arXiv subjects

Mingchen Li

Publications and source records attributed to Mingchen Li.

At least 37 records · Page 2Linked to original sources

arXiv2025

Benchmarking Retrieval-Augmented Large Language Models in Biomedical NLP: Application, Robustness, and Self-Awareness

Large language models (LLM) have demonstrated remarkable capabilities in various biomedical natural language processing (NLP) tasks, leveraging the demonstration within the input context to adapt to new tasks. However, LLM is sensitive to the selection of demonstrations. To address the hallucination issue inherent in LLM, retrieval-augmented LLM (RAL) offers a solution by retrieving pertinent information from an established database. Nonetheless, existing research work lacks rigorous evaluation of the impact of retrieval-augmented large language models on different biomedical NLP tasks. This deficiency makes it challenging to ascertain the capabilities of RAL within the biomedical domain. Moreover, the outputs from RAL are affected by retrieving the unlabeled, counterfactual, or diverse knowledge that is not well studied in the biomedical domain. However, such knowledge is common in the real world. Finally, exploring the self-awareness ability is also crucial for the RAL system. So, in this paper, we systematically investigate the impact of RALs on 5 different biomedical tasks (triple extraction, link prediction, classification, question answering, and natural language inference). We analyze the performance of RALs in four fundamental abilities, including unlabeled robustness, counterfactual robustness, diverse robustness, and negative awareness. To this end, we proposed an evaluation framework to assess the RALs' performance on different biomedical NLP tasks and establish four different testbeds based on the aforementioned fundamental abilities. Then, we evaluate 3 representative LLMs with 3 different retrievers on 5 tasks over 9 datasets.

cs.CL↗

arXiv2025

Cross-Platform Short-Video Diplomacy: Topic and Sentiment Analysis of China-US Relations on Douyin and TikTok

We examine discussions surrounding China-U.S. relations on the Chinese and American social media platforms \textit{Douyin} and \textit{TikTok}. Both platforms, owned by \textit{ByteDance}, operate under different regulatory and cultural environments, providing a unique perspective for analyzing China-U.S. public discourse. This study analyzed 4,040 videos and 338,209 user comments to assess the public discussions and sentiments on social media regarding China-U.S. relations. Through topic clustering and sentiment analysis, we identified key themes, including economic strength, technological and industrial interdependence, cultural cognition and value pursuits, and responses to global challenges. There are significant emotional differences between China and the US on various themes. Since April 2022, the Chinese government has implemented a new regulation requiring all social media accounts to disclose their provincial-level geolocation information. Utilizing this publicly available data, along with factors such as GDP per capita, minority index, and internet penetration rate, we investigate the changes in sentiment towards the U.S. in mainland China. This study links socioeconomic indicators with online discussions, deeply analyzing how regional and economic factors influence Chinese comments on their views of the US, providing important insights for China-U.S. relationship research and policy making.

cs.SI↗

arXiv2025

Hollywood Town: Long-Video Generation via Cross-Modal Multi-Agent Orchestration

Recent advancements in multi-agent systems have demonstrated significant potential for enhancing creative task performance, such as long video generation. This study introduces three innovations to improve multi-agent collaboration. First, we propose OmniAgent, a hierarchical, graph-based multi-agent framework for long video generation that leverages a film-production-inspired architecture to enable modular specialization and scalable inter-agent collaboration. Second, inspired by context engineering, we propose hypergraph nodes that enable temporary group discussions among agents lacking sufficient context, reducing individual memory requirements while ensuring adequate contextual information. Third, we transition from directed acyclic graphs (DAGs) to directed cyclic graphs with limited retries, allowing agents to reflect and refine outputs iteratively, thereby improving earlier stages through feedback from subsequent nodes. These contributions lay the groundwork for developing more robust multi-agent systems in creative tasks.

