Objective: To develop a corpus annotated for diet-microbiome associations from the biomedical literature and train natural language processing (NLP) models to identify these associations, thereby improving the understanding of their role in health and disease, and supporting personalized nutrition strategies. Materials and Methods: We constructed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., INCREASES, IMPROVES) capturing diet-microbiome associations. We fine-tuned and evaluated state-of-the-art NLP models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. In addition, we benchmarked two generative large language models (GPT-4o-mini and GPT-4o) on a subset of the dataset in zero- and one-shot settings. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 publications (including 30 full-text Results sections). Fine-tuned NLP models performed reasonably well for named entity recognition (0.800 F1 score), while end-to-end relation extraction performance was modest (0.445 F1). The use of Results section annotations improved relation extraction. The impact of trigger detection was mixed. Generative models showed lower accuracy compared to fine-tuned models. Discussion: To our knowledge, DiMB-RE is the largest and most diverse corpus focusing on diet-microbiome interactions. NLP models fine-tuned on DiMB-RE exhibit lower performance compared to similar corpora, highlighting the complexity of information extraction in this domain. Misclassified entities, missed triggers, and cross-sentence relations are the major sources of relation extraction errors. Conclusions: DiMB-RE can serve as a benchmark corpus for biomedical literature mining. DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.
With the rapid growth of the Natural Language Processing (NLP) field, a vast variety of Large Language Models (LLMs) continue to emerge for diverse NLP tasks. As more papers are published, researchers and developers face the challenge of information overload. Thus, developing a system that can automatically extract and organise key information about LLMs from academic papers is particularly important. The standard format for documenting information about LLMs is the LLM model card (\textbf{LLM-Card}). We propose a method for automatically generating LLM model cards from scientific publications. We use Named Entity Recognition (\textbf{NER}) and Relation Extraction (\textbf{RE}) methods that automatically extract key information about LLMs from the papers, helping researchers to access information about LLMs efficiently. These features include model \textit{licence}, model \textit{name}, and model \textit{application}. With these features, we can form a model card for each paper. We processed 106 academic papers by defining three dictionaries -- LLM's name, licence, and application. 11,051 sentences were extracted through dictionary lookup, and the dataset was constructed through manual review of the final selection of 129 sentences with a link between the name and the \textit{licence}, and 106 sentences with a link between the model name and the \textit{application}. The resulting resource is relevant for LLM card illustrations using relational knowledge graphs. Our code and findings can contribute to automatic LLM card generation. Data and code in \textsc{autoLLM-Card} will be shared and freely available at \url{https://github.com/shengwei-tian/dependency-parser-visualization}
Relation extraction as an important natural Language processing (NLP) task is to identify relations between named entities in text. Recently, graph convolutional networks over dependency trees have been widely used to capture syntactic features and achieved attractive performance. However, most existing dependency-based approaches ignore the positive influence of the words outside the dependency trees, sometimes conveying rich and useful information on relation extraction. In this paper, we propose a novel model, Entity-aware Self-attention Contextualized GCN (ESC-GCN), which efficiently incorporates syntactic structure of input sentences and semantic context of sequences. To be specific, relative position self-attention obtains the overall semantic pairwise correlation related to word position, and contextualized graph convolutional networks capture rich intra-sentence dependencies between words by adequately pruning operations. Furthermore, entity-aware attention layer dynamically selects which token is more decisive to make final relation prediction. In this way, our proposed model not only reduces the noisy impact from dependency trees, but also obtains easily-ignored entity-related semantic representation. Extensive experiments on various tasks demonstrate that our model achieves encouraging performance as compared to existing dependency-based and sequence-based models. Specially, our model excels in extracting relations between entities of long sentences.
