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MagicDock: Toward Docking-oriented De Novo Ligand Design via Gradient Inversion

arXiv.org Artificial Intelligence

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the docking process, leveraging learnable 3D point-cloud representations to precisely capture binding details, thereby ensuring that the generated ligands preserve docking validity through direct and interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide rigorous theoretical guarantees for each component of MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 27.1\% and 11.7\% over SOTA baselines specialized for protein or molecule ligand design, respectively.


Analytical Survey of Learning with Low-Resource Data: From Analysis to Investigation

arXiv.org Artificial Intelligence

Learning with high-resource data has demonstrated substantial success in artificial intelligence (AI); however, the costs associated with data annotation and model training remain significant. A fundamental objective of AI research is to achieve robust generalization with limited-resource data. This survey employs agnostic active sampling theory within the Probably Approximately Correct (PAC) framework to analyze the generalization error and label complexity associated with learning from low-resource data in both model-agnostic supervised and unsupervised settings. Based on this analysis, we investigate a suite of optimization strategies tailored for low-resource data learning, including gradient-informed optimization, meta-iteration optimization, geometry-aware optimization, and LLMs-powered optimization. Furthermore, we provide a comprehensive overview of multiple learning paradigms that can benefit from low-resource data, including domain transfer, reinforcement feedback, and hierarchical structure modeling. Finally, we conclude our analysis and investigation by summarizing the key findings and highlighting their implications for learning with low-resource data.


Velocity and Density-Aware RRI Analysis and Optimization for AoI Minimization in IoV SPS

arXiv.org Artificial Intelligence

Abstract--Addressing the problem of Age of Information (AoI) deterioration caused by packet collisions and vehicle speed-related channel uncertainties in Semi-Persistent Scheduling (SPS) for the Internet of V ehicles (IoV), this letter proposes an optimization approach based on Large Language Models (LLM) and Deep Deterministic Policy Gradient (DDPG). First, an AoI calculation model influenced by vehicle speed, vehicle density, and Resource Reservation Interval (RRI) is established, followed by the design of a dual-path optimization scheme. The DDPG is guided by the state space and reward function, while the LLM leverages contextual learning to generate optimal parameter configurations. Experimental results demonstrate that LLM can significantly reduce AoI after accumulating a small number of exemplars without requiring model training, whereas the DDPG method achieves more stable performance after training. HE Internet of V ehicles (IoV) is pivotal in enabling intelligent transportation systems [1], [2], [3].


Reinforcement Learning-Based Optimization of CT Acquisition and Reconstruction Parameters Through Virtual Imaging Trials

arXiv.org Artificial Intelligence

Protocol optimization is critical in Computed Tomography (CT) to achieve high diagnostic image quality while minimizing radiation dose. However, due to the complex interdependencies among CT acquisition and reconstruction parameters, traditional optimization methods rely on exhaustive testing of combinations of these parameters, which is often impractical. This study introduces a novel methodology that combines virtual imaging tools with reinforcement learning to optimize CT protocols more efficiently. Human models with liver lesions were imaged using a validated CT simulator and reconstructed with a novel CT reconstruction toolkit. The optimization parameter space included tube voltage, tube current, reconstruction kernel, slice thickness, and pixel size. The optimization process was performed using a Proximal Policy Optimization (PPO) agent, which was trained to maximize an image quality objective, specifically the detectability index (d') of liver lesions in the reconstructed images. Optimization performance was compared against an exhaustive search performed on a supercomputer. The proposed reinforcement learning approach achieved the global maximum d' across test cases while requiring 79.7% fewer steps than the exhaustive search, demonstrating both accuracy and computational efficiency. The proposed framework is flexible and can accommodate various image quality objectives. The findings highlight the potential of integrating virtual imaging tools with reinforcement learning for CT protocol management.


Whole Body Model Predictive Control for Spin-Aware Quadrupedal Table Tennis

arXiv.org Artificial Intelligence

Developing table tennis robots that mirror human speed, accuracy, and ability to predict and respond to the full range of ball spins remains a significant challenge for legged robots. To demonstrate these capabilities we present a system to play dynamic table tennis for quadrupedal robots that integrates high speed perception, trajectory prediction, and agile control. Our system uses external cameras for high-speed ball localization, physical models with learned residuals to infer spin and predict trajectories, and a novel model predictive control (MPC) formulation for agile full-body control. Notably, a continuous set of stroke strategies emerge automatically from different ball return objectives using this control paradigm. We demonstrate our system in the real world on a Spot quadruped, evaluate accuracy of each system component, and exhibit coordination through the system's ability to aim and return balls with varying spin types. As a further demonstration, the system is able to rally with human players.


VAGPO: Vision-augmented Asymmetric Group Preference Optimization for Graph Routing Problems

arXiv.org Artificial Intelligence

Graph routing problems play a vital role in web-related networks, where finding optimal paths across graphs is essential for efficient data transmission and content delivery. Classic routing formulations such as the Traveling Salesman Problem (TSP) and the Capacitated Vehicle Routing Problem (CVRP) represent fundamental graph optimization challenges. Recent data-driven optimization methods have made significant progress, yet they often face limitations in training efficiency and generalization to large-scale instances. In this paper, we propose a novel Vision-augmented Asymmetric Group Preference Optimization (VAGPO) approach. By leveraging ResNet-based visual encoding and Transformer-based sequential modeling, VAGPO captures both spatial structure and temporal dependencies. Furthermore, we introduce an asymmetric group preference optimization strategy that significantly accelerates convergence compared to commonly used policy gradient methods. Experimental results on generated TSP and CVRP instances, as well as real-world datasets, demonstrate that the proposed VAGPO approach achieves highly competitive solution quality. Additionally, VAGPO exhibits strong generalization to larger instances (up to 1000 nodes) without re-training, highlighting its effectiveness in both learning efficiency and scalability.



Differentiable Structure Learning with Partial Orders T aiyu Ban Lyuzhou Chen Xiangyu Wang

Neural Information Processing Systems

Differentiable structure learning is a novel line of causal discovery research that transforms the combinatorial optimization of structural models into a continuous optimization problem. However, the field has lacked feasible methods to integrate partial order constraints, a critical prior information typically used in real-world scenarios, into the differentiable structure learning framework. The main difficulty lies in adapting these constraints, typically suited for the space of total orderings, to the continuous optimization context of structure learning in the graph space. To bridge this gap, this paper formalizes a set of equivalent constraints that map partial orders onto graph spaces and introduces a plug-and-play module for their efficient application. This module preserves the equivalent effect of partial order constraints in the graph space, backed by theoretical validations of correctness and completeness. It significantly enhances the quality of recovered structures while maintaining good efficiency, which learns better structures using 90% fewer samples than the data-based method on a real-world dataset. This result, together with a comprehensive evaluation on synthetic cases, demonstrates our method's ability to effectively improve differentiable structure learning with partial orders.


c3010e98dc44b6f76df7cf82b5e12c77-Paper-Conference.pdf

Neural Information Processing Systems

From the learning theory perspective, the learning guarantees of SCO algorithms with known derivatives have been studied in the literature.