Yujia Zhou

Yujia Zhou, Yan Liu, Xiaoxi Li et al.

Retrieval-Augmented Generation (RAG) has quickly grown into a pivotal paradigm in the development of Large Language Models (LLMs). While much of the current research in this field focuses on performance optimization, particularly in terms of accuracy and efficiency, the trustworthiness of RAG systems remains an area still under exploration. From a positive perspective, RAG systems are promising to enhance LLMs by providing them with useful and up-to-date knowledge from vast external databases, thereby mitigating the long-standing problem of hallucination. While from a negative perspective, RAG systems are at the risk of generating undesirable contents if the retrieved information is either inappropriate or poorly utilized. To address these concerns, we propose a unified framework that assesses the trustworthiness of RAG systems across six key dimensions: factuality, robustness, fairness, transparency, accountability, and privacy. Within this framework, we thoroughly review the existing literature on each dimension. Additionally, we create the evaluation benchmark regarding the six dimensions and conduct comprehensive evaluations for a variety of proprietary and open-source models. Finally, we identify the potential challenges for future research based on our investigation results. Through this work, we aim to lay a structured foundation for future investigations and provide practical insights for enhancing the trustworthiness of RAG systems in real-world applications.

Shuqi Zhu, Yi Zhong, Ziyi Ye et al.

While AI-generated hallucinations pose considerable risks, the underlying cognitive mechanisms by which humans can successfully recognize or be misled by these hallucinations remain unclear. To address this problem, this paper explores humans' neural dynamics to characterize how the brain processes hallucinated content. We record EEG signals from 27 participants while they are performing a verification task to judge the correctness of image descriptions generated by a multi-modal large language model (MLLM). Based on an averaged event-related potential (ERP) study, we reveal that multiple cognitive processes, e.g., semantic integration, inferential processing, memory retrieval, and cognitive load, exhibit distinct patterns when humans process hallucinated versus non-hallucinated content. Notably, neural responses to hallucinations that were misjudged versus correctly judged by human participants showed significant differences. This indicates that misjudged AI-generated hallucinations failed to trigger the standard neurocognitive fact verification pathway.

Xiaoxi Li, Guanting Dong, Jiajie Jin et al.

Large reasoning models (LRMs) like OpenAI-o1 have demonstrated impressive long stepwise reasoning capabilities through large-scale reinforcement learning. However, their extended reasoning processes often suffer from knowledge insufficiency, leading to frequent uncertainties and potential errors. To address this limitation, we introduce \textbf{Search-o1}, a framework that enhances LRMs with an agentic retrieval-augmented generation (RAG) mechanism and a Reason-in-Documents module for refining retrieved documents. Search-o1 integrates an agentic search workflow into the reasoning process, enabling dynamic retrieval of external knowledge when LRMs encounter uncertain knowledge points. Additionally, due to the verbose nature of retrieved documents, we design a separate Reason-in-Documents module to deeply analyze the retrieved information before injecting it into the reasoning chain, minimizing noise and preserving coherent reasoning flow. Extensive experiments on complex reasoning tasks in science, mathematics, and coding, as well as six open-domain QA benchmarks, demonstrate the strong performance of Search-o1. This approach enhances the trustworthiness and applicability of LRMs in complex reasoning tasks, paving the way for more reliable and versatile intelligent systems. The code is available at \url{https://github.com/sunnynexus/Search-o1}.

Xiaoxi Li, Jiajie Jin, Yujia Zhou et al.

Information Retrieval (IR) systems are crucial tools for users to access information, which have long been dominated by traditional methods relying on similarity matching. With the advancement of pre-trained language models, generative information retrieval (GenIR) emerges as a novel paradigm, attracting increasing attention. Based on the form of information provided to users, current research in GenIR can be categorized into two aspects: \textbf{(1) Generative Document Retrieval} (GR) leverages the generative model's parameters for memorizing documents, enabling retrieval by directly generating relevant document identifiers without explicit indexing. \textbf{(2) Reliable Response Generation} employs language models to directly generate information users seek, breaking the limitations of traditional IR in terms of document granularity and relevance matching while offering flexibility, efficiency, and creativity to meet practical needs. This paper aims to systematically review the latest research progress in GenIR. We will summarize the advancements in GR regarding model training and structure, document identifier, incremental learning, etc., as well as progress in reliable response generation in aspects of internal knowledge memorization, external knowledge augmentation, etc. We also review the evaluation, challenges and future developments in GenIR systems. This review aims to offer a comprehensive reference for researchers, encouraging further development in the GenIR field. Github Repository: https://github.com/RUC-NLPIR/GenIR-Survey

Xiaoxi Li, Jiajie Jin, Yujia Zhou et al.

