Rare diseases affect millions worldwide but often face limited research focus due to their low prevalence. This results in prolonged diagnoses and a lack of approved therapies. Recent advancements in Large Language Models (LLMs) have shown promise in automating the extraction of medical information, offering potential to improve medical diagnosis and management. However, most LLMs lack professional medical knowledge, especially concerning rare diseases, and struggle to handle the latest rare disease information. They also cannot effectively manage rare disease data and are not directly suitable for diagnosis and management tasks. Our objective is to create an end-to-end system called AutoRD, which automates the extraction of information from medical texts about rare diseases, focusing on entities and their relations. AutoRD integrates up-to-date structured knowledge and demonstrates superior performance in rare disease extraction tasks. We conduct various experiments to evaluate AutoRD's performance, aiming to surpass common LLMs and traditional methods.
In recent years, large language models have achieved state-of-the-art performance across various NLP tasks. However, investigations have shown that these models tend to rely on shortcut features, leading to inaccurate predictions and causing the models to be unreliable at generalization to out-of-distribution (OOD) samples. For instance, in the context of relation extraction (RE), we would expect a model to identify the same relation independently of the entities involved in it. For example, consider the sentence "Leonardo da Vinci painted the Mona Lisa" expressing the created(Leonardo_da_Vinci, Mona_Lisa) relation. If we substiute "Leonardo da Vinci" with "Barack Obama", then the sentence still expresses the created relation. A robust model is supposed to detect the same relation in both cases. In this work, we describe several semantically-motivated strategies to generate adversarial examples by replacing entity mentions and investigate how state-of-the-art RE models perform under pressure. Our analyses show that the performance of these models significantly deteriorates on the modified datasets (avg. of -48.5% in F1), which indicates that these models rely to a great extent on shortcuts, such as surface forms (or patterns therein) of entities, without making full use of the information present in the sentences.
With the AI revolution in place, the trend for building automated systems to support professionals in different domains such as the open source software systems, healthcare systems, banking systems, transportation systems and many others have become increasingly prominent. A crucial requirement in the automation of support tools for such systems is the early identification of named entities, which serves as a foundation for developing specialized functionalities. However, due to the specific nature of each domain, different technical terminologies and specialized languages, expert annotation of available data becomes expensive and challenging. In light of these challenges, this paper proposes a novel named entity recognition (NER) technique specifically tailored for the open-source software systems. Our approach aims to address the scarcity of annotated software data by employing a comprehensive two-step distantly supervised annotation process. This process strategically leverages language heuristics, unique lookup tables, external knowledge sources, and an active learning approach. By harnessing these powerful techniques, we not only enhance model performance but also effectively mitigate the limitations associated with cost and the scarcity of expert annotators. It is noteworthy that our model significantly outperforms the state-of-the-art LLMs by a substantial margin. We also show the effectiveness of NER in the downstream task of relation extraction.
Continual Few-shot Relation Extraction (CFRE) is a practical problem that requires the model to continuously learn novel relations while avoiding forgetting old ones with few labeled training data. The primary challenges are catastrophic forgetting and overfitting. This paper harnesses prompt learning to explore the implicit capabilities of pre-trained language models to address the above two challenges, thereby making language models better continual few-shot relation extractors. Specifically, we propose a Contrastive Prompt Learning framework, which designs prompt representation to acquire more generalized knowledge that can be easily adapted to old and new categories, and margin-based contrastive learning to focus more on hard samples, therefore alleviating catastrophic forgetting and overfitting issues. To further remedy overfitting in low-resource scenarios, we introduce an effective memory augmentation strategy that employs well-crafted prompts to guide ChatGPT in generating diverse samples. Extensive experiments demonstrate that our method outperforms state-of-the-art methods by a large margin and significantly mitigates catastrophic forgetting and overfitting in low-resource scenarios.
Recently, large language models (LLMs) have been successful in relational extraction (RE) tasks, especially in the few-shot learning. An important problem in the field of RE is long-tailed data, while not much attention is paid to this problem using LLM approaches. Therefore, in this paper, we propose SLCoLM, a model collaboration framework, to mitigate the data long-tail problem. In our framework, we use the ``\textit{Training-Guide-Predict}'' strategy to combine the strengths of small pre-trained language models (SLMs) and LLMs, where a task-specific SLM framework acts as a guider, transfers task knowledge to the LLM and guides the LLM in performing RE tasks. Our experiments on an ancient Chinese RE dataset rich in relation types show that the approach facilitates RE of long-tail relation types.