The remarkable capabilities of Large Language Models (LLMs) in text comprehension and generation have revolutionized Information Extraction (IE). One such advancement is in Document-level Relation Triplet Extraction (DocRTE), a critical task in information systems that aims to extract entities and their semantic relationships from documents. However, existing methods are primarily designed for Sentence level Relation Triplet Extraction (SentRTE), which typically handles a limited set of relations and triplet facts within a single sentence. Additionally, some approaches treat relations as candidate choices integrated into prompt templates, resulting in inefficient processing and suboptimal performance when determining the relation elements in triplets. To address these limitations, we introduce a Discriminative and Voice Aware Paradigm DiVA. DiVA involves only two steps: performing document-level relation extraction (DocRE) and then identifying the subject object entities based on the relation. No additional processing is required simply input the document to directly obtain the triplets. This streamlined process more accurately reflects real-world scenarios for triplet extraction. Our innovation lies in transforming DocRE into a discriminative task, where the model pays attention to each relation and to the often overlooked issue of active vs. passive voice within the triplet. Our experiments on the Re-DocRED and DocRED datasets demonstrate state-of-the-art results for the DocRTE task.
NLP datasets may still contain annotation errors, even when they are manually annotated. Researchers have attempted to develop methods to automatically reduce the adverse effect of errors in datasets. However, existing methods are time-consuming because they require many trained models to detect errors. This paper proposes a time-saving method that utilizes a tokenization technique called subword regularization to simulate multiple error detection models for detecting errors. Our proposed method, SubRegWeigh, can perform annotation weighting four to five times faster than the existing method. Additionally, SubRegWeigh improved performance in document classification and named entity recognition tasks. In experiments with pseudo-incorrect labels, SubRegWeigh clearly identifies pseudo-incorrect labels as annotation errors. Our code is available at https://github.com/4ldk/SubRegWeigh .
Relation extraction is a Natural Language Processing task that aims to extract relationships from textual data. It is a critical step for information extraction. Due to its wide-scale applicability, research in relation extraction has rapidly scaled to using highly advanced neural networks. Despite their computational superiority, modern relation extractors fail to handle complicated extraction scenarios. However, a comprehensive performance analysis of the state-of-the-art extractors that compile these challenges has been missing from the literature, and this paper aims to bridge this gap. The goal has been to investigate the possible data-centric characteristics that impede neural relation extraction. Based on extensive experiments conducted using 15 state-of-the-art relation extraction algorithms ranging from recurrent architectures to large language models and seven large-scale datasets, this research suggests that modern relation extractors are not robust to complex data and relation characteristics. It emphasizes pivotal issues, such as contextual ambiguity, correlating relations, long-tail data, and fine-grained relation distributions. In addition, it sets a marker for future directions to alleviate these issues, thereby proving to be a critical resource for novice and advanced researchers. Efficient handling of the challenges described can have significant implications for the field of information extraction, which is a critical part of popular systems such as search engines and chatbots. Data and relevant code can be found at \url{https://aaig.ece.ufl.edu/projects/relation-extraction}.
Clinical notes contain unstructured representations of patient histories, including the relationships between medical problems and prescription drugs. To investigate the relationship between cancer drugs and their associated symptom burden, we extract structured, semantic representations of medical problem and drug information from the clinical narratives of oncology notes. We present Clinical Concept Annotations for Cancer Events and Relations (CACER), a novel corpus with fine-grained annotations for over 48,000 medical problems and drug events and 10,000 drug-problem and problem-problem relations. Leveraging CACER, we develop and evaluate transformer-based information extraction (IE) models such as BERT, Flan-T5, Llama3, and GPT-4 using fine-tuning and in-context learning (ICL). In event extraction, the fine-tuned BERT and Llama3 models achieved the highest performance at 88.2-88.0 F1, which is comparable to the inter-annotator agreement (IAA) of 88.4 F1. In relation extraction, the fine-tuned BERT, Flan-T5, and Llama3 achieved the highest performance at 61.8-65.3 F1. GPT-4 with ICL achieved the worst performance across both tasks. The fine-tuned models significantly outperformed GPT-4 in ICL, highlighting the importance of annotated training data and model optimization. Furthermore, the BERT models performed similarly to Llama3. For our task, LLMs offer no performance advantage over the smaller BERT models. The results emphasize the need for annotated training data to optimize models. Multiple fine-tuned transformer models achieved performance comparable to IAA for several extraction tasks.
