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Applications · Physics

Darya Biparva, Maarten Schoukens, Donatello Materassi

State-of-the-art machine learning models often incorporate prior knowledge or structural information about the task or data distribution. In some tasks, such knowledge may arise from first principles or emerge as simplified, learned functions that distill essential aspects of the data distribution. Model augmentation has emerged as a strategy to leverage this structured knowledge by coupling it with an auxiliary model to improve predictive performance, while preserving the interpretability offered by the simpler component. In this work, we present a new augmentation framework called the Tutor-Pupil scheme, which is designed to enhance both performance and interpretability. The Pupil is a fixed model, structurally designed for the core task, while the Tutor is a more flexible model trained to apply minimal input-level corrections to improve the Pupil’s performance on the modified input. This strict separation of roles enables the Tutor not only to compensate for the Pupil’s limitations but also to act as a diagnostic instrument. By examining the Tutor’s targeted interventions, we can identify failure modes, detect regions where the Pupil struggles to generalize, and uncover residual patterns or higher-order structures in the data not captured by the original model.

Computer Vision · 3D Rendering & Reconstruction

Shin Dong-Yeon, Kim Jun-Seong, Kwon Byung-Ki, Tae-Hyun Oh

Radiance of real-world scenes typically spans a much wider dynamic range than what standard cameras can capture. While conventional HDR methods merge alternating-exposure frames, these approaches are inherently constrained to 2D pixel-level alignment, often leading to ghosting artifacts and temporal inconsistency in dynamic scenes. To address these limitations, we present HDR-NSFF, a paradigm shift from 2D-based merging to 4D spatio-temporal modeling. Our framework reconstructs dynamic HDR radiance fields from alternating-exposure monocular videos by representing the scene as a continuous function of space and time, and is compatible with both neural radiance field and 4D Gaussian Splatting (4DGS) based dynamic representations. This unified end-to-end pipeline explicitly models HDR radiance, 3D scene flow, geometry, and tone-mapping, ensuring physical plausibility and global coherence. We further enhance robustness by (i) extending semantic-based optical flow with DINO features to achieve exposure-invariant motion estimation, and (ii) incorporating a generative prior as a regularizer to compensate for limited observation in monocular captures and saturation-induced information loss. To evaluate HDR space-time view synthesis, we present the first real-world HDR-GoPro dataset specifically designed for dynamic HDR scenes. Experiments demonstrate that HDR-NSFF recovers fine radiance details and coherent dynamics even under challenging exposure variations, thereby achieving state-of-the-art performance in novel space-time view synthesis. Project page: https://shin-dong-yeon.github.io/HDR-NSFF

Computer Vision · Image and Video Generation

Wanhee Lee, Klemen Kotar, Rahul Venkatesh, Jared Watrous, Honglin Chen, Khai Loong Aw, Daniel Yamins

Understanding 3D scenes requires flexible combinations of visual reasoning tasks, including depth estimation, novel view synthesis, and object manipulation, all of which are essential for perception and interaction. Existing approaches have typically addressed these tasks in isolation, preventing them from sharing a common representation or transferring knowledge across tasks. A conceptually simpler but practically non-trivial alternative is to unify these diverse tasks into a single model, reducing different tasks from separate training objectives to merely different prompts and allowing for joint training across all datasets. In this work, we present a physical world model for unified 3D understanding and interaction 3WM, formulated as a probabilistic graphical model in which nodes represent multimodal scene elements such as RGB, optical flow, and camera pose. Diverse tasks emerge from different inference pathways through the graph: novel view synthesis from RGB and dense flow prompts, object manipulation from RGB and sparse flow prompts, and depth estimation from RGB and camera conditioning, all zero-shot without task-specific training. 3WM outperforms specialized baselines without the need for finetuning by offering precise controllability, strong geometric consistency, and robustness in real-world scenarios, achieving state-of-the-art performance on NVS and 3D object manipulation. Beyond predefined tasks, the model supports composable inference pathways, such as moving objects aside while navigating a 3D environment, enabling complex geometric reasoning. This demonstrates that a unified model can serve as a practical alternative to fragmented task-specific systems, taking a step towards a general-purpose visual world model.