Relation extraction is an efficient way of mining the extraordinary wealth of human knowledge on the Web. Existing methods rely on domain-specific training data or produce noisy outputs. We focus here on extracting targeted relations from semi-structured web pages given only a short description of the relation. We present GraphScholarBERT, an open-domain information extraction method based on a joint graph and language model structure. GraphScholarBERT can generalize to previously unseen domains without additional data or training and produces only clean extraction results matched to the search keyword. Experiments show that GraphScholarBERT can improve extraction F1 scores by as much as 34.8\% compared to previous work in a zero-shot domain and zero-shot website setting.
Standard English and Malaysian English exhibit notable differences, posing challenges for natural language processing (NLP) tasks on Malaysian English. Unfortunately, most of the existing datasets are mainly based on standard English and therefore inadequate for improving NLP tasks in Malaysian English. An experiment using state-of-the-art Named Entity Recognition (NER) solutions on Malaysian English news articles highlights that they cannot handle morphosyntactic variations in Malaysian English. To the best of our knowledge, there is no annotated dataset available to improvise the model. To address these issues, we constructed a Malaysian English News (MEN) dataset, which contains 200 news articles that are manually annotated with entities and relations. We then fine-tuned the spaCy NER tool and validated that having a dataset tailor-made for Malaysian English could improve the performance of NER in Malaysian English significantly. This paper presents our effort in the data acquisition, annotation methodology, and thorough analysis of the annotated dataset. To validate the quality of the annotation, inter-annotator agreement was used, followed by adjudication of disagreements by a subject matter expert. Upon completion of these tasks, we managed to develop a dataset with 6,061 entities and 3,268 relation instances. Finally, we discuss on spaCy fine-tuning setup and analysis on the NER performance. This unique dataset will contribute significantly to the advancement of NLP research in Malaysian English, allowing researchers to accelerate their progress, particularly in NER and relation extraction. The dataset and annotation guideline has been published on Github.
Cutting edge techniques developed in the general NLP domain are often subsequently applied to the high-value, data-rich biomedical domain. The past few years have seen generative language models (LMs), instruction finetuning, and few-shot learning become foci of NLP research. As such, generative LMs pretrained on biomedical corpora have proliferated and biomedical instruction finetuning has been attempted as well, all with the hope that domain specificity improves performance on downstream tasks. Given the nontrivial effort in training such models, we investigate what, if any, benefits they have in the key biomedical NLP task of relation extraction. Specifically, we address two questions: (1) Do LMs trained on biomedical corpora outperform those trained on general domain corpora? (2) Do models instruction finetuned on biomedical datasets outperform those finetuned on assorted datasets or those simply pretrained? We tackle these questions using existing LMs, testing across four datasets. In a surprising result, general-domain models typically outperformed biomedical-domain models. However, biomedical instruction finetuning improved performance to a similar degree as general instruction finetuning, despite having orders of magnitude fewer instructions. Our findings suggest it may be more fruitful to focus research effort on larger-scale biomedical instruction finetuning of general LMs over building domain-specific biomedical LMs
Large language models (LLMs) have demonstrated impressive abilities in generating unstructured natural language according to instructions. However, their performance can be inconsistent when tasked with producing text that adheres to specific structured formats, which is crucial in applications like named entity recognition (NER) or relation extraction (RE). To address this issue, this paper introduces an efficient method, G&O, to enhance their structured text generation capabilities. It breaks the generation into a two-step pipeline: initially, LLMs generate answers in natural language as intermediate responses. Subsequently, LLMs are asked to organize the output into the desired structure, using the intermediate responses as context. G&O effectively separates the generation of content from the structuring process, reducing the pressure of completing two orthogonal tasks simultaneously. Tested on zero-shot NER and RE, the results indicate a significant improvement in LLM performance with minimal additional efforts. This straightforward and adaptable prompting technique can also be combined with other strategies, like self-consistency, to further elevate LLM capabilities in various structured text generation tasks.
