arXiv subjects

Yuxuan Chen

Publications and source records attributed to Yuxuan Chen.

At least 109 records · Page 6Linked to original sources

arXiv2025

An Inclusive Foundation Model for Generalizable Cytogenetics in Precision Oncology

Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and diversity of chromosomal abnormalities, requiring extensive annotation efforts, while automated methods remain task-specific and lack generalizability due to the scarcity of comprehensive datasets spanning diverse resource conditions. Here, we introduce CHROMA, a foundation model for cytogenomics, designed to overcome these challenges by learning generalizable representations of chromosomal abnormalities. Pre-trained on over 84,000 specimens (~4 million chromosomal images) via self-supervised learning, CHROMA outperforms other methods across all types of abnormalities, even when trained on fewer labelled data and more imbalanced datasets. By facilitating comprehensive mapping of instability and clonal leisons across various aberration types, CHROMA offers a scalable and generalizable solution for reliable and automated clinical analysis, reducing the annotation workload for experts and advancing precision oncology through the early detection of rare genomic abnormalities, enabling broad clinical AI applications and making advanced genomic analysis more accessible.

q-bio.QM↗

arXiv2025

LLM-Enhanced Feature Engineering for Multi-Factor Electricity Price Predictions

Accurately forecasting electricity price volatility is crucial for effective risk management and decision-making. Traditional forecasting models often fall short in capturing the complex, non-linear dynamics of electricity markets, particularly when external factors like weather conditions and market volatility are involved. These limitations hinder their ability to provide reliable predictions in markets with high volatility, such as the New South Wales (NSW) electricity market. To address these challenges, we introduce FAEP, a Feature-Augmented Electricity Price Prediction framework. FAEP leverages Large Language Models (LLMs) combined with advanced feature engineering to enhance prediction accuracy. By incorporating external features such as weather data and price volatility jumps, and utilizing Retrieval-Augmented Generation (RAG) for effective feature extraction, FAEP overcomes the shortcomings of traditional approaches. A hybrid XGBoost-LSTM model in FAEP further refines these augmented features, resulting in a more robust prediction framework. Experimental results demonstrate that FAEP achieves state-of-art (SOTA) performance compared to other electricity price prediction models in the Australian New South Wale electricity market, showcasing the efficiency of LLM-enhanced feature engineering and hybrid machine learning architectures.

cs.CE↗

arXiv2025

PersLLM: A Personified Training Approach for Large Language Models

Large language models (LLMs) exhibit human-like intelligence, enabling them to simulate human behavior and support various applications that require both humanized communication and extensive knowledge reserves. Efforts are made to personify LLMs with special training data or hand-crafted prompts, while correspondingly faced with challenges such as insufficient data usage or rigid behavior patterns. Consequently, personified LLMs fail to capture personified knowledge or express persistent opinion. To fully unlock the potential of LLM personification, we propose PersLLM, a framework for better data construction and model tuning. For insufficient data usage, we incorporate strategies such as Chain-of-Thought prompting and anti-induction, improving the quality of data construction and capturing the personality experiences, knowledge, and thoughts more comprehensively. For rigid behavior patterns, we design the tuning process and introduce automated DPO to enhance the specificity and dynamism of the models' personalities, which leads to a more natural opinion communication. Both automated metrics and expert human evaluations demonstrate the effectiveness of our approach. Case studies in human-machine interactions and multi-agent systems further suggest potential application scenarios and future directions for LLM personification.

cs.CL↗

arXiv2025

KBAlign: Efficient Self Adaptation on Specific Knowledge Bases

Although retrieval-augmented generation (RAG) remains essential for knowledge-based question answering (KBQA), current paradigms face critical challenges under specific domains. Existing methods struggle with targeted adaptation on small-scale KBs: vanilla unsupervised training exhibits poor effectiveness, while fine-tuning incurs prohibitive costs of external signals. We present KBAlign, a self-supervised framework that enhances RAG systems through efficient model adaptation. Our key insight is to leverage the model's intrinsic capabilities for knowledge alignment through two innovative mechanisms: multi-grained self-annotation that captures global knowledge for data construction, and iterative tuning that accelerates convergence through self verification. This framework enables cost-effective model adaptation to specific textual KBs, without human supervision or external model assistance. Experiments demonstrate that KBAlign can achieve 90\% of the performance gain obtained through GPT-4-supervised adaptation, while relying entirely on self-annotation of much smaller models. KBAlign significantly improves downstream QA accuracy across multiple domains with tiny costs, particularly benefiting scenarios requiring deep knowledge integration from specialized corpora. We release our experimental data, models, and process analyses to the community for further exploration (https://github.com/thunlp/KBAlign).

