arXiv subjects

Weitao Du

Publications and source records attributed to Weitao Du.

At least 19 recordsLinked to original sources

arXiv2026

InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames

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 tokens that is invariant to both SE(3) transformations and atom index permutations, and (2) how to design an architecture capable of modeling hybrid atom-based tokens that couple discrete atom types with continuous 3D coordinates. To address these challenges, we introduce InertialAR. It first performs generation-oriented canonical tokenization by aligning each molecule to a canonical inertial frame and reordering atoms, thereby converting arbitrary 3D structures into a unique, SE(3)- and permutation-invariant sequence of tokens for autoregressive generation. Built upon this canonical tokenization, we propose geometric positional encoding (GeoPE), which endows Transformer attention with 3D geometric awareness. Finally, InertialAR utilizes a hierarchical autoregressive paradigm to decode the next atom, consecutively predicting the atom type and 3D coordinates via Diffusion Loss. Experimentally, InertialAR achieves state-of-the-art performance on 8 of the 10 evaluation metrics for unconditional generation across QM9, GEOM-Drugs, and B3LYP. Moreover, it significantly outperforms baselines in controllable generation for targeted chemical functionality, attaining state-of-the-art results across all 5 metrics. Code is available at github.com/HaoruiLi46/InertialAR.

cs.LG↗

arXiv2026

Frequency-Forcing: From Scaling-as-Time to Soft Frequency Guidance

While standard flow-matching models transport noise to data uniformly, incorporating an explicit generation order - specifically, establishing coarse, low-frequency structure before fine detail - has proven highly effective for synthesizing natural images. Two recent works offer distinct paradigms for this. K-Flow imposes a hard frequency constraint by reinterpreting a frequency scaling variable as flow time, running the trajectory inside a transformed amplitude space. Latent Forcing provides a soft ordering mechanism by coupling the pixel flow with an auxiliary semantic latent flow via asynchronous time schedules, leaving the pixel interpolation path itself untouched. Viewed from the angle of improving pixel generation, we observe that forcing - guiding generation with an earlier-maturing auxiliary stream - offers a highly compatible route to scale-ordered generation without rewriting the core flow coordinate. Building on this, we propose Frequency-Forcing, which realizes K-Flow's frequency ordering through Latent Forcing's soft mechanism: a standard pixel flow is guided by an auxiliary low-frequency stream that matures earlier in time. Unlike Latent Forcing, whose scratchpad relies on a heavy pretrained encoder (e.g., DINO), our frequency scratchpad is derived from the data itself via a lightweight learnable wavelet packet transform. We term this a self-forcing signal, which avoids external dependencies while learning a basis better adapted to data statistics than the fixed bases used in hard frequency flows. On ImageNet-256, Frequency-Forcing consistently improves FID over strong pixel- and latent-space baselines, and naturally composes with a semantic stream to yield further gains. This illustrates that forcing-based scale ordering is a versatile, path-preserving alternative to hard frequency flows.

cs.LG↗

arXiv2025

Flow Along the K-Amplitude for Generative Modeling

In this work, we propose a novel generative learning paradigm, K-Flow, an algorithm that flows along the $K$-amplitude. Here, $k$ is a scaling parameter that organizes frequency bands (or projected coefficients), and amplitude describes the norm of such projected coefficients. By incorporating the $K$-amplitude decomposition, K-Flow enables flow matching across the scaling parameter as time. We discuss three venues and six properties of K-Flow, from theoretical foundations, energy and temporal dynamics, and practical applications, respectively. Specifically, from the practical usage perspective, K-Flow allows steerable generation by controlling the information at different scales. To demonstrate the effectiveness of K-Flow, we conduct experiments on unconditional image generation, class-conditional image generation, and molecule assembly generation. Additionally, we conduct three ablation studies to demonstrate how K-Flow steers scaling parameter to effectively control the resolution of image generation.

