Jiyue Jiang

Jingqi Zhou, Sheng Wang, Dezhao Deng et al.

LLM-powered agentic systems excel at complex long-horizon tasks, but remain constrained by static configurations fixed before execution. Such rigidity forces a trade-off between domain-specific performance and cross-task generalization: strong priors and compact tool spaces aid specialization but weaken transfer, while task-agnostic workflows and broad action spaces expand coverage but dilute guidance. Existing pre-execution optimization, planner-worker orchestration, and configuration patching fall short of resolving this tension, as they decouple adaptation from execution, causing information loss, fragmented optimization, and ambiguous credit assignment. We propose ToolSelf, a tool-driven runtime self-reconfiguration paradigm that abstracts configuration updates as a standardized tool interface and unifies execution and adaptation within one policy's action space. The execution agent can dynamically update sub-goals, strategies, toolboxes, context, and context-management modes based on task progress and feedback. We further introduce Configuration-Aware Two-stage Training (CAT), which combines rejection sampling fine-tuning with trajectory-level KTO reinforcement learning to internalize self-reconfiguration. Across diverse benchmarks, zero-shot ToolSelf rivals task-specialized agents; after CAT training, ToolSelf gains 28.8 points over the static-configuration baseline on average, illuminating a path toward emergent adaptivity that obviates manually injected guidance.

Jiyue Jiang, Pengan Chen, Liheng Chen et al. · oxford

The rapid evolution of large language models (LLMs) has transformed the competitive landscape in natural language processing (NLP), particularly for English and other data-rich languages. However, underrepresented languages like Cantonese, spoken by over 85 million people, face significant development gaps, which is particularly concerning given the economic significance of the Guangdong-Hong Kong-Macau Greater Bay Area, and in substantial Cantonese-speaking populations in places like Singapore and North America. Despite its wide use, Cantonese has scant representation in NLP research, especially compared to other languages from similarly developed regions. To bridge these gaps, we outline current Cantonese NLP methods and introduce new benchmarks designed to evaluate LLM performance in factual generation, mathematical logic, complex reasoning, and general knowledge in Cantonese, which aim to advance open-source Cantonese LLM technology. We also propose future research directions and recommended models to enhance Cantonese LLM development.

Yanyu Chen, Jiyue Jiang, Dianzhi Yu et al.

The evolution of Large Language Model (LLM) reasoning is bottlenecked by the scarcity of high-quality process data. While self-alignment via endogenous rewards offers a solution, mining valid supervision faces three challenges: (1) Label Noise via Mimetic Bias, where rewards prioritize statistical likelihood over logical truth, creating a "correctness illusion" that masks compounding errors; (2) Coarse-Grained Supervision, where sparse global outcomes (e.g., in GRPO) fail to provide granular guidance, treating reasoning chains as monolithic; and (3) Distributional Collapse, where signals fail to generalize without amplifying pre-training biases. To address these, we introduce LC-ERD (Logic-Consistent Endogenous Reward Decomposition), a framework framing self-alignment as latent structure mining. We derive a Variational Logic Potential by aggregating consensus from the model's Latent Logic Expertise (LLE) to denoise the reasoning manifold, and introduce a Multi-Agent Value Decomposition protocol based on the IGM principle to quantify individual step utility. Experiments show LC-ERD delivers a robust self-evolution path, uncovering trade-offs between logic consistency and accuracy while identifying high-value reasoning patterns missed by standard rewards. Our code is available at https://github.com/Reinhardmannn/LC-ERD.

Yanyu Chen, Jiyue Jiang, Jiahong Liu et al.

