Molecular conformations, the stable three-dimensional structures corresponding to local minima on the potential energy surface, govern key molecular properties and consequently underpin a wide range of downstream tasks. However, contemporary learning-based methods often lack scalability, interpretability, and robustness, thereby significantly constraining their practical effectiveness and reliability. In this context, I will introduce my ongoing explorations and the proposed research plan to address these challenges, with the ultimate objective of developing conformation‑centric universal foundation models to accelerate scientific discovery.

The generative mechanisms behind real-world event sequences are often heterogeneous, leading to data that possesses inherent clustering structures. However, most existing temporal point processes (TPPs) treat different event sequences independently, without leveraging the clustering structures when predicting events. In this study, we design and learn a novel semi-transductive temporal point process (ST-TPP), which explicitly improves prediction performance by co-training sequence clusters. In particular, given a set of event sequences, our method learns a neural TPP together with cluster centers of the sequences. Besides maximizing the likelihood of the event sequences, we leverage a data-based kernel matrix and prior knowledge to regularize the sequence embeddings, leading to a Gromov-Wasserstein barycentric (GWB) regularizer. Based on the optimal transport plans associated with the GWB regularizer, we derive the cluster centers by the push-forward of the sequence embeddings. When a new sequence comes, the learned model first assigns a cluster center to the sequence and then jointly encodes the sequence and the cluster center to predict future events, leading to a semi-transductive prediction scheme. Experiments demonstrate that ST-TPP achieves competitive sequence clustering results and strong prediction performance.

Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing conformation generation methods for small molecules and proteins, these methods struggle to generate polymer conformations due to their unique structural characteristics. Meanwhile, the scarcity of polymer conformation datasets further limits progress, making this important area largely unexplored. In this work, we propose PolyConf, a pioneering tailored polymer conformation generation method that leverages hierarchical generative models to unlock new possibilities. Specifically, we decompose the polymer conformation into a series of local conformations (i.e., the conformations of its repeating units), generating these local conformations through an autoregressive model, and then generating their orientation transformations via a diffusion model to assemble them into the complete polymer conformation. Moreover, we develop the first benchmark with a high-quality polymer conformation dataset derived from molecular dynamics simulations to boost related research in this area. The comprehensive evaluation demonstrates that PolyConf consistently outperforms existing conformation generation methods, thus facilitating advancements in polymer modeling and simulation. The whole work is available at https://polyconf-icml25.github.io.

Predicting molecular ground-state conformation (i.e., energy-minimized conformation) is crucial for many chemical applications such as molecular docking and property prediction. Classic energy-based simulation is time-consuming when solving this problem, while existing learning-based methods have advantages in computational efficiency but sacrifice accuracy and interpretability. In this work, we propose a novel and effective method to bridge the energy-based simulation and the learning-based strategy, which designs and learns a Wasserstein gradient flow-driven SE(3)-Transformer, called WGFormer, for ground-state conformation prediction. Specifically, our method tackles this task within an auto-encoding framework, which encodes low-quality conformations by the proposed WGFormer and decodes corresponding ground-state conformations by an MLP. The architecture of WGFormer corresponds to Wasserstein gradient flows --- it optimizes conformations by minimizing an energy function defined on the latent mixture models of atoms, thereby significantly improving performance and interpretability. Extensive experiments demonstrate that our method consistently outperforms state-of-the-art competitors, providing a new and insightful paradigm to predict ground-state conformation. The code is available at https://github.com/FanmengWang/WGFormer.

Polymers are high-molecular-weight compounds constructed by the covalent bonding of numerous identical or similar monomers so that their 3D structures are complex yet exhibit unignorable regularity. Typically, the properties of a polymer, such as plasticity, conductivity, bio-compatibility, and so on, are highly correlated with its 3D structure. However, existing polymer property prediction methods heavily rely on the information learned from polymer SMILES sequences (P-SMILES strings) while ignoring crucial 3D structural information, resulting in sub-optimal performance. In this work, we propose MMPolymer, a novel multimodal multitask pretraining framework incorporating polymer 1D sequential and 3D structural information to encourage downstream polymer property prediction tasks. Besides, considering the scarcity of polymer 3D data, we further introduce the "Star Substitution" strategy to extract 3D structural information effectively. During pretraining, in addition to predicting masked tokens and recovering clear 3D coordinates, MMPolymer achieves the cross-modal alignment of latent representations. Then we further fine-tune the pretrained MMPolymer for downstream polymer property prediction tasks in the supervised learning paradigm. Experiments show that MMPolymer achieves state-of-the-art performance in downstream property prediction tasks. Moreover, given the pretrained MMPolymer, utilizing merely a single modality in the fine-tuning phase can also outperform existing methods, showcasing the exceptional capability of MMPolymer in polymer feature extraction and utilization.

Molecular perception aims to construct 3D molecules from 3D atom clouds (i.e., atom types and corresponding 3D coordinates), determining bond connections, bond orders, and other molecular attributes within molecules. It is essential for realizing many applications in cheminformatics and bioinformatics, such as modeling quantum chemistry-derived molecular structures in protein-ligand complexes. Additionally, many molecular generation methods can only generate molecular 3D atom clouds, requiring molecular perception as a necessary post-processing. However, existing molecular perception methods mainly rely on predefined chemical rules and fail to leverage 3D geometric information, whose performance is sub-optimal fully. In this study, we propose MPerformer, an SE(3) Transformer-based molecular perceptron exhibiting SE(3)-invariance, to construct 3D molecules from 3D atom clouds efficiently. Besides, we propose a multi-task pretraining-and-finetuning paradigm to learn this model. In the pretraining phase, we jointly minimize an attribute prediction loss and an atom cloud reconstruction loss, mitigating the data imbalance issue of molecular attributes and enhancing the robustness and generalizability of the model. Experiments show that MPerformer significantly outperforms state-of-the-art molecular perception methods in precision and robustness, benefiting various molecular generation scenarios.