cs.MA↗

arXiv2025

Exploiting Meta-Learning-based Poisoning Attacks for Graph Link Prediction

Link prediction in graph data uses various algorithms and Graph Nerual Network (GNN) models to predict potential relationships between graph nodes. These techniques have found widespread use in numerous real-world applications, including recommendation systems, community/social networks, and biological structures. However, recent research has highlighted the vulnerability of GNN models to adversarial attacks, such as poisoning and evasion attacks. Addressing the vulnerability of GNN models is crucial to ensure stable and robust performance in GNN applications. Although many works have focused on enhancing the robustness of node classification on GNN models, the robustness of link prediction has received less attention. To bridge this gap, this article introduces an unweighted graph poisoning attack that leverages meta-learning with weighted scheme strategies to degrade the link prediction performance of GNNs. We conducted comprehensive experiments on diverse datasets across multiple link prediction applications to evaluate the proposed method and its parameters, comparing it with existing approaches under similar conditions. Our results demonstrate that our approach significantly reduces link prediction performance and consistently outperforms other state-of-the-art baselines.

cs.LG↗

arXiv2025

MS-DFTVNet:A Long-Term Time Series Prediction Method Based on Multi-Scale Deformable Convolution

Research on long-term time series prediction has primarily relied on Transformer and MLP models, while the potential of convolutional networks in this domain remains underexplored. To address this, we propose a novel multi-scale time series reshape module that effectively captures cross-period patch interactions and variable dependencies. Building on this, we develop MS-DFTVNet, the multi-scale 3D deformable convolutional framework tailored for long-term forecasting. Moreover, to handle the inherently uneven distribution of temporal features, we introduce a context-aware dynamic deformable convolution mechanism, which further enhances the model's ability to capture complex temporal patterns. Extensive experiments demonstrate that MS-DFTVNet not only significantly outperforms strong baselines but also achieves an average improvement of about 7.5% across six public datasets, setting new state-of-the-art results.

cs.LG↗

arXiv2025

DP-GTR: Differentially Private Prompt Protection via Group Text Rewriting

Prompt privacy is crucial, especially when using online large language models (LLMs), due to the sensitive information often contained within prompts. While LLMs can enhance prompt privacy through text rewriting, existing methods primarily focus on document-level rewriting, neglecting the rich, multi-granular representations of text. This limitation restricts LLM utilization to specific tasks, overlooking their generalization and in-context learning capabilities, thus hindering practical application. To address this gap, we introduce DP-GTR, a novel three-stage framework that leverages local differential privacy (DP) and the composition theorem via group text rewriting. DP-GTR is the first framework to integrate both document-level and word-level information while exploiting in-context learning to simultaneously improve privacy and utility, effectively bridging local and global DP mechanisms at the individual data point level. Experiments on CommonSense QA and DocVQA demonstrate that DP-GTR outperforms existing approaches, achieving a superior privacy-utility trade-off. Furthermore, our framework is compatible with existing rewriting techniques, serving as a plug-in to enhance privacy protection. Our code is publicly available at github.com/ResponsibleAILab/DP-GTR.

cs.CL↗

arXiv2025

Rejection or Inclusion in the Emotion-Identity Dynamics of TikTok Refugees on RedNote

This study examines cross-cultural interactions between Chinese users and self-identified "TikTok Refugees"(foreign users who migrated to RedNote after TikTok's U.S. ban). Based on a dataset of 1,862 posts and 403,054 comments, we use large language model-based sentiment classification and BERT-based topic modelling to explore how both groups engage with the TikTok refugee phenomenon. We analyse what themes foreign users express, how Chinese users respond, how stances (Pro-China, Neutral, Pro-Foreign) shape emotional expression, and how affective responses differ across topics and identities. Results show strong affective asymmetry: Chinese users respond with varying emotional intensities across topics and stances: pride and praise dominate cultural threads, while political discussions elicit high levels of contempt and anger, especially from Pro-China commenters. Pro-Foreign users exhibit the strongest negative emotions across all topics, whereas neutral users express curiosity and joy but still reinforce mainstream discursive norms. Cross-topic comparisons reveal that appearance-related content produces the most emotionally balanced interactions, while politics generates the highest polarization. Our findings reveal distinct emotion-stance structures in Sino-foreign online interactions and offer empirical insights into identity negotiation in transnational digital publics.