Most available data is unstructured, making it challenging to access valuable information. Automatically building Knowledge Graphs (KGs) is crucial for structuring data and making it accessible, allowing users to search for information effectively. KGs also facilitate insights, inference, and reasoning. Traditional NLP methods, such as named entity recognition and relation extraction, are key in information retrieval but face limitations, including the use of predefined entity types and the need for supervised learning. Current research leverages large language models' capabilities, such as zero- or few-shot learning. However, unresolved and semantically duplicated entities and relations still pose challenges, leading to inconsistent graphs and requiring extensive post-processing. Additionally, most approaches are topic-dependent. In this paper, we propose iText2KG, a method for incremental, topic-independent KG construction without post-processing. This plug-and-play, zero-shot method is applicable across a wide range of KG construction scenarios and comprises four modules: Document Distiller, Incremental Entity Extractor, Incremental Relation Extractor, and Graph Integrator and Visualization. Our method demonstrates superior performance compared to baseline methods across three scenarios: converting scientific papers to graphs, websites to graphs, and CVs to graphs.
The relation extraction (RE) in complex scenarios faces challenges such as diverse relation types and ambiguous relations between entities within a single sentence, leading to the poor performance of pure "text-in, text-out" language models (LMs). To address these challenges, in this paper, we propose an agent-based RE framework, namely AgentRE, which fully leverages the potential of large language models (LLMs) including memory, retrieval and reflection, to achieve RE in complex scenarios. Specifically, three major modules are built in AgentRE serving as the tools to help the agent acquire and process various useful information, thereby obtaining improved RE performance. Our extensive experimental results upon two datasets in English and Chinese demonstrate our AgentRE's superior performance, especially in low-resource scenarios. Additionally, the trajectories generated by AgentRE can be refined to construct a high-quality training dataset incorporating different reasoning methods, which can be used to fine-tune smaller models. Code is available at https://github.com/Lightblues/AgentRE.
Large language models (LLMs) have created a new paradigm for natural language processing. Despite their advancement, LLM-based methods still lag behind traditional approaches in document-level relation extraction (DocRE), a critical task for understanding complex entity relations within long context. This paper investigates the causes of this performance gap, identifying the dispersion of attention by LLMs due to entity pairs without relations as a key factor. We then introduce a novel classifier-LLM approach to DocRE. Particularly, the proposed approach begins with a classifier designed to select entity pair candidates that exhibit potential relations and then feed them to LLM for final relation classification. This method ensures that the LLM's attention is directed at relation-expressing entity pairs instead of those without relations during inference. Experiments on DocRE benchmarks reveal that our method significantly outperforms recent LLM-based DocRE models and narrows the performance gap with state-of-the-art BERT-based models.
Multimodal Relation Extraction is crucial for constructing flexible and realistic knowledge graphs. Recent studies focus on extracting the relation type with entity pairs present in different modalities, such as one entity in the text and another in the image. However, existing approaches require entities and objects given beforehand, which is costly and impractical. To address the limitation, we propose a novel task, Multimodal Entity-Object Relational Triple Extraction, which aims to extract all triples (entity span, relation, object region) from image-text pairs. To facilitate this study, we modified a multimodal relation extraction dataset MORE, which includes 21 relation types, to create a new dataset containing 20,264 triples, averaging 5.75 triples per image-text pair. Moreover, we propose QEOT, a query-based model with a selective attention mechanism, to dynamically explore the interaction and fusion of textual and visual information. In particular, the proposed method can simultaneously accomplish entity extraction, relation classification, and object detection with a set of queries. Our method is suitable for downstream applications and reduces error accumulation due to the pipeline-style approaches. Extensive experimental results demonstrate that our proposed method outperforms the existing baselines by 8.06% and achieves state-of-the-art performance.
In today's globalized economy, comprehensive supply chain visibility is crucial for effective risk management. Achieving visibility remains a significant challenge due to limited information sharing among supply chain partners. This paper presents a novel framework leveraging Knowledge Graphs (KGs) and Large Language Models (LLMs) to enhance supply chain visibility without relying on direct stakeholder information sharing. Our zero-shot, LLM-driven approach automates the extraction of supply chain information from diverse public sources and constructs KGs to capture complex interdependencies between supply chain entities. We employ zero-shot prompting for Named Entity Recognition (NER) and Relation Extraction (RE) tasks, eliminating the need for extensive domain-specific training. We validate the framework with a case study on electric vehicle supply chains, focusing on tracking critical minerals for battery manufacturing. Results show significant improvements in supply chain mapping, extending visibility beyond tier-2 suppliers. The framework reveals critical dependencies and alternative sourcing options, enhancing risk management and strategic planning. With high accuracy in NER and RE tasks, it provides an effective tool for understanding complex, multi-tiered supply networks. This research offers a scalable, flexible method for constructing domain-specific supply chain KGs, addressing longstanding challenges in visibility and paving the way for advancements in digital supply chain surveillance.