Large language models (LLMs) exhibit remarkable generative capabilities but often suffer from hallucinations. Retrieval-augmented generation (RAG) offers an effective solution by incorporating external knowledge, but existing methods still face several limitations: additional deployment costs of separate retrievers, redundant input tokens from retrieved text chunks, and the lack of joint optimization of retrieval and generation. To address these issues, we propose \textbf{RetroLLM}, a unified framework that integrates retrieval and generation into a single, cohesive process, enabling LLMs to directly generate fine-grained evidence from the corpus with constrained decoding. Moreover, to mitigate false pruning in the process of constrained evidence generation, we introduce (1) hierarchical FM-Index constraints, which generate corpus-constrained clues to identify a subset of relevant documents before evidence generation, reducing irrelevant decoding space; and (2) a forward-looking constrained decoding strategy, which considers the relevance of future sequences to improve evidence accuracy. Extensive experiments on five open-domain QA datasets demonstrate RetroLLM's superior performance across both in-domain and out-of-domain tasks. The code is available at \url{https://github.com/sunnynexus/RetroLLM}.

Yan Hu, Qingyu Chen, Jingcheng Du et al.

Objective: This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance. Materials and Methods: We evaluated these models on two clinical NER tasks: (1) to extract medical problems, treatments, and tests from clinical notes in the MTSamples corpus, following the 2010 i2b2 concept extraction shared task, and (2) identifying nervous system disorder-related adverse events from safety reports in the vaccine adverse event reporting system (VAERS). To improve the GPT models' performance, we developed a clinical task-specific prompt framework that includes (1) baseline prompts with task description and format specification, (2) annotation guideline-based prompts, (3) error analysis-based instructions, and (4) annotated samples for few-shot learning. We assessed each prompt's effectiveness and compared the models to BioClinicalBERT. Results: Using baseline prompts, GPT-3.5 and GPT-4 achieved relaxed F1 scores of 0.634, 0.804 for MTSamples, and 0.301, 0.593 for VAERS. Additional prompt components consistently improved model performance. When all four components were used, GPT-3.5 and GPT-4 achieved relaxed F1 socres of 0.794, 0.861 for MTSamples and 0.676, 0.736 for VAERS, demonstrating the effectiveness of our prompt framework. Although these results trail BioClinicalBERT (F1 of 0.901 for the MTSamples dataset and 0.802 for the VAERS), it is very promising considering few training samples are needed. Conclusion: While direct application of GPT models to clinical NER tasks falls short of optimal performance, our task-specific prompt framework, incorporating medical knowledge and training samples, significantly enhances GPT models' feasibility for potential clinical applications.

Yan Hu, Xu Zuo, Yujia Zhou et al.

Backgrounds: Information extraction (IE) is critical in clinical natural language processing (NLP). While large language models (LLMs) excel on generative tasks, their performance on extractive tasks remains debated. Methods: We investigated Named Entity Recognition (NER) and Relation Extraction (RE) using 1,588 clinical notes from four sources (UT Physicians, MTSamples, MIMIC-III, and i2b2). We developed an annotated corpus covering 4 clinical entities and 16 modifiers, and compared instruction-tuned LLaMA-2 and LLaMA-3 against BERT in terms of performance, generalizability, computational resources, and throughput to BERT. Results: LLaMA models outperformed BERT across datasets. With sufficient training data, LLaMA showed modest improvements (1% on NER, 1.5-3.7% on RE); improvements were larger with limited training data. On unseen i2b2 data, LLaMA-3-70B outperformed BERT by 7% (F1) on NER and 4% on RE. However, LLaMA models required more computing resources and ran up to 28 times slower. We implemented "Kiwi," a clinical IE package featuring both models, available at https://kiwi.clinicalnlp.org/. Conclusion: This study is among the first to develop and evaluate a comprehensive clinical IE system using open-source LLMs. Results indicate that LLaMA models outperform BERT for clinical NER and RE but with higher computational costs and lower throughputs. These findings highlight that choosing between LLMs and traditional deep learning methods for clinical IE applications should remain task-specific, taking into account both performance metrics and practical considerations such as available computing resources and the intended use case scenarios.