Computer Vision · Everything Else

George Webber, Andrew Reader

Recovering true signals from noisy measurements is a central challenge in inverse problems spanning medical imaging, geophysics, and signal processing. Current solutions nearly always balance prior assumptions regarding the true signal (regularization) with agreement to noisy measured data (data-fidelity). Conventional data-fidelity loss functions, such as mean-squared error (MSE) or negative log-likelihood, seek pointwise agreement with noisy measurements, often leading to overfitting to noise. In this work, we instead evaluate data-fidelity collectively by testing whether the observed measurements are statistically consistent with the noise distributions implied by the current estimate. We adopt this aggregated perspective and introduce $\textit{distributional consistency (DC) loss}$, a data-fidelity objective that replaces pointwise matching with distribution-level calibration. DC loss acts as a direct and practical plug-in replacement for standard data consistency terms: i) it is compatible with modern unsupervised regularizers that operate without paired measurement–ground-truth data, ii) it is optimized in the same way as traditional losses, and iii) it avoids overfitting to measurement noise without early stopping or the use of priors. Its scope naturally fits many practical inverse problems where the measurement-noise distribution is known and where the measured dataset consists of many independent noisy values. We demonstrate efficacy in two key example application areas: i) in image denoising with deep image prior, using DC instead of MSE loss removes the need for early stopping and achieves higher PSNR; ii) in medical image reconstruction from Poisson-noisy data, DC loss reduces artifacts in highly-iterated reconstructions and enhances the efficacy of hand-crafted regularization. These results position DC loss as a statistically grounded, performance-enhancing alternative to conventional fidelity losses for an important class of unsupervised noise-dominated inverse problems.

Applications · Physics

Youjin Kim, Dagyeong Na, JaeYong Lee, Junseok Kwon

The problem of physical dynamics, which involves predicting the 3D trajectories of particles, is a fundamental task with wide-ranging applications across science and engineering. However, accurately forecasting long-horizon trajectories from initial states remains challenging, due to complex particle interactions and entangled multi-scale dynamics involving both low- and high-frequency components. To address this, we propose a novel knowledge-distillation-based framework, SGDD (Spectral-Guided Dynamics Distillation), which integrates a spectral-guided enhancement to adaptively prioritize key frequency components within a unified spatio-temporal representation. Through knowledge distillation, SGDD leverages future trajectories as privileged information during training, guiding a teacher encoder to generate comprehensive dynamics representations while a student encoder approximates them using only the initial state. This enables the student to generate effective dynamics representations at inference, even without privileged information, thereby enabling accurate long-horizon trajectory prediction. Experimental results on molecule, protein, and human motion datasets demonstrate that our method achieves more accurate and stable long-term predictions than previous physical dynamics models, successfully capturing the complex spatio-temporal structures of real-world systems.

Computer Vision · 3D Rendering & Reconstruction

Zhongwen Wang, Han Ling, Weihao Zhang, Yinghui Sun, Quansen Sun

We propose ETGS, a method for reconstructing dynamic thermal scenes by embedding explicit thermodynamic modeling into 3D Gaussian Splatting. Each Gaussian is equipped with physically interpretable thermal parameters, and its thermodynamics evolution is described by a first-order heat-transfer ODE with an analytical closed-form solution. This formulation avoids numerical integration, enables efficient rendering at arbitrary timestamps, and naturally handles irregular sampling and out-of-order observations. We also introduce the Rapid Heat Dynamics (RHD) dataset, which provides millisecond-aligned RGB–IR image pairs covering typical thermal processes such as cooling, warming, heating, and heat transfer. Experiments on RHD show that ETGS captures rapid thermal dynamics more accurately than existing static and dynamic baselines, while maintaining training and rendering efficiency close to that of static 3DGS. Code and dataset are available at https://github.com/jankin-wang/ETGS.

