The deployment of large language models (LLMs) within the healthcare sector has sparked both enthusiasm and apprehension. These models exhibit the remarkable capability to provide proficient responses to free-text queries, demonstrating a nuanced understanding of professional medical knowledge. This comprehensive survey delves into the functionalities of existing LLMs designed for healthcare applications, elucidating the trajectory of their development, starting from traditional Pretrained Language Models (PLMs) to the present state of LLMs in healthcare sector. First, we explore the potential of LLMs to amplify the efficiency and effectiveness of diverse healthcare applications, particularly focusing on clinical language understanding tasks. These tasks encompass a wide spectrum, ranging from named entity recognition and relation extraction to natural language inference, multi-modal medical applications, document classification, and question-answering. Additionally, we conduct an extensive comparison of the most recent state-of-the-art LLMs in the healthcare domain, while also assessing the utilization of various open-source LLMs and highlighting their significance in healthcare applications. Furthermore, we present the essential performance metrics employed to evaluate LLMs in the biomedical domain, shedding light on their effectiveness and limitations. Finally, we summarize the prominent challenges and constraints faced by large language models in the healthcare sector, offering a holistic perspective on their potential benefits and shortcomings. This review provides a comprehensive exploration of the current landscape of LLMs in healthcare, addressing their role in transforming medical applications and the areas that warrant further research and development.
Medical knowledge extraction methods based on edge computing deploy deep learning models on edge devices to achieve localized entity and relation extraction. This approach avoids transferring substantial sensitive data to cloud data centers, effectively safeguarding the privacy of healthcare services. However, existing relation extraction methods mainly employ a sequential pipeline approach, which classifies relations between determined entities after entity recognition. This mode faces challenges such as error propagation between tasks, insufficient consideration of dependencies between the two subtasks, and the neglect of interrelations between different relations within a sentence. To address these challenges, a joint extraction model with parameter sharing in edge computing is proposed, named CoEx-Bert. This model leverages shared parameterization between two models to jointly extract entities and relations. Specifically, CoEx-Bert employs two models, each separately sharing hidden layer parameters, and combines these two loss functions for joint backpropagation to optimize the model parameters. Additionally, it effectively resolves the issue of entity overlapping when extracting knowledge from unstructured Uyghur medical texts by considering contextual relations. Finally, this model is deployed on edge devices for real-time extraction and inference of Uyghur medical knowledge. Experimental results demonstrate that CoEx-Bert outperforms existing state-of-the-art methods, achieving accuracy, recall, and F1 scores of 90.65\%, 92.45\%, and 91.54\%, respectively, in the Uyghur traditional medical literature dataset. These improvements represent a 6.45\% increase in accuracy, a 9.45\% increase in recall, and a 7.95\% increase in F1 score compared to the baseline.
Information extraction techniques, including named entity recognition (NER) and relation extraction (RE), are crucial in many domains to support making sense of vast amounts of unstructured text data by identifying and connecting relevant information. Such techniques can assist researchers in extracting valuable insights. In this paper, we introduce the Entity-aware Masking for Biomedical Relation Extraction (EMBRE) method for biomedical relation extraction, as applied in the context of the BioRED challenge Task 1, in which human-annotated entities are provided as input. Specifically, we integrate entity knowledge into a deep neural network by pretraining the backbone model with an entity masking objective. We randomly mask named entities for each instance and let the model identify the masked entity along with its type. In this way, the model is capable of learning more specific knowledge and more robust representations. Then, we utilize the pre-trained model as our backbone to encode language representations and feed these representations into two multilayer perceptron (MLPs) to predict the logits for relation and novelty, respectively. The experimental results demonstrate that our proposed method can improve the performances of entity pair, relation and novelty extraction over our baseline.
