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Xiangyu Shi

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4 papers

2 author rows

AAAI Conference 2026 Conference Paper

DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design

Yanting Li
Zikang Wang
Jiyue Jiang
Ziqian Lin
Dongchen He
Yuheng Shan
Yanruisheng Shao
Jiayi Li

Inverse Protein Folding (IPF) is a critical subtask in the field of protein design, aiming to engineer amino acid sequences capable of folding correctly into a specified three-dimensional (3D) conformation. Although substantial progress has been achieved in recent years, existing methods generally rely on either backbone coordinates or molecular surface features alone, which restricts their ability to fully capture the complex chemical and geometric constraints necessary for precise sequence prediction. To address this limitation, we present DS-ProGen, a dual-structure deep language model for functional protein design, which integrates both backbone geometry and surface-level representations. By incorporating backbone coordinates as well as surface chemical and geometric descriptors into a next-amino-acid prediction paradigm, DS-ProGen is able to generate functionally relevant and structurally stable sequences while satisfying both global and local conformational constraints. On the PRIDE dataset, DS-ProGen attains the current state-of-the-art recovery rate of 61.47%, demonstrating the synergistic advantage of multi-modal structural encoding in protein design. Furthermore, DS-ProGen excels in predicting interactions with a variety of biological partners, including ligands, ions, and RNA, confirming its robust functional retention capabilities.

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AAAI Conference 2026 Conference Paper

RMSAGen: Integrating Multiple Sequence Alignment for Function RNA Design

Jiyue Jiang
Yanyu Chen
Qingchuan Zhang
Jiayi Li
Xiangyu Shi
Chang Zhou
Ziqian Lin
Jiuming Wang

Biological sequences, including RNAs and proteins, share similarities with natural languages, enabling the application of advanced language models to various biological tasks. However, due to its flexibility and lack of experimental data, RNA is a particularly challenging biological ``language'' compared to other biological sequences like proteins. RNA multiple sequence alignments (MSAs), which align evolutionarily related RNA sequences, can greatly enhance RNA biology modeling, as evidenced by their significant roles in structure prediction and function annotation. This raises the question of whether RNA MSAs can also benefit RNA design, which remains unexplored. This paper introduces RMSAGen, a model comprising RMSA-Encoder and RMSA-Decoder, that leverages MSAs to design functional RNA sequences. RMSA-Encoder effectively extracts MSA features, enhancing performance in functional prediction and solvent accessibility prediction tasks and supporting RMSA-Decoder in accurate RNA generation. RMSAGen can design RNA sequences that effectively bind to target RNA-binding proteins, and the design performance improves with an increasing number of sequences. In addition, the ribozymes designed with structural features by RMSAGen show strong computational metrics and exhibit biological activity during gel electrophoresis. These results highlight the effectiveness of RMSAGen, establishing it as a powerful tool and a new direction for RNA design.

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IROS Conference 2025 Conference Paper

Embodied Domain Adaptation for Object Detection

Xiangyu Shi
Yanyuan Qiao
Lingqiao Liu
Feras Dayoub

Mobile robots rely on object detectors for perception and object localization in indoor environments. However, standard closed-set methods struggle to handle the diverse objects and dynamic conditions encountered in real homes and labs. Open-vocabulary object detection (OVOD), driven by Vision Language Models (VLMs), extends beyond fixed labels but still struggles with domain shifts in indoor environments. We introduce a Source-Free Domain Adaptation (SFDA) approach that adapts a pre-trained model without accessing source data. We refine pseudo labels via temporal clustering, employ multi-scale threshold fusion, and apply a Mean Teacher framework with contrastive learning. Our Embodied Domain Adaptation for Object Detection (EDAOD) benchmark evaluates adaptation under sequential changes in lighting, layout, and object diversity. Our experiments show significant gains in zero-shot detection performance and flexible adaptation to dynamic indoor conditions.

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IROS Conference 2025 Conference Paper

SmartWay: Enhanced Waypoint Prediction and Backtracking for Zero-Shot Vision-and-Language Navigation

Xiangyu Shi
Zerui Li
Wenqi Lyu
Jiatong Xia
Feras Dayoub
Yanyuan Qiao
Qi Wu 0001

Vision-and-Language Navigation (VLN) in continuous environments requires agents to interpret natural language instructions while navigating unconstrained 3D spaces. Existing VLN-CE frameworks rely on a two-stage approach: a waypoint predictor to generate waypoints and a navigator to execute movements. However, current waypoint predictors struggle with spatial awareness, while navigators lack historical reasoning and backtracking capabilities, limiting adaptability. We propose a zero-shot VLN-CE framework integrating an enhanced waypoint predictor with a Multi-modal Large Language Model (MLLM)-based navigator. Our predictor employs a stronger vision encoder, masked cross-attention fusion, and an occupancy-aware loss for better waypoint quality. The navigator incorporates history-aware reasoning and adaptive path planning with backtracking, improving robustness. Experiments on R2R-CE and MP3D benchmarks show our method achieves state-of-the-art (SOTA) performance in zero-shot settings, demonstrating competitive results compared to fully supervised methods. Real-world validation on Turtlebot 4 further highlights its adaptability.

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