Related papers: Unlocking High-Fidelity Molecular Generation from …

Brain network analysis plays an increasingly important role in studying brain function and the exploring of disease mechanisms. However, existing brain network construction tools have some limitations, including dependency on empirical…

Generating molecular structures with desired properties is a critical task with broad applications in drug discovery and materials design. We propose 3M-Diffusion, a novel multi-modal molecular graph generation method, to generate diverse,…

We introduce a new graph diffusion model for small molecule generation, DMol, which outperforms the state-of-the-art DiGress model in terms of validity by roughly 1.5% across all benchmarking datasets while reducing the number of diffusion…

Fine-tuned autoregressive models for graph-to-sequence generation (G2S) often struggle with factual grounding and edit sensitivity. To tackle these issues, we propose a non-autoregressive diffusion framework that generates text by iterative…

We introduce SeaDAG, a semi-autoregressive diffusion model for conditional generation of Directed Acyclic Graphs (DAGs). Considering their inherent layer-wise structure, we simulate layer-wise autoregressive generation by designing…

We present a novel model-based deep learning solution for the inverse problem of localizing sources of network diffusion. Starting from first graph signal processing (GSP) principles, we show that the problem reduces to joint (blind)…

Graph Neural Networks (GNNs) have proven effective in various medical imaging applications, such as automated disease diagnosis. However, due to the local neighborhood aggregation paradigm in message passing which characterizes these…

Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable…

Generating diverse, all-atom conformational ensembles of dynamic proteins such as G-protein-coupled receptors (GPCRs) is critical for understanding their function, yet most generative models simplify atomic detail or ignore conformational…

The efficiency of multi-agent systems driven by large language models (LLMs) largely hinges on their communication topology. However, designing an optimal topology is a non-trivial challenge, as it requires balancing competing objectives…

Graph domain adaptation (GDA) aims to transfer knowledge from a labeled source graph to an unlabeled target graph under distribution shifts. However, existing methods are largely feature-centric and overlook structural discrepancies, which…

Masked Diffusion Models (MDMs) offer a promising alternative to autoregressive language models by enabling parallel token generation and bidirectional context modeling. However, their inference speed is significantly limited by the…

Dual-target therapeutic strategies have become a compelling approach and attracted significant attention due to various benefits, such as their potential in overcoming drug resistance in cancer therapy. Considering the tremendous success…

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are…

Molecular representation learning has shown great success in advancing AI-based drug discovery. The core of many recent works is based on the fact that the 3D geometric structure of molecules provides essential information about their…

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) using one formulation. We first formulate prediction…

The open-world test dataset is often mixed with out-of-distribution (OOD) samples, where the deployed models will struggle to make accurate predictions. Traditional detection methods need to trade off OOD detection and in-distribution (ID)…

Graph generation is a critical yet challenging task, as empirical analyses require a deep understanding of complex, non-Euclidean structures. Diffusion models have recently made significant advances in graph generation, but these models are…

Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…