Changyue Wang, Weihang Su, Qingyao Ai et al.

Knowledge editing aims to efficiently update Large Language Models (LLMs) by modifying specific knowledge without retraining the entire model. Among knowledge editing approaches, in-context editing (ICE) offers a lightweight solution by injecting new knowledge directly into the input context, leaving model parameters unchanged. However, existing ICE approaches do not explicitly separate the newly injected knowledge from the model's original reasoning process. This entanglement often results in conflicts between external updates and internal parametric knowledge, undermining the consistency and accuracy of the reasoning path.In this work, we conduct preliminary experiments to examine how parametric knowledge influences reasoning path planning. We find that the model's reasoning is tightly coupled with its internal knowledge, and that naively injecting new information without adapting the reasoning path often leads to performance degradation, particularly in multi-hop tasks. To this end, we propose DecKER, a novel ICE framework that decouples reasoning from knowledge editing by generating a masked reasoning path and then resolving knowledge edits via hybrid retrieval and model-based validation. Experiments on multi-hop QA benchmarks show that DecKER significantly outperforms existing ICE methods by mitigating knowledge conflicts and preserving reasoning consistency. Our code is available at: https://github.com/bebr2/DecKER .

Laila Rasmy, Jie Zhu, Zhiheng Li et al.

Recently, there is great interest to investigate the application of deep learning models for the prediction of clinical events using electronic health records (EHR) data. In EHR data, a patient's history is often represented as a sequence of visits, and each visit contains multiple events. As a result, deep learning models developed for sequence modeling, like recurrent neural networks (RNNs) are common architecture for EHR-based clinical events predictive models. While a large variety of RNN models were proposed in the literature, it is unclear if complex architecture innovations will offer superior predictive performance. In order to move this field forward, a rigorous evaluation of various methods is needed. In this study, we conducted a thorough benchmark of RNN architectures in modeling EHR data. We used two prediction tasks: the risk for developing heart failure and the risk of early readmission for inpatient hospitalization. We found that simple gated RNN models, including GRUs and LSTMs, often offer competitive results when properly tuned with Bayesian Optimization, which is in line with similar to findings in the natural language processing (NLP) domain. For reproducibility, Our codebase is shared at https://github.com/ZhiGroup/pytorch_ehr.

Weihang Su, Changyue Wang, Qingyao Ai et al. · tsinghua

Hallucinations in large language models (LLMs) refer to the phenomenon of LLMs producing responses that are coherent yet factually inaccurate. This issue undermines the effectiveness of LLMs in practical applications, necessitating research into detecting and mitigating hallucinations of LLMs. Previous studies have mainly concentrated on post-processing techniques for hallucination detection, which tend to be computationally intensive and limited in effectiveness due to their separation from the LLM's inference process. To overcome these limitations, we introduce MIND, an unsupervised training framework that leverages the internal states of LLMs for real-time hallucination detection without requiring manual annotations. Additionally, we present HELM, a new benchmark for evaluating hallucination detection across multiple LLMs, featuring diverse LLM outputs and the internal states of LLMs during their inference process. Our experiments demonstrate that MIND outperforms existing state-of-the-art methods in hallucination detection.

Jiajie Jin, Yutao Zhu, Yujia Zhou et al.

Retrieval-augmented large language models (LLMs) have demonstrated efficacy in knowledge-intensive tasks such as open-domain QA, addressing inherent challenges in knowledge update and factual inadequacy. However, inconsistencies between retrieval knowledge and the necessary knowledge for LLMs, leading to a decline in LLM's answer quality. This paper introduces BIDER, an approach that refines retrieval documents into Key Supporting Evidence (KSE) through knowledge synthesis, supervised fine-tuning (SFT), and preference alignment. We train BIDER by learning from crafting KSE, while maximizing its output to align with LLM's information acquisition preferences through reinforcement learning. Evaluations across five datasets show BIDER boosts LLMs' answer quality by 7% while reducing input content length in retrieval documents by 80%, outperforming existing methods. The proposed KSE simulation effectively equips LLMs with essential information for accurate question answering.