ChatGPT explores a strategic blueprint of question answering (QA) in delivering medical diagnosis, treatment recommendations, and other healthcare support. This is achieved through the increasing incorporation of medical domain data via natural language processing (NLP) and multimodal paradigms. By transitioning the distribution of text, images, videos, and other modalities from the general domain to the medical domain, these techniques have expedited the progress of medical domain question answering (MDQA). They bridge the gap between human natural language and sophisticated medical domain knowledge or expert manual annotations, handling large-scale, diverse, unbalanced, or even unlabeled data analysis scenarios in medical contexts. Central to our focus is the utilizing of language models and multimodal paradigms for medical question answering, aiming to guide the research community in selecting appropriate mechanisms for their specific medical research requirements. Specialized tasks such as unimodal-related question answering, reading comprehension, reasoning, diagnosis, relation extraction, probability modeling, and others, as well as multimodal-related tasks like vision question answering, image caption, cross-modal retrieval, report summarization, and generation, are discussed in detail. Each section delves into the intricate specifics of the respective method under consideration. This paper highlights the structures and advancements of medical domain explorations against general domain methods, emphasizing their applications across different tasks and datasets. It also outlines current challenges and opportunities for future medical domain research, paving the way for continued innovation and application in this rapidly evolving field.
We introduce a novel task, called Generalized Relation Discovery (GRD), for open-world relation extraction. GRD aims to identify unlabeled instances in existing pre-defined relations or discover novel relations by assigning instances to clusters as well as providing specific meanings for these clusters. The key challenges of GRD are how to mitigate the serious model biases caused by labeled pre-defined relations to learn effective relational representations and how to determine the specific semantics of novel relations during classifying or clustering unlabeled instances. We then propose a novel framework, SFGRD, for this task to solve the above issues by learning from semi-factuals in two stages. The first stage is semi-factual generation implemented by a tri-view debiased relation representation module, in which we take each original sentence as the main view and design two debiased views to generate semi-factual examples for this sentence. The second stage is semi-factual thinking executed by a dual-space tri-view collaborative relation learning module, where we design a cluster-semantic space and a class-index space to learn relational semantics and relation label indices, respectively. In addition, we devise alignment and selection strategies to integrate two spaces and establish a self-supervised learning loop for unlabeled data by doing semi-factual thinking across three views. Extensive experimental results show that SFGRD surpasses state-of-the-art models in terms of accuracy by 2.36\% $\sim$5.78\% and cosine similarity by 32.19\%$\sim$ 84.45\% for relation label index and relation semantic quality, respectively. To the best of our knowledge, we are the first to exploit the efficacy of semi-factuals in relation extraction.
Document pair extraction aims to identify key and value entities as well as their relationships from visually-rich documents. Most existing methods divide it into two separate tasks: semantic entity recognition (SER) and relation extraction (RE). However, simply concatenating SER and RE serially can lead to severe error propagation, and it fails to handle cases like multi-line entities in real scenarios. To address these issues, this paper introduces a novel framework, PEneo (Pair Extraction new decoder option), which performs document pair extraction in a unified pipeline, incorporating three concurrent sub-tasks: line extraction, line grouping, and entity linking. This approach alleviates the error accumulation problem and can handle the case of multi-line entities. Furthermore, to better evaluate the model's performance and to facilitate future research on pair extraction, we introduce RFUND, a re-annotated version of the commonly used FUNSD and XFUND datasets, to make them more accurate and cover realistic situations. Experiments on various benchmarks demonstrate PEneo's superiority over previous pipelines, boosting the performance by a large margin (e.g., 19.89%-22.91% F1 score on RFUND-EN) when combined with various backbones like LiLT and LayoutLMv3, showing its effectiveness and generality. Codes and the new annotations are available at https://github.com/ZeningLin/PEneo.