cs.CL↗

arXiv2025

MAGI: Multi-Agent Guided Interview for Psychiatric Assessment

Automating structured clinical interviews could revolutionize mental healthcare accessibility, yet existing large language models (LLMs) approaches fail to align with psychiatric diagnostic protocols. We present MAGI, the first framework that transforms the gold-standard Mini International Neuropsychiatric Interview (MINI) into automatic computational workflows through coordinated multi-agent collaboration. MAGI dynamically navigates clinical logic via four specialized agents: 1) an interview tree guided navigation agent adhering to the MINI's branching structure, 2) an adaptive question agent blending diagnostic probing, explaining, and empathy, 3) a judgment agent validating whether the response from participants meet the node, and 4) a diagnosis Agent generating Psychometric Chain-of- Thought (PsyCoT) traces that explicitly map symptoms to clinical criteria. Experimental results on 1,002 real-world participants covering depression, generalized anxiety, social anxiety and suicide shows that MAGI advances LLM- assisted mental health assessment by combining clinical rigor, conversational adaptability, and explainable reasoning.

cs.CL↗

arXiv2025

Crisp: Cognitive Restructuring of Negative Thoughts through Multi-turn Supportive Dialogues

Cognitive Restructuring (CR) is a psychotherapeutic process aimed at identifying and restructuring an individual's negative thoughts, arising from mental health challenges, into more helpful and positive ones via multi-turn dialogues. Clinician shortage and stigma urge the development of human-LLM interactive psychotherapy for CR. Yet, existing efforts implement CR via simple text rewriting, fixed-pattern dialogues, or a one-shot CR workflow, failing to align with the psychotherapeutic process for effective CR. To address this gap, we propose CRDial, a novel framework for CR, which creates multi-turn dialogues with specifically designed identification and restructuring stages of negative thoughts, integrates sentence-level supportive conversation strategies, and adopts a multi-channel loop mechanism to enable iterative CR. With CRDial, we distill Crisp, a large-scale and high-quality bilingual dialogue dataset, from LLM. We then train Crispers, Crisp-based conversational LLMs for CR, at 7B and 14B scales. Extensive human studies show the superiority of Crispers in pointwise, pairwise, and intervention evaluations.

cs.CL↗

arXiv2025

TransST: Transfer Learning Embedded Spatial Factor Modeling of Spatial Transcriptomics Data

Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However, limitations of the technology such as the relatively low resolution and comparatively insufficient sequencing depth make it difficult to reliably extract real biological signals from these data. To alleviate this challenge, we propose a novel transfer learning framework, referred to as TransST, to adaptively leverage the cell-labeled information from external sources in inferring cell-level heterogeneity of a target spatial transcriptomics data. Results: Applications in several real studies as well as a number of simulation settings show that our approach significantly improves existing techniques. For example, in the breast cancer study, TransST successfully identifies five biologically meaningful cell clusters, including the two subgroups of cancer in situ and invasive cancer; in addition, only TransST is able to separate the adipose tissues from the connective issues among all the studied methods. Conclusions: In summary, the proposed method TransST is both effective and robust in identifying cell subclusters and detecting corresponding driving biomarkers in spatial transcriptomics data.

q-bio.GN↗

arXiv2025

AimTS: Augmented Series and Image Contrastive Learning for Time Series Classification

Time series classification (TSC) is an important task in time series analysis. Existing TSC methods mainly train on each single domain separately, suffering from a degradation in accuracy when the samples for training are insufficient in certain domains. The pre-training and fine-tuning paradigm provides a promising direction for solving this problem. However, time series from different domains are substantially divergent, which challenges the effective pre-training on multi-source data and the generalization ability of pre-trained models. To handle this issue, we introduce Augmented Series and Image Contrastive Learning for Time Series Classification (AimTS), a pre-training framework that learns generalizable representations from multi-source time series data. We propose a two-level prototype-based contrastive learning method to effectively utilize various augmentations in multi-source pre-training, which learns representations for TSC that can be generalized to different domains. In addition, considering augmentations within the single time series modality are insufficient to fully address classification problems with distribution shift, we introduce the image modality to supplement structural information and establish a series-image contrastive learning to improve the generalization of the learned representations for TSC tasks. Extensive experiments show that after multi-source pre-training, AimTS achieves good generalization performance, enabling efficient learning and even few-shot learning on various downstream TSC datasets.