Event Temporal Relation Extraction (ETRE) aims to identify the temporal relationship between two events, which plays an important role in natural language understanding. Most previous works follow a single-label classification style, classifying an event pair into either a specific temporal relation (e.g., \textit{Before}, \textit{After}), or a special label \textit{Vague} when there may be multiple possible temporal relations between the pair. In our work, instead of directly making predictions on \textit{Vague}, we propose a multi-label classification solution for ETRE (METRE) to infer the possibility of each temporal relation independently, where we treat \textit{Vague} as the cases when there is more than one possible relation between two events. We design a speculation mechanism to explore the possible relations hidden behind \textit{Vague}, which enables the latent information to be used efficiently. Experiments on TB-Dense, MATRES and UDS-T show that our method can effectively utilize the \textit{Vague} instances to improve the recognition for specific temporal relations and outperforms most state-of-the-art methods.
In recent years, there has been an increasing number of frameworks developed for biomedical entity and relation extraction. This research effort aims to address the accelerating growth in biomedical publications and the intricate nature of biomedical texts, which are written for mainly domain experts. To handle these challenges, we develop a novel framework that utilizes external knowledge to construct a task-independent and reusable background knowledge graph for biomedical entity and relation extraction. The design of our model is inspired by how humans learn domain-specific topics. In particular, humans often first acquire the most basic and common knowledge regarding a field to build the foundational knowledge and then use that as a basis for extending to various specialized topics. Our framework employs such common-knowledge-sharing mechanism to build a general neural-network knowledge graph that is learning transferable to different domain-specific biomedical texts effectively. Experimental evaluations demonstrate that our model, equipped with this generalized and cross-transferable knowledge base, achieves competitive performance benchmarks, including BioRelEx for binding interaction detection and ADE for Adverse Drug Effect identification.
Entity Linking (EL) and Relation Extraction (RE) are fundamental tasks in Natural Language Processing, serving as critical components in a wide range of applications. In this paper, we propose ReLiK, a Retriever-Reader architecture for both EL and RE, where, given an input text, the Retriever module undertakes the identification of candidate entities or relations that could potentially appear within the text. Subsequently, the Reader module is tasked to discern the pertinent retrieved entities or relations and establish their alignment with the corresponding textual spans. Notably, we put forward an innovative input representation that incorporates the candidate entities or relations alongside the text, making it possible to link entities or extract relations in a single forward pass and to fully leverage pre-trained language models contextualization capabilities, in contrast with previous Retriever-Reader-based methods, which require a forward pass for each candidate. Our formulation of EL and RE achieves state-of-the-art performance in both in-domain and out-of-domain benchmarks while using academic budget training and with up to 40x inference speed compared to competitors. Finally, we show how our architecture can be used seamlessly for Information Extraction (cIE), i.e. EL + RE, and setting a new state of the art by employing a shared Reader that simultaneously extracts entities and relations.
Event-argument extraction is a challenging task, particularly in Arabic due to sparse linguistic resources. To fill this gap, we introduce the \hadath corpus ($550$k tokens) as an extension of Wojood, enriched with event-argument annotations. We used three types of event arguments: $agent$, $location$, and $date$, which we annotated as relation types. Our inter-annotator agreement evaluation resulted in $82.23\%$ $Kappa$ score and $87.2\%$ $F_1$-score. Additionally, we propose a novel method for event relation extraction using BERT, in which we treat the task as text entailment. This method achieves an $F_1$-score of $94.01\%$. To further evaluate the generalization of our proposed method, we collected and annotated another out-of-domain corpus (about $80$k tokens) called \testNLI and used it as a second test set, on which our approach achieved promising results ($83.59\%$ $F_1$-score). Last but not least, we propose an end-to-end system for event-arguments extraction. This system is implemented as part of SinaTools, and both corpora are publicly available at {\small \url{https://sina.birzeit.edu/wojood}}
Document-level relation extraction (DocRE) aims to extract relations between entities from unstructured document text. Compared to sentence-level relation extraction, it requires more complex semantic understanding from a broader text context. Currently, some studies are utilizing logical rules within evidence sentences to enhance the performance of DocRE. However, in the data without provided evidence sentences, researchers often obtain a list of evidence sentences for the entire document through evidence retrieval (ER). Therefore, DocRE suffers from two challenges: firstly, the relevance between evidence and entity pairs is weak; secondly, there is insufficient extraction of complex cross-relations between long-distance multi-entities. To overcome these challenges, we propose GEGA, a novel model for DocRE. The model leverages graph neural networks to construct multiple weight matrices, guiding attention allocation to evidence sentences. It also employs multi-scale representation aggregation to enhance ER. Subsequently, we integrate the most efficient evidence information to implement both fully supervised and weakly supervised training processes for the model. We evaluate the GEGA model on three widely used benchmark datasets: DocRED, Re-DocRED, and Revisit-DocRED. The experimental results indicate that our model has achieved comprehensive improvements compared to the existing SOTA model.