In this paper, we propose a novel method for joint entity and relation extraction from unstructured text by framing it as a conditional sequence generation problem. In contrast to conventional generative information extraction models that are left-to-right token-level generators, our approach is \textit{span-based}. It generates a linearized graph where nodes represent text spans and edges represent relation triplets. Our method employs a transformer encoder-decoder architecture with pointing mechanism on a dynamic vocabulary of spans and relation types. Our model can capture the structural characteristics and boundaries of entities and relations through span representations while simultaneously grounding the generated output in the original text thanks to the pointing mechanism. Evaluation on benchmark datasets validates the effectiveness of our approach, demonstrating competitive results. Code is available at https://github.com/urchade/ATG.
Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately $200,000$ instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.
Recently, prompt-tuning with pre-trained language models (PLMs) has demonstrated the significantly enhancing ability of relation extraction (RE) tasks. However, in low-resource scenarios, where the available training data is scarce, previous prompt-based methods may still perform poorly for prompt-based representation learning due to a superficial understanding of the relation. To this end, we highlight the importance of learning high-quality relation representation in low-resource scenarios for RE, and propose a novel prompt-based relation representation method, named MVRE (\underline{M}ulti-\underline{V}iew \underline{R}elation \underline{E}xtraction), to better leverage the capacity of PLMs to improve the performance of RE within the low-resource prompt-tuning paradigm. Specifically, MVRE decouples each relation into different perspectives to encompass multi-view relation representations for maximizing the likelihood during relation inference. Furthermore, we also design a Global-Local loss and a Dynamic-Initialization method for better alignment of the multi-view relation-representing virtual words, containing the semantics of relation labels during the optimization learning process and initialization. Extensive experiments on three benchmark datasets show that our method can achieve state-of-the-art in low-resource settings.
A comprehensive understanding of videos is inseparable from describing the action with its contextual action-object interactions. However, many current video understanding tasks prioritize general action classification and overlook the actors and relationships that shape the nature of the action, resulting in a superficial understanding of the action. Motivated by this, we introduce Open-vocabulary Video Relation Extraction (OVRE), a novel task that views action understanding through the lens of action-centric relation triplets. OVRE focuses on pairwise relations that take part in the action and describes these relation triplets with natural languages. Moreover, we curate the Moments-OVRE dataset, which comprises 180K videos with action-centric relation triplets, sourced from a multi-label action classification dataset. With Moments-OVRE, we further propose a crossmodal mapping model to generate relation triplets as a sequence. Finally, we benchmark existing cross-modal generation models on the new task of OVRE.
Few-shot Relation Extraction (FSRE) aims to extract relational facts from a sparse set of labeled corpora. Recent studies have shown promising results in FSRE by employing Pre-trained Language Models (PLMs) within the framework of supervised contrastive learning, which considers both instances and label facts. However, how to effectively harness massive instance-label pairs to encompass the learned representation with semantic richness in this learning paradigm is not fully explored. To address this gap, we introduce a novel synergistic anchored contrastive pre-training framework. This framework is motivated by the insight that the diverse viewpoints conveyed through instance-label pairs capture incomplete yet complementary intrinsic textual semantics. Specifically, our framework involves a symmetrical contrastive objective that encompasses both sentence-anchored and label-anchored contrastive losses. By combining these two losses, the model establishes a robust and uniform representation space. This space effectively captures the reciprocal alignment of feature distributions among instances and relational facts, simultaneously enhancing the maximization of mutual information across diverse perspectives within the same relation. Experimental results demonstrate that our framework achieves significant performance enhancements compared to baseline models in downstream FSRE tasks. Furthermore, our approach exhibits superior adaptability to handle the challenges of domain shift and zero-shot relation extraction. Our code is available online at https://github.com/AONE-NLP/FSRE-SaCon.