cs.LG↗

arXiv2025

MaRI: Material Retrieval Integration across Domains

Accurate material retrieval is critical for creating realistic 3D assets. Existing methods rely on datasets that capture shape-invariant and lighting-varied representations of materials, which are scarce and face challenges due to limited diversity and inadequate real-world generalization. Most current approaches adopt traditional image search techniques. They fall short in capturing the unique properties of material spaces, leading to suboptimal performance in retrieval tasks. Addressing these challenges, we introduce MaRI, a framework designed to bridge the feature space gap between synthetic and real-world materials. MaRI constructs a shared embedding space that harmonizes visual and material attributes through a contrastive learning strategy by jointly training an image and a material encoder, bringing similar materials and images closer while separating dissimilar pairs within the feature space. To support this, we construct a comprehensive dataset comprising high-quality synthetic materials rendered with controlled shape variations and diverse lighting conditions, along with real-world materials processed and standardized using material transfer techniques. Extensive experiments demonstrate the superior performance, accuracy, and generalization capabilities of MaRI across diverse and complex material retrieval tasks, outperforming existing methods.

cs.CV↗

arXiv2025

DeepNote: Note-Centric Deep Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) mitigates factual errors and hallucinations in Large Language Models (LLMs) for question-answering (QA) by incorporating external knowledge. However, existing adaptive RAG methods rely on LLMs to predict retrieval timing and directly use retrieved information for generation, often failing to reflect real information needs and fully leverage retrieved knowledge. We develop DeepNote, an adaptive RAG framework that achieves in-depth and robust exploration of knowledge sources through note-centric adaptive retrieval. DeepNote employs notes as carriers for refining and accumulating knowledge. During in-depth exploration, it uses these notes to determine retrieval timing, formulate retrieval queries, and iteratively assess knowledge growth, ultimately leveraging the best note for answer generation. Extensive experiments and analyses demonstrate that DeepNote significantly outperforms all baselines (+10.2% to +20.1%) and exhibits the ability to gather knowledge with both high density and quality. Additionally, DPO further improves the performance of DeepNote. The code and data are available at https://github.com/thunlp/DeepNote.

cs.CL↗

arXiv2025

UltraRAG: A Modular and Automated Toolkit for Adaptive Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) significantly enhances the performance of large language models (LLMs) in downstream tasks by integrating external knowledge. To facilitate researchers in deploying RAG systems, various RAG toolkits have been introduced. However, many existing RAG toolkits lack support for knowledge adaptation tailored to specific application scenarios. To address this limitation, we propose UltraRAG, a RAG toolkit that automates knowledge adaptation throughout the entire workflow, from data construction and training to evaluation, while ensuring ease of use. UltraRAG features a user-friendly WebUI that streamlines the RAG process, allowing users to build and optimize systems without coding expertise. It supports multimodal input and provides comprehensive tools for managing the knowledge base. With its highly modular architecture, UltraRAG delivers an end-to-end development solution, enabling seamless knowledge adaptation across diverse user scenarios. The code, demonstration videos, and installable package for UltraRAG are publicly available at https://github.com/OpenBMB/UltraRAG.

cs.IR↗

arXiv2025

Cross-Modal Prototype Allocation: Unsupervised Slide Representation Learning via Patch-Text Contrast in Computational Pathology

With the rapid advancement of pathology foundation models (FMs), the representation learning of whole slide images (WSIs) attracts increasing attention. Existing studies develop high-quality patch feature extractors and employ carefully designed aggregation schemes to derive slide-level representations. However, mainstream weakly supervised slide representation learning methods, primarily based on multiple instance learning (MIL), are tailored to specific downstream tasks, which limits their generalizability. To address this issue, some studies explore unsupervised slide representation learning. However, these approaches focus solely on the visual modality of patches, neglecting the rich semantic information embedded in textual data. In this work, we propose ProAlign, a cross-modal unsupervised slide representation learning framework. Specifically, we leverage a large language model (LLM) to generate descriptive text for the prototype types present in a WSI, introducing patch-text contrast to construct initial prototype embeddings. Furthermore, we propose a parameter-free attention aggregation strategy that utilizes the similarity between patches and these prototypes to form unsupervised slide embeddings applicable to a wide range of downstream tasks. Extensive experiments on four public datasets show that ProAlign outperforms existing unsupervised frameworks and achieves performance comparable to some weakly supervised models.