Computer Vision · Everything Else

Qinhong Zhou, Hongxin Zhang, Xiangye Lin, Zheyuan Zhang, Yutian Chen, Wenjun Liu, Zunzhe Zhang, Sunli Chen, Lixing Fang, Qiushi Lyu 等

The rapid progress of AI and robotics may profoundly transform society, as humans and robots begin to coexist in shared communities, bringing both opportunities and challenges. To explore this future, we present Virtual Community—an open-world platform for humans, robots, and society—built on a universal physics engine and grounded in real-world 3D scenes. With Virtual Community, we aim to enable the study of embodied social intelligence at scale. To support these, Virtual Community features: 1) An open-source multi-agent physics simulator that supports robot, human, and their interactions within a society; 2) A large‑scale, real‑world aligned environment generation pipeline, including vast outdoor space, diverse indoor scenes, and a community of grounded agents with rich characters and appearances. Leveraging Virtual Community, we propose two novel challenges. The Community Planning Challenge evaluates multi‑agent reasoning and planning in open‑world settings, such as cooperating to help agents with daily activities and efficiently connecting other agents. The Community Robot Challenge requires multiple heterogeneous robots to collaborate in solving complex open‑world tasks. We evaluate various baselines and demonstrate the challenges in both high‑level open‑world task planning and low‑level cooperation controls. We have open-sourced our project and hope that Virtual Community will unlock further study of human-robot coexistence in open worlds.

Computer Vision · Vision Models & Multimodal

Lu Ling, Chen-Hsuan Lin, Tsung-Yi Lin, Yifan Ding, Yu Zeng, Yichen Sheng, Yunhao Ge, Ming-Yu Liu, Aniket Bera, Max Li

Generating interactive 3D scenes from text requires not only synthesizing assets but arranging them with spatial intelligence—support, affordances, and plausibility. However, training data for interactive scenes is dominated by a few indoor datasets, so learning-based methods overfit to in-distribution layouts and struggle to compose diverse arrangements (e.g., outdoor settings and small-on-large relations). Meanwhile, LLM-based layout planners can propose diverse arrangements, but the lack of visual grounding often yields implausible placements that violate commonsense physics. We propose Scenethesis, a training-free, agentic framework that couples LLM-based scene planning with vision-guided layout refinement. Given a text prompt, Scenethesis first drafts a coarse layout with an LLM; a vision module refines the layout and extracts scene structure to capture inter-object relations. A novel optimization stage enforces pose alignment and physical plausibility, and a final judge verifies spatial coherence and triggers targeted repair when needed. Across indoor and outdoor prompts, Scenethesis produces realistic, relation-rich, and physically plausible 3D interactive scenes, reducing collisions and stability failures compared to SOTA methods, making it practical for virtual content creation, simulation, and embodied AI.

Applications · Robotics

Jinbang Huang, Yixin Xiao, Zhanguang Zhang, Mark Coates, Jianye Hao, Yingxue Zhang

Pre-trained large language models (LLMs) show promise for robotic task planning but often struggle to guarantee correctness in long-horizon problems. Task and motion planning (TAMP) addresses this by grounding symbolic plans in low-level execution, yet it relies heavily on manually engineered planning domains. To improve long-horizon planning reliability and reduce human intervention, we present Planning Domain Derivation with LLMs (PDDLLM), a framework that automatically induces symbolic predicates and actions directly from demonstration trajectories by combining LLM reasoning with physical simulation roll-outs. Unlike prior domain-inference methods that rely on partially predefined or language descriptions of planning domains, PDDLLM constructs domains with minimal manual domain initialization and automatically integrates them with motion planners to produce executable plans, enhancing long-horizon planning automation. Across 1,200 tasks in nine environments, PDDLLM outperforms six LLM-based planning baselines, achieving at least 20% higher success rates, reduced token costs, and successful deployment on multiple physical robot platforms.