cs.LG↗

arXiv2025

AlphaNet: Scaling Up Local-frame-based Atomistic Interatomic Potential

Molecular dynamics simulations demand an unprecedented combination of accuracy and scalability to tackle grand challenges in catalysis and materials design. To bridge this gap, we present AlphaNet, a local-frame-based equivariant model that simultaneously improves computational efficiency and predictive precision for interatomic interactions. By constructing equivariant local frames with learnable geometric transitions, AlphaNet encodes atomic environments with enhanced representational capacity, achieving state-of-the-art accuracy in energy and force predictions. Extensive benchmarks on large-scale datasets spanning molecular reactions, crystal stability, and surface catalysis (Matbench Discovery and OC2M) demonstrate its superior performance over existing neural network interatomic potentials while ensuring scalability across diverse system sizes with varying types of interatomic interactions. The synergy of accuracy, efficiency, and transferability positions AlphaNet as a transformative tool for modeling multiscale phenomena, decoding dynamics in catalysis and functional interfaces, with direct implications for accelerating the discovery of complex molecular systems and functional materials.

cs.LG↗

arXiv2025

A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining

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 has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

cs.LG↗

arXiv2025

GDiffRetro: Retrosynthesis Prediction with Dual Graph Enhanced Molecular Representation and Diffusion Generation

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 two phases: (i) Existing models do not adequately capture the ``face'' information in molecular graphs for the reaction center identification. (ii) Current approaches for the reactant generation predominantly use sequence generation in a 2D space, which lacks versatility in generating reasonable distributions for completed reactive groups and overlooks molecules' inherent 3D properties. To overcome the above limitations, we propose GDiffRetro. For the reaction center identification, GDiffRetro uniquely integrates the original graph with its corresponding dual graph to represent molecular structures, which helps guide the model to focus more on the faces in the graph. For the reactant generation, GDiffRetro employs a conditional diffusion model in 3D to further transform the obtained synthon into a complete reactant. Our experimental findings reveal that GDiffRetro outperforms state-of-the-art semi-template models across various evaluative metrics.

cs.AI↗

arXiv2024

Sculpting Molecules in Text-3D Space: A Flexible Substructure Aware Framework for Text-Oriented Molecular Optimization

The integration of deep learning, particularly AI-Generated Content, with high-quality data derived from ab initio calculations has emerged as a promising avenue for transforming the landscape of scientific research. However, the challenge of designing molecular drugs or materials that incorporate multi-modality prior knowledge remains a critical and complex undertaking. Specifically, achieving a practical molecular design necessitates not only meeting the diversity requirements but also addressing structural and textural constraints with various symmetries outlined by domain experts. In this article, we present an innovative approach to tackle this inverse design problem by formulating it as a multi-modality guidance optimization task. Our proposed solution involves a textural-structure alignment symmetric diffusion framework for the implementation of molecular optimization tasks, namely 3DToMolo. 3DToMolo aims to harmonize diverse modalities including textual description features and graph structural features, aligning them seamlessly to produce molecular structures adhere to specified symmetric structural and textural constraints by experts in the field. Experimental trials across three guidance optimization settings have shown a superior hit optimization performance compared to state-of-the-art methodologies. Moreover, 3DToMolo demonstrates the capability to discover potential novel molecules, incorporating specified target substructures, without the need for prior knowledge. This work not only holds general significance for the advancement of deep learning methodologies but also paves the way for a transformative shift in molecular design strategies. 3DToMolo creates opportunities for a more nuanced and effective exploration of the vast chemical space, opening new frontiers in the development of molecular entities with tailored properties and functionalities.

cs.LG↗

arXiv2024

A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of improving the efficiency of MD simulations through better numerical methods and, more recently, by utilizing machine learning (ML) methods. Yet, challenges remain, such as accurate modeling of extended-timescale simulations. To address this issue, we propose NeuralMD, the first ML surrogate that can facilitate numerical MD and provide accurate simulations in protein-ligand binding dynamics. We propose a principled approach that incorporates a novel physics-informed multi-grained group symmetric framework. Specifically, we propose (1) the BindingNet model that satisfies group symmetry using vector frames and captures the multi-level protein-ligand interactions, and (2) an augmented neural differential equation solver that learns the trajectory under Newtonian mechanics. For the experiment, we design ten single-trajectory and three multi-trajectory binding simulation tasks. We demonstrate the efficiency and effectiveness of NeuralMD, achieving over 1K$\times$ speedup compared to standard numerical MD simulations. NeuralMD also outperforms all other ML approaches, achieving up to 15$\times$ reduction in reconstruction error and 70% increase in validity. Additionally, we qualitatively illustrate that the oscillations in the predicted trajectories align more closely with ground-truth dynamics than those of other machine-learning methods. We believe NeuralMD paves the foundation for a new research paradigm in simulating protein-ligand dynamics.

