Xiuying Chen

Juexiao Zhou, Bin Zhang, Xiuying Chen et al.

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the analytical process by requiring minimal user input while delivering detailed step-by-step plans for various bioinformatics tasks. Through rigorous validation by expert bioinformaticians, AutoBA's robustness and adaptability are affirmed across a diverse range of omics analysis cases, including whole genome sequencing (WGS), RNA sequencing (RNA-seq), single-cell RNA-seq, ChIP-seq, and spatial transcriptomics. AutoBA's unique capacity to self-design analysis processes based on input data variations further underscores its versatility. Compared with online bioinformatic services, AutoBA deploys the analysis locally, preserving data privacy. Moreover, different from the predefined pipeline, AutoBA has adaptability in sync with emerging bioinformatics tools. Overall, AutoBA represents a convenient tool, offering robustness and adaptability for complex omics data analysis.

Xiuying Chen, Tairan Wang, Juexiao Zhou et al.

Artificial intelligence (AI) systems, particularly those based on deep learning models, have increasingly achieved expert-level performance in medical applications. However, there is growing concern that such AI systems may reflect and amplify human bias, and reduce the quality of their performance in historically under-served populations. The fairness issue has attracted considerable research interest in the medical imaging classification field, yet it remains understudied in the text generation domain. In this study, we investigate the fairness problem in text generation within the medical field and observe significant performance discrepancies across different races, sexes, and age groups, including intersectional groups, various model scales, and different evaluation metrics. To mitigate this fairness issue, we propose an algorithm that selectively optimizes those underperformed groups to reduce bias. The selection rules take into account not only word-level accuracy but also the pathology accuracy to the target reference, while ensuring that the entire process remains fully differentiable for effective model training. Our evaluations across multiple backbones, datasets, and modalities demonstrate that our proposed algorithm enhances fairness in text generation without compromising overall performance. Specifically, the disparities among various groups across different metrics were diminished by more than 30% with our algorithm, while the relative change in text generation accuracy was typically within 2%. By reducing the bias generated by deep learning models, our proposed approach can potentially alleviate concerns about the fairness and reliability of text generation diagnosis in medical domain. Our code is publicly available to facilitate further research at https://github.com/iriscxy/GenFair.

Yanbo Wang, Zixiang Xu, Yue Huang et al.

Large Language Models (LLMs) often struggle to maintain their original performance when faced with semantically coherent but task-irrelevant contextual information. Although prior studies have explored this issue using fixed-template or retrieval-based distractions, such static methods show limited effectiveness against contemporary models. To address this problem, we propose a dynamic distraction generation framework based on tree search, where the generation process is guided by model behavior. Without modifying the original question or answer, the method efficiently produces challenging adaptive distractions across multiple datasets, enabling systematic stress testing of LLMs' contextual robustness. Experiments on four benchmarks demonstrate that the generated distractions lead to an average performance drop of over 45\% for mainstream models. Further comparisons of mitigation strategies show that prompt-based optimization methods yield limited gains, whereas post-training approaches (e.g., DPO) significantly enhance the model's contextual robustness. The results indicate that these issues do not stem from knowledge deficits in LLMs, but from a fundamental inability to maintain consistent reasoning under contextual distraction, posing a major challenge to the reliability of LLMs in real-world applications. The code is publicly available at https://github.com/wyf23187/Adaptive_Distractions.

Qiang Yang, Xiuying Chen, Changsheng Ma et al.

