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Statistical shape modeling (SSM) is an enabling quantitative tool to study anatomical shapes in various medical applications. However, directly using 3D images in these applications still has a long way to go. Recent deep learning methods…

Understanding molecular structure and related knowledge is crucial for scientific research. Recent studies integrate molecular graphs with their textual descriptions to enhance molecular representation learning. However, they focus on the…

In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…

A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined…

Molecular property prediction is essential for applications such as drug discovery and toxicity assessment. While Graph Neural Networks (GNNs) have shown promising results by modeling molecules as molecular graphs, their reliance on…

Missing input sequences are common in medical imaging data, posing a challenge for deep learning models reliant on complete input data. In this work, inspired by MultiMAE [2], we develop a masked autoencoder (MAE) paradigm for multi-modal,…

Current 3D self-supervised learning methods of 3D scenes face a data desert issue, resulting from the time-consuming and expensive collecting process of 3D scene data. Conversely, 3D shape datasets are easier to collect. Despite this,…

Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage…

Accurate prediction of drug-target interactions (DTI) is critical for drug discovery. Existing methods often rely on single-modal representations (e.g., sequences or graphs) or combine only two modalities, overlooking 3D structural…

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts…

Fast and accurate simulation of dynamical systems is a fundamental challenge across scientific and engineering domains. Traditional numerical integrators often face a trade-off between accuracy and computational efficiency, while existing…

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount…

Learning-based simulators show great potential for simulating particle dynamics when 3D groundtruth is available, but per-particle correspondences are not always accessible. The development of neural rendering presents a new solution to…

Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we…

Learning representations through deep generative modeling is a powerful approach for dynamical modeling to discover the most simplified and compressed underlying description of the data, to then use it for other tasks such as prediction.…

Molecular property prediction constitutes a cornerstone of drug discovery and materials science, necessitating models capable of disentangling complex structure-property relationships across diverse molecular modalities. Existing approaches…

Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…

Quantifying similarity between neural representations -- e.g. hidden layer activation vectors -- is a perennial problem in deep learning and neuroscience research. Existing methods compare deterministic responses (e.g. artificial networks…

As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular…

Large-scale multimodal contrastive learning has recently achieved impressive success in learning rich and transferable representations, yet it remains fundamentally limited by the uniform treatment of feature dimensions and the neglect of…