cs.CV↗

arXiv2025

OptMetaOpenFOAM: Large Language Model Driven Chain of Thought for Sensitivity Analysis and Parameter Optimization based on CFD

Merging natural language interfaces with computational fluid dynamics (CFD) workflows presents transformative opportunities for both industry and research. In this study, we introduce OptMetaOpenFOAM - a novel framework that bridges MetaOpenFOAM with external analysis and optimization tool libraries through a large language model (LLM)-driven chain-of-thought (COT) methodology. By automating complex CFD tasks via natural language inputs, the framework empowers non-expert users to perform sensitivity analyses and parameter optimizations with markedly improved efficiency. The test dataset comprises 11 distinct CFD analysis or optimization tasks, including a baseline simulation task derived from an OpenFOAM tutorial covering fluid dynamics, combustion, and heat transfer. Results confirm that OptMetaOpenFOAM can accurately interpret user requirements expressed in natural language and effectively invoke external tool libraries alongside MetaOpenFOAM to complete the tasks. Furthermore, validation on a non-OpenFOAM tutorial case - namely, a hydrogen combustion chamber - demonstrates that a mere 200-character natural language input can trigger a sequence of simulation, postprocessing, analysis, and optimization tasks spanning over 2,000 lines of code. These findings underscore the transformative potential of LLM-driven COT methodologies in linking external tool for advanced analysis and optimization, positioning OptMetaOpenFOAM as an effective tool that streamlines CFD simulations and enhances their convenience and efficiency for both industrial and research applications. Code is available at https://github.com/Terry-cyx/MetaOpenFOAM.

cs.AI↗

arXiv2025

Multimodal Distillation-Driven Ensemble Learning for Long-Tailed Histopathology Whole Slide Images Analysis

Multiple Instance Learning (MIL) plays a significant role in computational pathology, enabling weakly supervised analysis of Whole Slide Image (WSI) datasets. The field of WSI analysis is confronted with a severe long-tailed distribution problem, which significantly impacts the performance of classifiers. Long-tailed distributions lead to class imbalance, where some classes have sparse samples while others are abundant, making it difficult for classifiers to accurately identify minority class samples. To address this issue, we propose an ensemble learning method based on MIL, which employs expert decoders with shared aggregators and consistency constraints to learn diverse distributions and reduce the impact of class imbalance on classifier performance. Moreover, we introduce a multimodal distillation framework that leverages text encoders pre-trained on pathology-text pairs to distill knowledge and guide the MIL aggregator in capturing stronger semantic features relevant to class information. To ensure flexibility, we use learnable prompts to guide the distillation process of the pre-trained text encoder, avoiding limitations imposed by specific prompts. Our method, MDE-MIL, integrates multiple expert branches focusing on specific data distributions to address long-tailed issues. Consistency control ensures generalization across classes. Multimodal distillation enhances feature extraction. Experiments on Camelyon+-LT and PANDA-LT datasets show it outperforms state-of-the-art methods.

cs.CV↗

arXiv2025

OptMATH: A Scalable Bidirectional Data Synthesis Framework for Optimization Modeling

Despite the rapid development of large language models (LLMs), a fundamental challenge persists: the lack of high-quality optimization modeling datasets hampers LLMs' robust modeling of practical optimization problems from natural language descriptions (NL). This data scarcity also contributes to the generalization difficulties experienced by learning-based methods. To address these challenges, we propose a scalable framework for synthesizing a high-quality dataset, named OptMATH. Starting from curated seed data with mathematical formulations (MF), this framework automatically generates problem data (PD) with controllable complexity. Then, a back-translation step is employed to obtain NL. To verify the correspondence between the NL and the PD, a forward modeling step followed by rejection sampling is used. The accepted pairs constitute the training part of OptMATH. Then a collection of rejected pairs is identified and further filtered. This collection serves as a new benchmark for optimization modeling, containing difficult instances whose lengths are much longer than these of NL4OPT and MAMO. Through extensive experiments, we demonstrate that models of various sizes (0.5B-32B parameters) trained on OptMATH achieve superior results on multiple modeling benchmarks, thereby validating the effectiveness and scalability of our approach. Our dataset is publicly available at https://github.com/AuroraLHL/OptMATH.

cs.AI↗

arXiv2025

MetaOpenFOAM 2.0: Large Language Model Driven Chain of Thought for Automating CFD Simulation and Post-Processing

