michael M. Bronstein, Xavier Bresson et al.

In this paper, we consider the problem of finding dense intrinsic correspondence between manifolds using the recently introduced functional framework. We pose the functional correspondence problem as matrix completion with manifold geometric structure and inducing functional localization with the $L_1$ norm. We discuss efficient numerical procedures for the solution of our problem. Our method compares favorably to the accuracy of state-of-the-art correspondence algorithms on non-rigid shape matching benchmarks, and is especially advantageous in settings when only scarce data is available.

Nicolas Garcia Trillos, Dejan Slepcev, James von Brecht et al.

This paper establishes the consistency of a family of graph-cut-based algorithms for clustering of data clouds. We consider point clouds obtained as samples of a ground-truth measure. We investigate approaches to clustering based on minimizing objective functionals defined on proximity graphs of the given sample. Our focus is on functionals based on graph cuts like the Cheeger and ratio cuts. We show that minimizers of the these cuts converge as the sample size increases to a minimizer of a corresponding continuum cut (which partitions the ground truth measure). Moreover, we obtain sharp conditions on how the connectivity radius can be scaled with respect to the number of sample points for the consistency to hold. We provide results for two-way and for multiway cuts. Furthermore we provide numerical experiments that illustrate the results and explore the optimality of scaling in dimension two.

Vassilis Kalofolias, Xavier Bresson, Michael Bronstein et al.

The problem of finding the missing values of a matrix given a few of its entries, called matrix completion, has gathered a lot of attention in the recent years. Although the problem under the standard low rank assumption is NP-hard, Candès and Recht showed that it can be exactly relaxed if the number of observed entries is sufficiently large. In this work, we introduce a novel matrix completion model that makes use of proximity information about rows and columns by assuming they form communities. This assumption makes sense in several real-world problems like in recommender systems, where there are communities of people sharing preferences, while products form clusters that receive similar ratings. Our main goal is thus to find a low-rank solution that is structured by the proximities of rows and columns encoded by graphs. We borrow ideas from manifold learning to constrain our solution to be smooth on these graphs, in order to implicitly force row and column proximities. Our matrix recovery model is formulated as a convex non-smooth optimization problem, for which a well-posed iterative scheme is provided. We study and evaluate the proposed matrix completion on synthetic and real data, showing that the proposed structured low-rank recovery model outperforms the standard matrix completion model in many situations.

Xavier Bresson, Huiyi Hu, Thomas Laurent et al.

In this work we propose a simple and easily parallelizable algorithm for multiway graph partitioning. The algorithm alternates between three basic components: diffusing seed vertices over the graph, thresholding the diffused seeds, and then randomly reseeding the thresholded clusters. We demonstrate experimentally that the proper combination of these ingredients leads to an algorithm that achieves state-of-the-art performance in terms of cluster purity on standard benchmarks datasets. Moreover, the algorithm runs an order of magnitude faster than the other algorithms that achieve comparable results in terms of accuracy. We also describe a coarsen, cluster and refine approach similar to GRACLUS and METIS that removes an additional order of magnitude from the runtime of our algorithm while still maintaining competitive accuracy.

Xavier Bresson, Thomas Laurent, David Uminsky et al.

Ideas from the image processing literature have recently motivated a new set of clustering algorithms that rely on the concept of total variation. While these algorithms perform well for bi-partitioning tasks, their recursive extensions yield unimpressive results for multiclass clustering tasks. This paper presents a general framework for multiclass total variation clustering that does not rely on recursion. The results greatly outperform previous total variation algorithms and compare well with state-of-the-art NMF approaches.

Virginia Estellers, Jean-Philippe Thiran, Xavier Bresson

We propose a compressive sensing algorithm that exploits geometric properties of images to recover images of high quality from few measurements. The image reconstruction is done by iterating the two following steps: 1) estimation of normal vectors of the image level curves and 2) reconstruction of an image fitting the normal vectors, the compressed sensing measurements and the sparsity constraint. The proposed technique can naturally extend to non local operators and graphs to exploit the repetitive nature of textured images in order to recover fine detail structures. In both cases, the problem is reduced to a series of convex minimization problems that can be efficiently solved with a combination of variable splitting and augmented Lagrangian methods, leading to fast and easy-to-code algorithms. Extended experiments show a clear improvement over related state-of-the-art algorithms in the quality of the reconstructed images and the robustness of the proposed method to noise, different kind of images and reduced measurements.

Xavier Bresson, Ruiliang Zhang

We introduce semi-supervised data classification algorithms based on total variation (TV), Reproducing Kernel Hilbert Space (RKHS), support vector machine (SVM), Cheeger cut, labeled and unlabeled data points. We design binary and multi-class semi-supervised classification algorithms. We compare the TV-based classification algorithms with the related Laplacian-based algorithms, and show that TV classification perform significantly better when the number of labeled data is small.