Daily Papers

Relation Extraction (RE) is a task that identifies relationships between entities in a text, enabling the acquisition of relational facts and bridging the gap between natural language and structured knowledge. However, current RE models often rely on small datasets with low coverage of relation types, particularly when working with languages other than English. In this paper, we address the above issue and provide two new resources that enable the training and evaluation of multilingual RE systems. First, we present SRED^{rm FM}, an automatically annotated dataset covering 18 languages, 400 relation types, 13 entity types, totaling more than 40 million triplet instances. Second, we propose RED^{rm FM}, a smaller, human-revised dataset for seven languages that allows for the evaluation of multilingual RE systems. To demonstrate the utility of these novel datasets, we experiment with the first end-to-end multilingual RE model, mREBEL, that extracts triplets, including entity types, in multiple languages. We release our resources and model checkpoints at https://www.github.com/babelscape/rebel

Relation extraction (RE) has achieved remarkable progress with the help of pre-trained language models. However, existing RE models are usually incapable of handling two situations: implicit expressions and long-tail relation classes, caused by language complexity and data sparsity. Further, these approaches and models are largely inaccessible to users who don't have direct access to large language models (LLMs) and/or infrastructure for supervised training or fine-tuning. Rule-based systems also struggle with implicit expressions. Apart from this, Real world financial documents such as various 10-X reports (including 10-K, 10-Q, etc.) of publicly traded companies pose another challenge to rule-based systems in terms of longer and complex sentences. In this paper, we introduce a simple approach that consults training relations at test time through a nearest-neighbor search over dense vectors of lexico-syntactic patterns and provides a simple yet effective means to tackle the above issues. We evaluate our approach on REFinD and show that our method achieves state-of-the-art performance. We further show that it can provide a good start for human in the loop setup when a small number of annotations are available and it is also beneficial when domain experts can provide high quality patterns.

Relation Extraction (RE) has been extended to cross-document scenarios because many relations are not simply described in a single document. This inevitably brings the challenge of efficient open-space evidence retrieval to support the inference of cross-document relations, along with the challenge of multi-hop reasoning on top of entities and evidence scattered in an open set of documents. To combat these challenges, we propose MR.COD (Multi-hop evidence retrieval for Cross-document relation extraction), which is a multi-hop evidence retrieval method based on evidence path mining and ranking. We explore multiple variants of retrievers to show evidence retrieval is essential in cross-document RE. We also propose a contextual dense retriever for this setting. Experiments on CodRED show that evidence retrieval with MR.COD effectively acquires crossdocument evidence and boosts end-to-end RE performance in both closed and open settings.

Relation extraction (RE) models have been challenged by their reliance on training data with expensive annotations. Considering that summarization tasks aim at acquiring concise expressions of synoptical information from the longer context, these tasks naturally align with the objective of RE, i.e., extracting a kind of synoptical information that describes the relation of entity mentions. We present SuRE, which converts RE into a summarization formulation. SuRE leads to more precise and resource-efficient RE based on indirect supervision from summarization tasks. To achieve this goal, we develop sentence and relation conversion techniques that essentially bridge the formulation of summarization and RE tasks. We also incorporate constraint decoding techniques with Trie scoring to further enhance summarization-based RE with robust inference. Experiments on three RE datasets demonstrate the effectiveness of SuRE in both full-dataset and low-resource settings, showing that summarization is a promising source of indirect supervision to improve RE models.

Relation Extraction (RE) is a fundamental task in Natural Language Processing, and its document-level variant poses significant challenges, due to the need to model complex interactions between entities across sentences. Current approaches, largely based on the ATLOP architecture, are commonly evaluated on benchmarks like DocRED and Re-DocRED. However, their performance in zero-shot or few-shot settings remains largely underexplored due to the task's complexity. Recently, the GLiNER model has shown that a compact NER model can outperform much larger Large Language Models. With a similar motivation, we introduce GLiDRE, a new model for document-level relation extraction that builds on the key ideas of GliNER. We benchmark GLiDRE against state-of-the-art models across various data settings on the Re-DocRED dataset. Our results demonstrate that GLiDRE achieves state-of-the-art performance in few-shot scenarios. Our code is publicly available.

Relation extraction (RE) is a fundamental task in information extraction, whose extension to multilingual settings has been hindered by the lack of supervised resources comparable in size to large English datasets such as TACRED (Zhang et al., 2017). To address this gap, we introduce the MultiTACRED dataset, covering 12 typologically diverse languages from 9 language families, which is created by machine-translating TACRED instances and automatically projecting their entity annotations. We analyze translation and annotation projection quality, identify error categories, and experimentally evaluate fine-tuned pretrained mono- and multilingual language models in common transfer learning scenarios. Our analyses show that machine translation is a viable strategy to transfer RE instances, with native speakers judging more than 83% of the translated instances to be linguistically and semantically acceptable. We find monolingual RE model performance to be comparable to the English original for many of the target languages, and that multilingual models trained on a combination of English and target language data can outperform their monolingual counterparts. However, we also observe a variety of translation and annotation projection errors, both due to the MT systems and linguistic features of the target languages, such as pronoun-dropping, compounding and inflection, that degrade dataset quality and RE model performance.