In this study, we investigate the potential of GPT-4 and its advanced iteration, GPT-4 Turbo, in autonomously developing a detailed entity type taxonomy. Our objective is to construct a comprehensive taxonomy, starting from a broad classification of entity types - including objects, time, locations, organizations, events, actions, and subjects - similar to existing manually curated taxonomies. This classification is then progressively refined through iterative prompting techniques, leveraging GPT-4's internal knowledge base. The result is an extensive taxonomy comprising over 5000 nuanced entity types, which demonstrates remarkable quality upon subjective evaluation. We employed a straightforward yet effective prompting strategy, enabling the taxonomy to be dynamically expanded. The practical applications of this detailed taxonomy are diverse and significant. It facilitates the creation of new, more intricate branches through pattern-based combinations and notably enhances information extraction tasks, such as relation extraction and event argument extraction. Our methodology not only introduces an innovative approach to taxonomy creation but also opens new avenues for applying such taxonomies in various computational linguistics and AI-related fields.
There has been increasing interest in exploring the capabilities of advanced large language models (LLMs) in the field of information extraction (IE), specifically focusing on tasks related to named entity recognition (NER) and relation extraction (RE). Although researchers are exploring the use of few-shot information extraction through in-context learning with LLMs, they tend to focus only on using correct or positive examples for demonstration, neglecting the potential value of incorporating incorrect or negative examples into the learning process. In this paper, we present c-ICL, a novel few-shot technique that leverages both correct and incorrect sample constructions to create in-context learning demonstrations. This approach enhances the ability of LLMs to extract entities and relations by utilizing prompts that incorporate not only the positive samples but also the reasoning behind them. This method allows for the identification and correction of potential interface errors. Specifically, our proposed method taps into the inherent contextual information and valuable information in hard negative samples and the nearest positive neighbors to the test and then applies the in-context learning demonstrations based on LLMs. Our experiments on various datasets indicate that c-ICL outperforms previous few-shot in-context learning methods, delivering substantial enhancements in performance across a broad spectrum of related tasks. These improvements are noteworthy, showcasing the versatility of our approach in miscellaneous scenarios.
Relation extraction (RE) aims to identify semantic relationships between entities within text. Despite considerable advancements, existing models predominantly require extensive annotated training data, which is both costly and labor-intensive to collect. Moreover, these models often struggle to adapt to new or unseen relations. Few-shot learning, aiming to lessen annotation demands, typically provides incomplete and biased supervision for target relations, leading to degraded and unstable performance. To accurately and explicitly describe relation semantics while minimizing annotation demands, we explore the definition only zero-shot RE setting where only relation definitions expressed in natural language are used to train a RE model. We introduce REPaL, comprising three stages: (1) We leverage large language models (LLMs) to generate initial seed instances from relation definitions and an unlabeled corpus. (2) We fine-tune a bidirectional Small Language Model (SLM) with initial seeds to learn relations for the target domain. (3) We expand pattern coverage and mitigate bias from initial seeds by integrating feedback from the SLM's predictions on the unlabeled corpus and the synthesis history. To accomplish this, we leverage the multi-turn conversation ability of LLMs to generate new instances in follow-up dialogues, informed by both the feedback and synthesis history. Studies reveal that definition-oriented seed synthesis enhances pattern coverage whereas indiscriminately increasing seed quantity leads to performance saturation. Experiments on two datasets show REPaL significantly improved cost-effective zero-shot performance by large margins.
The field of relation extraction (RE) is experiencing a notable shift towards generative relation extraction (GRE), leveraging the capabilities of large language models (LLMs). However, we discovered that traditional relation extraction (RE) metrics like precision and recall fall short in evaluating GRE methods. This shortfall arises because these metrics rely on exact matching with human-annotated reference relations, while GRE methods often produce diverse and semantically accurate relations that differ from the references. To fill this gap, we introduce GenRES for a multi-dimensional assessment in terms of the topic similarity, uniqueness, granularity, factualness, and completeness of the GRE results. With GenRES, we empirically identified that (1) precision/recall fails to justify the performance of GRE methods; (2) human-annotated referential relations can be incomplete; (3) prompting LLMs with a fixed set of relations or entities can cause hallucinations. Next, we conducted a human evaluation of GRE methods that shows GenRES is consistent with human preferences for RE quality. Last, we made a comprehensive evaluation of fourteen leading LLMs using GenRES across document, bag, and sentence level RE datasets, respectively, to set the benchmark for future research in GRE
Modelling learning objects (LO) within their context enables the learner to advance from a basic, remembering-level, learning objective to a higher-order one, i.e., a level with an application- and analysis objective. While hierarchical data models are commonly used in digital learning platforms, using graph-based models enables representing the context of LOs in those platforms. This leads to a foundation for personalized recommendations of learning paths. In this paper, the transformation of hierarchical data models into knowledge graph (KG) models of LOs using text mining is introduced and evaluated. We utilize custom text mining pipelines to mine semantic relations between elements of an expert-curated hierarchical model. We evaluate the KG structure and relation extraction using graph quality-control metrics and the comparison of algorithmic semantic-similarities to expert-defined ones. The results show that the relations in the KG are semantically comparable to those defined by domain experts, and that the proposed KG improves representing and linking the contexts of LOs through increasing graph communities and betweenness centrality.