cs.LG↗

arXiv2024

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

q-bio.QM↗

arXiv2024

Structure-based Drug Design with Equivariant Diffusion Models

Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. Generative SBDD methods leverage structural data of drugs in complex with their protein targets to propose new drug candidates. These approaches typically place one atom at a time in an autoregressive fashion using the binding pocket as well as previously added ligand atoms as context in each step. Recently a surge of diffusion generative models has entered this domain which hold promise to capture the statistical properties of natural ligands more faithfully. However, most existing methods focus exclusively on bottom-up de novo design of compounds or tackle other drug development challenges with task-specific models. The latter requires curation of suitable datasets, careful engineering of the models and retraining from scratch for each task. Here we show how a single pre-trained diffusion model can be applied to a broader range of problems, such as off-the-shelf property optimization, explicit negative design, and partial molecular design with inpainting. We formulate SBDD as a 3D-conditional generation problem and present DiffSBDD, an SE(3)-equivariant diffusion model that generates novel ligands conditioned on protein pockets. Our in silico experiments demonstrate that DiffSBDD captures the statistics of the ground truth data effectively. Furthermore, we show how additional constraints can be used to improve the generated drug candidates according to a variety of computational metrics. These results support the assumption that diffusion models represent the complex distribution of structural data more accurately than previous methods, and are able to incorporate additional design objectives and constraints changing nothing but the sampling strategy.

q-bio.BM↗

arXiv2024

CGCL: Collaborative Graph Contrastive Learning without Handcrafted Graph Data Augmentations

Unsupervised graph representation learning is a non-trivial topic. The success of contrastive methods in the unsupervised representation learning on structured data inspires similar attempts on the graph. Existing graph contrastive learning (GCL) aims to learn the invariance across multiple augmentation views, which renders it heavily reliant on the handcrafted graph augmentations. However, inappropriate graph data augmentations can potentially jeopardize such invariance. In this paper, we show the potential hazards of inappropriate augmentations and then propose a novel Collaborative Graph Contrastive Learning framework (CGCL). This framework harnesses multiple graph encoders to observe the graph. Features observed from different encoders serve as the contrastive views in contrastive learning, which avoids inducing unstable perturbation and guarantees the invariance. To ensure the collaboration among diverse graph encoders, we propose the concepts of asymmetric architecture and complementary encoders as the design principle. To further prove the rationality, we utilize two quantitative metrics to measure the assembly of CGCL respectively. Extensive experiments demonstrate the advantages of CGCL in unsupervised graph-level representation learning and the potential of collaborative framework. The source code for reproducibility is available at https://github.com/zhangtia16/CGCL

cs.LG↗

arXiv2024

A quatum inspired neural network for geometric modeling

By conceiving physical systems as 3D many-body point clouds, geometric graph neural networks (GNNs), such as SE(3)/E(3) equivalent GNNs, have showcased promising performance. In particular, their effective message-passing mechanics make them adept at modeling molecules and crystalline materials. However, current geometric GNNs only offer a mean-field approximation of the many-body system, encapsulated within two-body message passing, thus falling short in capturing intricate relationships within these geometric graphs. To address this limitation, tensor networks, widely employed by computational physics to handle manybody systems using high-order tensors, have been introduced. Nevertheless, integrating these tensorized networks into the message-passing framework of GNNs faces scalability and symmetry conservation (e.g., permutation and rotation) challenges. In response, we introduce an innovative equivariant Matrix Product State (MPS)-based message-passing strategy, through achieving an efficient implementation of the tensor contraction operation. Our method effectively models complex many-body relationships, suppressing mean-field approximations, and captures symmetries within geometric graphs. Importantly, it seamlessly replaces the standard message-passing and layer-aggregation modules intrinsic to geometric GNNs. We empirically validate the superior accuracy of our approach on benchmark tasks, including predicting classical Newton systems and quantum tensor Hamiltonian matrices. To our knowledge, our approach represents the inaugural utilization of parameterized geometric tensor networks.

