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Thomas Laurent

Thomas Laurent contributes to research discovery and scholarly infrastructure.

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Machine Learning cs.CY Genomics Software Engineering

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preprint2026arXiv

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.

preprint2026arXiv

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. 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.

preprint2022arXiv

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.

preprint2022arXiv

Learning the Travelling Salesperson Problem Requires Rethinking Generalization

End-to-end training of neural network solvers for graph combinatorial optimization problems such as the Travelling Salesperson Problem (TSP) have seen a surge of interest recently, but remain intractable and inefficient beyond graphs with few hundreds of nodes. While state-of-the-art learning-driven approaches for TSP perform closely to classical solvers when trained on trivially small sizes, they are unable to generalize the learnt policy to larger instances at practical scales. This work presents an end-to-end neural combinatorial optimization pipeline that unifies several recent papers in order to identify the inductive biases, model architectures and learning algorithms that promote generalization to instances larger than those seen in training. Our controlled experiments provide the first principled investigation into such zero-shot generalization, revealing that extrapolating beyond training data requires rethinking the neural combinatorial optimization pipeline, from network layers and learning paradigms to evaluation protocols. Additionally, we analyze recent advances in deep learning for routing problems through the lens of our pipeline and provide new directions to stimulate future research.

preprint2022arXiv

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.

preprint2022arXiv

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.

preprint2022arXiv

The Forgotten Margins of AI Ethics

How has recent AI Ethics literature addressed topics such as fairness and justice in the context of continued social and structural power asymmetries? We trace both the historical roots and current landmark work that have been shaping the field and categorize these works under three broad umbrellas: (i) those grounded in Western canonical philosophy, (ii) mathematical and statistical methods, and (iii) those emerging from critical data/algorithm/information studies. We also survey the field and explore emerging trends by examining the rapidly growing body of literature that falls under the broad umbrella of AI Ethics. To that end, we read and annotated peer-reviewed papers published over the past four years in two premier conferences: FAccT and AIES. We organize the literature based on an annotation scheme we developed according to three main dimensions: whether the paper deals with concrete applications, use-cases, and/or people's lived experience; to what extent it addresses harmed, threatened, or otherwise marginalized groups; and if so, whether it explicitly names such groups. We note that although the goals of the majority of FAccT and AIES papers were often commendable, their consideration of the negative impacts of AI on traditionally marginalized groups remained shallow. Taken together, our conceptual analysis and the data from annotated papers indicate that the field would benefit from an increased focus on ethical analysis grounded in concrete use-cases, people's experiences, and applications as well as from approaches that are sensitive to structural and historical power asymmetries.

preprint2021arXiv

The Transformer Network for the Traveling Salesman Problem

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.

preprint2019arXiv

A Mutation-based Approach for Assessing Weight Coverage of a Path Planner

Autonomous cars are subjected to several different kind of inputs (other cars, road structure, etc.) and, therefore, testing the car under all possible conditions is impossible. To tackle this problem, scenario-based testing for automated driving defines categories of different scenarios that should be covered. Although this kind of coverage is a necessary condition, it still does not guarantee that any possible behaviour of the autonomous car is tested. In this paper, we consider the path planner of an autonomous car that decides, at each timestep, the short-term path to follow in the next few seconds; such decision is done by using a weighted cost function that considers different aspects (safety, comfort, etc.). In order to assess whether all the possible decisions that can be taken by the path planner are covered by a given test suite T, we propose a mutation-based approach that mutates the weights of the cost function and then checks if at least one scenario of T kills the mutant. Preliminary experiments on a manually designed test suite show that some weights are easier to cover as they consider aspects that more likely occur in a scenario, and that more complicated scenarios (that generate more complex paths) are those that allow to cover more weights.

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