Applications · Physics

Ruihua Chen, Yisi Luo, Bangyu Wu, Deyu Meng

Full-waveform inversion (FWI) estimates physical parameters in the wave equation from limited measurements and has been widely applied in geophysical exploration, medical imaging, and non-destructive testing. Conventional FWI methods are limited by their notorious sensitivity to the accuracy of the initial models. Recent progress in continuous representation FWI (CR-FWI) demonstrates that representing parameter models with a coordinate-based neural network, such as implicit neural representation (INR), can mitigate the dependence on initial models. However, its underlying mechanism remains unclear, and INR-based FWI shows slower high-frequency convergence. In this work, we investigate the general CR-FWI framework and develop a unified theoretical understanding by extending the neural tangent kernel (NTK) for FWI to establish a wave-based NTK framework. Unlike standard NTK, our analysis reveals that wave-based NTK is not constant, both at initialization and during training, due to the inherent nonlinearity of FWI. We further show that the eigenvalue decay behavior of the wave-based NTK can explain why CR-FWI alleviates the dependency on initial models and shows slower high-frequency convergence. Building on these insights, we propose several CR-FWI methods with tailored eigenvalue decay properties for FWI, including a novel hybrid representation combining INR and multi-resolution grid (termed IG-FWI) that achieves a more balanced trade-off between robustness and high-frequency convergence rate. Applications in geophysical exploration on Marmousi, 2D SEG/EAGE Salt and Overthrust, 2004 BP model, and the more realistic 2014 Chevron models show the superior performance of our proposed methods compared to conventional FWI and existing INR-based FWI methods.

Theory · Learning Theory

Zhuo Liu, Tao Chen

Brain-like intelligent systems need brain-like learning methods. Equilibrium Propagation (EP) is a biologically plausible learning framework with strong potential for brain-inspired computing hardware. However, existing implementations of EP suffer from instability and prohibitively high computational costs. Inspired by the structure and dynamics of the brain, we propose a biologically plausible Feedback-regulated REsidual recurrent neural network (FRE-RNN) and study its learning performance in EP framework. Feedback regulation enables rapid convergence by attenuating feedback signals and reducing the disturbance of feedback path to feedforward path. The improvement in convergence property reduces the computational cost and training time of EP by orders of magnitude, delivering performance on par with backpropagation (BP) in benchmark tasks. Meanwhile, residual connections with brain-inspired topologies help alleviate the vanishing gradient problem that arises when feedback pathways are weak in deep RNNs. Our approach substantially enhances the applicability and practicality of EP. The techniques developed here also offer guidance to implementing in-situ learning in physical neural networks.

Computer Vision · Classification and Understanding

Jiajing Lin, Shu Jiang, Qingyuan Zeng, Zhenzhong Wang, Min Jiang

The intrinsic dynamics of an object governs its physical behavior in the real world, playing a critical role in enabling physically plausible interactive simulation with 3D assets. Existing methods have attempted to infer the intrinsic dynamics of objects from visual observations, but generally face two major challenges: one line of work relies on manually defined constitutive priors, making it difficult to align with actual intrinsic dynamics; the other models intrinsic dynamics using neural networks, resulting in limited interpretability and poor generalization. To address these challenges, we propose VisionLaw, a bilevel optimization framework that infers interpretable expressions of intrinsic dynamics from visual observations. At the upper level, we introduce an LLMs-driven decoupled constitutive evolution strategy, where LLMs are prompted to act as physics experts to generate and revise constitutive laws, with a built-in decoupling mechanism that substantially reduces the search complexity of LLMs. At the lower level, we introduce a vision-guided constitutive evaluation mechanism, which utilizes visual simulation to evaluate the consistency between the generated constitutive law and the underlying intrinsic dynamics, thereby guiding the upper-level evolution. Experiments on both synthetic and real-world datasets demonstrate that VisionLaw can effectively infer interpretable intrinsic dynamics from visual observations. It significantly outperforms existing state-of-the-art methods and exhibits strong generalization for interactive simulation in novel scenarios.

