Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, proteins, diseases, and chemicals. The vast growth of biomedical literature poses significant challenges updating the network knowledge. The recent Biomedical Relation Extraction Dataset (BioRED) provides valuable manual annotations, facilitating the develop-ment of machine-learning and pre-trained language model approaches for automatically identifying novel document-level (inter-sentence context) relationships. Nonetheless, its annotations lack directionality (subject/object) for the entity roles, essential for studying complex biological networks. Herein we annotate the entity roles of the relationships in the BioRED corpus and subsequently propose a novel multi-task language model with soft-prompt learning to jointly identify the relationship, novel findings, and entity roles. Our results in-clude an enriched BioRED corpus with 10,864 directionality annotations. Moreover, our proposed method outperforms existing large language models such as the state-of-the-art GPT-4 and Llama-3 on two benchmarking tasks. Our source code and dataset are available at https://github.com/ncbi-nlp/BioREDirect.
Cyber Threat Intelligence (CTI) is critical for mitigating threats to organizations, governments, and institutions, yet the necessary data are often dispersed across diverse formats. AI-driven solutions for CTI Information Extraction (IE) typically depend on high-quality, annotated data, which are not always available. This paper introduces 0-CTI, a scalable AI-based framework designed for efficient CTI Information Extraction. Leveraging advanced Natural Language Processing (NLP) techniques, particularly Transformer-based architectures, the proposed system processes complete text sequences of CTI reports to extract a cyber ontology of named entities and their relationships. Our contribution is the development of 0-CTI, the first modular framework for CTI Information Extraction that supports both supervised and zero-shot learning. Unlike existing state-of-the-art models that rely heavily on annotated datasets, our system enables fully dataless operation through zero-shot methods for both Entity and Relation Extraction, making it adaptable to various data availability scenarios. Additionally, our supervised Entity Extractor surpasses current state-of-the-art performance in cyber Entity Extraction, highlighting the dual strength of the framework in both low-resource and data-rich environments. By aligning the system's outputs with the Structured Threat Information Expression (STIX) format, a standard for information exchange in the cybersecurity domain, 0-CTI standardizes extracted knowledge, enhancing communication and collaboration in cybersecurity operations.
Document-Level Biomedical Relation Extraction (Bio-RE) aims to identify relations between biomedical entities within extensive texts, serving as a crucial subfield of biomedical text mining. Existing Bio-RE methods struggle with cross-sentence inference, which is essential for capturing relations spanning multiple sentences. Moreover, previous methods often overlook the incompleteness of documents and lack the integration of external knowledge, limiting contextual richness. Besides, the scarcity of annotated data further hampers model training. Recent advancements in large language models (LLMs) have inspired us to explore all the above issues for document-level Bio-RE. Specifically, we propose a document-level Bio-RE framework via LLM Adaptive Document-Relation Cross-Mapping (ADRCM) Fine-Tuning and Concept Unique Identifier (CUI) Retrieval-Augmented Generation (RAG). First, we introduce the Iteration-of-REsummary (IoRs) prompt for solving the data scarcity issue. In this way, Bio-RE task-specific synthetic data can be generated by guiding ChatGPT to focus on entity relations and iteratively refining synthetic data. Next, we propose ADRCM fine-tuning, a novel fine-tuning recipe that establishes mappings across different documents and relations, enhancing the model's contextual understanding and cross-sentence inference capabilities. Finally, during the inference, a biomedical-specific RAG approach, named CUI RAG, is designed to leverage CUIs as indexes for entities, narrowing the retrieval scope and enriching the relevant document contexts. Experiments conducted on three Bio-RE datasets (GDA, CDR, and BioRED) demonstrate the state-of-the-art performance of our proposed method by comparing it with other related works.
Generative relation extraction (RE) commonly involves first reformulating RE as a linguistic modeling problem easily tackled with pre-trained language models (PLM) and then fine-tuning a PLM with supervised cross-entropy loss. Although having achieved promising performance, existing approaches assume only one deterministic relation between each pair of entities without considering real scenarios where multiple relations may be valid, i.e., entity pair overlap, causing their limited applications. To address this problem, we introduce a novel contrastive prompt tuning method for RE, CPTuning, which learns to associate a candidate relation between two in-context entities with a probability mass above or below a threshold, corresponding to whether the relation exists. Beyond learning schema, CPTuning also organizes RE as a verbalized relation generation task and uses Trie-constrained decoding to ensure a model generates valid relations. It adaptively picks out the generated candidate relations with a high estimated likelihood in inference, thereby achieving multi-relation extraction. We conduct extensive experiments on four widely used datasets to validate our method. Results show that T5-large fine-tuned with CPTuning significantly outperforms previous methods, regardless of single or multiple relations extraction.
