Author name cluster

Lihao Wang

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7 papers

2 author rows

ICLR Conference 2025 Conference Paper

ProteinBench: A Holistic Evaluation of Protein Foundation Models

Fei Ye
Zaixiang Zheng
Dongyu Xue
Yuning Shen
Lihao Wang
Yiming Ma
Yan Wang
Xinyou Wang

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

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NeurIPS Conference 2025 Conference Paper

Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression

Yuning Shen
Lihao Wang
Huizhuo Yuan
Yan Wang
Bangji Yang
Quanquan Gu

Understanding protein dynamics is critical for elucidating their biological functions. The increasing availability of molecular dynamics (MD) data enables the training of deep generative models to efficiently explore the conformational space of proteins. However, existing approaches either fail to explicitly capture the temporal dependencies between conformations or do not support direct generation of time-independent samples. To address these limitations, we introduce ConfRover, an autoregressive model that simultaneously learns protein conformation and dynamics from MD trajectory data, supporting both time-dependent and time-independent sampling. At the core of our model is a modular architecture comprising: (i) an encoding layer, adapted from protein folding models, that embeds protein-specific information and conformation at each time frame into a latent space; (ii) a temporal module, a sequence model that captures conformational dynamics across frames; and (iii) an SE(3) diffusion model as the structure decoder, generating conformations in continuous space. Experiments on ATLAS, a large-scale protein MD dataset of diverse structures, demonstrate the effectiveness of our model in learning conformational dynamics and supporting a wide range of downstream tasks. ConfRover is the first model to sample both protein conformations and trajectories within a single framework, offering a novel and flexible approach for learning from protein MD data.

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ICML Conference 2024 Conference Paper

Autaptic Synaptic Circuit Enhances Spatio-temporal Predictive Learning of Spiking Neural Networks

Lihao Wang
Zhaofei Yu

Spiking Neural Networks (SNNs) emulate the integrated-fire-leak mechanism found in biological neurons, offering a compelling combination of biological realism and energy efficiency. In recent years, they have gained considerable research interest. However, existing SNNs predominantly rely on the Leaky Integrate-and-Fire (LIF) model and are primarily suited for simple, static tasks. They lack the ability to effectively model long-term temporal dependencies and facilitate spatial information interaction, which is crucial for tackling complex, dynamic spatio-temporal prediction tasks. To tackle these challenges, this paper draws inspiration from the concept of autaptic synapses in biology and proposes a novel Spatio-Temporal Circuit (STC) model. The STC model integrates two learnable adaptive pathways, enhancing the spiking neurons’ temporal memory and spatial coordination. We conduct theoretical analysis of the dynamic parameters in the STC model, highlighting their contribution in establishing long-term memory and mitigating the issue of gradient vanishing. Through extensive experiments on multiple spatio-temporal prediction datasets, we demonstrate that our model outperforms other adaptive models. Furthermore, our model is compatible with existing spiking neuron models, thereby augmenting their dynamic representations. In essence, our work enriches the specificity and topological complexity of SNNs.

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ICML Conference 2024 Conference Paper

Protein Conformation Generation via Force-Guided SE(3) Diffusion Models

Yan Wang
Lihao Wang
Yuning Shen
Yiqun Wang
Huizhuo Yuan
Yue Wu
Quanquan Gu

The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event sampling and long equilibration time problems, hindering their applications in general protein systems. Recently, deep generative modeling techniques, especially diffusion models, have been employed to generate novel protein conformations. However, existing score-based diffusion methods cannot properly incorporate important physical prior knowledge to guide the generation process, causing large deviations in the sampled protein conformations from the equilibrium distribution. In this paper, to overcome these limitations, we propose a force-guided $\mathrm{SE}(3)$ diffusion model, ConfDiff, for protein conformation generation. By incorporating a force-guided network with a mixture of data-based score models, ConfDiff can generate protein conformations with rich diversity while preserving high fidelity. Experiments on a variety of protein conformation prediction tasks, including 12 fast-folding proteins and the Bovine Pancreatic Trypsin Inhibitor (BPTI), demonstrate that our method surpasses the state-of-the-art method.

