Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2601.02138

Edge-aware GAT-based protein binding site prediction

Weisen Yang·Hanqing Zhang·Wangren Qiu·Xuan Xiao·Weizhong Lin
View original source ↗Read source document ↗Export metadata ↓

Abstract

Accurate identification of protein binding sites is crucial for understanding biomolecular interaction mechanisms and for the rational design of drug targets. Traditional predictive methods often struggle to balance prediction accuracy with computational efficiency when capturing complex spatial conformations. To address this challenge, we propose an Edge-aware Graph Attention Network (Edge-aware GAT) model for the fine-grained prediction of binding sites across various biomolecules, including proteins, DNA/RNA, ions, ligands, and lipids. Our method constructs atom-level graphs and integrates multidimensional structural features, including geometric descriptors, DSSP-derived secondary structure, and relative solvent accessibility (RSA), to generate spatially aware embedding vectors. By incorporating interatomic distances and directional vectors as edge features within the attention mechanism, the model significantly enhances its representation capacity. On benchmark datasets, our model achieves an ROC-AUC of 0.93 for protein-protein binding site prediction, outperforming several state-of-the-art methods. The use of directional tensor propagation and residue-level attention pooling further improves both binding site localization and the capture of local structural details. Visualizations using PyMOL confirm the model's practical utility and interpretability. To facilitate community access and application, we have deployed a publicly accessible web server at http://119.45.201.89:5000/. In summary, our approach offers a novel and efficient solution that balances prediction accuracy, generalization, and interpretability for identifying functional sites in proteins.

Explore related subjects

cs.LGq-bio.QM

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Weisen Yang, Hanqing Zhang, Wangren Qiu, Xuan Xiao, Weizhong Lin. 2026-01-05. Edge-aware GAT-based protein binding site prediction. https://arxiv.org/abs/2601.02138

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Rollout Total Correlation for Deep Reinforcement Learning

Learning task-relevant representations is crucial for reinforcement learning. Recent approaches aim to learn such representations by improving the temporal consistency in the observed transitions. However, they only consider individual transitions and can fail to achieve long-term consistency. Instead, we argue that capturing aspects of the state that correlate with other states and actions of the trajectory---even more distant in the future---could further help in extracting task-relevant information. Hence, in this paper we investigate how to learn representations by maximizing the rollout total correlation, the correlation among all learned representations and actions within the trajectories produced by the agent. For improving rollout total correlation, we propose to combine two complementary lower bounds based on a generative and a discriminative model, combined with a simple and effective technique of chunk-wise mini-batching. Furthermore, we propose an intrinsic reward based on the learned representation for better exploration. Experimental evaluations on a set of challenging image-based simulated control tasks show that our method achieves better sample efficiency, and robustness to both white noise and natural video backgrounds compared to leading baselines.

cs.LG↗
arXiv2026

Reward Shaping to Mitigate Reward Hacking in RLHF

Reinforcement learning from human feedback (RLHF) is widely used to align large language models (LLMs) with human preferences. However, RLHF remains vulnerable to \emph{reward hacking}, whereby a policy exploits imperfections in the reward function instead of learning the intended behavior, thereby undermining alignment. Although reward shaping can stabilize RLHF training and partially mitigate reward hacking, shaping methods and their underlying design principles have not been systematically investigated. To address this gap, we conduct a comprehensive study of prevalent reward-shaping techniques. Our analysis identifies two key design principles: (1) the reinforcement-learning reward should be bounded, and (2) it should grow rapidly at first and then gradually saturate. Motivated by these principles, we propose Preference as Reward (PAR), a novel method that uses the latent preferences encoded in the reward model as the reinforcement-learning signal. We further show that PAR possesses two variance-reduction properties that stabilize RLHF training and substantially widen the practical window for early stopping. Our evaluation consists of two parts. First, we compare PAR with several other reward-shaping strategies using Proximal Policy Optimization (PPO) as the reinforcement-learning algorithm and Gemma2-2B as the base model. Second, we compare PAR with the vanilla baseline (i.e., unshaped reward) across four base models and four reinforcement-learning algorithms. In the first set of experiments, PAR consistently outperforms other reward-shaping methods and also reflects high data efficiency and robustness. The second set of experiments shows that PAR is particularly effective for actor-critic RL algorithms when value estimates become unstable and demonstrates its effectiveness across different base models. The code is available at https://github.com/PorUna-byte/PAR.

cs.LG↗
arXiv2026

Trajectory Entropy Reinforcement Learning for Robust Robot Motor Skill Learning

Simplicity is a critical inductive bias for designing data-driven controllers, especially when robustness is important. Despite the impressive results of deep reinforcement learning in complex control tasks, it is prone to capturing intricate and spurious correlations between observations and actions, leading to failure under slight perturbations to the environment. To tackle this problem, in this work we introduce a novel inductive bias towards simple policies in reinforcement learning. The simplicity inductive bias is introduced by minimizing the entropy of entire action trajectories, corresponding to the number of bits required to describe information in action trajectories after the agent observes state trajectories. Our reinforcement learning agent, Trajectory Entropy Reinforcement Learning, is optimized to minimize the trajectory entropy while maximizing rewards. We show that the trajectory entropy can be effectively estimated by learning a variational parameterized action prediction model, and use the prediction model to construct an information-regularized reward function. Furthermore, we construct a practical algorithm that enables the joint optimization of models, including the policy and the prediction model. Experimental evaluations on several high-dimensional locomotion tasks show that our learned policies produce more cyclical and consistent action trajectories, and achieve superior performance, and robustness to noise and dynamic changes than the state-of-the-art.

cs.LG↗