cs.SI↗

arXiv2025

Unsafe LLM-Based Search: Quantitative Analysis and Mitigation of Safety Risks in AI Web Search

Recent advancements in Large Language Models (LLMs) have significantly enhanced the capabilities of AI-Powered Search Engines (AIPSEs), offering precise and efficient responses by integrating external databases with pre-existing knowledge. However, we observe that these AIPSEs raise risks such as quoting malicious content or citing malicious websites, leading to harmful or unverified information dissemination. In this study, we conduct the first safety risk quantification on seven production AIPSEs by systematically defining the threat model, risk type, and evaluating responses to various query types. With data collected from PhishTank, ThreatBook, and LevelBlue, our findings reveal that AIPSEs frequently generate harmful content that contains malicious URLs even with benign queries (e.g., with benign keywords). We also observe that directly querying a URL will increase the number of main risk-inclusive responses, while querying with natural language will slightly mitigate such risk. Compared to traditional search engines, AIPSEs outperform in both utility and safety. We further perform two case studies on online document spoofing and phishing to show the ease of deceiving AIPSEs in the real-world setting. To mitigate these risks, we develop an agent-based defense with a GPT-4.1-based content refinement tool and a URL detector. Our evaluation shows that our defense can effectively reduce the risk, with only a minor cost of reducing available information by approximately 10.7%. Our research highlights the urgent need for robust safety measures in AIPSEs.

cs.CR↗

arXiv2025

Sequence-Only Prediction of Binding Affinity Changes: A Robust and Interpretable Model for Antibody Engineering

A pivotal area of research in antibody engineering is to find effective modifications that enhance antibody-antigen binding affinity. Traditional wet-lab experiments assess mutants in a costly and time-consuming manner. Emerging deep learning solutions offer an alternative by modeling antibody structures to predict binding affinity changes. However, they heavily depend on high-quality complex structures, which are frequently unavailable in practice. Therefore, we propose ProtAttBA, a deep learning model that predicts binding affinity changes based solely on the sequence information of antibody-antigen complexes. ProtAttBA employs a pre-training phase to learn protein sequence patterns, following a supervised training phase using labeled antibody-antigen complex data to train a cross-attention-based regressor for predicting binding affinity changes. We evaluated ProtAttBA on three open benchmarks under different conditions. Compared to both sequence- and structure-based prediction methods, our approach achieves competitive performance, demonstrating notable robustness, especially with uncertain complex structures. Notably, our method possesses interpretability from the attention mechanism. We show that the learned attention scores can identify critical residues with impacts on binding affinity. This work introduces a rapid and cost-effective computational tool for antibody engineering, with the potential to accelerate the development of novel therapeutic antibodies.

q-bio.QM↗

arXiv2025

CancerLLM: A Large Language Model in Cancer Domain

Medical Large Language Models (LLMs) have demonstrated impressive performance on a wide variety of medical NLP tasks; however, there still lacks a LLM specifically designed for phenotyping identification and diagnosis in cancer domain. Moreover, these LLMs typically have several billions of parameters, making them computationally expensive for healthcare systems. Thus, in this study, we propose CancerLLM, a model with 7 billion parameters and a Mistral-style architecture, pre-trained on nearly 2.7M clinical notes and over 515K pathology reports covering 17 cancer types, followed by fine-tuning on two cancer-relevant tasks, including cancer phenotypes extraction and cancer diagnosis generation. Our evaluation demonstrated that the CancerLLM achieves state-of-the-art results with F1 score of 91.78% on phenotyping extraction and 86.81% on disganois generation. It outperformed existing LLMs, with an average F1 score improvement of 9.23%. Additionally, the CancerLLM demonstrated its efficiency on time and GPU usage, and robustness comparing with other LLMs. We demonstrated that CancerLLM can potentially provide an effective and robust solution to advance clinical research and practice in cancer domain

cs.CL↗

arXiv2025

VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating $40+$ protein-related datasets and $40+$ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