Document-level relation extraction (DocRE) poses the challenge of identifying relationships between entities within a document as opposed to the traditional RE setting where a single sentence is input. Existing approaches rely on logical reasoning or contextual cues from entities. This paper reframes document-level RE as link prediction over a knowledge graph with distinct benefits: 1) Our approach combines entity context with document-derived logical reasoning, enhancing link prediction quality. 2) Predicted links between entities offer interpretability, elucidating employed reasoning. We evaluate our approach on three benchmark datasets: DocRED, ReDocRED, and DWIE. The results indicate that our proposed method outperforms the state-of-the-art models and suggests that incorporating context-based link prediction techniques can enhance the performance of document-level relation extraction models.
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.
Material science literature is a rich source of factual information about various categories of entities (like materials and compositions) and various relations between these entities, such as conductivity, voltage, etc. Automatically extracting this information to generate a material science knowledge base is a challenging task. In this paper, we propose MatSciRE (Material Science Relation Extractor), a Pointer Network-based encoder-decoder framework, to jointly extract entities and relations from material science articles as a triplet ($entity1, relation, entity2$). Specifically, we target the battery materials and identify five relations to work on - conductivity, coulombic efficiency, capacity, voltage, and energy. Our proposed approach achieved a much better F1-score (0.771) than a previous attempt using ChemDataExtractor (0.716). The overall graphical framework of MatSciRE is shown in Fig 1. The material information is extracted from material science literature in the form of entity-relation triplets using MatSciRE.
The task of Information Extraction (IE) involves automatically converting unstructured textual content into structured data. Most research in this field concentrates on extracting all facts or a specific set of relationships from documents. In this paper, we present a method for the extraction and categorisation of an unrestricted set of relationships from text. Our method relies on morpho-syntactic extraction patterns obtained by a distant supervision method, and creates Syntactic and Semantic Indices to extract and classify candidate graphs. We evaluate our approach on six datasets built on Wikidata and Wikipedia. The evaluation shows that our approach can achieve Precision scores of up to 0.85, but with lower Recall and F1 scores. Our approach allows to quickly create rule-based systems for Information Extraction and to build annotated datasets to train machine-learning and deep-learning based classifiers.
The development and integration of knowledge graphs and language models has significance in artificial intelligence and natural language processing. In this study, we introduce the BERTologyNavigator -- a two-phased system that combines relation extraction techniques and BERT embeddings to navigate the relationships within the DBLP Knowledge Graph (KG). Our approach focuses on extracting one-hop relations and labelled candidate pairs in the first phases. This is followed by employing BERT's CLS embeddings and additional heuristics for relation selection in the second phase. Our system reaches an F1 score of 0.2175 on the DBLP QuAD Final test dataset for Scholarly QALD and 0.98 F1 score on the subset of the DBLP QuAD test dataset during the QA phase.
Contextual Text Block Detection (CTBD) is the task of identifying coherent text blocks within the complexity of natural scenes. Previous methodologies have treated CTBD as either a visual relation extraction challenge within computer vision or as a sequence modeling problem from the perspective of natural language processing. We introduce a new framework that frames CTBD as a graph generation problem. This methodology consists of two essential procedures: identifying individual text units as graph nodes and discerning the sequential reading order relationships among these units as graph edges. Leveraging the cutting-edge capabilities of DQ-DETR for node detection, our framework innovates further by integrating a novel mechanism, a Dynamic Relation Transformer (DRFormer), dedicated to edge generation. DRFormer incorporates a dual interactive transformer decoder that deftly manages a dynamic graph structure refinement process. Through this iterative process, the model systematically enhances the graph's fidelity, ultimately resulting in improved precision in detecting contextual text blocks. Comprehensive experimental evaluations conducted on both SCUT-CTW-Context and ReCTS-Context datasets substantiate that our method achieves state-of-the-art results, underscoring the effectiveness and potential of our graph generation framework in advancing the field of CTBD.