arXiv subjects

Mohamed Amine Ketata

Publications and source records attributed to Mohamed Amine Ketata.

5 recordsLinked to original sources

arXiv2026

CDMD: A Cross-Dataset Mixed-Type Diffusion Model for Tabular Data

Generative models for tabular data are typically trained separately for each dataset, limiting knowledge transfer and requiring the storage of many specialized models. In this paper, we introduce CDMD, a tabular diffusion model trained jointly across heterogeneous datasets with different schemas and variable numbers of numerical and categorical features. Unlike existing cross-dataset tabular diffusion models that operate in continuous representation spaces, CDMD defines diffusion directly over the mixed-type feature space and is trained end-to-end. To accommodate heterogeneous categorical domains, we introduce a schema-restricted reverse-process parameterization for masked diffusion models, in which the output space dynamically adapts to each feature's vocabulary. We then compose numerical and categorical feature-level diffusion processes into a schema-dependent row-level process. A shared schema-aware Transformer denoiser captures dependencies between features and parameterizes the reverse process across varying schemas. On seven real-world datasets, a single jointly trained CDMD achieves the highest average generation quality among strong single-dataset and cross-dataset baselines, while using substantially fewer total parameters than the collection of separately trained models. Furthermore, pre-training on a corpus of 337 datasets improves generation on previously unseen datasets under both limited target data and limited adaptation epochs. These results demonstrate the potential of direct mixed-type diffusion for shared and transferable tabular data generation. Our code is available at https://github.com/ketatam/cdmd.

cs.LG↗

arXiv2026

Joint Relational Database Generation via Graph-Conditional Diffusion Models

Building generative models for relational databases (RDBs) is important for many applications, such as privacy-preserving data release and augmenting real datasets. However, most prior works either focus on single-table generation or adapt single-table models to the multi-table setting by relying on autoregressive factorizations and sequential generation. These approaches limit parallelism, restrict flexibility in downstream applications, and compound errors due to commonly made conditional independence assumptions. In this paper, we propose a fundamentally different approach: jointly modeling all tables in an RDB without imposing any table order. By using a natural graph representation of RDBs, we propose the Graph-Conditional Relational Diffusion Model (GRDM), which leverages a graph neural network to jointly denoise row attributes and capture complex inter-table dependencies. Extensive experiments on six real-world RDBs demonstrate that our approach substantially outperforms autoregressive baselines in modeling multi-hop inter-table correlations and achieves state-of-the-art performance on single-table fidelity metrics. Our code is available at https://github.com/ketatam/rdb-diffusion.

cs.LG↗

arXiv2024

Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space

We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and learns the inverse map using an E(n)-Equivariant Graph Neural Network (EGNN). The induced point cloud-structured latent space is well-suited to apply existing 3D molecular generative models. This approach simplifies the graph generation problem - without relying on molecular fragments nor autoregressive decoding - into a point cloud generation problem followed by node and edge classification tasks. Further, we propose a novel similarity-constrained optimization scheme for 3D diffusion models based on inpainting and guidance. As a concrete implementation of our framework, we develop EDM-SyCo based on the E(3) Equivariant Diffusion Model (EDM). EDM-SyCo achieves state-of-the-art performance in distribution learning of molecular graphs, outperforming the best non-autoregressive methods by more than 30% on ZINC250K and 16% on the large-scale GuacaMol dataset while improving conditional generation by up to 3.9 times.

cs.LG↗

arXiv2023

Uncertainty Estimation for Molecules: Desiderata and Methods

Graph Neural Networks (GNNs) are promising surrogates for quantum mechanical calculations as they establish unprecedented low errors on collections of molecular dynamics (MD) trajectories. Thanks to their fast inference times they promise to accelerate computational chemistry applications. Unfortunately, despite low in-distribution (ID) errors, such GNNs might be horribly wrong for out-of-distribution (OOD) samples. Uncertainty estimation (UE) may aid in such situations by communicating the model's certainty about its prediction. Here, we take a closer look at the problem and identify six key desiderata for UE in molecular force fields, three 'physics-informed' and three 'application-focused' ones. To overview the field, we survey existing methods from the field of UE and analyze how they fit to the set desiderata. By our analysis, we conclude that none of the previous works satisfies all criteria. To fill this gap, we propose Localized Neural Kernel (LNK) a Gaussian Process (GP)-based extension to existing GNNs satisfying the desiderata. In our extensive experimental evaluation, we test four different UE with three different backbones and two datasets. In out-of-equilibrium detection, we find LNK yielding up to 2.5 and 2.1 times lower errors in terms of AUC-ROC score than dropout or evidential regression-based methods while maintaining high predictive performance.

physics.chem-ph↗

arXiv2023

DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models

Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem with significant performance boosts over both traditional and deep learning baselines. In this work, we propose a similar approach for rigid protein-protein docking: DiffDock-PP is a diffusion generative model that learns to translate and rotate unbound protein structures into their bound conformations. We achieve state-of-the-art performance on DIPS with a median C-RMSD of 4.85, outperforming all considered baselines. Additionally, DiffDock-PP is faster than all search-based methods and generates reliable confidence estimates for its predictions. Our code is publicly available at $\texttt{https://github.com/ketatam/DiffDock-PP}$

q-bio.BM↗