We introduce GLiREL (Generalist Lightweight model for zero-shot Relation Extraction), an efficient architecture and training paradigm for zero-shot relation classification. Inspired by recent advancements in zero-shot named entity recognition, this work presents an approach to efficiently and accurately predict zero-shot relationship labels between multiple entities in a single forward pass. Experiments using the FewRel and WikiZSL benchmarks demonstrate that our approach achieves state-of-the-art results on the zero-shot relation classification task. In addition, we contribute a protocol for synthetically-generating datasets with diverse relation labels.
Benchmarks are crucial for evaluating machine learning algorithm performance, facilitating comparison and identifying superior solutions. However, biases within datasets can lead models to learn shortcut patterns, resulting in inaccurate assessments and hindering real-world applicability. This paper addresses the issue of entity bias in relation extraction tasks, where models tend to rely on entity mentions rather than context. We propose a debiased relation extraction benchmark DREB that breaks the pseudo-correlation between entity mentions and relation types through entity replacement. DREB utilizes Bias Evaluator and PPL Evaluator to ensure low bias and high naturalness, providing a reliable and accurate assessment of model generalization in entity bias scenarios. To establish a new baseline on DREB, we introduce MixDebias, a debiasing method combining data-level and model training-level techniques. MixDebias effectively improves model performance on DREB while maintaining performance on the original dataset. Extensive experiments demonstrate the effectiveness and robustness of MixDebias compared to existing methods, highlighting its potential for improving the generalization ability of relation extraction models. We will release DREB and MixDebias publicly.
Document-level relation extraction (Doc-RE) aims to extract relations between entities across multiple sentences. Therefore, Doc-RE requires more comprehensive reasoning abilities like humans, involving complex cross-sentence interactions between entities, contexts, and external general knowledge, compared to the sentence-level RE. However, most existing Doc-RE methods focus on optimizing single reasoning ability, but lack the ability to utilize external knowledge for comprehensive reasoning on long documents. To solve these problems, a knowledge retrieval augmented method, named KnowRA, was proposed with comprehensive reasoning to autonomously determine whether to accept external knowledge to assist DocRE. Firstly, we constructed a document graph for semantic encoding and integrated the co-reference resolution model to augment the co-reference reasoning ability. Then, we expanded the document graph into a document knowledge graph by retrieving the external knowledge base for common-sense reasoning and a novel knowledge filtration method was presented to filter out irrelevant knowledge. Finally, we proposed the axis attention mechanism to build direct and indirect associations with intermediary entities for achieving cross-sentence logical reasoning. Extensive experiments conducted on two datasets verified the effectiveness of our method compared to the state-of-the-art baselines. Our code is available at https://anonymous.4open.science/r/KnowRA.
Existing datasets for relation classification and extraction often exhibit limitations such as restricted relation types and domain-specific biases. This work presents a generic framework to generate well-structured sentences from given tuples with the help of Large Language Models (LLMs). This study has focused on the following major questions: (i) how to generate sentences from relation tuples, (ii) how to compare and rank them, (iii) can we combine strengths of individual methods and amalgamate them to generate an even bette quality of sentences, and (iv) how to evaluate the final dataset? For the first question, we employ a multifaceted 5-stage pipeline approach, leveraging LLMs in conjunction with template-guided generation. We introduce Sentence Evaluation Index(SEI) that prioritizes factors like grammatical correctness, fluency, human-aligned sentiment, accuracy, and complexity to answer the first part of the second question. To answer the second part of the second question, this work introduces a SEI-Ranker module that leverages SEI to select top candidate generations. The top sentences are then strategically amalgamated to produce the final, high-quality sentence. Finally, we evaluate our dataset on LLM-based and SOTA baselines for relation classification. The proposed dataset features 255 relation types, with 15K sentences in the test set and around 150k in the train set organized in, significantly enhancing relational diversity and complexity. This work not only presents a new comprehensive benchmark dataset for RE/RC task, but also compare different LLMs for generation of quality sentences from relational tuples.