Computational Fluid Dynamics (CFD) is widely used in aerospace, energy, and biology to model fluid flow, heat transfer, and chemical reactions. While Large Language Models (LLMs) have transformed various domains, their application in CFD remains limited, particularly for complex tasks like post-processing. To bridge this gap, we introduce MetaOpenFOAM 2.0, which leverages Chain of Thought (COT) decomposition and iterative verification to enhance accessibility for non-expert users through natural language inputs. Tested on a new benchmark covering simulation (fluid flow, heat transfer, combustion) and post-processing (extraction, visualization), MetaOpenFOAM 2.0 achieved an Executability score of 6.3/7 and a pass rate of 86.9%, significantly outperforming MetaOpenFOAM 1.0 (2.1/7, 0%). Additionally, it proved cost-efficient, averaging $0.15 per case. An ablation study confirmed that COT-driven decomposition and iterative refinement substantially improved task performance. Furthermore, scaling laws showed that increasing COT steps enhanced accuracy while raising token usage, aligning with LLM post-training scaling trends. These results highlight the transformative potential of LLMs in automating CFD workflows for industrial and research applications. Code is available at https://github.com/Terry-cyx/MetaOpenFOAM

cs.AI↗

arXiv2025

Dynamic Hypergraph Representation for Bone Metastasis Cancer Analysis

Bone metastasis analysis is a significant challenge in pathology and plays a critical role in determining patient quality of life and treatment strategies. The microenvironment and specific tissue structures are essential for pathologists to predict the primary bone cancer origins and primary bone cancer subtyping. By digitizing bone tissue sections into whole slide images (WSIs) and leveraging deep learning to model slide embeddings, this analysis can be enhanced. However, tumor metastasis involves complex multivariate interactions with diverse bone tissue structures, which traditional WSI analysis methods such as multiple instance learning (MIL) fail to capture. Moreover, graph neural networks (GNNs), limited to modeling pairwise relationships, are hard to represent high-order biological associations. To address these challenges, we propose a dynamic hypergraph neural network (DyHG) that overcomes the edge construction limitations of traditional graph representations by connecting multiple nodes via hyperedges. A low-rank strategy is used to reduce the complexity of parameters in learning hypergraph structures, while a Gumbel-Softmax-based sampling strategy optimizes the patch distribution across hyperedges. An MIL aggregator is then used to derive a graph-level embedding for comprehensive WSI analysis. To evaluate the effectiveness of DyHG, we construct two large-scale datasets for primary bone cancer origins and subtyping classification based on real-world bone metastasis scenarios. Extensive experiments demonstrate that DyHG significantly outperforms state-of-the-art (SOTA) baselines, showcasing its ability to model complex biological interactions and improve the accuracy of bone metastasis analysis.

cs.CV↗

arXiv2025

RAG-WM: An Efficient Black-Box Watermarking Approach for Retrieval-Augmented Generation of Large Language Models

In recent years, tremendous success has been witnessed in Retrieval-Augmented Generation (RAG), widely used to enhance Large Language Models (LLMs) in domain-specific, knowledge-intensive, and privacy-sensitive tasks. However, attackers may steal those valuable RAGs and deploy or commercialize them, making it essential to detect Intellectual Property (IP) infringement. Most existing ownership protection solutions, such as watermarks, are designed for relational databases and texts. They cannot be directly applied to RAGs because relational database watermarks require white-box access to detect IP infringement, which is unrealistic for the knowledge base in RAGs. Meanwhile, post-processing by the adversary's deployed LLMs typically destructs text watermark information. To address those problems, we propose a novel black-box "knowledge watermark" approach, named RAG-WM, to detect IP infringement of RAGs. RAG-WM uses a multi-LLM interaction framework, comprising a Watermark Generator, Shadow LLM & RAG, and Watermark Discriminator, to create watermark texts based on watermark entity-relationship tuples and inject them into the target RAG. We evaluate RAG-WM across three domain-specific and two privacy-sensitive tasks on four benchmark LLMs. Experimental results show that RAG-WM effectively detects the stolen RAGs in various deployed LLMs. Furthermore, RAG-WM is robust against paraphrasing, unrelated content removal, knowledge insertion, and knowledge expansion attacks. Lastly, RAG-WM can also evade watermark detection approaches, highlighting its promising application in detecting IP infringement of RAG systems.

cs.CR↗