The global impact of the COVID-19 pandemic has highlighted the need for a comprehensive understanding of public sentiment and reactions. Despite the availability of numerous public datasets on COVID-19, some reaching volumes of up to 100 billion data points, challenges persist regarding the availability of labeled data and the presence of coarse-grained or inappropriate sentiment labels. In this paper, we introduce SenWave, a novel fine-grained multi-language sentiment analysis dataset specifically designed for analyzing COVID-19 tweets, featuring ten sentiment categories across five languages. The dataset comprises 10,000 annotated tweets each in English and Arabic, along with 30,000 translated tweets in Spanish, French, and Italian, derived from English tweets. Additionally, it includes over 105 million unlabeled tweets collected during various COVID-19 waves. To enable accurate fine-grained sentiment classification, we fine-tuned pre-trained transformer-based language models using the labeled tweets. Our study provides an in-depth analysis of the evolving emotional landscape across languages, countries, and topics, revealing significant insights over time. Furthermore, we assess the compatibility of our dataset with ChatGPT, demonstrating its robustness and versatility in various applications. Our dataset and accompanying code are publicly accessible on the repository\footnote{https://github.com/gitdevqiang/SenWave}. We anticipate that this work will foster further exploration into fine-grained sentiment analysis for complex events within the NLP community, promoting more nuanced understanding and research innovations.

Zirui Song, Guangxian Ouyang, Mingzhe Li et al.

Large Vision-Language Models (LVLMs) have recently advanced robotic manipulation by leveraging vision for scene perception and language for instruction following. However, existing methods rely heavily on costly human-annotated training datasets, which limits their generalization and causes them to struggle in out-of-domain (OOD) scenarios, reducing real-world adaptability. To address these challenges, we propose ManipLVM-R1, a novel reinforcement learning framework that replaces traditional supervision with Reinforcement Learning using Verifiable Rewards (RLVR). By directly optimizing for task-aligned outcomes, our method enhances generalization and physical reasoning while removing the dependence on costly annotations. Specifically, we design two rule-based reward functions targeting key robotic manipulation subtasks: an Affordance Perception Reward to enhance localization of interaction regions, and a Trajectory Match Reward to ensure the physical plausibility of action paths. These rewards provide immediate feedback and impose spatial-logical constraints, encouraging the model to go beyond shallow pattern matching and instead learn deeper, more systematic reasoning about physical interactions.

Songhao Wu, Quan Tu, Hong Liu et al.

Session search involves a series of interactive queries and actions to fulfill user's complex information need. Current strategies typically prioritize sequential modeling for deep semantic understanding, overlooking the graph structure in interactions. While some approaches focus on capturing structural information, they use a generalized representation for documents, neglecting the word-level semantic modeling. In this paper, we propose Symbolic Graph Ranker (SGR), which aims to take advantage of both text-based and graph-based approaches by leveraging the power of recent Large Language Models (LLMs). Concretely, we first introduce a set of symbolic grammar rules to convert session graph into text. This allows integrating session history, interaction process, and task instruction seamlessly as inputs for the LLM. Moreover, given the natural discrepancy between LLMs pre-trained on textual corpora, and the symbolic language we produce using our graph-to-text grammar, our objective is to enhance LLMs' ability to capture graph structures within a textual format. To achieve this, we introduce a set of self-supervised symbolic learning tasks including link prediction, node content generation, and generative contrastive learning, to enable LLMs to capture the topological information from coarse-grained to fine-grained. Experiment results and comprehensive analysis on two benchmark datasets, AOL and Tiangong-ST, confirm the superiority of our approach. Our paradigm also offers a novel and effective methodology that bridges the gap between traditional search strategies and modern LLMs.

Qingqing Zhu, Xiuying Chen, Qiao Jin et al.

In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging. Current metrics, such as Conventional Natural Language Generation (NLG) and Clinical Efficacy (CE), often fall short in capturing the semantic intricacies of clinical contexts or overemphasize clinical details, undermining report clarity. To overcome these issues, our proposed method synergizes the expertise of professional radiologists with Large Language Models (LLMs), like GPT-3.5 and GPT-4 1. Utilizing In-Context Instruction Learning (ICIL) and Chain of Thought (CoT) reasoning, our approach aligns LLM evaluations with radiologist standards, enabling detailed comparisons between human and AI generated reports. This is further enhanced by a Regression model that aggregates sentence evaluation scores. Experimental results show that our "Detailed GPT-4 (5-shot)" model achieves a 0.48 score, outperforming the METEOR metric by 0.19, while our "Regressed GPT-4" model shows even greater alignment with expert evaluations, exceeding the best existing metric by a 0.35 margin. Moreover, the robustness of our explanations has been validated through a thorough iterative strategy. We plan to publicly release annotations from radiology experts, setting a new standard for accuracy in future assessments. This underscores the potential of our approach in enhancing the quality assessment of AI-driven medical reports.