This paper proposes a novel approach to develop an open-domain and long-form Over-The-Top (OTT) Question-Answering (QA) dataset, DragonVerseQA, specifically oriented to the fantasy universe of "House of the Dragon" and "Game Of Thrones" TV series. Most existing QA datasets focus on short, fact-based answers sourced almost solely from Wikipedia articles, devoid of depth and contextual richness for sophisticated narrative understanding. We curate a dataset that combines full episode summaries sourced from HBO and fandom wiki websites, user reviews from sources like IMDb and Rotten Tomatoes, and high-quality, open-domain, legally admissible sources, and structured data from repositories like WikiData into one dataset. The dataset provides a multi-dimensional context, reflecting complex character dynamics and plot developments from these varied sources. That means, on equal footing, only after heavy data preprocessing and filtering methods will meaningful, non-spam unbiased reviews be available in this enriched dataset. The comprehensive insights are given through the long-form answers generated from this enriched context. This is what makes this valuable dataset for improving conversational AI, narrative analysis, sentiment analysis, summarization techniques, and relation extraction. A comparative analysis with state-of-the-art QA datasets such as SQuAD 2.0, TriviaQA, and Natural Questions brings to light the unique advantages of our dataset in terms of contextual complexity and answer length. Detailed reviews add layers to audience sentiment and narrative interpretation, raising the bar for domain-specific QA with a new quality benchmark. Our work also allows a deeper understanding of entertainment-industry content and opens the door to more knowledgeable and creative AI-driven interactions within digital media environments.
Integrating Large Language Models (LLMs) in healthcare diagnosis demands systematic frameworks that can handle complex medical scenarios while maintaining specialized expertise. We present KG4Diagnosis, a novel hierarchical multi-agent framework that combines LLMs with automated knowledge graph construction, encompassing 362 common diseases across medical specialties. Our framework mirrors real-world medical systems through a two-tier architecture: a general practitioner (GP) agent for initial assessment and triage, coordinating with specialized agents for in-depth diagnosis in specific domains. The core innovation lies in our end-to-end knowledge graph generation methodology, incorporating: (1) semantic-driven entity and relation extraction optimized for medical terminology, (2) multi-dimensional decision relationship reconstruction from unstructured medical texts, and (3) human-guided reasoning for knowledge expansion. KG4Diagnosis serves as an extensible foundation for specialized medical diagnosis systems, with capabilities to incorporate new diseases and medical knowledge. The framework's modular design enables seamless integration of domain-specific enhancements, making it valuable for developing targeted medical diagnosis systems. We provide architectural guidelines and protocols to facilitate adoption across medical contexts.
Document-level Relation Extraction (DocRE) aims to identify relationships between entity pairs within a document. However, most existing methods assume a uniform label distribution, resulting in suboptimal performance on real-world, imbalanced datasets. To tackle this challenge, we propose a novel data augmentation approach using generative models to enhance data from the embedding space. Our method leverages the Variational Autoencoder (VAE) architecture to capture all relation-wise distributions formed by entity pair representations and augment data for underrepresented relations. To better capture the multi-label nature of DocRE, we parameterize the VAE's latent space with a Diffusion Model. Additionally, we introduce a hierarchical training framework to integrate the proposed VAE-based augmentation module into DocRE systems. Experiments on two benchmark datasets demonstrate that our method outperforms state-of-the-art models, effectively addressing the long-tail distribution problem in DocRE.
The rise of chronic diseases and pandemics like COVID-19 has emphasized the need for effective patient data processing while ensuring privacy through anonymization and de-identification of protected health information (PHI). Anonymized data facilitates research without compromising patient confidentiality. This paper introduces expert small AI models developed using the LLM-in-the-loop methodology to meet the demand for domain-specific de-identification NER models. These models overcome the privacy risks associated with large language models (LLMs) used via APIs by eliminating the need to transmit or store sensitive data. More importantly, they consistently outperform LLMs in de-identification tasks, offering superior performance and reliability. Our de-identification NER models, developed in eight languages (English, German, Italian, French, Romanian, Turkish, Spanish, and Arabic) achieved f1-micro score averages of 0.966, 0.975, 0.976, 0.970, 0.964, 0.974, 0.978, and 0.953 respectively. These results establish them as the most accurate healthcare anonymization solutions, surpassing existing small models and even general-purpose LLMs such as GPT-4o. While Part-1 of this series introduced the LLM-in-the-loop methodology for bio-medical document translation, this second paper showcases its success in developing cost-effective expert small NER models in de-identification tasks. Our findings lay the groundwork for future healthcare AI innovations, including biomedical entity and relation extraction, demonstrating the value of specialized models for domain-specific challenges.