Guying Lin, Kemeng Huang, Michael Liu, Ruihan Gao, Hanke Chen, Lyuhao Chen, Beijia Lu, Taku Komura, Yuan Liu, Jun-Yan Zhu 等

We introduce PAT3D, the first physics-augmented text-to-3D scene generation framework that integrates vision–language models with physics-based simulation to produce physically plausible, simulation-ready, and intersection-free 3D scenes. Given a text prompt, PAT3D generates 3D objects, infers their spatial relations, and organizes them into a hierarchical scene tree, which is then converted into initial simulation conditions. A rigid-body simulator ensures realistic object interactions under gravity, driving the scene toward static equilibrium without interpenetrations. To further enhance scene quality, we introduce a simulation-in-the-loop optimization procedure that guarantees physical stability and non-intersection, while improving semantic consistency with the input prompt. Experiments demonstrate that PAT3D substantially outperforms prior approaches in physical plausibility, semantic accuracy, and visual quality. Beyond high-quality generation, PAT3D uniquely enables simulation-ready 3D scenes for downstream tasks such as scene editing and robotic manipulation. Our code and data are available at https://github.com/Simulation-Intelligence/PAT3D.

General Machine Learning · Representation Learning

Vivek Anand, Alec Helbling, Mark Davenport, Gordon Berman, Sankaraleengam Alagapan, Christopher Rozell

Learning the intrinsic dimensionality of subjective perceptual spaces such as taste, smell, or aesthetics from ordinal data is a challenging problem. We introduce LORE (Low Rank Ordinal Embedding), a scalable framework that jointly learns both the intrinsic dimensionality and an ordinal embedding from noisy triplet comparisons of the form, "Is A more similar to B than C?". Unlike existing methods that require the embedding dimension to be set apriori, LORE regularizes the solution using the nonconvex Schatten-$p$ quasi norm, enabling automatic joint recovery of both the ordinal embedding and its dimensionality. We optimize this joint objective via an iteratively reweighted algorithm and establish convergence guarantees. Extensive experiments on synthetic datasets, simulated perceptual spaces, and real world crowdsourced ordinal judgements show that LORE learns compact, interpretable and highly accurate low dimensional embeddings that recover the latent geometry of subjective percepts. By simultaneously inferring both the intrinsic dimensionality and ordinal embeddings, LORE enables more interpretable and data efficient perceptual modeling in psychophysics and opens new directions for scalable discovery of low dimensional structure from ordinal data in machine learning.

Applications · Health

Hanchen Wang, Yixuan Wu, Yinan Feng, Peng Jin, Luoyuan Zhang, Shihang Feng, James Wiskin, Baris Turkbey, Peter Pinto, Bradford Wood 等

Prostate cancer is one of the most common and lethal cancers among men, making its early detection critically important. Ultrasound computed tomography (USCT) has emerged as an accessible and cost-effective method that reconstructs quantitative tissue parameters, which can serve as potential biomarkers for malignancy. However, current prostate USCT faces considerable barriers: limited-angle acquisitions due to anatomical constraints, tissue heterogeneity, proximity to organs and bony pelvic structures, and lengthy processing times. The lack of large-scale, anatomically precise datasets significantly hampers the development of high-quality, efficient, and generalizable methods. To address this gap, we introduce OpenPros, the first large-scale benchmark dataset for limited-angle prostate USCT, designed to evaluate machine learning algorithms for inverse problems systematically. Our dataset includes over 280,000 paired samples of realistic 2D speed-of-sound (SOS) phantoms and corresponding ultrasound full-waveform data, generated from anatomically accurate 3D digital prostate models derived from 4 real clinical MRI/CT scans and 62 ex vivo prostate specimens with experimental ultrasound measurements, annotated by medical experts. Simulations are conducted under clinically realistic configurations using advanced finite-difference time-domain (FDTD) and Runge-Kutta acoustic wave solvers, both provided as open-source components. Through comprehensive benchmarking, we find that deep learning methods significantly outperform traditional physics-based algorithms in inference efficiency and reconstruction accuracy. However, our results also reveal that current machine learning methods fail to deliver clinically acceptable, high-resolution reconstructions, underscoring critical gaps in generalization, robustness, and uncertainty quantification. By publicly releasing OpenPros, we provide the community with a rigorous benchmark that not only enables fair method comparison but also motivates new advances in physics-informed learning, foundation models for scientific imaging, and uncertainty-aware reconstruction—bridging the gap between academic ML research and real-world clinical deployment. The dataset is publicly accessible at https://open-pros.github.io/.