cs.CL↗

arXiv2025

VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data

In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (DMS) experiments that use surrogate readouts, which may not adequately capture the complex biochemical properties of interest. Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties, and this is particularly true for the real industrial application scenario. Therefore, the desired testing datasets, will be small-size (~10-100) experimental data for each protein, and involve as many proteins as possible and as many properties as possible, which is, however, lacking. Here, we present VenusMutHub, a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases, spanning 527 proteins across diverse functional properties including stability, activity, binding affinity, and selectivity. These datasets feature direct biochemical measurements rather than surrogate readouts, providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions. We evaluate 23 computational models across various methodological paradigms, such as sequence-based, structure-informed and evolutionary approaches. This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.

q-bio.QM↗

arXiv2025

TVNet: A Novel Time Series Analysis Method Based on Dynamic Convolution and 3D-Variation

With the recent development and advancement of Transformer and MLP architectures, significant strides have been made in time series analysis. Conversely, the performance of Convolutional Neural Networks (CNNs) in time series analysis has fallen short of expectations, diminishing their potential for future applications. Our research aims to enhance the representational capacity of Convolutional Neural Networks (CNNs) in time series analysis by introducing novel perspectives and design innovations. To be specific, We introduce a novel time series reshaping technique that considers the inter-patch, intra-patch, and cross-variable dimensions. Consequently, we propose TVNet, a dynamic convolutional network leveraging a 3D perspective to employ time series analysis. TVNet retains the computational efficiency of CNNs and achieves state-of-the-art results in five key time series analysis tasks, offering a superior balance of efficiency and performance over the state-of-the-art Transformer-based and MLP-based models. Additionally, our findings suggest that TVNet exhibits enhanced transferability and robustness. Therefore, it provides a new perspective for applying CNN in advanced time series analysis tasks.

cs.LG↗

arXiv2024

A Condensed Transition Graph Framework for Zero-shot Link Prediction with Large Language Models

Zero-shot link prediction (ZSLP) on knowledge graphs aims at automatically identifying relations between given entities. Existing methods primarily employ auxiliary information to predict tail entity given head entity and its relation, yet face challenges due to the occasional unavailability of such detailed information and the inherent simplicity of predicting tail entities based on semantic similarities. Even though Large Language Models (LLMs) offer a promising solution to predict unobserved relations between the head and tail entity in a zero-shot manner, their performance is still restricted due to the inability to leverage all the (exponentially many) paths' information between two entities, which are critical in collectively indicating their relation types. To address this, in this work, we introduce a Condensed Transition Graph Framework for Zero-Shot Link Prediction (CTLP), which encodes all the paths' information in linear time complexity to predict unseen relations between entities, attaining both efficiency and information preservation. Specifically, we design a condensed transition graph encoder with theoretical guarantees on its coverage, expressiveness, and efficiency. It is learned by a transition graph contrastive learning strategy. Subsequently, we design a soft instruction tuning to learn and map the all-path embedding to the input of LLMs. Experimental results show that our proposed CTLP method achieves state-of-the-art performance on three standard ZSLP datasets

cs.CL↗

arXiv2024

RAMIE: Retrieval-Augmented Multi-task Information Extraction with Large Language Models on Dietary Supplements

\textbf{Objective:} We aimed to develop an advanced multi-task large language model (LLM) framework to extract multiple types of information about dietary supplements (DS) from clinical records. \textbf{Methods:} We used four core DS information extraction tasks - namely, named entity recognition (NER: 2,949 clinical sentences), relation extraction (RE: 4,892 sentences), triple extraction (TE: 2,949 sentences), and usage classification (UC: 2,460 sentences) as our multitasks. We introduced a novel Retrieval-Augmented Multi-task Information Extraction (RAMIE) Framework, including: 1) employed instruction fine-tuning techniques with task-specific prompts, 2) trained LLMs for multiple tasks with improved storage efficiency and lower training costs, and 3) incorporated retrieval augmentation generation (RAG) techniques by retrieving similar examples from the training set. We compared RAMIE's performance to LLMs with instruction fine-tuning alone and conducted an ablation study to assess the contributions of multi-task learning and RAG to improved multitasking performance. \textbf{Results:} With the aid of the RAMIE framework, Llama2-13B achieved an F1 score of 87.39 (3.51\% improvement) on the NER task and demonstrated outstanding performance on the RE task with an F1 score of 93.74 (1.15\% improvement). For the TE task, Llama2-7B scored 79.45 (14.26\% improvement), and MedAlpaca-7B achieved the highest F1 score of 93.45 (0.94\% improvement) on the UC task. The ablation study revealed that while MTL increased efficiency with a slight trade-off in performance, RAG significantly boosted overall accuracy. \textbf{Conclusion:} This study presents a novel RAMIE framework that demonstrates substantial improvements in multi-task information extraction for DS-related data from clinical records. Our framework can potentially be applied to other domains.

