The structure of protein-protein complexes is critical for understanding binding dynamics, biological mechanisms, and intervention strategies.

The structure of protein-protein complexes is critical for understanding binding dynamics, biological mechanisms, and intervention strategies. Rigid protein docking, a fundamental problem in this field, aims to predict the 3D structure of complexes from their unbound states without conformational changes. In this scenario, we have access to two types of valuable information: sequence-modal information, such as coevolutionary data obtained from multiple sequence alignments, and structure-modal information, including the 3D conformations of rigid structures. However, existing docking methods typically utilize single-modal information, resulting in suboptimal predictions. In this paper, we propose xTrimoBiDock (or BiDock for short), a novel rigid docking model that effectively integrates sequence-and structure-modal information through bi-level optimization. Specifically, a cross-modal transformer combines multimodal information to predict an inter-protein distance map. To achieve rigid docking, the roto-translation transformation is optimized to align the docked pose with the predicted distance map. In order to tackle this bi-level optimization problem, we unroll the gradient descent of the inner loop and further derive a better initialization for roto-translation transformation based on spectral estimation. Compared to baselines, BiDock achieves a promising result of a maximum 234% relative improvement in challenging antibody-antigen docking problem.

Challenges in traversing dynamic clutters lie mainly in the efficient perception of the environmental dynamics and the generation of evasive behaviors considering obstacle movement. Previous solutions have made progress in explicitly modeling the dynamic obstacle motion for avoidance, but this key dependency of decision-making is time-consuming and unreliable in highly dynamic scenarios with occlusions. On the contrary, without introducing object detection, tracking, and prediction, we empower the reinforcement learning (RL) with single LiDAR sensing to realize an autonomous flight system directly from point to motion. For exteroception, a depth sensing distance map achieving fixed-shape, low-resolution, and detail-safe is encoded from raw point clouds, and an environment change sensing point flow is adopted as motion features extracted from multi-frame observations. These two are integrated into a lightweight and easy-to-learn representation of complex dynamic environments. For action generation, the behavior of avoiding dynamic threats in advance is implicitly driven by the proposed change-aware sensing representation, where the policy optimization is indicated by the relative motion modulated distance field. With the deployment-friendly sensing simulation and dynamics model-free acceleration control, the proposed system shows a superior success rate and adaptability to alternatives, and the policy derived from the simulator can drive a real-world quadrotor with safe maneuvers.

Abstract--This paper presents a novel and sustainable approach for improving beam selection in 5G and beyond networks using transfer learning and Reinforcement Learning (RL). Traditional RL-based beam selection models require extensive training time and computational resources, particularly when deployed in diverse environments with varying propagation characteristics posing a major challenge for scalability and energy efficiency. T o address this, we propose modeling the environment as a point cloud, where each point represents the locations of gNodeBs (gNBs) and surrounding scatterers. By computing the Chamfer distance between point clouds, structurally similar environments can be efficiently identified, enabling the reuse of pre-trained models through transfer learning. This methodology leads to a 16 reduction in training time and computational overhead, directly contributing to energy efficiency. By minimizing the need for retraining in each new deployment, our approach significantly lowers power consumption and supports the development of green and sustainable Artificial Intelligence (AI) in wireless systems. Furthermore, it accelerates time-to-deployment, reduces carbon emissions associated with training, and enhances the viability of deploying AI-driven communication systems at the edge. Simulation results confirm that our approach maintains high performance while drastically cutting energy costs, demonstrating the potential of transfer learning to enable scalable, adaptive, and environmentally conscious RL-based beam selection strategies in dynamic and diverse propagation environments.

Illuminating interactions between proteins and small drug molecules is a longstanding challenge in the field of drug discovery.

Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due to their strong, enduring binding nature. However, most existing docking methods and deep learning approaches hardly account for the formation of covalent bonds and the associated structural changes. To address this gap, we introduce a comprehensive benchmark for covalent docking, CovDocker, which is designed to better capture the complexities of covalent binding. We decompose the covalent docking process into three main tasks: reactive location prediction, covalent reaction prediction, and covalent docking. By adapting state-of-the-art models, such as Uni-Mol and Chemformer, we establish baseline performances and demonstrate the effectiveness of the benchmark in accurately predicting interaction sites and modeling the molecular transformations involved in covalent binding. These results confirm the role of the benchmark as a rigorous framework for advancing research in covalent drug design. It underscores the potential of data-driven approaches to accelerate the discovery of selective covalent inhibitors and addresses critical challenges in therapeutic development.

Accurate and efficient quantification of cardiac function is essential for the estimation of prognosis of cardiovascular diseases (CVDs). One of the most commonly used metrics for evaluating cardiac pumping performance is left ventricular ejection fraction (LVEF). However, LVEF can be affected by factors such as inter-observer variability and varying pre-load and after-load conditions, which can reduce its reproducibility. Additionally, cardiac dysfunction may not always manifest as alterations in LVEF, such as in heart failure and cardiotoxicity diseases. An alternative measure that can provide a relatively load-independent quantitative assessment of myocardial contractility is myocardial strain and strain rate. By using LVEF in combination with myocardial strain, it is possible to obtain a thorough description of cardiac function. Automated estimation of LVEF and other volumetric measures from cine-MRI sequences can be achieved through segmentation models, while strain calculation requires the estimation of tissue displacement between sequential frames, which can be accomplished using registration models. These tasks are often performed separately, potentially limiting the assessment of cardiac function. To address this issue, in this study we propose an end-to-end deep learning (DL) model that jointly estimates groupwise (GW) registration and segmentation for cardiac cine-MRI images. The proposed anatomically-guided Deep GW network was trained and validated on a large dataset of 4-chamber view cine-MRI image series of 374 subjects. A quantitative comparison with conventional GW registration using elastix and two DL-based methods showed that the proposed model improved performance and substantially reduced computation time.

Abstract--AI-powered drug discovery typically relies on the successful prediction of compound-protein interactions, which are pivotal for the evaluation of designed compound molecules in structure-based drug design and represent a core challenge in the field. However, accurately predicting compound-protein affinity via regression models usually requires adequate-binding pose, which are derived from costly and complex experimental methods or time-consuming simulations with docking software. In response, we have introduced the GenShin model, which constructs a geometry-enhanced structural graph module that separately extracts additional features from proteins and compounds. Consequently, it attains an accuracy on par with mainstream models in predicting compound-protein affinities, while eliminating the need for adequate-binding pose as input. Our experimental findings demonstrate that the GenShin model vastly outperforms other models that rely on non-input docking conformations, achieving, or in some cases even exceeding, the performance of those requiring adequate-binding pose. Further experiments indicate that our GenShin model is more robust to inadequate-binding pose, affirming its higher suitability for real-world drug discovery scenarios. We hope our work will inspire more endeavors to bridge the gap between AI models and practical drug discovery challenges. Currently, compound-protein binding affinity can be measured via various experimental techniques, including isothermal titration calorimetry (ITC) [1] and surface plasmon resonance (SPR) [2]. Y et, these traditional methods are both time-intensive and costly .