arXiv subjects

Xavier Bresson

Publications and source records attributed to Xavier Bresson.

At least 19 recordsLinked to original sources

arXiv2026

Crys-JEPA: Accelerating Crystal Discovery via Embedding Screening and Generative Refinement

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. Our empirical analysis shows that current crystal generative models exhibit a clear conflict between stability and novelty: samples near the observed distribution tend to retain stability but offer limited novelty, whereas samples farther from it often lose stability rapidly. This suggests that the useful region for discovering crystals that are both stable and novel is extremely narrow. To move beyond this limitation, 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 53.8% and 72.7% on V.S.U.N. metric, respectively.

cs.LG↗

arXiv2026

Composable Crystals: Controllable Materials Discovery via Concept Learning

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.

cs.LG↗

arXiv2025

AI4X Roadmap: Artificial Intelligence for the advancement of scientific pursuit and its future directions

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.

physics.soc-ph↗

arXiv2025

Haystack Engineering: Context Engineering for Heterogeneous and Agentic Long-Context Evaluation

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.

cs.CL↗

arXiv2025

A General Graph Spectral Wavelet Convolution via Chebyshev Order Decomposition

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.

cs.LG↗

arXiv2025

Through the Dual-Prism: A Spectral Perspective on Graph Data Augmentation for Graph Classification

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.

cs.LG↗

arXiv2024

Navigating Complexity: Toward Lossless Graph Condensation via Expanding Window Matching

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.

cs.LG↗

arXiv2024

G-Retriever: Retrieval-Augmented Generation for Textual Graph Understanding and Question Answering

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}}

cs.LG↗

arXiv2024

Harnessing Explanations: LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation Learning

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.

cs.LG↗

arXiv2023

Graph Transformers for Large Graphs

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.

cs.LG↗

arXiv2023

A Generalization of ViT/MLP-Mixer to Graphs

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}.

cs.CV↗

arXiv2023

Feature Collapse

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.

cs.LG↗

arXiv2022

Long-Tailed Learning Requires Feature Learning

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.

cs.LG↗

arXiv2022

Benchmarking Graph Neural Networks

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.

cs.LG↗

arXiv2022

Semantic Role Aware Correlation Transformer for Text to Video Retrieval

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.

cs.CV↗

arXiv2022

Learning to Untangle Genome Assembly with Graph Convolutional Networks

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.

q-bio.GN↗

arXiv2022

Combining Reinforcement Learning and Optimal Transport for the Traveling Salesman Problem

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.

cs.LG↗

arXiv2022

Graph Neural Networks with Learnable Structural and Positional Representations

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.

cs.LG↗