Nagham Osman

Clement Vignac, Nagham Osman, Laura Toni et al.

This work introduces MiDi, a novel diffusion model for jointly generating molecular graphs and their corresponding 3D arrangement of atoms. Unlike existing methods that rely on predefined rules to determine molecular bonds based on the 3D conformation, MiDi offers an end-to-end differentiable approach that streamlines the molecule generation process. Our experimental results demonstrate the effectiveness of this approach. On the challenging GEOM-DRUGS dataset, MiDi generates 92% of stable molecules, against 6% for the previous EDM model that uses interatomic distances for bond prediction, and 40% using EDM followed by an algorithm that directly optimize bond orders for validity. Our code is available at github.com/cvignac/MiDi.

Nagham Osman, Vittorio Lembo, Giovanni Bottegoni et al.

Hit identification is a critical yet resource-intensive step in the drug discovery pipeline, traditionally relying on high-throughput screening of large compound libraries. Despite advancements in virtual screening, these methods remain time-consuming and costly. Recent progress in deep learning has enabled the development of generative models capable of learning complex molecular representations and generating novel compounds de novo. However, using ML to replace the entire drug-discovery pipeline is highly challenging. In this work, we rather investigate whether generative models can replace one step of the pipeline: hit-like molecule generation. To the best of our knowledge, this is the first study to explicitly frame hit-like molecule generation as a standalone task and empirically test whether generative models can directly support this stage of the drug discovery pipeline. Specifically, we investigate if such models can be trained to generate hit-like molecules, enabling direct incorporation into, or even substitution of, traditional hit identification workflows. We propose an evaluation framework tailored to this task, integrating physicochemical, structural, and bioactivity-related criteria within a multi-stage filtering pipeline that defines the hit-like chemical space. Two autoregressive and one diffusion-based generative models were benchmarked across various datasets and training settings, with outputs assessed using standard metrics and target-specific docking scores. Our results show that these models can generate valid, diverse, and biologically relevant compounds across multiple targets, with a few selected GSK-3$β$ hits synthesized and confirmed active in vitro. We also identify key limitations in current evaluation metrics and available training data.

Nagham Osman, Keyue Jiang, Davide Buffelli et al.

Graph generation is a critical task across scientific domains. Existing methods fall broadly into two categories: autoregressive models, which iteratively expand graphs, and one-shot models, such as diffusion, which generate the full graph at once. In this work, we provide an analysis of these two paradigms and reveal a key trade-off: autoregressive models stand out in capturing fine-grained local structures, such as degree and clustering properties, whereas one-shot models excel at modeling global patterns, such as spectral distributions. Building on this, we propose LGDC (latent graph diffusion via spectrum-preserving coarsening), a hybrid framework that combines strengths of both approaches. LGDC employs a spectrum-preserving coarsening-decoarsening to bidirectionally map between graphs and a latent space, where diffusion efficiently generates latent graphs before expansion restores detail. This design captures both local and global properties with improved efficiency. Empirically, LGDC matches autoregressive models on locally structured datasets (Tree) and diffusion models on globally structured ones (Planar, Community-20), validating the benefits of hybrid generation.