Relation extraction is essentially a text classification problem, which can be tackled by fine-tuning a pre-trained language model (LM). However, a key challenge arises from the fact that relation extraction cannot straightforwardly be reduced to sequence or token classification. Existing approaches therefore solve the problem in an indirect way: they fine-tune an LM to learn embeddings of the head and tail entities, and then predict the relationship from these entity embeddings. Our hypothesis in this paper is that relation extraction models can be improved by capturing relationships in a more direct way. In particular, we experiment with appending a prompt with a [MASK] token, whose contextualised representation is treated as a relation embedding. While, on its own, this strategy significantly underperforms the aforementioned approach, we find that the resulting relation embeddings are highly complementary to what is captured by embeddings of the head and tail entity. By jointly considering both types of representations, we end up with a simple model that outperforms the state-of-the-art across several relation extraction benchmarks.
Automatic extraction of information from publications is key to making scientific knowledge machine readable at a large scale. The extracted information can, for example, facilitate academic search, decision making, and knowledge graph construction. An important type of information not covered by existing approaches is hyperparameters. In this paper, we formalize and tackle hyperparameter information extraction (HyperPIE) as an entity recognition and relation extraction task. We create a labeled data set covering publications from a variety of computer science disciplines. Using this data set, we train and evaluate BERT-based fine-tuned models as well as five large language models: GPT-3.5, GALACTICA, Falcon, Vicuna, and WizardLM. For fine-tuned models, we develop a relation extraction approach that achieves an improvement of 29% F1 over a state-of-the-art baseline. For large language models, we develop an approach leveraging YAML output for structured data extraction, which achieves an average improvement of 5.5% F1 in entity recognition over using JSON. With our best performing model we extract hyperparameter information from a large number of unannotated papers, and analyze patterns across disciplines. All our data and source code is publicly available at https://github.com/IllDepence/hyperpie
Objective: To develop a high-throughput biomedical relation extraction system that takes advantage of the large language models'(LLMs) reading comprehension ability and biomedical world knowledge in a scalable and evidential manner. Methods: We formulate the relation extraction task as binary classifications for large language models. Specifically, LLMs make the decision based on the external corpus and its world knowledge, giving the reason for the judgment for factual verification. This method is tailored for semi-structured web articles, wherein we designate the main title as the tail entity and explicitly incorporate it into the context, and the potential head entities are matched based on a biomedical thesaurus. Moreover, lengthy contents are sliced into text chunks, embedded, and retrieved with additional embedding models. Results: Using an open-source LLM, we extracted 248659 relation triplets of three distinct relation types from three reputable biomedical websites. To assess the efficacy of the basic pipeline employed for biomedical relation extraction, we curated a benchmark dataset annotated by a medical expert. Evaluation results indicate that the pipeline exhibits performance comparable to that of GPT-4. Case studies further illuminate challenges faced by contemporary LLMs in the context of biomedical relation extraction for semi-structured web articles. Conclusion: The proposed method has demonstrated its effectiveness in leveraging the strengths of LLMs for high-throughput biomedical relation extraction. Its adaptability is evident, as it can be seamlessly extended to diverse semi-structured biomedical websites, facilitating the extraction of various types of biomedical relations with ease.
Incremental Learning (IL) has been a long-standing problem in both vision and Natural Language Processing (NLP) communities. In recent years, as Pre-trained Language Models (PLMs) have achieved remarkable progress in various NLP downstream tasks, utilizing PLMs as backbones has become a common practice in recent research of IL in NLP. Most assume that catastrophic forgetting is the biggest obstacle to achieving superior IL performance and propose various techniques to overcome this issue. However, we find that this assumption is problematic. Specifically, we revisit more than 20 methods on four classification tasks (Text Classification, Intent Classification, Relation Extraction, and Named Entity Recognition) under the two most popular IL settings (Class-Incremental and Task-Incremental) and reveal that most of them severely underestimate the inherent anti-forgetting ability of PLMs. Based on the observation, we propose a frustratingly easy method called SEQ* for IL with PLMs. The results show that SEQ* has competitive or superior performance compared to state-of-the-art (SOTA) IL methods and requires considerably less trainable parameters and training time. These findings urge us to revisit the IL with PLMs and encourage future studies to have a fundamental understanding of the catastrophic forgetting in PLMs. The data, code and scripts are publicly available at https://github.com/zzz47zzz/codebase-for-incremental-learning-with-llm.