The evaluation of Deep Research Agents is a critical challenge, as conventional outcome-based metrics fail to capture the nuances of their complex reasoning. Current evaluation faces two primary challenges: 1) a reliance on singular metrics like Pass@1, creating a "high-score illusion" that ignores the quality, efficiency, and soundness of the reasoning process; and 2) the failure of static benchmarks to quantify crucial attributes like robustness and latent capability. To address these gaps, we introduce TRACE (Trajectory-Aware Comprehensive Evaluation), a framework that holistically assesses the entire problem-solving trajectory. To counter the "high-score illusion", we propose a Hierarchical Trajectory Utility Function that quantifies process efficiency and cognitive quality, including evidence grounding, alongside accuracy. To measure deeper attributes, TRACE introduces a Scaffolded Capability Assessment protocol, quantifying an agent's latent ability by determining the minimum guidance needed for success. Our contributions include the TRACE framework, its novel metrics, and the accompanying DeepResearch-Bench with controllable complexity. Experiments show TRACE delivers a granular ranking that uncovers critical trade-offs between agent accuracy, efficiency, and robustness entirely missed by singular metrics.

Jingqi Zhou, Sheng Wang, Jingwei Dong et al.

Large vision-language models (LVLMs) have witnessed significant progress on visual understanding tasks. However, they often prioritize language knowledge over image information on visual reasoning tasks, incurring performance degradation. To tackle this issue, we first identify the drawbacks of existing solutions (i.e., limited multi-modal reasoning capacities, and insufficient and irrelevant visual descriptions). We then decompose visual reasoning process into two stages: proactive visual perception (i.e., eyesight) and textual reasoning (i.e., wisdom), and introduce a novel visual reasoning framework named ProReason. This framework features decoupled vision-reasoning capabilities and multi-run proactive perception. Briefly, given a multi-modal question, ProReason iterates proactive information collection and reasoning until the answer can be concluded with necessary and sufficient visual descriptions. Notably, the disassociation of capabilities allows seamless integration of existing large language models (LLMs) to compensate for the reasoning deficits of LVLMs. Our extensive experiments demonstrate that ProReason outperforms existing multi-step reasoning frameworks on various benchmarks for both open-source and closed-source models, with the average performance gain reaching 13.2%. Besides, the integration of LLMs allows ProReason to produce high-quality visual reasoning data, which empowers ProReason-distilled models (i.e., ProReason-VL and ProReason-Q3) to achieve superior performance in downstream tasks. Our insights into existing solutions and the decoupled perspective for feasible integration of LLMs illuminate future research on visual reasoning techniques, especially LLM-assisted ones.

Sheng Wang, Pengan Chen, Jingqi Zhou et al.

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 distributions 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 dividing-and-synthesizing 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 rebalancing of existing datasets for more balanced and comprehensive distributions. Empirically, extensive experiments across diverse benchmarks consistently demonstrate the superior data diversity, model performance, and robust scalability of TREESYNTH compared to both human-crafted datasets and peer data synthesis methods, with an 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.

Jiyue Jiang, Alfred Kar Yin Truong, Yanyu Chen et al.

High-quality data resources play a crucial role in learning large language models (LLMs), particularly for low-resource languages like Cantonese. Despite having more than 85 million native speakers, Cantonese is still considered a low-resource language in the field of natural language processing (NLP) due to factors such as the dominance of Mandarin, lack of cohesion within the Cantonese-speaking community, diversity in character encoding and input methods, and the tendency of overseas Cantonese speakers to prefer using English. In addition, rich colloquial vocabulary of Cantonese, English loanwords, and code-switching characteristics add to the complexity of corpus collection and processing. To address these challenges, we collect Cantonese texts from a variety of sources, including open source corpora, Hong Kong-specific forums, Wikipedia, and Common Crawl data. We conduct rigorous data processing through language filtering, quality filtering, content filtering, and de-duplication steps, successfully constructing a high-quality Cantonese corpus of over 2 billion tokens for training large language models. We further refined the model through supervised fine-tuning (SFT) on curated Cantonese tasks, enhancing its ability to handle specific applications. Upon completion of the training, the model achieves state-of-the-art (SOTA) performance on four Cantonese benchmarks. After training on our dataset, the model also exhibits improved performance on other mainstream language tasks.