Large Language Models (LLMs) have demonstrated unprecedented prowess across various natural language processing tasks in various application domains. Recent studies show that LLMs can be leveraged to perform lexical semantic tasks, such as Knowledge Base Completion (KBC) or Ontology Learning (OL). However, it has not effectively been verified whether their success is due to their ability to reason over unstructured or semi-structured data, or their effective learning of linguistic patterns and senses alone. This unresolved question is particularly crucial when dealing with domain-specific data, where the lexical senses and their meaning can completely differ from what a LLM has learned during its training stage. This paper investigates the following question: Do LLMs really adapt to domains and remain consistent in the extraction of structured knowledge, or do they only learn lexical senses instead of reasoning? To answer this question and, we devise a controlled experiment setup that uses WordNet to synthesize parallel corpora, with English and gibberish terms. We examine the differences in the outputs of LLMs for each corpus in two OL tasks: relation extraction and taxonomy discovery. Empirical results show that, while adapting to the gibberish corpora, off-the-shelf LLMs do not consistently reason over semantic relationships between concepts, and instead leverage senses and their frame. However, fine-tuning improves the performance of LLMs on lexical semantic tasks even when the domain-specific terms are arbitrary and unseen during pre-training, hinting at the applicability of pre-trained LLMs for OL.
Large Language Models (LLMs) have demonstrated proficiency in a wide array of natural language processing tasks. However, its effectiveness over discourse-level event relation extraction (ERE) tasks remains unexplored. In this paper, we assess the effectiveness of LLMs in addressing discourse-level ERE tasks characterized by lengthy documents and intricate relations encompassing coreference, temporal, causal, and subevent types. Evaluation is conducted using an commercial model, GPT-3.5, and an open-source model, LLaMA-2. Our study reveals a notable underperformance of LLMs compared to the baseline established through supervised learning. Although Supervised Fine-Tuning (SFT) can improve LLMs performance, it does not scale well compared to the smaller supervised baseline model. Our quantitative and qualitative analysis shows that LLMs have several weaknesses when applied for extracting event relations, including a tendency to fabricate event mentions, and failures to capture transitivity rules among relations, detect long distance relations, or comprehend contexts with dense event mentions.
Generative pre-trained transformer (GPT) models have shown promise in clinical entity and relation extraction tasks because of their precise extraction and contextual understanding capability. In this work, we further leverage the Unified Medical Language System (UMLS) knowledge base to accurately identify medical concepts and improve clinical entity and relation extraction at the document level. Our framework selects UMLS concepts relevant to the text and combines them with prompts to guide language models in extracting entities. Our experiments demonstrate that this initial concept mapping and the inclusion of these mapped concepts in the prompts improves extraction results compared to few-shot extraction tasks on generic language models that do not leverage UMLS. Further, our results show that this approach is more effective than the standard Retrieval Augmented Generation (RAG) technique, where retrieved data is compared with prompt embeddings to generate results. Overall, we find that integrating UMLS concepts with GPT models significantly improves entity and relation identification, outperforming the baseline and RAG models. By combining the precise concept mapping capability of knowledge-based approaches like UMLS with the contextual understanding capability of GPT, our method highlights the potential of these approaches in specialized domains like healthcare.