Relation Extraction (RE) has attracted increasing attention, but current RE evaluation is limited to in-domain evaluation setups. Little is known on how well a RE system fares in challenging, but realistic out-of-distribution evaluation setups. To address this gap, we propose CrossRE, a new, freely-available cross-domain benchmark for RE, which comprises six distinct text domains and includes multi-label annotations. An additional innovation is that we release meta-data collected during annotation, to include explanations and flags of difficult instances. We provide an empirical evaluation with a state-of-the-art model for relation classification. As the meta-data enables us to shed new light on the state-of-the-art model, we provide a comprehensive analysis on the impact of difficult cases and find correlations between model and human annotations. Overall, our empirical investigation highlights the difficulty of cross-domain RE. We release our dataset, to spur more research in this direction.

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.

Information Extraction (IE) is crucial for converting unstructured data into structured formats like Knowledge Graphs (KGs). A key task within IE is Relation Extraction (RE), which identifies relationships between entities in text. Various RE methods exist, including supervised, unsupervised, weakly supervised, and rule-based approaches. Recent studies leveraging pre-trained language models (PLMs) have shown significant success in this area. In the current era dominated by Large Language Models (LLMs), fine-tuning these models can overcome limitations associated with zero-shot LLM prompting-based RE methods, especially regarding domain adaptation challenges and identifying implicit relations between entities in sentences. These implicit relations, which cannot be easily extracted from a sentence's dependency tree, require logical inference for accurate identification. This work explores the performance of fine-tuned LLMs and their integration into the Retrieval Augmented-based (RAG) RE approach to address the challenges of identifying implicit relations at the sentence level, particularly when LLMs act as generators within the RAG framework. Empirical evaluations on the TACRED, TACRED-Revisited (TACREV), Re-TACRED, and SemEVAL datasets show significant performance improvements with fine-tuned LLMs, including Llama2-7B, Mistral-7B, and T5 (Large). Notably, our approach achieves substantial gains on SemEVAL, where implicit relations are common, surpassing previous results on this dataset. Additionally, our method outperforms previous works on TACRED, TACREV, and Re-TACRED, demonstrating exceptional performance across diverse evaluation scenarios.

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine. The BioRED dataset and annotation guideline are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.

A number of datasets for Relation Extraction (RE) have been created to aide downstream tasks such as information retrieval, semantic search, question answering and textual entailment. However, these datasets fail to capture financial-domain specific challenges since most of these datasets are compiled using general knowledge sources such as Wikipedia, web-based text and news articles, hindering real-life progress and adoption within the financial world. To address this limitation, we propose REFinD, the first large-scale annotated dataset of relations, with sim29K instances and 22 relations amongst 8 types of entity pairs, generated entirely over financial documents. We also provide an empirical evaluation with various state-of-the-art models as benchmarks for the RE task and highlight the challenges posed by our dataset. We observed that various state-of-the-art deep learning models struggle with numeric inference, relational and directional ambiguity.

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.

Document-level Relation Extraction (RE) is a more challenging task than sentence RE as it often requires reasoning over multiple sentences. Yet, human annotators usually use a small number of sentences to identify the relationship between a given entity pair. In this paper, we present an embarrassingly simple but effective method to heuristically select evidence sentences for document-level RE, which can be easily combined with BiLSTM to achieve good performance on benchmark datasets, even better than fancy graph neural network based methods. We have released our code at https://github.com/AndrewZhe/Three-Sentences-Are-All-You-Need.

Real-world Relation Extraction (RE) tasks are challenging to deal with, either due to limited training data or class imbalance issues. In this work, we present Data Augmented Relation Extraction(DARE), a simple method to augment training data by properly fine-tuning GPT-2 to generate examples for specific relation types. The generated training data is then used in combination with the gold dataset to train a BERT-based RE classifier. In a series of experiments we show the advantages of our method, which leads in improvements of up to 11 F1 score points against a strong base-line. Also, DARE achieves new state of the art in three widely used biomedical RE datasets surpassing the previous best results by 4.7 F1 points on average.

This paper presents an empirical study to build relation extraction systems in low-resource settings. Based upon recent pre-trained language models, we comprehensively investigate three schemes to evaluate the performance in low-resource settings: (i) different types of prompt-based methods with few-shot labeled data; (ii) diverse balancing methods to address the long-tailed distribution issue; (iii) data augmentation technologies and self-training to generate more labeled in-domain data. We create a benchmark with 8 relation extraction (RE) datasets covering different languages, domains and contexts and perform extensive comparisons over the proposed schemes with combinations. Our experiments illustrate: (i) Though prompt-based tuning is beneficial in low-resource RE, there is still much potential for improvement, especially in extracting relations from cross-sentence contexts with multiple relational triples; (ii) Balancing methods are not always helpful for RE with long-tailed distribution; (iii) Data augmentation complements existing baselines and can bring much performance gain, while self-training may not consistently achieve advancement to low-resource RE. Code and datasets are in https://github.com/zjunlp/LREBench.