Sheng Wang, Liheng Chen, Jiyue Jiang et al. · oxford

With the remarkable capabilities, large language models (LLMs) have emerged as essential elements in numerous NLP applications, while parameter-efficient finetuning, especially LoRA, has gained popularity as a lightweight approach for model customization. Meanwhile, various dropout methods, initially designed for full finetuning with all the parameters updated, alleviates overfitting associated with excessive parameter redundancy. Hence, a possible contradiction arises from negligible trainable parameters of LoRA and the effectiveness of previous dropout methods, which has been largely overlooked. To fill this gap, we first confirm that parameter-efficient LoRA is also overfitting-prone. We then revisit transformer-specific dropout methods, and establish their equivalence and distinctions mathematically and empirically. Building upon this comparative analysis, we introduce a unified framework for a comprehensive investigation, which instantiates these methods based on dropping position, structural pattern and compensation measure. Through this framework, we reveal the new preferences and performance comparisons of them when involved with limited trainable parameters. This framework also allows us to amalgamate the most favorable aspects into a novel dropout method named HiddenKey. Extensive experiments verify the remarkable superiority and sufficiency of HiddenKey across multiple models and tasks, which highlights it as the preferred approach for high-performance and parameter-efficient finetuning of LLMs.

Sheng Wang, Boyang Xue, Jiacheng Ye et al. · oxford

With the rapid scaling of large language models (LLMs), serving numerous low-rank adaptations (LoRAs) concurrently has become increasingly impractical, leading to unaffordable costs and necessitating more parameter-efficient finetuning methods. In this work, we introduce Partially Rotation-enhanced Low-Rank Adaptation (PRoLoRA), an intra-layer sharing mechanism comprising four essential components: broadcast reduction, rotation enhancement, partially-sharing refinement, and rectified initialization strategy. As a superset of LoRA, PRoLoRA retains its advantages, and effectively circumvent the drawbacks of peer parameter-sharing methods with superior model capacity, practical feasibility, and broad applicability. Empirical experiments demonstrate the remarkably higher parameter efficiency of PRoLoRA in both specific parameter budget and performance target scenarios, and its scalability to larger LLMs. Notably, with one time less trainable parameters, PRoLoRA still outperforms LoRA on multiple instruction tuning datasets. Subsequently, an ablation study is conducted to validate the necessity of individual components and highlight the superiority of PRoLoRA over three potential variants. Hopefully, the conspicuously higher parameter efficiency can establish PRoLoRA as a resource-friendly alternative to LoRA.

Zhenyu Wang, Zikang Wang, Jiyue Jiang et al.

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling, RNA structure prediction, protein function inference, and single-cell transcriptomics. Meanwhile, we also discuss several key challenges, including data scarcity, computational complexity, and cross-omics integration, and explore future directions such as multimodal learning, hybrid AI models, and clinical applications. By offering a comprehensive perspective, this paper underscores the transformative potential of LLMs in driving innovations in bioinformatics and precision medicine.

Jiyue Jiang, Pengan Chen, Jiuming Wang et al.

Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of these LLMs. However, current benchmarks can hardly evaluate the performance of these models across diverse tasks effectively. In this paper, we introduce a comprehensive prompting-based benchmarking framework, termed Bio-benchmark, which includes 30 key bioinformatics tasks covering areas such as proteins, RNA, drugs, electronic health records, and traditional Chinese medicine. Using this benchmark, we evaluate six mainstream LLMs, including GPT-4o and Llama-3.1-70b, etc., using 0-shot and few-shot Chain-of-Thought (CoT) settings without fine-tuning to reveal their intrinsic capabilities. To improve the efficiency of our evaluations, we demonstrate BioFinder, a new tool for extracting answers from LLM responses, which increases extraction accuracy by round 30% compared to existing methods. Our benchmark results show the biological tasks suitable for current LLMs and identify specific areas requiring enhancement. Furthermore, we propose targeted prompt engineering strategies for optimizing LLM performance in these contexts. Based on these findings, we provide recommendations for the development of more robust LLMs tailored for various biological applications. This work offers a comprehensive evaluation framework and robust tools to support the application of LLMs in bioinformatics.

