Xiaotong Xu

Xiaotong Xu, Alexandre M. J. J. Bonvin

Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere with those or to guide drug design. Various strategies can be followed to model those complexes, all typically resulting in a large number of models. A challenging step in this process is the identification of good models (near-native PPI conformations) from the large pool of generated models. To address this challenge, we previously developed DeepRank-GNN-esm, a graph-based deep learning algorithm for ranking modelled PPI structures harnessing the power of protein language models. Here, we detail the use of our software with examples. DeepRank-GNN-esm is freely available at https://github.com/haddocking/DeepRank-GNN-esm

Xuejun Cheng, Qian Zhang, Yuhui Jiao et al.

Beyond diagonal reconfigurable intelligent surfaces (BD-RIS) can realize the interconnection between reflecting elements through the impedance network, thereby providing a new approach for the performance improvement of integrated sensing and communication (ISAC) systems. This paper investigates the optimization problem of BD-RIS-aided multiuser ISAC system, aiming to achieve the flexible design of trade-offs between communication and sensing performance. Specifically, we propose an optimization framework jointly combining the multiuser interference management and sensing beam gain approximation method. By jointly optimizing the precoding vector and RIS phase-shift matrix, improving the multiuser communication sum rate through the proposed interference management method, and enhancing the system sensing performance through the beam gain approximation method. For the resulting non-convex weighted optimization problem, we employ the alternating optimization (AO) algorithm to decouple it into two subproblems of precoding vector and phase-shift matrix optimization, with each step admitting closed-form solutions.Simulation results demonstrate that the proposed BD-RIS-aided ISAC system can achieve significant improvement in the trade-offs between communication and sensing performance than the traditional diagonal RIS, verifying the effectiveness of the proposed optimization framework.

Xiaotong Xu, Qian Zhang, Yunxiao Li et al.

This paper studies an extremely large-scale reconfigurable intelligent surface (XL-RIS)-aided near-field physical layer security (PLS) communication system, aiming to maximize the secrecy rate by jointly optimizing precoding vector at the BS and the reflection coefficient matrix at the XL-RIS. Artifi-cial jamming was introduced to further enhance communication security. To solve the non-convex secrecy rate problem, an alternate optimization-based algorithm is adopted to decompose it into two sub-problems. Specifically, when optimizing the transmit beamformer at the BS, the non-convex prob-lem is transformed into a convex one through the weighted minimum mean-square error and the successive convex approximation-based algorithms. For the optimization problem of the XL-RIS phase-shifting matrix, a low-complexity alternating direction method of multipliers-based algorithm is employed to enhance the flexibility of the design. The proposed algorithm is capable of accommodating discrete phase optimization for the XL-RIS, thus better aligning with practical system requirements. Simulation results demonstrate that when the eavesdropper reside in the same direction as the legitimate user and is located closer to the XL-RIS, the proposed scheme in this paper can still ensure the secure communication.