Information Extraction (IE) is a transformative process that converts unstructured text data into a structured format by employing entity and relation extraction (RE) methodologies. The identification of the relation between a pair of entities plays a crucial role within this framework. Despite the existence of various techniques for relation extraction, their efficacy heavily relies on access to labeled data and substantial computational resources. In addressing these challenges, Large Language Models (LLMs) emerge as promising solutions; however, they might return hallucinating responses due to their own training data. To overcome these limitations, Retrieved-Augmented Generation-based Relation Extraction (RAG4RE) in this work is proposed, offering a pathway to enhance the performance of relation extraction tasks. This work evaluated the effectiveness of our RAG4RE approach utilizing different LLMs. Through the utilization of established benchmarks, such as TACRED, TACREV, Re-TACRED, and SemEval RE datasets, our aim is to comprehensively evaluate the efficacy of our RAG4RE approach. In particularly, we leverage prominent LLMs including Flan T5, Llama2, and Mistral in our investigation. The results of our study demonstrate that our RAG4RE approach surpasses performance of traditional RE approaches based solely on LLMs, particularly evident in the TACRED dataset and its variations. Furthermore, our approach exhibits remarkable performance compared to previous RE methodologies across both TACRED and TACREV datasets, underscoring its efficacy and potential for advancing RE tasks in natural language processing.

Many datasets have been developed to train and evaluate document-level relation extraction (RE) models. Most of these are constructed using real-world data. It has been shown that RE models trained on real-world data suffer from factual biases. To evaluate and address this issue, we present CovEReD, a counterfactual data generation approach for document-level relation extraction datasets using entity replacement. We first demonstrate that models trained on factual data exhibit inconsistent behavior: while they accurately extract triples from factual data, they fail to extract the same triples after counterfactual modification. This inconsistency suggests that models trained on factual data rely on spurious signals such as specific entities and external knowledge x2013 rather than on the input context x2013 to extract triples. We show that by generating document-level counterfactual data with CovEReD and training models on them, consistency is maintained with minimal impact on RE performance. We release our CovEReD pipeline as well as Re-DocRED-CF, a dataset of counterfactual RE documents, to assist in evaluating and addressing inconsistency in document-level RE.

We present the first human-annotated dialogue-based relation extraction (RE) dataset DialogRE, aiming to support the prediction of relation(s) between two arguments that appear in a dialogue. We further offer DialogRE as a platform for studying cross-sentence RE as most facts span multiple sentences. We argue that speaker-related information plays a critical role in the proposed task, based on an analysis of similarities and differences between dialogue-based and traditional RE tasks. Considering the timeliness of communication in a dialogue, we design a new metric to evaluate the performance of RE methods in a conversational setting and investigate the performance of several representative RE methods on DialogRE. Experimental results demonstrate that a speaker-aware extension on the best-performing model leads to gains in both the standard and conversational evaluation settings. DialogRE is available at https://dataset.org/dialogre/.

Two key obstacles in biomedical relation extraction (RE) are the scarcity of annotations and the prevalence of instances without explicitly pre-defined labels due to low annotation coverage. Existing approaches, which treat biomedical RE as a multi-class classification task, often result in poor generalization in low-resource settings and do not have the ability to make selective prediction on unknown cases but give a guess from seen relations, hindering the applicability of those approaches. We present NBR, which converts biomedical RE as natural language inference formulation through indirect supervision. By converting relations to natural language hypotheses, NBR is capable of exploiting semantic cues to alleviate annotation scarcity. By incorporating a ranking-based loss that implicitly calibrates abstinent instances, NBR learns a clearer decision boundary and is instructed to abstain on uncertain instances. Extensive experiments on three widely-used biomedical RE benchmarks, namely ChemProt, DDI and GAD, verify the effectiveness of NBR in both full-set and low-resource regimes. Our analysis demonstrates that indirect supervision benefits biomedical RE even when a domain gap exists, and combining NLI knowledge with biomedical knowledge leads to the best performance gains.

This paper introduces a framework for relation extraction (RE) that enhances both accuracy and explainability. The framework has two key components: (i) a reasoning mechanism that formulates relation extraction as a series of text-processing steps inspired by cognitive science, and (ii) an optimization process driven by reinforcement learning (RL) with a novel reward function designed to improve both task accuracy and explanation quality. We call our approach CogRE. Our framework addresses the lack of supervision for language-based explanations in traditional RE by promoting outputs that include important relation keywords. These keywords are drawn from a high-quality dictionary that is automatically constructed using an LLM. We evaluate our approach for the task of one-shot RE using two LLMs and two RE datasets. Our experiments show that CogRE improves explanation quality by addressing two common failure patterns in one-shot RE: poor attention focus and limited one-shot learning capability. For example, our cognitive-structured reasoning with Qwen2.5-15B-Instruct on One-shot NYT29 achieves 24.65% F1, surpassing prior reasoning-based designs. Optimizing this approach with RL using our reward further improves performance by +23.46% (absolute). Finally, human evaluation shows that our best model generates relational keywords closely aligned with gold labels, increasing human explanation quality ratings by 54% (relative).