cs.CL↗

arXiv2024

Selective Attention: Enhancing Transformer through Principled Context Control

The attention mechanism within the transformer architecture enables the model to weigh and combine tokens based on their relevance to the query. While self-attention has enjoyed major success, it notably treats all queries $q$ in the same way by applying the mapping $V^\top\text{softmax}(Kq)$, where $V,K$ are the value and key embeddings respectively. In this work, we argue that this uniform treatment hinders the ability to control contextual sparsity and relevance. As a solution, we introduce the $\textit{Selective Self-Attention}$ (SSA) layer that augments the softmax nonlinearity with a principled temperature scaling strategy. By controlling temperature, SSA adapts the contextual sparsity of the attention map to the query embedding and its position in the context window. Through theory and experiments, we demonstrate that this alleviates attention dilution, aids the optimization process, and enhances the model's ability to control softmax spikiness of individual queries. We also incorporate temperature scaling for value embeddings and show that it boosts the model's ability to suppress irrelevant/noisy tokens. Notably, SSA is a lightweight method which introduces less than 0.5% new parameters through a weight-sharing strategy and can be fine-tuned on existing LLMs. Extensive empirical evaluations demonstrate that SSA-equipped models achieve a noticeable and consistent accuracy improvement on language modeling benchmarks.

cs.LG↗

arXiv2024

Pro-PRIME: A general Temperature-Guided Language model to engineer enhanced Stability and Activity in Proteins

Designing protein mutants of both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants of improved stability and activity without any prior experimental mutagenesis data of the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive power compared to current state-of-the-art models on the public mutagenesis dataset over 283 protein assays. Furthermore, we validated PRIME's predictions on five proteins, examining the top 30-45 single-site mutations' impact on various protein properties, including thermal stability, antigen-antibody binding affinity, and the ability to polymerize non-natural nucleic acid or resilience to extreme alkaline conditions. Remarkably, over 30% of the AI-recommended mutants exhibited superior performance compared to their pre-mutation counterparts across all proteins and desired properties. Moreover, we have developed an efficient, and successful method based on PRIME to rapidly obtain multi-site mutants with enhanced activity and stability. Hence, PRIME demonstrates the general applicability in protein engineering.

q-bio.BM↗

arXiv2024

CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation

Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for distinguishing between experimentally resolved and computationally predicted structures, evaluating the reliability of prediction methods, and guiding downstream biological studies. Building on works in structure prediction, We developed a structure-sensitive supervised deep learning model, Crystal vs Predicted Evaluator for Protein Structure (CPE-Pro), to represent and discriminate the origin of protein structures. CPE-Pro learns the structural information of proteins and captures inter-structural differences to achieve accurate traceability on four data classes, and is expected to be extended to more. Simultaneously, we utilized Foldseek to encode protein structures into "structure-sequences" and trained a protein Structural Sequence Language Model, SSLM. Preliminary experiments demonstrated that, compared to large-scale protein language models pre-trained on vast amounts of amino acid sequences, the "structure-sequence" enables the language model to learn more informative protein features, enhancing and optimizing structural representations. We have provided the code, model weights, and all related materials on https://github.com/GouWenrui/CPE-Pro-main.git.

q-bio.BM↗