arXiv subjects

Jiyue Jiang

Publications and source records attributed to Jiyue Jiang.

At least 19 recordsLinked to original sources

arXiv2026

CONDUIT: A Unified Residual-Stream Restoration Framework for KV Cache Reuse in Vision-Language Models

Vision-language models (VLMs) often answer new questions about recurring visual content, where reusing the key-value (KV) cache can avoid re-encoding expensive visual prefixes. Exact-prefix reuse, however, fails when the same visual content appears under a changed prefix. Selective recomputation can recover quality under a small visual-token budget, but only when the right stale tokens are refreshed. Raw-attention selection can waste budget on high-attention tokens with small value-norm proxy scores and on query-irrelevant images. To address these failure modes, we propose CONDUIT, a training-free refresh policy that unifies single- and multi-image reuse as residual-stream restoration. Building on norm-weighted attention, CONDUIT ranks cached visual tokens using cached-key query attention and an accessible pre-output cached-value-norm proxy, then applies empirical image-level relevance amplification before one global selection. With one image, the coefficient is one and the rule reduces to intra-image token selection. The method preserves model architecture and weights, adding only a single query-conditioned scoring pass at inference. At a 10% refresh budget, CONDUIT achieves 97.0-99.5% of the corresponding full-prefill five-dataset average across three VLM backbones and leads budgeted methods on average; on the MMLongBench-Doc latency subset, it uses 13.5% of full-prefill FLOPs and achieves a 2.99x time-to-first-token speedup.

cs.CL↗

arXiv2026

Think Before You Comfort: Reflective Cognitive Alignment for Protocol-Grounded Elderly Stimulation Agents

Cognitive Stimulation Therapy (CST) offers non-pharmacological support for elders with cognitive impairment, yet scalability remains constrained by reliance on trained facilitators and severe data scarcity, particularly for privacy-sensitive, low-resource languages such as Cantonese. While Large Language Models (LLMs) show promise for automated companionship, they often struggle to balance empathetic engagement with adherence to cognitive stimulation guidelines. We propose a framework addressing these challenges along two complementary axes. First, STaR-CS (Style-Transfer and Role-Conditioned Cognitive Stimulation) synthesizes multi-party dialogues through facilitator style modeling and structured skeleton extraction, mitigating data barriers. Building upon this corpus, the Reflective Cognitive Alignment (RCA) framework models stimulation interactions as a sequential decision process, integrating Protocol-Constrained Chain-of-Cognition (PC-CoC) for structured reasoning and Inference-Time Value Alignment (IVA) for principled response selection based on safety and engagement goals. Evaluations across six backbone LLMs and two independent judges show that RCA consistently improves protocol adherence, safety, and group facilitation over standard prompting baselines. Our code is available at https://github.com/jiangjyjy/RCA_Agent.

cs.CL↗

arXiv2026

ToolSelf: Unifying Task Execution and Self-Reconfiguration via Tool-Driven Emergent Adaptation

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. The code is available at https://github.com/lian-tian-mo-zun/ToolSelf.

cs.AI↗

arXiv2026

LC-ERD: Mining Latent Logic for Self-Evolving Reasoning via Consistency-Regulated Reward Decomposition

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/LC-ERD-repo/LC-ERD.

cs.AI↗

arXiv2026

Large Language Models in Bioinformatics: A Survey

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.

cs.CL↗

arXiv2026

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

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.

cs.CL↗

arXiv2026

Investigating Data Pruning for Pretraining Biological Foundation Models at Scale

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.

cs.LG↗

arXiv2026

TRACE: Trajectory-Aware Comprehensive Evaluation for Deep Research Agents

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.

cs.CL↗

arXiv2025

ProReason: Multi-Modal Proactive Reasoning with Decoupled Eyesight and Wisdom

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.

cs.CV↗

arXiv2025

Design and Implementation of a Lightweight Object Detection System for Resource-Constrained Edge Environments

This project aims to develop a system to run the object detection model under low power consumption conditions. The detection scene is set as an outdoor traveling scene, and the detection categories include people and vehicles. In this system, users data does not need to be uploaded to the cloud, which is suitable for use in environments with portable needs and strict requirements for data privacy. The MCU device used in this system is STM32H7, which has better performance among low power devices. The YOLOv5 system is selected to train the object detection model. To overcome the resource limitation of the embedded devices, this project uses several model compression techniques such as pruned, quantization, and distillation, which could improve the performance and efficiency of the detection model. Through these processes, the model s computation and the quantity of model parameters could be reduced, in order to run computer vision models on micro-controller devices for the development of embedded vision applications.

eess.SY↗

arXiv2025

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

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.

cs.LG↗

arXiv2025

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

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.

cs.CL↗

arXiv2025

Benchmarking Large Language Models on Multiple Tasks in Bioinformatics NLP with Prompting

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.

cs.CL↗

arXiv2025

Biological Sequence with Language Model Prompting: A Survey

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.

cs.CL↗

arXiv2025

Developing and Utilizing a Large-Scale Cantonese Dataset for Multi-Tasking in Large Language Models

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.

cs.CL↗

arXiv2025

How Well Do LLMs Handle Cantonese? Benchmarking Cantonese Capabilities of Large Language Models

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.

cs.CL↗

arXiv2025

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

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 8x 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.

cs.LG↗

arXiv2024

Data Augmentation of Multi-turn Psychological Dialogue via Knowledge-driven Progressive Thought Prompting

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.

cs.CL↗