Victor Shirasuna

Eduardo Soares, Victor Shirasuna, Emilio Vital Brazil et al.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and $8\times289M$). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

Eduardo Soares, Emilio Vital Brazil, Victor Shirasuna et al.

We present PDE-FM, a modular foundation model for physics-informed machine learning that unifies spatial, spectral, and temporal reasoning across heterogeneous partial differential equation (PDE) systems. PDE-FM combines spatial-spectral tokenization, physics-aware conditioning, and a Mamba-based state-space backbone with an operator-theoretic decoder, enabling scalable and data-efficient modeling of complex physical dynamics. In contrast to task-specific neural operators, PDE-FM is pretrained once on diverse PDE datasets and can be transferred to new physical regimes without architectural or data-specific modifications. Evaluated on twelve 2D and 3D datasets from The Well benchmark - spanning hydrodynamic, radiative, elastic, and astrophysical phenomena - PDE-FM achieves state-of-the-art accuracy in six domains, reducing mean VRMSE by 46% relative to prior operator-learning baselines. The model demonstrates robust cross-physics generalization, excelling in turbulent and radiative systems while maintaining strong performance in linear and steady-state regimes. These results suggest that large-scale pretraining across diverse physical processes can yield transferable representations of dynamics, marking a step toward unified, foundation-level surrogates for multi-physics simulation and scientific discovery.