Section identification is an important task for library science, especially knowledge management. Identifying the sections of a paper would help filter noise in entity and relation extraction. In this research, we studied the paper section identification problem in the context of Chinese medical literature analysis, where the subjects, methods, and results are more valuable from a physician's perspective. Based on previous studies on English literature section identification, we experiment with the effective features to use with classic machine learning algorithms to tackle the problem. It is found that Conditional Random Fields, which consider sentence interdependency, is more effective in combining different feature sets, such as bag-of-words, part-of-speech, and headings, for Chinese literature section identification. Moreover, we find that classic machine learning algorithms are more effective than generic deep learning models for this problem. Based on these observations, we design a novel deep learning model, the Structural Bidirectional Long Short-Term Memory (SLSTM) model, which models word and sentence interdependency together with the contextual information. Experiments on a human-curated asthma literature dataset show that our approach outperforms the traditional machine learning methods and other deep learning methods and achieves close to 90% precision and recall in the task. The model shows good potential for use in other text mining tasks. The research has significant methodological and practical implications.
Information extraction from the scientific literature is one of the main techniques to transform unstructured knowledge hidden in the text into structured data which can then be used for decision-making in down-stream tasks. One such area is Trust in AI, where factors contributing to human trust in artificial intelligence applications are studied. The relationships of these factors with human trust in such applications are complex. We hence explore this space from the lens of information extraction where, with the input of domain experts, we carefully design annotation guidelines, create the first annotated English dataset in this domain, investigate an LLM-guided annotation, and benchmark it with state-of-the-art methods using large language models in named entity and relation extraction. Our results indicate that this problem requires supervised learning which may not be currently feasible with prompt-based LLMs.
To efficiently select optimal dataset combinations for enhancing multi-task learning (MTL) performance in large language models, we proposed a novel framework that leverages a neural network to predict the best dataset combinations. The framework iteratively refines the selection, greatly improving efficiency, while being model-, dataset-, and domain-independent. Through experiments on 12 biomedical datasets across four tasks - named entity recognition, relation extraction, event extraction, and text classification-we demonstrate that our approach effectively identifies better combinations, even for tasks that may seem unpromising from a human perspective. This verifies that our framework provides a promising solution for maximizing MTL potential.
The delivery of appropriate targeted therapies to cancer patients requires the complete analysis of the molecular profiling of tumors and the patient's clinical characteristics in the context of existing knowledge and recent findings described in biomedical literature and several other sources. We evaluated the potential contributions of specific natural language processing solutions to support knowledge discovery from biomedical literature. Two models from the Bidirectional Encoder Representations from Transformers (BERT) family, two Large Language Models, and PubTator 3.0 were tested for their ability to support the named entity recognition (NER) and the relation extraction (RE) tasks. PubTator 3.0 and the BioBERT model performed best in the NER task (best F1-score equal to 0.93 and 0.89, respectively), while BioBERT outperformed all other solutions in the RE task (best F1-score 0.79) and a specific use case it was applied to by recognizing nearly all entity mentions and most of the relations.
To address catastrophic forgetting in Continual Relation Extraction (CRE), many current approaches rely on memory buffers to rehearse previously learned knowledge while acquiring new tasks. Recently, prompt-based methods have emerged as potent alternatives to rehearsal-based strategies, demonstrating strong empirical performance. However, upon analyzing existing prompt-based approaches for CRE, we identified several critical limitations, such as inaccurate prompt selection, inadequate mechanisms for mitigating forgetting in shared parameters, and suboptimal handling of cross-task and within-task variances. To overcome these challenges, we draw inspiration from the relationship between prefix-tuning and mixture of experts, proposing a novel approach that employs a prompt pool for each task, capturing variations within each task while enhancing cross-task variances. Furthermore, we incorporate a generative model to consolidate prior knowledge within shared parameters, eliminating the need for explicit data storage. Extensive experiments validate the efficacy of our approach, demonstrating superior performance over state-of-the-art prompt-based and rehearsal-free methods in continual relation extraction.