Xiaoxi Li, Zhicheng Dou, Yujia Zhou et al.

Large language models (LLMs) have gained significant attention in various fields but prone to hallucination, especially in knowledge-intensive (KI) tasks. To address this, retrieval-augmented generation (RAG) has emerged as a popular solution to enhance factual accuracy. However, traditional retrieval modules often rely on large document index and disconnect with generative tasks. With the advent of generative retrieval (GR), language models can retrieve by directly generating document identifiers (DocIDs), offering superior performance in retrieval tasks. However, the potential relationship between GR and downstream tasks remains unexplored. In this paper, we propose \textbf{CorpusLM}, a unified language model that leverages external corpus to tackle various knowledge-intensive tasks by integrating generative retrieval, closed-book generation, and RAG through a unified greedy decoding process. We design the following mechanisms to facilitate effective retrieval and generation, and improve the end-to-end effectiveness of KI tasks: (1) We develop a ranking-oriented DocID list generation strategy, which refines GR by directly learning from a DocID ranking list, to improve retrieval quality. (2) We design a continuous DocIDs-References-Answer generation strategy, which facilitates effective and efficient RAG. (3) We employ well-designed unsupervised DocID understanding tasks, to comprehend DocID semantics and their relevance to downstream tasks. We evaluate our approach on the widely used KILT benchmark with two variants of backbone models, i.e., T5 and Llama2. Experimental results demonstrate the superior performance of our models in both retrieval and downstream tasks.

Hongjin Qian, Zheng Liu, Peitian Zhang et al.

The learning and deployment of long-LLMs remains a challenging problem despite recent progresses. In this work, we argue that the long-LLMs are not a necessity to solve long-context tasks, as common long-context tasks are short-context solvable, i.e. they can be solved by purely working with oracle short-contexts within the long-context tasks' inputs. On top of this argument, we propose a framework called LC-Boost (Long-Context Bootstrapper), which enables a short-LLM to address the long-context tasks in a bootstrapping manner. In our framework, the short-LLM prompts itself to reason for two critical decisions: 1) how to access to the appropriate part of context within the input, 2) how to make effective use of the accessed context. By adaptively accessing and utilizing the context based on the presented tasks, LC-Boost can serve as a general framework to handle diversified long-context processing problems. We comprehensively evaluate different types of tasks from popular long-context benchmarks, where LC-Boost is able to achieve a substantially improved performance with a much smaller consumption of resource.

Yiteng Tu, Weihang Su, Yujia Zhou et al.

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by integrating external knowledge retrieved from a knowledge base. However, its effectiveness is fundamentally constrained by the reliability of both the retriever and the knowledge base. In real-world scenarios, imperfections in these components often lead to the retrieval of noisy, irrelevant, or misleading counterfactual information, ultimately undermining the trustworthiness of RAG systems. To address this challenge, we propose Robust Fine-Tuning (RbFT), a method designed to enhance the resilience of LLMs against retrieval defects through two targeted fine-tuning tasks. Experimental results demonstrate that RbFT significantly improves the robustness of RAG systems across diverse retrieval conditions, surpassing existing methods while maintaining high inference efficiency and compatibility with other robustness techniques.

Yujia Zhou, Zheng Liu, Zhicheng Dou

The emergence of Large Language Models (LLMs) has significantly advanced natural language processing, but these models often generate factually incorrect information, known as "hallucination". Initial retrieval-augmented generation (RAG) methods like the "Retrieve-Read" framework was inadequate for complex reasoning tasks. Subsequent prompt-based RAG strategies and Supervised Fine-Tuning (SFT) methods improved performance but required frequent retraining and risked altering foundational LLM capabilities. To cope with these challenges, we propose Assistant-based Retrieval-Augmented Generation (AssistRAG), integrating an intelligent information assistant within LLMs. This assistant manages memory and knowledge through tool usage, action execution, memory building, and plan specification. Using a two-phase training approach, Curriculum Assistant Learning and Reinforced Preference Optimization. AssistRAG enhances information retrieval and decision-making. Experiments show AssistRAG significantly outperforms benchmarks, especially benefiting less advanced LLMs, by providing superior reasoning capabilities and accurate responses.

Yichen Tang, Weihang Su, Yujia Zhou et al.