Despite the extensive applications of relation extraction (RE) tasks in various domains, little has been explored in the historical context, which contains promising data across hundreds and thousands of years. To promote the historical RE research, we present HistRED constructed from Yeonhaengnok. Yeonhaengnok is a collection of records originally written in Hanja, the classical Chinese writing, which has later been translated into Korean. HistRED provides bilingual annotations such that RE can be performed on Korean and Hanja texts. In addition, HistRED supports various self-contained subtexts with different lengths, from a sentence level to a document level, supporting diverse context settings for researchers to evaluate the robustness of their RE models. To demonstrate the usefulness of our dataset, we propose a bilingual RE model that leverages both Korean and Hanja contexts to predict relations between entities. Our model outperforms monolingual baselines on HistRED, showing that employing multiple language contexts supplements the RE predictions. The dataset is publicly available at: https://huggingface.co/datasets/Soyoung/HistRED under CC BY-NC-ND 4.0 license.

With the advent of artificial intelligence (AI), many researchers are attempting to extract structured information from document-level biomedical literature by fine-tuning large language models (LLMs). However, they face significant challenges such as the need for expensive hardware, like high-performance GPUs and the high labor costs associated with annotating training datasets, especially in biomedical realm. Recent research on LLMs, such as GPT-4 and Llama3, has shown promising performance in zero-shot settings, inspiring us to explore a novel approach to achieve the same results from unannotated full documents using general LLMs with lower hardware and labor costs. Our approach combines two major stages: named entity recognition (NER) and relation extraction (RE). NER identifies chemical, disease and gene entities from the document with synonym and hypernym extraction using an LLM with a crafted prompt. RE extracts relations between entities based on predefined relation schemas and prompts. To enhance the effectiveness of prompt, we propose a five-part template structure and a scenario-based prompt design principles, along with evaluation method to systematically assess the prompts. Finally, we evaluated our approach against fine-tuning and pre-trained models on two biomedical datasets: ChemDisGene and CDR. The experimental results indicate that our proposed method can achieve comparable accuracy levels to fine-tuning and pre-trained models but with reduced human and hardware expenses.

Large Language Models (LLMs) have demonstrated exceptional abilities in comprehending and generating text, motivating numerous researchers to utilize them for Information Extraction (IE) purposes, including Relation Extraction (RE). Nonetheless, most existing methods are predominantly designed for Sentence-level Relation Extraction (SentRE) tasks, which typically encompass a restricted set of relations and triplet facts within a single sentence. Furthermore, certain approaches resort to treating relations as candidate choices integrated into prompt templates, leading to inefficient processing and suboptimal performance when tackling Document-Level Relation Extraction (DocRE) tasks, which entail handling multiple relations and triplet facts distributed across a given document, posing distinct challenges. To overcome these limitations, we introduce AutoRE, an end-to-end DocRE model that adopts a novel RE extraction paradigm named RHF (Relation-Head-Facts). Unlike existing approaches, AutoRE does not rely on the assumption of known relation options, making it more reflective of real-world scenarios. Additionally, we have developed an easily extensible RE framework using a Parameters Efficient Fine Tuning (PEFT) algorithm (QLoRA). Our experiments on the RE-DocRED dataset showcase AutoRE's best performance, achieving state-of-the-art results, surpassing TAG by 10.03\% and 9.03\% respectively on the dev and test set. The code is available at https://github.com/THUDM/AutoRE and the demonstration video is provided at https://www.youtube.com/watch?v=IhKRsZUAxKk.

Clinical texts, represented in electronic medical records (EMRs), contain rich medical information and are essential for disease prediction, personalised information recommendation, clinical decision support, and medication pattern mining and measurement. Relation extractions between medication mentions and temporal information can further help clinicians better understand the patients' treatment history. To evaluate the performances of deep learning (DL) and large language models (LLMs) in medication extraction and temporal relations classification, we carry out an empirical investigation of MedTem project using several advanced learning structures including BiLSTM-CRF and CNN-BiLSTM for a clinical domain named entity recognition (NER), and BERT-CNN for temporal relation extraction (RE), in addition to the exploration of different word embedding techniques. Furthermore, we also designed a set of post-processing roles to generate structured output on medications and the temporal relation. Our experiments show that CNN-BiLSTM slightly wins the BiLSTM-CRF model on the i2b2-2009 clinical NER task yielding 75.67, 77.83, and 78.17 for precision, recall, and F1 scores using Macro Average. BERT-CNN model also produced reasonable evaluation scores 64.48, 67.17, and 65.03 for P/R/F1 using Macro Avg on the temporal relation extraction test set from i2b2-2012 challenges. Code and Tools from MedTem will be hosted at https://github.com/HECTA-UoM/MedTem

Multiple entities in a document generally exhibit complex inter-sentence relations, and cannot be well handled by existing relation extraction (RE) methods that typically focus on extracting intra-sentence relations for single entity pairs. In order to accelerate the research on document-level RE, we introduce DocRED, a new dataset constructed from Wikipedia and Wikidata with three features: (1) DocRED annotates both named entities and relations, and is the largest human-annotated dataset for document-level RE from plain text; (2) DocRED requires reading multiple sentences in a document to extract entities and infer their relations by synthesizing all information of the document; (3) along with the human-annotated data, we also offer large-scale distantly supervised data, which enables DocRED to be adopted for both supervised and weakly supervised scenarios. In order to verify the challenges of document-level RE, we implement recent state-of-the-art methods for RE and conduct a thorough evaluation of these methods on DocRED. Empirical results show that DocRED is challenging for existing RE methods, which indicates that document-level RE remains an open problem and requires further efforts. Based on the detailed analysis on the experiments, we discuss multiple promising directions for future research.