Despite the rapid progress that existing automated feedback methods have made in correcting the output of large language models (LLMs), these methods cannot be well applied to the relation extraction (RE) task due to their designated feedback objectives and correction manner. To address this problem, we propose a novel automated feedback framework for RE, which presents a rationale supervisor to verify the rationale and provides re-selected demonstrations as feedback to correct the initial prediction. Specifically, we first design a causal intervention and observation method to collect biased/unbiased rationales for contrastive training the rationale supervisor. Then, we present a verification-feedback-correction procedure to iteratively enhance LLMs' capability of handling the RE task. Extensive experiments prove that our proposed framework significantly outperforms existing methods.
Objective: This paper aims to prompt large language models (LLMs) for clinical temporal relation extraction (CTRE) in both few-shot and fully supervised settings. Materials and Methods: This study utilizes four LLMs: Encoder-based GatorTron-Base (345M)/Large (8.9B); Decoder-based LLaMA3-8B/MeLLaMA-13B. We developed full (FFT) and parameter-efficient (PEFT) fine-tuning strategies and evaluated these strategies on the 2012 i2b2 CTRE task. We explored four fine-tuning strategies for GatorTron-Base: (1) Standard Fine-Tuning, (2) Hard-Prompting with Unfrozen LLMs, (3) Soft-Prompting with Frozen LLMs, and (4) Low-Rank Adaptation (LoRA) with Frozen LLMs. For GatorTron-Large, we assessed two PEFT strategies-Soft-Prompting and LoRA with Frozen LLMs-leveraging Quantization techniques. Additionally, LLaMA3-8B and MeLLaMA-13B employed two PEFT strategies: LoRA strategy with Quantization (QLoRA) applied to Frozen LLMs using instruction tuning and standard fine-tuning. Results: Under fully supervised settings, Hard-Prompting with Unfrozen GatorTron-Base achieved the highest F1 score (89.54%), surpassing the SOTA model (85.70%) by 3.74%. Additionally, two variants of QLoRA adapted to GatorTron-Large and Standard Fine-Tuning of GatorTron-Base exceeded the SOTA model by 2.36%, 1.88%, and 0.25%, respectively. Decoder-based models with frozen parameters outperformed their Encoder-based counterparts in this setting; however, the trend reversed in few-shot scenarios. Discussions and Conclusions: This study presented new methods that significantly improved CTRE performance, benefiting downstream tasks reliant on CTRE systems. The findings underscore the importance of selecting appropriate models and fine-tuning strategies based on task requirements and data availability. Future work will explore larger models and broader CTRE applications.
Multimodal information extraction (IE) tasks have attracted increasing attention because many studies have shown that multimodal information benefits text information extraction. However, existing multimodal IE datasets mainly focus on sentence-level image-facilitated IE in English text, and pay little attention to video-based multimodal IE and fine-grained visual grounding. Therefore, in order to promote the development of multimodal IE, we constructed a multimodal multilingual multitask dataset, named M$^{3}$D, which has the following features: (1) It contains paired document-level text and video to enrich multimodal information; (2) It supports two widely-used languages, namely English and Chinese; (3) It includes more multimodal IE tasks such as entity recognition, entity chain extraction, relation extraction and visual grounding. In addition, our dataset introduces an unexplored theme, i.e., biography, enriching the domains of multimodal IE resources. To establish a benchmark for our dataset, we propose an innovative hierarchical multimodal IE model. This model effectively leverages and integrates multimodal information through a Denoised Feature Fusion Module (DFFM). Furthermore, in non-ideal scenarios, modal information is often incomplete. Thus, we designed a Missing Modality Construction Module (MMCM) to alleviate the issues caused by missing modalities. Our model achieved an average performance of 53.80% and 53.77% on four tasks in English and Chinese datasets, respectively, which set a reasonable standard for subsequent research. In addition, we conducted more analytical experiments to verify the effectiveness of our proposed module. We believe that our work can promote the development of the field of multimodal IE.