Zirui Song, Qian Jiang, Mingxuan Cui et al.

The rise of Large Audio Language Models (LAMs) brings both potential and risks, as their audio outputs may contain harmful or unethical content. However, current research lacks a systematic, quantitative evaluation of LAM safety especially against jailbreak attacks, which are challenging due to the temporal and semantic nature of speech. To bridge this gap, we introduce AJailBench, the first benchmark specifically designed to evaluate jailbreak vulnerabilities in LAMs. We begin by constructing AJailBench-Base, a dataset of 1,495 adversarial audio prompts spanning 10 policy-violating categories, converted from textual jailbreak attacks using realistic text to speech synthesis. Using this dataset, we evaluate several state-of-the-art LAMs and reveal that none exhibit consistent robustness across attacks. To further strengthen jailbreak testing and simulate more realistic attack conditions, we propose a method to generate dynamic adversarial variants. Our Audio Perturbation Toolkit (APT) applies targeted distortions across time, frequency, and amplitude domains. To preserve the original jailbreak intent, we enforce a semantic consistency constraint and employ Bayesian optimization to efficiently search for perturbations that are both subtle and highly effective. This results in AJailBench-APT, an extended dataset of optimized adversarial audio samples. Our findings demonstrate that even small, semantically preserved perturbations can significantly reduce the safety performance of leading LAMs, underscoring the need for more robust and semantically aware defense mechanisms.

Xiuying Chen, Tairan Wang, Qingqing Zhu et al.

The summarization capabilities of pretrained and large language models (LLMs) have been widely validated in general areas, but their use in scientific corpus, which involves complex sentences and specialized knowledge, has been less assessed. This paper presents conceptual and experimental analyses of scientific summarization, highlighting the inadequacies of traditional evaluation methods, such as $n$-gram, embedding comparison, and QA, particularly in providing explanations, grasping scientific concepts, or identifying key content. Subsequently, we introduce the Facet-aware Metric (FM), employing LLMs for advanced semantic matching to evaluate summaries based on different aspects. This facet-aware approach offers a thorough evaluation of abstracts by decomposing the evaluation task into simpler subtasks.Recognizing the absence of an evaluation benchmark in this domain, we curate a Facet-based scientific summarization Dataset (FD) with facet-level annotations. Our findings confirm that FM offers a more logical approach to evaluating scientific summaries. In addition, fine-tuned smaller models can compete with LLMs in scientific contexts, while LLMs have limitations in learning from in-context information in scientific domains. This suggests an area for future enhancement of LLMs.

Xiuying Chen, Shen Gao, Mingzhe Li et al.

Nowadays, neural text generation has made tremendous progress in abstractive summarization tasks. However, most of the existing summarization models take in the whole document all at once, which sometimes cannot meet the needs in practice. Practically, social text streams such as news events and tweets keep growing from time to time, and can only be fed to the summarization system step by step. Hence, in this paper, we propose the task of Stepwise Summarization, which aims to generate a new appended summary each time a new document is proposed. The appended summary should not only summarize the newly added content but also be coherent with the previous summary, to form an up-to-date complete summary. To tackle this challenge, we design an adversarial learning model, named Stepwise Summary Generator (SSG). First, SSG selectively processes the new document under the guidance of the previous summary, obtaining polished document representation. Next, SSG generates the summary considering both the previous summary and the document. Finally, a convolutional-based discriminator is employed to determine whether the newly generated summary is coherent with the previous summary. For the experiment, we extend the traditional two-step update summarization setting to a multi-step stepwise setting, and re-propose a large-scale stepwise summarization dataset based on a public story generation dataset. Extensive experiments on this dataset show that SSG achieves state-of-the-art performance in terms of both automatic metrics and human evaluations. Ablation studies demonstrate the effectiveness of each module in our framework. We also discuss the benefits and limitations of recent large language models on this task.