Multi-agent techniques such as role playing or multi-turn debates have been shown to be effective in improving the performance of large language models (LLMs) in downstream tasks. Despite their differences in workflows, existing multi-agent systems constructed from a single base LLM mostly use natural language for agent communication. While this is appealing for its simplicity and interpretability, it also introduces inevitable information loss as one model must down sample its continuous state vectors to discrete tokens before transferring them to the other model. Such losses are particularly significant when the information to transfer is not simple facts, but reasoning logics or abstractive thoughts. To tackle this problem, we propose a new communication protocol that transfers both natural language tokens and token-wise state transition trajectory from one agent to another. Particularly, compared to the actual state value, we find that the sequence of state changes in LLMs after generating each token can better reflect the information hidden behind the inference process. We propose a State Delta Encoding (SDE) method to represent state transition trajectories. The experimental results show that multi-agent systems with SDE achieve SOTA performance compared to other communication protocols, particularly in tasks that involve complex reasoning.

Hao Liu, Yiqing Dai, Haotian Tan et al.

Emotions guide human decisions, but whether large language models (LLMs) use emotion similarly remains unknown. We tested this using altruistic third-party punishment, where an observer incurs a personal cost to enforce fairness, a hallmark of human morality and often driven by negative emotion. In a large-scale comparison of 4,068 LLM agents with 1,159 adults across 796,100 decisions, LLMs used emotion to guide punishment, sometimes even more strongly than humans did: Unfairness elicited stronger negative emotion that led to more punishment; punishing unfairness produced more positive emotion than accepting; and critically, prompting self-reports of emotion causally increased punishment. However, mechanisms diverged: LLMs prioritized emotion over cost, enforcing norms in an almost all-or-none manner with reduced cost sensitivity, whereas humans balanced fairness and cost. Notably, reasoning models (o3-mini, DeepSeek-R1) were more cost-sensitive and closer to human behavior than foundation models (GPT-3.5, DeepSeek-V3), yet remained heavily emotion-driven. These findings provide the first causal evidence of emotion-guided moral decisions in LLMs and reveal deficits in cost calibration and nuanced fairness judgements, reminiscent of early-stage human responses. We propose that LLMs progress along a trajectory paralleling human development; future models should integrate emotion with context-sensitive reasoning to achieve human-like emotional intelligence.

Yujia Zhou, Zhicheng Dou, Huaying Yuan et al.

Utilizing pre-trained language models has achieved great success for neural document ranking. Limited by the computational and memory requirements, long document modeling becomes a critical issue. Recent works propose to modify the full attention matrix in Transformer by designing sparse attention patterns. However, most of them only focus on local connections of terms within a fixed-size window. How to build suitable remote connections between terms to better model document representation remains underexplored. In this paper, we propose the model Socialformer, which introduces the characteristics of social networks into designing sparse attention patterns for long document modeling in document ranking. Specifically, we consider several attention patterns to construct a graph like social networks. Endowed with the characteristic of social networks, most pairs of nodes in such a graph can reach with a short path while ensuring the sparsity. To facilitate efficient calculation, we segment the graph into multiple subgraphs to simulate friend circles in social scenarios. Experimental results confirm the effectiveness of our model on long document modeling.

Jingqi Wang, Noor Abu-el-rub, Josh Gray et al.

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.

Yujia Zhou, Shumao Pang, Jun Cheng et al.

Deformation field estimation is an important and challenging issue in many medical image registration applications. In recent years, deep learning technique has become a promising approach for simplifying registration problems, and has been gradually applied to medical image registration. However, most existing deep learning registrations do not consider the problem that when the receptive field cannot cover the corresponding features in the moving image and the fixed image, it cannot output accurate displacement values. In fact, due to the limitation of the receptive field, the 3 x 3 kernel has difficulty in covering the corresponding features at high/original resolution. Multi-resolution and multi-convolution techniques can improve but fail to avoid this problem. In this study, we constructed pyramidal feature sets on moving and fixed images and used the warped moving and fixed features to estimate their "residual" deformation field at each scale, called the Pyramidal Residual Deformation Field Estimation module (PRDFE-Module). The "total" deformation field at each scale was computed by upsampling and weighted summing all the "residual" deformation fields at all its previous scales, which can effectively and accurately transfer the deformation fields from low resolution to high resolution and is used for warping the moving features at each scale. Simulation and real brain data results show that our method improves the accuracy of the registration and the rationality of the deformation field.