cs.LG↗

arXiv2023

Molecule Joint Auto-Encoding: Trajectory Pretraining with 2D and 3D Diffusion

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 machine learning techniques for drug discovery. In this work, we propose a pretraining method for molecule joint auto-encoding (MoleculeJAE). MoleculeJAE can learn both the 2D bond (topology) and 3D conformation (geometry) information, and a diffusion process model is applied to mimic the augmented trajectories of such two modalities, based on which, MoleculeJAE will learn the inherent chemical structure in a self-supervised manner. Thus, the pretrained geometrical representation in MoleculeJAE is expected to benefit downstream geometry-related tasks. Empirically, MoleculeJAE proves its effectiveness by reaching state-of-the-art performance on 15 out of 20 tasks by comparing it with 12 competitive baselines.

cs.LG↗

arXiv2023

Power-law Dynamic arising from machine learning

We study a kind of new SDE that was arisen from the research on optimization in machine learning, we call it power-law dynamic because its stationary distribution cannot have sub-Gaussian tail and obeys power-law. We prove that the power-law dynamic is ergodic with unique stationary distribution, provided the learning rate is small enough. We investigate its first exist time. In particular, we compare the exit times of the (continuous) power-law dynamic and its discretization. The comparison can help guide machine learning algorithm.

stat.ML↗

arXiv2023

Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials

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 blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science (e.g., physics, chemistry, & biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 46 diverse datasets, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications.

cs.LG↗

arXiv2023

A new perspective on building efficient and expressive 3D equivariant graph neural networks

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 networks through a local-to-global analysis lacks today. In this paper, we propose a local hierarchy of 3D isomorphism to evaluate the expressive power of equivariant GNNs and investigate the process of representing global geometric information from local patches. Our work leads to two crucial modules for designing expressive and efficient geometric GNNs; namely local substructure encoding (LSE) and frame transition encoding (FTE). To demonstrate the applicability of our theory, we propose LEFTNet which effectively implements these modules and achieves state-of-the-art performance on both scalar-valued and vector-valued molecular property prediction tasks. We further point out the design space for future developments of equivariant graph neural networks. Our codes are available at \url{https://github.com/yuanqidu/LeftNet}.

cs.LG↗

arXiv2022

An Efficient Lorentz Equivariant Graph Neural Network for Jet Tagging

Deep learning methods have been increasingly adopted to study jets in particle physics. Since symmetry-preserving behavior has been shown to be an important factor for improving the performance of deep learning in many applications, Lorentz group equivariance - a fundamental spacetime symmetry for elementary particles - has recently been incorporated into a deep learning model for jet tagging. However, the design is computationally costly due to the analytic construction of high-order tensors. In this article, we introduce LorentzNet, a new symmetry-preserving deep learning model for jet tagging. The message passing of LorentzNet relies on an efficient Minkowski dot product attention. Experiments on two representative jet tagging benchmarks show that LorentzNet achieves the best tagging performance and improves significantly over existing state-of-the-art algorithms. The preservation of Lorentz symmetry also greatly improves the efficiency and generalization power of the model, allowing LorentzNet to reach highly competitive performance when trained on only a few thousand jets. Code and models are available at \url{https://github.com/sdogsq/LorentzNet-release}.

hep-ph↗

arXiv2022

SE(3) Equivariant Graph Neural Networks with Complete Local Frames

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 symmetry into deep neural networks, which has been shown to improve the generalization performance and data efficiency for downstream tasks. Constructing an equivariant neural network generally brings high computational costs to ensure expressiveness. Therefore, how to better trade-off the expressiveness and computational efficiency plays a core role in the design of the equivariant deep learning models. In this paper, we propose a framework to construct SE(3) equivariant graph neural networks that can approximate the geometric quantities efficiently. Inspired by differential geometry and physics, we introduce equivariant local complete frames to graph neural networks, such that tensor information at given orders can be projected onto the frames. The local frame is constructed to form an orthonormal basis that avoids direction degeneration and ensure completeness. Since the frames are built only by cross product operations, our method is computationally efficient. We evaluate our method on two tasks: Newton mechanics modeling and equilibrium molecule conformation generation. Extensive experimental results demonstrate that our model achieves the best or competitive performance in two types of datasets.

cs.CE↗