Canonical relation extraction aims to extract relational triples from sentences, where the triple elements (entity pairs and their relationship) are mapped to the knowledge base. Recently, methods based on the encoder-decoder architecture are proposed and achieve promising results. However, these methods cannot well utilize the entity information, which is merely used as augmented training data. Moreover, they are incapable of representing novel entities, since no embeddings have been learned for them. In this paper, we propose a novel framework, Bi-Encoder-Decoder (BED), to solve the above issues. Specifically, to fully utilize entity information, we employ an encoder to encode semantics of this information, leading to high-quality entity representations. For novel entities, given a trained entity encoder, their representations can be easily generated. Experimental results on two datasets show that, our method achieves a significant performance improvement over the previous state-of-the-art and handle novel entities well without retraining.
Objective To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning. Methods We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (i.e., trainable vectors) with frozen LLM, where the LLM parameters were not updated (i.e., frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models. Results and Conclusion The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ~3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4~10% for clinical abbreviation disambiguation, and 5.5~9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the ``one model for all`` promise from training to deployment using a unified generative LLM.
In this paper, we delve into the advancement of domain-specific Large Language Models (LLMs) with a focus on their application in software development. We introduce DevAssistLlama, a model developed through instruction tuning, to assist developers in processing software-related natural language queries. This model, a variant of instruction tuned LLM, is particularly adept at handling intricate technical documentation, enhancing developer capability in software specific tasks. The creation of DevAssistLlama involved constructing an extensive instruction dataset from various software systems, enabling effective handling of Named Entity Recognition (NER), Relation Extraction (RE), and Link Prediction (LP). Our results demonstrate DevAssistLlama's superior capabilities in these tasks, in comparison with other models including ChatGPT. This research not only highlights the potential of specialized LLMs in software development also the pioneer LLM for this domain.
The task of multimodal relation extraction has attracted significant research attention, but progress is constrained by the scarcity of available training data. One natural thought is to extend existing datasets with cross-modal generative models. In this paper, we consider a novel problem setting, where only unimodal data, either text or image, are available during training. We aim to train a multimodal classifier from synthetic data that perform well on real multimodal test data. However, training with synthetic data suffers from two obstacles: lack of data diversity and label information loss. To alleviate the issues, we propose Mutual Information-aware Multimodal Iterated Relational dAta GEneration (MI2RAGE), which applies Chained Cross-modal Generation (CCG) to promote diversity in the generated data and exploits a teacher network to select valuable training samples with high mutual information with the ground-truth labels. Comparing our method to direct training on synthetic data, we observed a significant improvement of 24.06% F1 with synthetic text and 26.42% F1 with synthetic images. Notably, our best model trained on completely synthetic images outperforms prior state-of-the-art models trained on real multimodal data by a margin of 3.76% in F1. Our codebase will be made available upon acceptance.
Unsupervised relation extraction (URE) aims to extract relations between named entities from raw text without requiring manual annotations or pre-existing knowledge bases. In recent studies of URE, researchers put a notable emphasis on contrastive learning strategies for acquiring relation representations. However, these studies often overlook two important aspects: the inclusion of diverse positive pairs for contrastive learning and the exploration of appropriate loss functions. In this paper, we propose AugURE with both within-sentence pairs augmentation and augmentation through cross-sentence pairs extraction to increase the diversity of positive pairs and strengthen the discriminative power of contrastive learning. We also identify the limitation of noise-contrastive estimation (NCE) loss for relation representation learning and propose to apply margin loss for sentence pairs. Experiments on NYT-FB and TACRED datasets demonstrate that the proposed relation representation learning and a simple K-Means clustering achieves state-of-the-art performance.