Applications · Physics

Siying (Sydney) Ma, Mehrdad Momeni Zadeh, Mauricio Soroco, Wuyang Chen, Jiguo Cao, Vijay Ganesh

Recent advances in scientific machine learning (SciML) have enabled neural operators (NOs) to serve as powerful surrogates for modeling the dynamic evolution of physical systems governed by partial differential equations (PDEs). While existing approaches focus primarily on learning simulations from the target PDE, they often overlook more fundamental physical principles underlying these equations. Inspired by how numerical solvers are compatible with simulations of different settings of PDEs, we propose a multiphysics training framework that jointly learns from both the original PDEs and their simplified basic forms. Our framework enhances data efficiency, reduces predictive errors, and improves out-of-distribution (OOD) generalization, particularly in scenarios involving shifts of physical parameters and synthetic-to-real transfer. Our method is architecture-agnostic and demonstrates consistent improvements in normalized root mean square error (nRMSE) across a wide range of 1D/2D/3D PDE problems. Through extensive experiments, we show that explicit incorporation of fundamental physics knowledge significantly strengthens the generalization ability of neural operators. We will release models and codes at https://sites.google.com/view/sciml-fundemental-pde.

Computer Vision · 3D Rendering & Reconstruction

Iris Zheng, Guojun Tang, Alexander Doronin, Paul Teal, Fang-Lue Zhang

We present SSD-GS, a physically-based relighting framework built upon 3D Gaussian Splatting (3DGS) that achieves high-quality reconstruction and photorealistic relighting under novel lighting conditions. In physically-based relighting, accurately modeling light-material interactions is essential for faithful appearance reproduction. However, existing 3DGS-based relighting methods adopt coarse shading decompositions, either modeling only diffuse and specular reflections or relying on neural networks to approximate shadows and scattering. This leads to limited fidelity and poor physical interpretability, particularly for anisotropic metals and translucent materials. To address these limitations, SSD-GS decomposes reflectance into four components: diffuse, specular, shadow, and subsurface scattering. We introduce a learnable dipole-based scattering module for subsurface transport, an occlusion-aware shadow formulation that integrates visibility estimates with a refinement network, and an enhanced specular component with an anisotropic Fresnel-based model. Through progressive integration of all components during training, SSD-GS effectively disentangles lighting and material properties, even for unseen illumination conditions, as demonstrated on the challenging OLAT dataset. Experiments demonstrate superior quantitative and perceptual relighting quality compared to prior methods and pave the way for downstream tasks including controllable light source editing and interactive scene relighting. The source code is available at: [https://github.com/irisfreesiri/SSD-GS](https://github.com/irisfreesiri/SSD-GS).

Applications · Robotics

Sixu Lin, Guanren Qiao, Yunxin Tai, Ang Li, Kui Jia, Guiliang Liu

Humanoid robots, capable of assuming human roles in various workplaces, have become essential to embodied intelligence. However, as robots with complex physical structures, learning a control model that can operate robustly across diverse environments remains inherently challenging, particularly under the discrepancies between training and deployment environments. In this study, we propose HWC-Loco, a robust whole-body control algorithm tailored for humanoid locomotion tasks. By reformulating policy learning as a robust optimization problem, HWC-Loco explicitly learns to recover from safety-critical scenarios. While prioritizing safety guarantees, overly conservative behavior can compromise the robot's ability to complete the given tasks. To tackle this challenge, HWC-Loco leverages a hierarchical policy for robust control. This policy can dynamically resolve the trade-off between goal-tracking and safety recovery, guided by human behavior norms and dynamic constraints. To evaluate the performance of HWC-Loco, we conduct extensive comparisons against state-of-the-art humanoid control models, demonstrating HWC-Loco's superior performance across diverse terrains, robot structures, and locomotion tasks under both simulated and real-world environments.

