11 accepted papers
In this work, we propose K-Flow, a novel generative learning paradigm that flows along the $K$-amplitude domain, where $K$ is a scaling parameter that organizes projected coefficients (frequency bands), and amplitude refers to the norm of such coefficients. We instantiate K-Flow with three concrete…
Transformer-based autoregressive models have emerged as a unifying paradigm across modalities such as text and images, but their extension to 3D molecule generation remains underexplored. The gap stems from two fundamental challenges: (1) how to tokenize molecules into a canonical 1D sequence of tok…
Retrosynthesis prediction focuses on identifying reactants capable of synthesizing a target product. Typically, the retrosynthesis prediction involves two phases: Reaction Center Identification and Reactant Generation. However, we argue that most existing methods suffer from two limitations in the t…
Denoising diffusion (score-based) generative models have become a popular choice for modeling complex data. Recently, a deep connection between forward-backward stochastic differential equations (SDEs) and diffusion-based models has been established, leading to the development of new SDE variants su…
Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research…
Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these network architectures through a local-to-global analysis lacks tod…
Recently, artificial intelligence for drug discovery has raised increasing interest in both machine learning and chemistry domains. The fundamental building block for drug discovery is molecule geometry and thus, the molecule's geometrical representation is the main bottleneck to better utilize mach…
Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building b…
Group equivariance (e.g. SE(3) equivariance) is a critical physical symmetry in science, from classical and quantum physics to computational biology. It enables robust and accurate prediction under arbitrary reference transformations. In light of this, great efforts have been put on encoding this sy…
Graph convolutional networks (GCNs) and their variants have achieved great success in dealing with graph-structured data. Nevertheless, it is well known that deep GCNs suffer from the over-smoothing problem, where node representations tend to be indistinguishable as more layers are stacked up. The t…
The prevailing thinking is that orthogonal weights are crucial to enforcing dynamical isometry and speeding up training. The increase in learning speed that results from orthogonal initialization in linear networks has been well-proven. However, while the same is believed to also hold for nonlinear…