OpenNRE is an open-source and extensible toolkit that provides a unified framework to implement neural models for relation extraction (RE). Specifically, by implementing typical RE methods, OpenNRE not only allows developers to train custom models to extract structured relational facts from the plain text but also supports quick model validation for researchers. Besides, OpenNRE provides various functional RE modules based on both TensorFlow and PyTorch to maintain sufficient modularity and extensibility, making it becomes easy to incorporate new models into the framework. Besides the toolkit, we also release an online system to meet real-time extraction without any training and deploying. Meanwhile, the online system can extract facts in various scenarios as well as aligning the extracted facts to Wikidata, which may benefit various downstream knowledge-driven applications (e.g., information retrieval and question answering). More details of the toolkit and online system can be obtained from http://github.com/thunlp/OpenNRE.

The DocRED dataset is one of the most popular and widely used benchmarks for document-level relation extraction (RE). It adopts a recommend-revise annotation scheme so as to have a large-scale annotated dataset. However, we find that the annotation of DocRED is incomplete, i.e., false negative samples are prevalent. We analyze the causes and effects of the overwhelming false negative problem in the DocRED dataset. To address the shortcoming, we re-annotate 4,053 documents in the DocRED dataset by adding the missed relation triples back to the original DocRED. We name our revised DocRED dataset Re-DocRED. We conduct extensive experiments with state-of-the-art neural models on both datasets, and the experimental results show that the models trained and evaluated on our Re-DocRED achieve performance improvements of around 13 F1 points. Moreover, we conduct a comprehensive analysis to identify the potential areas for further improvement. Our dataset is publicly available at https://github.com/tonytan48/Re-DocRED.

Distant supervision (DS) is a well established technique for creating large-scale datasets for relation extraction (RE) without using human annotations. However, research in DS-RE has been mostly limited to the English language. Constraining RE to a single language inhibits utilization of large amounts of data in other languages which could allow extraction of more diverse facts. Very recently, a dataset for multilingual DS-RE has been released. However, our analysis reveals that the proposed dataset exhibits unrealistic characteristics such as 1) lack of sentences that do not express any relation, and 2) all sentences for a given entity pair expressing exactly one relation. We show that these characteristics lead to a gross overestimation of the model performance. In response, we propose a new dataset, DiS-ReX, which alleviates these issues. Our dataset has more than 1.5 million sentences, spanning across 4 languages with 36 relation classes + 1 no relation (NA) class. We also modify the widely used bag attention models by encoding sentences using mBERT and provide the first benchmark results on multilingual DS-RE. Unlike the competing dataset, we show that our dataset is challenging and leaves enough room for future research to take place in this field.

Despite efforts to distinguish three different evaluation setups (Bekoulis et al., 2018), numerous end-to-end Relation Extraction (RE) articles present unreliable performance comparison to previous work. In this paper, we first identify several patterns of invalid comparisons in published papers and describe them to avoid their propagation. We then propose a small empirical study to quantify the impact of the most common mistake and evaluate it leads to overestimating the final RE performance by around 5% on ACE05. We also seize this opportunity to study the unexplored ablations of two recent developments: the use of language model pretraining (specifically BERT) and span-level NER. This meta-analysis emphasizes the need for rigor in the report of both the evaluation setting and the datasets statistics and we call for unifying the evaluation setting in end-to-end RE.

TACRED (Zhang et al., 2017) is one of the largest, most widely used crowdsourced datasets in Relation Extraction (RE). But, even with recent advances in unsupervised pre-training and knowledge enhanced neural RE, models still show a high error rate. In this paper, we investigate the questions: Have we reached a performance ceiling or is there still room for improvement? And how do crowd annotations, dataset, and models contribute to this error rate? To answer these questions, we first validate the most challenging 5K examples in the development and test sets using trained annotators. We find that label errors account for 8% absolute F1 test error, and that more than 50% of the examples need to be relabeled. On the relabeled test set the average F1 score of a large baseline model set improves from 62.1 to 70.1. After validation, we analyze misclassifications on the challenging instances, categorize them into linguistically motivated error groups, and verify the resulting error hypotheses on three state-of-the-art RE models. We show that two groups of ambiguous relations are responsible for most of the remaining errors and that models may adopt shallow heuristics on the dataset when entities are not masked.