Jiyue Jiang, Zikang Wang, Yuheng Shan et al.

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis and synthesis, attracting widespread attention from academics and medicine. In this paper, we systematically investigate the application of prompt-based methods with LLMs to biological sequences, including DNA, RNA, proteins, and drug discovery tasks. Specifically, we focus on how prompt engineering enables LLMs to tackle domain-specific problems, such as promoter sequence prediction, protein structure modeling, and drug-target binding affinity prediction, often with limited labeled data. Furthermore, our discussion highlights the transformative potential of prompting in bioinformatics while addressing key challenges such as data scarcity, multimodal fusion, and computational resource limitations. Our aim is for this paper to function both as a foundational primer for newcomers and a catalyst for continued innovation within this dynamic field of study.

Yanting Li, Jiyue Jiang, Zikang Wang et al.

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.

Yifan Wu, Jiyue Jiang, Xichen Ye et al.

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 introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost, and builds upon it two simple yet effective selection strategies, namely Top-k Influence (Top I) and Coverage-Centric Influence (CCI). 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 percent, demonstrating its effectiveness. Furthermore, we show the generalizability of our framework on protein-related tasks using ESM-C. In particular, our coreset even outperforms random subsets that are ten times larger 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.

Jiyue Jiang, Liheng Chen, Sheng Wang et al.

Existing dialogue data augmentation (DA) techniques predominantly focus on augmenting utterance-level dialogues, which makes it difficult to take dialogue contextual information into account. The advent of large language models (LLMs) has simplified the implementation of multi-turn dialogues. Due to absence of professional understanding and knowledge, it remains challenging to deliver satisfactory performance in low-resource domain, like psychological dialogue dialogue. DA involves creating new training or prompting data based on the existing data, which help the model better understand and generate psychology-related responses. In this paper, we aim to address the issue of multi-turn dialogue data augmentation for boosted performance in the psychology domain. We propose a knowledge-driven progressive thought prompting method to guide LLM to generate multi-turn psychology-related dialogue. This method integrates a progressive thought generator, a psychology knowledge generator, and a multi-turn dialogue generator. The thought generated by the progressive thought generator serves as a prompt to prevent the generated dialogue from having significant semantic deviations, while the psychology knowledge generator produces psychological knowledge to serve as the dialogue history for the LLM, guiding the dialogue generator to create multi-turn psychological dialogue. To ensure the precision of multi-turn psychological dialogue generation by LLM, a meticulous professional evaluation is required. Extensive experiments conducted on three datasets related to psychological dialogue verify the effectiveness of the proposed method.

Jiyue Jiang, Sheng Wang, Qintong Li et al.

When communicating with elders with cognitive impairment, cognitive stimulation (CS) help to maintain the cognitive health of elders. Data sparsity is the main challenge in building CS-based dialogue systems, particularly in the Chinese language. To fill this gap, we construct a Chinese CS conversation (CSConv) dataset, which contains about 2.6K groups of dialogues with CS principles and emotional support strategy labels. Making chit chat while providing emotional support is overlooked by the majority of existing cognitive dialogue systems. In this paper, we propose a multi-source knowledge fusion method for CS dialogue (CSD), to generate open-ended responses guided by the CS principle and emotional support strategy. We first use a progressive mask method based on external knowledge to learn encoders as effective classifiers, which is the prerequisite to predict the CS principle and emotional support strategy of the target response. Then a decoder interacts with the perceived CS principle and emotional support strategy to generate responses. Extensive experiments conducted on the CSConv dataset demonstrate the effectiveness of the proposed method, while there is still a large space for improvement compared to human performance.