Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models?

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 BiomedBERT in terms of performance, generalizability, computational resources, and throughput to BiomedBERT. Results: LLaMA models outperformed BiomedBERT 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 BiomedBERT 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 BiomedBERT 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.

CalibraEval: Calibrating Prediction Distribution to Mitigate Selection Bias in LLMs-as-Judges

The use of large language models (LLMs) as automated evaluation tools to assess the quality of generated natural language, known as LLMs-as-Judges, has demonstrated promising capabilities and is rapidly gaining widespread attention. However, when applied to pairwise comparisons of candidate responses, LLM-based evaluators often exhibit selection bias. Specifically, their judgments may become inconsistent when the option positions or ID tokens are swapped, compromising the effectiveness and fairness of the evaluation result. To address this challenge, we introduce CalibraEval, a novel label-free method for mitigating selection bias during inference. Specifically, CalibraEval reformulates debiasing as an optimization task aimed at adjusting observed prediction distributions to align with unbiased prediction distributions. To solve this optimization problem, we propose a non-parametric order-preserving algorithm (NOA). This algorithm leverages the partial order relationships between model prediction distributions, thereby eliminating the need for explicit labels and precise mathematical function modeling.Empirical evaluations of LLMs in multiple representative benchmarks demonstrate that CalibraEval effectively mitigates selection bias and improves performance compared to existing debiasing methods. This work marks a step toward building more robust and unbiased automated evaluation frameworks, paving the way for improved reliability in AI-driven assessments

Trustworthiness in Retrieval-Augmented Generation Systems: A Survey

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.

Are Long-LLMs A Necessity For Long-Context Tasks?

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.

From Matching to Generation: A Survey on Generative Information Retrieval

Information Retrieval (IR) systems are crucial tools for users to access information, widely applied in scenarios like search engines, question answering, and recommendation systems. Traditional IR methods, based on similarity matching to return ranked lists of documents, have been reliable means of information acquisition, dominating the IR field for years. With the advancement of pre-trained language models, generative information retrieval (GenIR) has emerged as a novel paradigm, gaining increasing attention in recent years. Currently, research in GenIR can be categorized into two aspects: generative document retrieval (GR) and reliable response generation. GR leverages the generative model's parameters for memorizing documents, enabling retrieval by directly generating relevant document identifiers without explicit indexing. Reliable response generation, on the other hand, employs language models to directly generate the information users seek, breaking the limitations of traditional IR in terms of document granularity and relevance matching, offering more flexibility, efficiency, and creativity, thus better meeting practical needs. This paper aims to systematically review the latest research progress in GenIR. We will summarize the advancements in GR regarding model training, document identifier, incremental learning, downstream tasks adaptation, multi-modal GR and generative recommendation, as well as progress in reliable response generation in aspects of internal knowledge memorization, external knowledge augmentation, generating response with citations and personal information assistant. We also review the evaluation, challenges and future prospects in GenIR systems. This review aims to offer a comprehensive reference for researchers in the GenIR field, encouraging further development in this area.

Unsupervised Real-Time Hallucination Detection based on the Internal States of Large Language Models

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.

BIDER: Bridging Knowledge Inconsistency for Efficient Retrieval-Augmented LLMs via Key Supporting Evidence

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.

Metacognitive Retrieval-Augmented Large Language Models

Retrieval-augmented generation have become central in natural language processing due to their efficacy in generating factual content. While traditional methods employ single-time retrieval, more recent approaches have shifted towards multi-time retrieval for multi-hop reasoning tasks. However, these strategies are bound by predefined reasoning steps, potentially leading to inaccuracies in response generation. This paper introduces MetaRAG, an approach that combines the retrieval-augmented generation process with metacognition. Drawing from cognitive psychology, metacognition allows an entity to self-reflect and critically evaluate its cognitive processes. By integrating this, MetaRAG enables the model to monitor, evaluate, and plan its response strategies, enhancing its introspective reasoning abilities. Through a three-step metacognitive regulation pipeline, the model can identify inadequacies in initial cognitive responses and fixes them. Empirical evaluations show that MetaRAG significantly outperforms existing methods.

Cognitive Personalized Search Integrating Large Language Models with an Efficient Memory Mechanism

Traditional search engines usually provide identical search results for all users, overlooking individual preferences. To counter this limitation, personalized search has been developed to re-rank results based on user preferences derived from query logs. Deep learning-based personalized search methods have shown promise, but they rely heavily on abundant training data, making them susceptible to data sparsity challenges. This paper proposes a Cognitive Personalized Search (CoPS) model, which integrates Large Language Models (LLMs) with a cognitive memory mechanism inspired by human cognition. CoPS employs LLMs to enhance user modeling and user search experience. The cognitive memory mechanism comprises sensory memory for quick sensory responses, working memory for sophisticated cognitive responses, and long-term memory for storing historical interactions. CoPS handles new queries using a three-step approach: identifying re-finding behaviors, constructing user profiles with relevant historical information, and ranking documents based on personalized query intent. Experiments show that CoPS outperforms baseline models in zero-shot scenarios.

Grounding Language Model with Chunking-Free In-Context Retrieval

This paper presents a novel Chunking-Free In-Context (CFIC) retrieval approach, specifically tailored for Retrieval-Augmented Generation (RAG) systems. Traditional RAG systems often struggle with grounding responses using precise evidence text due to the challenges of processing lengthy documents and filtering out irrelevant content. Commonly employed solutions, such as document chunking and adapting language models to handle longer contexts, have their limitations. These methods either disrupt the semantic coherence of the text or fail to effectively address the issues of noise and inaccuracy in evidence retrieval. CFIC addresses these challenges by circumventing the conventional chunking process. It utilizes the encoded hidden states of documents for in-context retrieval, employing auto-aggressive decoding to accurately identify the specific evidence text required for user queries, eliminating the need for chunking. CFIC is further enhanced by incorporating two decoding strategies, namely Constrained Sentence Prefix Decoding and Skip Decoding. These strategies not only improve the efficiency of the retrieval process but also ensure that the fidelity of the generated grounding text evidence is maintained. Our evaluations of CFIC on a range of open QA datasets demonstrate its superiority in retrieving relevant and accurate evidence, offering a significant improvement over traditional methods. By doing away with the need for document chunking, CFIC presents a more streamlined, effective, and efficient retrieval solution, making it a valuable advancement in the field of RAG systems.