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

Recent work has shown that NLP tasks such as Relation Extraction (RE) can be recasted as Textual Entailment tasks using verbalizations, with strong performance in zero-shot and few-shot settings thanks to pre-trained entailment models. The fact that relations in current RE datasets are easily verbalized casts doubts on whether entailment would be effective in more complex tasks. In this work we show that entailment is also effective in Event Argument Extraction (EAE), reducing the need of manual annotation to 50% and 20% in ACE and WikiEvents respectively, while achieving the same performance as with full training. More importantly, we show that recasting EAE as entailment alleviates the dependency on schemas, which has been a road-block for transferring annotations between domains. Thanks to the entailment, the multi-source transfer between ACE and WikiEvents further reduces annotation down to 10% and 5% (respectively) of the full training without transfer. Our analysis shows that the key to good results is the use of several entailment datasets to pre-train the entailment model. Similar to previous approaches, our method requires a small amount of effort for manual verbalization: only less than 15 minutes per event argument type is needed, and comparable results can be achieved with users with different level of expertise.

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 will be open to the public.

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 (Multi-View Relation Extraction), 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.

Recent work has shown that fine-tuning large language models (LLMs) on large-scale instruction-following datasets substantially improves their performance on a wide range of NLP tasks, especially in the zero-shot setting. However, even advanced instruction-tuned LLMs still fail to outperform small LMs on relation extraction (RE), a fundamental information extraction task. We hypothesize that instruction-tuning has been unable to elicit strong RE capabilities in LLMs due to RE's low incidence in instruction-tuning datasets, making up less than 1% of all tasks (Wang et al., 2022). To address this limitation, we propose QA4RE, a framework that aligns RE with question answering (QA), a predominant task in instruction-tuning datasets. Comprehensive zero-shot RE experiments over four datasets with two series of instruction-tuned LLMs (six LLMs in total) demonstrate that our QA4RE framework consistently improves LLM performance, strongly verifying our hypothesis and enabling LLMs to outperform strong zero-shot baselines by a large margin. Additionally, we provide thorough experiments and discussions to show the robustness, few-shot effectiveness, and strong transferability of our QA4RE framework. This work illustrates a promising way of adapting LLMs to challenging and underrepresented tasks by aligning these tasks with more common instruction-tuning tasks like QA.

Universal Information Extraction (UIE) is an area of interest due to the challenges posed by varying targets, heterogeneous structures, and demand-specific schemas. However, previous works have only achieved limited success by unifying a few tasks, such as Named Entity Recognition (NER) and Relation Extraction (RE), which fall short of being authentic UIE models particularly when extracting other general schemas such as quadruples and quintuples. Additionally, these models used an implicit structural schema instructor, which could lead to incorrect links between types, hindering the model's generalization and performance in low-resource scenarios. In this paper, we redefine the authentic UIE with a formal formulation that encompasses almost all extraction schemas. To the best of our knowledge, we are the first to introduce UIE for any kind of schemas. In addition, we propose RexUIE, which is a Recursive Method with Explicit Schema Instructor for UIE. To avoid interference between different types, we reset the position ids and attention mask matrices. RexUIE shows strong performance under both full-shot and few-shot settings and achieves State-of-the-Art results on the tasks of extracting complex schemas.

This paper presents DWIE, the 'Deutsche Welle corpus for Information Extraction', a newly created multi-task dataset that combines four main Information Extraction (IE) annotation subtasks: (i) Named Entity Recognition (NER), (ii) Coreference Resolution, (iii) Relation Extraction (RE), and (iv) Entity Linking. DWIE is conceived as an entity-centric dataset that describes interactions and properties of conceptual entities on the level of the complete document. This contrasts with currently dominant mention-driven approaches that start from the detection and classification of named entity mentions in individual sentences. Further, DWIE presented two main challenges when building and evaluating IE models for it. First, the use of traditional mention-level evaluation metrics for NER and RE tasks on entity-centric DWIE dataset can result in measurements dominated by predictions on more frequently mentioned entities. We tackle this issue by proposing a new entity-driven metric that takes into account the number of mentions that compose each of the predicted and ground truth entities. Second, the document-level multi-task annotations require the models to transfer information between entity mentions located in different parts of the document, as well as between different tasks, in a joint learning setting. To realize this, we propose to use graph-based neural message passing techniques between document-level mention spans. Our experiments show an improvement of up to 5.5 F1 percentage points when incorporating neural graph propagation into our joint model. This demonstrates DWIE's potential to stimulate further research in graph neural networks for representation learning in multi-task IE. We make DWIE publicly available at https://github.com/klimzaporojets/DWIE.

This work addresses two important questions pertinent to Relation Extraction (RE). First, what are all possible relations that could exist between any two given entity types? Second, how do we define an unambiguous taxonomical (is-a) hierarchy among the identified relations? To address the first question, we use three resources Wikipedia Infobox, Wikidata, and DBpedia. This study focuses on relations between person, organization and location entity types. We exploit Wikidata and DBpedia in a data-driven manner, and Wikipedia Infobox templates manually to generate lists of relations. Further, to address the second question, we canonicalize, filter, and combine the identified relations from the three resources to construct a taxonomical hierarchy. This hierarchy contains 623 canonical relations with highest contribution from Wikipedia Infobox followed by DBpedia and Wikidata. The generated relation list subsumes an average of 85% of relations from RE datasets when entity types are restricted.

Knowledge graphs have shown promise for several cybersecurity tasks, such as vulnerability assessment and threat analysis. In this work, we present a new method for constructing a vulnerability knowledge graph from information in the National Vulnerability Database (NVD). Our approach combines named entity recognition (NER), relation extraction (RE), and entity prediction using a combination of neural models, heuristic rules, and knowledge graph embeddings. We demonstrate how our method helps to fix missing entities in knowledge graphs used for cybersecurity and evaluate the performance.