Applications · Physics

jiayi li, Flora Salim

Learning PDE dynamics with neural solvers can significantly improve wall-clock efficiency and accuracy compared with classical numerical solvers. In recent years, foundation models for PDEs have largely adopted multi-scale windowed self-attention, with the scOT backbone in Poseidon serving as a representative example. However, because of their locality, truly globally consistent spectral coupling can only be propagated gradually through deep stacking and window shifting. This weakens global coupling and leads to error accumulation and drift during closed-loop rollouts. To address this, we propose DRIFT-Net. It employs a dual-branch design comprising a spectral branch and an image branch. The spectral branch is responsible for capturing global, large-scale low-frequency information, whereas the image branch focuses on local details and nonstationary structures. Specifically, we first perform controlled, lightweight mixing within the low-frequency range. Then we fuse the spectral and image paths at each layer via bandwise weighting, which avoids the width inflation and training instability caused by naive concatenation. The fused result is transformed back into the spatial domain and added to the image branch, thereby preserving both global structure and high-frequency details across scales. Compared with strong attention-based baselines, DRIFT-Net achieves lower error and higher throughput with fewer parameters under identical training settings and budget. On Navier--Stokes benchmarks, the relative $L_{1}$ error is reduced by 7%-54%, the parameter count decreases by about 15%, and the throughput remains higher than scOT. Ablation studies and theoretical analyses further demonstrate the stability and effectiveness of this design. The code is available at https://github.com/cruiseresearchgroup/DRIFT-Net.

Applications · Chemistry and Drug Discovery

Yize Jiang, Xinze Li, Yuanyuan Zhang, Jin Han, Youjun Xu, Ayush Pandit, ZAIXI ZHANG, Mengdi Wang, Mengyang Wang, Chong Liu 等

Recently, significant progress has been made in protein-ligand docking, especially in deep learning methods, and some benchmarks were proposed, such as PoseBench and PLINDER. However, these studies typically focus on the self-docking scenario, which is less practical in real-world applications. Moreover, some studies employ complex frameworks that require extensive training, posing challenges for convenient and efficient assessment of docking methods. To address these gaps, we introduce PoseX, an open-source benchmark for evaluating both self-docking and cross-docking, enabling a practical and comprehensive assessment of algorithmic advances. Specifically, we curated a novel dataset comprising 718 entries for self-docking and 1,312 entries for cross-docking; secondly, we incorporated 23 docking methods in three methodological categories, including physics-based methods (e.g., Schrödinger Glide), AI docking methods (e.g., DiffDock) and AI co-folding methods (e.g., AlphaFold3); thirdly, we developed a relaxation method for post-processing to minimize conformational energy and refine binding poses; fourthly, we established a public leaderboard to rank submitted models in real-time. We derived some key insights and conclusions through extensive experiments: (1) AI-based approaches consistently outperform physics-based methods in overall docking success rate. (2) Most intra- and intermolecular clashes of AI-based approaches can be greatly alleviated with relaxation, which means combining AI modeling with physics-based post-processing could achieve excellent performance. (3) AI co-folding methods exhibit ligand chirality issues, except for Boltz-1x, which introduced physics-inspired potentials to fix hallucinations, suggesting that stereochemical modeling greatly improves the structural plausibility of the predicted protein-ligand complexes. (4) Specifying binding pockets significantly promotes docking performance, indicating that pocket information can be leveraged adequately, particularly for AI co-folding methods, in future modeling efforts.