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Jiyue Jiang

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6 papers

2 author rows

AAAI Conference 2026 Conference Paper

A Principle-Driven Adaptive Policy for Group Cognitive Stimulation Dialogue for Elderly with Cognitive Impairment

Jiyue Jiang
Yanyu Chen
Pengan CHEN
Kai Liu
Jingqi Zhou
Zheyong Zhu
He Hu
Fei Ma

Cognitive impairment is becoming a major public health challenge. Cognitive Stimulation Therapy (CST) is an effective intervention for cognitive impairment, but traditional methods are difficult to scale, and existing digital systems struggle with group dialogues and cognitive stimulation principles. While Large Language Models (LLMs) are powerful, their application in this context faces key challenges: cognitive stimulation dialogue paradigms, a lack of therapeutic reasoning, and static-only user modeling. To address these issues, we propose a principle-driven adaptive policy actualized through a Group Cognitive Stimulation Dialogue (GCSD) system. We first construct a dataset with over 500 hours of real-world CST conversations and 10,000+ simulated dialogues generated via our Principle-Guided Scenario Simulation strategy. Our GCSD system then integrates four core modules to overcome LLM limitations: (i) a multi-speaker context controller to resolve role confusion; (ii) dynamic participant cognitive state modeling for personalized interaction; (iii) a cognitive stimulation-focused attention loss to instill cognitive stimulation reasoning; and (iv) a multi-dimensional reward strategy to enhance response value. Experimental results demonstrate that GCSD significantly outperforms baseline models across various evaluation metrics. Future work will focus on long-term clinical validation to bridge the gap between computational performance and clinical efficacy.

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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

Investigating Data Pruning for Pretraining Biological Foundation Models at Scale

Yifan Wu
Jiyue Jiang
Xichen Ye
Yiqi Wang
Chang Zhou
Yitao Xu
Jiayang Chen
He Hu

Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely on millions to billions of training sequences and billions of parameters, resulting in prohibitive computational costs and significant barriers to reproducibility and accessibility—particularly for academic labs. To address these challenges, we investigate the feasibility of data pruning for BioFM pretraining and propose a post-hoc influence-guided data pruning framework tailored to biological domains. Our approach first introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost. Built upon this, we propose two simple yet effective selection strategies: Top-k Influence (Top I) and Coverage-Centric Influence (CCI). Then, we empirically validate our method on two representative BioFMs: RNA-FM and ESM-C. For RNA, our framework consistently outperforms random selection baselines under an extreme pruning rate of over 99%, which displays our framework's effectiveness. Furthermore, we demonstrate the generalizability of our framework on protein-related tasks using ESM-C. Specifically, our coreset even outperforms random 10x subsets in both RNA and protein settings, revealing substantial redundancy in biological sequence datasets. These findings underscore the potential of influence-guided data pruning to substantially reduce the computational cost of BioFM pretraining, paving the way for more efficient, accessible, and sustainable biological AI research.

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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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ICLR Conference 2025 Conference Paper

MoS: Unleashing Parameter Efficiency of Low-Rank Adaptation with Mixture of Shards

Sheng Wang
Liheng Chen
Pengan Chen
Jingwei Dong
Boyang Xue
Jiyue Jiang
Lingpeng Kong
Chuan Wu

The rapid scaling of large language models necessitates more lightweight finetuning methods to reduce the explosive GPU memory overhead when numerous customized models are served simultaneously. Targeting more parameter-efficient low-rank adaptation (LoRA), parameter sharing presents a promising solution. Empirically, our research into high-level sharing principles highlights the indispensable role of differentiation in reversing the detrimental effects of pure sharing. Guided by this finding, we propose Mixture of Shards (MoS), incorporating both inter-layer and intra-layer sharing schemes, and integrating four nearly cost-free differentiation strategies, namely subset selection, pair dissociation, vector sharding, and shard privatization. Briefly, it selects a designated number of shards from global pools with a Mixture-of-Experts (MoE)-like routing mechanism before sequentially concatenating them to low-rank matrices. Hence, it retains all the advantages of LoRA while offering enhanced parameter efficiency, and effectively circumvents the drawbacks of peer parameter-sharing methods. Our empirical experiments demonstrate approximately $8\times$ parameter savings in a standard LoRA setting. The ablation study confirms the significance of each component. Our insights into parameter sharing and MoS method may illuminate future developments of more parameter-efficient finetuning methods. The code is officially available at https://github.com/Forence1999/MoS.

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NeurIPS Conference 2025 Conference Paper

TreeSynth: Synthesizing Diverse Data from Scratch via Tree-Guided Subspace Partitioning

Sheng Wang
Pengan CHEN
Jingqi Zhou
Qintong Li
Jingwei Dong
Jiahui Gao
Boyang XUE
Jiyue Jiang

Model customization necessitates high-quality and diverse datasets, but acquiring such data remains time-consuming and labor-intensive. Despite the great potential of large language models (LLMs) for data synthesis, current approaches are constrained by limited seed data, model biases and low-variation prompts, resulting in limited diversity and biased distribution with the increase of data scales. To tackle this challenge, we introduce TreeSynth, a tree-guided subspace-based data synthesis approach inspired by decision trees. It constructs a spatial partitioning tree to recursively divide a task-specific full data space (i. e. , root node) into numerous atomic subspaces (i. e. , leaf nodes) with mutually exclusive and exhaustive attributes to ensure both distinctiveness and comprehensiveness, before synthesizing samples within each atomic subspace. This globally divide-and-synthesize method finally collects subspace samples into a comprehensive dataset, effectively circumventing repetition and space collapse to ensure the diversity of large-scale data synthesis. Furthermore, the spatial partitioning tree enables sample allocation into atomic subspaces, allowing the re-balancing of existing datasets for more balanced and comprehensive distributions. Empirically, extensive experiments across diverse benchmarks consistently validates the superior data diversity, model performance, and robust scalability of TreeSynth compared to both human-crafted datasets and peer data synthesis methods, with the average performance gain reaching 10%. Besides, the consistent improvements of TreeSynth-balanced datasets highlight its efficacious application to redistribute existing datasets for more comprehensive coverage and the induced performance enhancement. The code is available at https: //github. com/cpa2001/TreeSynth.

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