Natural language processing (NLP) practitioners are leveraging large language models (LLM) to create structured datasets from semi-structured and unstructured data sources such as patents, papers, and theses, without having domain-specific knowledge. At the same time, ecological experts are searching for a variety of means to preserve biodiversity. To contribute to these efforts, we focused on endangered species and through in-context learning, we distilled knowledge from GPT-4. In effect, we created datasets for both named entity recognition (NER) and relation extraction (RE) via a two-stage process: 1) we generated synthetic data from GPT-4 of four classes of endangered species, 2) humans verified the factual accuracy of the synthetic data, resulting in gold data. Eventually, our novel dataset contains a total of 3.6K sentences, evenly divided between 1.8K NER and 1.8K RE sentences. The constructed dataset was then used to fine-tune both general BERT and domain-specific BERT variants, completing the knowledge distillation process from GPT-4 to BERT, because GPT-4 is resource intensive. Experiments show that our knowledge transfer approach is effective at creating a NER model suitable for detecting endangered species from texts.

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

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.

In this work, we explore how to train task-specific language models aimed towards learning rich representation of keyphrases from text documents. We experiment with different masking strategies for pre-training transformer language models (LMs) in discriminative as well as generative settings. In the discriminative setting, we introduce a new pre-training objective - Keyphrase Boundary Infilling with Replacement (KBIR), showing large gains in performance (upto 8.16 points in F1) over SOTA, when the LM pre-trained using KBIR is fine-tuned for the task of keyphrase extraction. In the generative setting, we introduce a new pre-training setup for BART - KeyBART, that reproduces the keyphrases related to the input text in the CatSeq format, instead of the denoised original input. This also led to gains in performance (upto 4.33 points in F1@M) over SOTA for keyphrase generation. Additionally, we also fine-tune the pre-trained language models on named entity recognition (NER), question answering (QA), relation extraction (RE), abstractive summarization and achieve comparable performance with that of the SOTA, showing that learning rich representation of keyphrases is indeed beneficial for many other fundamental NLP tasks.

The current state of adoption of well-structured electronic health records and integration of digital methods for storing medical patient data in structured formats can often considered as inferior compared to the use of traditional, unstructured text based patient data documentation. Data mining in the field of medical data analysis often needs to rely solely on processing of unstructured data to retrieve relevant data. In natural language processing (NLP), statistical models have been shown successful in various tasks like part-of-speech tagging, relation extraction (RE) and named entity recognition (NER). In this work, we present GERNERMED, the first open, neural NLP model for NER tasks dedicated to detect medical entity types in German text data. Here, we avoid the conflicting goals of protection of sensitive patient data from training data extraction and the publication of the statistical model weights by training our model on a custom dataset that was translated from publicly available datasets in foreign language by a pretrained neural machine translation model. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED

External knowledge (a.k.a. side information) plays a critical role in zero-shot learning (ZSL) which aims to predict with unseen classes that have never appeared in training data. Several kinds of external knowledge, such as text and attribute, have been widely investigated, but they alone are limited with incomplete semantics. Some very recent studies thus propose to use Knowledge Graph (KG) due to its high expressivity and compatibility for representing kinds of knowledge. However, the ZSL community is still in short of standard benchmarks for studying and comparing different external knowledge settings and different KG-based ZSL methods. In this paper, we proposed six resources covering three tasks, i.e., zero-shot image classification (ZS-IMGC), zero-shot relation extraction (ZS-RE), and zero-shot KG completion (ZS-KGC). Each resource has a normal ZSL benchmark and a KG containing semantics ranging from text to attribute, from relational knowledge to logical expressions. We have clearly presented these resources including their construction, statistics, data formats and usage cases w.r.t. different ZSL methods. More importantly, we have conducted a comprehensive benchmarking study, with two general and state-of-the-art methods, two setting-specific methods and one interpretable method. We discussed and compared different ZSL paradigms w.r.t. different external knowledge settings, and found that our resources have great potential for developing more advanced ZSL methods and more solutions for applying KGs for augmenting machine learning. All the resources are available at https://github.com/China-UK-ZSL/Resources_for_KZSL.

Semantic matching is a mainstream paradigm of zero-shot relation extraction, which matches a given input with a corresponding label description. The entities in the input should exactly match their hypernyms in the description, while the irrelevant contexts should be ignored when matching. However, general matching methods lack explicit modeling of the above matching pattern. In this work, we propose a fine-grained semantic matching method tailored for zero-shot relation extraction. Following the above matching pattern, we decompose the sentence-level similarity score into entity and context matching scores. Due to the lack of explicit annotations of the redundant components, we design a feature distillation module to adaptively identify the relation-irrelevant features and reduce their negative impact on context matching. Experimental results show that our method achieves higher matching F_1 score and has an inference speed 10 times faster, when compared with the state-of-the-art methods.