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IROS Conference 2023 Conference Paper

Holistic Parking Slot Detection with Polygon-Shaped Representations

Lihao Wang
Antonyo Musabini
Christel Leonet
Rachid Benmokhtar
Amaury Breheret
Chaima Yedes
Fabian Bürger
Thomas Boulay

Current parking slot detection in advanced driver-assistance systems (ADAS) primarily relies on ultrasonic sen-sors. This method has several limitations such as the need to scan the entire parking slot before detecting it, the incapacity of detecting multiple slots in a row, and the difficulty of classifying them. Due to the complex visual environment, vehicles are equipped with surround view camera systems to detect vacant parking slots. Previous research works in this field mostly use image-domain models to solve the problem. These two-stage approaches separate the 2D detection and 3D pose estimation steps using camera calibration. In this paper, we propose one-step Holistic Parking Slot Network (HPS-Net), a tailor-made adaptation of the You Only Look Once (YOLO)v4 algorithm. This camera-based approach directly outputs the four vertex coordinates of the parking slot in topview domain, instead of a bounding box in raw camera images. Several visible points and shapes can be proposed from different angles. A novel regression loss function named polygon-corner Generalized Intersection over Union (GIoU) for polygon vertex position optimization is also proposed to manage the slot orientation and to distinguish the entrance line. Experiments show that HPS-Net can detect various vacant parking slots with a F1-score of 0. 92 on our internal Valeo Parking Slots Dataset (VPSD) and 0. 99 on the public dataset PS2. 0. It provides a satisfying generalization and robustness in various parking scenarios, such as indoor (F1: 0. 86) or paved ground (F1: 0. 91). Moreover, it achieves a realtime detection speed of 17 FPS on Nvidia Drive AGX Xavier. A demo video can be found at https://streamable.com/75j7sj.

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ICLR Conference 2023 Conference Paper

Learning Harmonic Molecular Representations on Riemannian Manifold

Yiqun Wang
Yuning Shen
Shi Chen 0003
Lihao Wang
Fei Ye
Hao Zhou

Molecular representation learning plays a crucial role in AI-assisted drug discovery research. Encoding 3D molecular structures through Euclidean neural networks has become the prevailing method in the geometric deep learning community. However, the equivariance constraints and message passing in Euclidean space may limit the network expressive power. In this work, we propose a Harmonic Molecular Representation learning (HMR) framework, which represents a molecule using the Laplace-Beltrami eigenfunctions of the molecular surface. HMR offers a multi-resolution representation of molecular geometric and chemical properties on 2D Riemannian manifold. We also introduce a harmonic message passing method to realize efficient spectral message passing over the surface manifold for better molecular encoding. Our proposed method shows comparable predictive power to current models in small molecule property prediction, and outperforms the state-of-the-art deep learning models for the rigid protein docking challenge, demonstrating its versatility in molecular representation learning.

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NeurIPS Conference 2022 Conference Paper

Regularized Molecular Conformation Fields

Lihao Wang
Yi Zhou
Yiqun Wang
Xiaoqing Zheng
Xuanjing Huang
Hao Zhou

Predicting energetically favorable 3-dimensional conformations of organic molecules frommolecular graph plays a fundamental role in computer-aided drug discovery research. However, effectively exploring the high-dimensional conformation space to identify (meta) stable conformers is anything but trivial. In this work, we introduce RMCF, a novel framework to generate a diverse set of low-energy molecular conformations through samplingfrom a regularized molecular conformation field. We develop a data-driven molecular segmentation algorithm to automatically partition each molecule into several structural building blocks to reduce the modeling degrees of freedom. Then, we employ a Markov Random Field to learn the joint probability distribution of fragment configurations and inter-fragment dihedral angles, which enables us to sample from different low-energy regions of a conformation space. Our model constantly outperforms state-of-the-art models for the conformation generation task on the GEOM-Drugs dataset. We attribute the success of RMCF to modeling in a regularized feature space and learning a global fragment configuration distribution for effective sampling. The proposed method could be generalized to deal with larger biomolecular systems.

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