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

Driven by the demand for cross-sentence and large-scale relation extraction, document-level relation extraction (DocRE) has attracted increasing research interest. Despite the continuous improvement in performance, we find that existing DocRE models which initially perform well may make more mistakes when merely changing the entity names in the document, hindering the generalization to novel entity names. To this end, we systematically investigate the robustness of DocRE models to entity name variations in this work. We first propose a principled pipeline to generate entity-renamed documents by replacing the original entity names with names from Wikidata. By applying the pipeline to DocRED and Re-DocRED datasets, we construct two novel benchmarks named Env-DocRED and Env-Re-DocRED for robustness evaluation. Experimental results show that both three representative DocRE models and two in-context learned large language models consistently lack sufficient robustness to entity name variations, particularly on cross-sentence relation instances and documents with more entities. Finally, we propose an entity variation robust training method which not only improves the robustness of DocRE models but also enhances their understanding and reasoning capabilities. We further verify that the basic idea of this method can be effectively transferred to in-context learning for DocRE as well.

Deep learning models have achieved state-of-the-art performances on many relation extraction datasets. A common element in these deep learning models involves the pooling mechanisms where a sequence of hidden vectors is aggregated to generate a single representation vector, serving as the features to perform prediction for RE. Unfortunately, the models in the literature tend to employ different strategies to perform pooling for RE, leading to the challenge to determine the best pooling mechanism for this problem, especially in the biomedical domain. In order to answer this question, in this work, we conduct a comprehensive study to evaluate the effectiveness of different pooling mechanisms for the deep learning models in biomedical RE. The experimental results suggest that dependency-based pooling is the best pooling strategy for RE in the biomedical domain, yielding the state-of-the-art performance on two benchmark datasets for this problem.

We present MobIE, a German-language dataset, which is human-annotated with 20 coarse- and fine-grained entity types and entity linking information for geographically linkable entities. The dataset consists of 3,232 social media texts and traffic reports with 91K tokens, and contains 20.5K annotated entities, 13.1K of which are linked to a knowledge base. A subset of the dataset is human-annotated with seven mobility-related, n-ary relation types, while the remaining documents are annotated using a weakly-supervised labeling approach implemented with the Snorkel framework. To the best of our knowledge, this is the first German-language dataset that combines annotations for NER, EL and RE, and thus can be used for joint and multi-task learning of these fundamental information extraction tasks. We make MobIE public at https://github.com/dfki-nlp/mobie.

Annotation noise is widespread in datasets, but manually revising a flawed corpus is time-consuming and error-prone. Hence, given the prior knowledge in Pre-trained Language Models and the expected uniformity across all annotations, we attempt to reduce annotation noise in the corpus through two tasks automatically: (1) Annotation Inconsistency Detection that indicates the credibility of annotations, and (2) Annotation Error Correction that rectifies the abnormal annotations. We investigate how to acquire semantic sensitive annotation representations from Pre-trained Language Models, expecting to embed the examples with identical annotations to the mutually adjacent positions even without fine-tuning. We proposed a novel credibility score to reveal the likelihood of annotation inconsistencies based on the neighbouring consistency. Then, we fine-tune the Pre-trained Language Models based classifier with cross-validation for annotation correction. The annotation corrector is further elaborated with two approaches: (1) soft labelling by Kernel Density Estimation and (2) a novel distant-peer contrastive loss. We study the re-annotation in relation extraction and create a new manually revised dataset, Re-DocRED, for evaluating document-level re-annotation. The proposed credibility scores show promising agreement with human revisions, achieving a Binary F1 of 93.4 and 72.5 in detecting inconsistencies on TACRED and DocRED respectively. Moreover, the neighbour-aware classifiers based on distant-peer contrastive learning and uncertain labels achieve Macro F1 up to 66.2 and 57.8 in correcting annotations on TACRED and DocRED respectively. These improvements are not merely theoretical: Rather, automatically denoised training sets demonstrate up to 3.6% performance improvement for state-of-the-art relation extraction models.

TACRED is one of the largest and most widely used sentence-level relation extraction datasets. Proposed models that are evaluated using this dataset consistently set new state-of-the-art performance. However, they still exhibit large error rates despite leveraging external knowledge and unsupervised pretraining on large text corpora. A recent study suggested that this may be due to poor dataset quality. The study observed that over 50% of the most challenging sentences from the development and test sets are incorrectly labeled and account for an average drop of 8% f1-score in model performance. However, this study was limited to a small biased sample of 5k (out of a total of 106k) sentences, substantially restricting the generalizability and broader implications of its findings. In this paper, we address these shortcomings by: (i) performing a comprehensive study over the whole TACRED dataset, (ii) proposing an improved crowdsourcing strategy and deploying it to re-annotate the whole dataset, and (iii) performing a thorough analysis to understand how correcting the TACRED annotations affects previously published results. After verification, we observed that 23.9% of TACRED labels are incorrect. Moreover, evaluating several models on our revised dataset yields an average f1-score improvement of 14.3% and helps uncover significant relationships between the different models (rather than simply offsetting or scaling their scores by a constant factor). Finally, aside from our analysis we also release Re-TACRED, a new completely re-annotated version of the TACRED dataset that can be used to perform reliable evaluation of relation extraction models.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed 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 also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.