The powerful capabilities of Large Language Models (LLMs) have led to their growing use in evaluating human-generated content, particularly in evaluating research ideas within academic settings. Existing solutions primarily rely on prompt-based LLM methods or fine-tuned lightweight language models for idea evaluation. However, these methods are often unstable and struggle to comprehend the complex semantic information embedded in the ideas, impeding their ability to perform high-quality evaluations. To address the above challenges, we propose GraphEval, a lightweight graph-based LLM framework for idea evaluation. Our insight is that a complex idea can be broken down into comprehensible viewpoint nodes using prompts from small LLMs. These viewpoint nodes can then be linked together through edges created from LLM-based relation extraction and/or BERT similarity scores. The created viewpoint-graph can be used to conveniently propagate scores across view-nodes to improve the robustness of the idea evaluations. In particular, we propose two lightweight graph-based methods for idea evaluation: (1) GraphEval-LP: a training-free label propagation algorithm that propagates evaluation scores from known view-nodes to unknown nodes; (2) GraphEval-GNN: a Graph Neural Networks (GNN) that is trained to predict the evaluation scores given the observed graph with minimal computation resources. Moreover, to overcome LLM's limitation in objectively assessing the novelty of ideas, we further propose a novelty detection model to GraphEval-GNN to enhance its capability in judging idea novelty. Experiments on two datasets show GraphEval improves F1 scores by at least 14% with low computation and API costs. Additionally, GraphEval can effectively detect plagiarized ideas.
In Biomedical Natural Language Processing (BioNLP) tasks, such as Relation Extraction, Named Entity Recognition, and Text Classification, the scarcity of high-quality data remains a significant challenge. This limitation poisons large language models to correctly understand relationships between biological entities, such as molecules and diseases, or drug interactions, and further results in potential misinterpretation of biomedical documents. To address this issue, current approaches generally adopt the Synthetic Data Augmentation method which involves similarity computation followed by word replacement, but counterfactual data are usually generated. As a result, these methods disrupt meaningful word sets or produce sentences with meanings that deviate substantially from the original context, rendering them ineffective in improving model performance. To this end, this paper proposes a biomedical-dedicated rationale-based synthetic data augmentation method. Beyond the naive lexicon similarity, specific bio-relation similarity is measured to hold the augmented instance having a strong correlation with bio-relation instead of simply increasing the diversity of augmented data. Moreover, a multi-agents-involved reflection mechanism helps the model iteratively distinguish different usage of similar entities to escape falling into the mis-replace trap. We evaluate our method on the BLURB and BigBIO benchmark, which includes 9 common datasets spanning four major BioNLP tasks. Our experimental results demonstrate consistent performance improvements across all tasks, highlighting the effectiveness of our approach in addressing the challenges associated with data scarcity and enhancing the overall performance of biomedical NLP models.
Dense retrieval models are commonly used in Information Retrieval (IR) applications, such as Retrieval-Augmented Generation (RAG). Since they often serve as the first step in these systems, their robustness is critical to avoid failures. In this work, by repurposing a relation extraction dataset (e.g. Re-DocRED), we design controlled experiments to quantify the impact of heuristic biases, such as favoring shorter documents, in retrievers like Dragon+ and Contriever. Our findings reveal significant vulnerabilities: retrievers often rely on superficial patterns like over-prioritizing document beginnings, shorter documents, repeated entities, and literal matches. Additionally, they tend to overlook whether the document contains the query's answer, lacking deep semantic understanding. Notably, when multiple biases combine, models exhibit catastrophic performance degradation, selecting the answer-containing document in less than 3% of cases over a biased document without the answer. Furthermore, we show that these biases have direct consequences for downstream applications like RAG, where retrieval-preferred documents can mislead LLMs, resulting in a 34% performance drop than not providing any documents at all.
Relation extraction (RE) is a standard information extraction task playing a major role in downstream applications such as knowledge discovery and question answering. Although decoder-only large language models are excelling in generative tasks, smaller encoder models are still the go to architecture for RE. In this paper, we revisit fine-tuning such smaller models using a novel dual-encoder architecture with a joint contrastive and cross-entropy loss. Unlike previous methods that employ a fixed linear layer for predicate representations, our approach uses a second encoder to compute instance-specific predicate representations by infusing them with real entity spans from corresponding input instances. We conducted experiments on two biomedical RE datasets and two general domain datasets. Our approach achieved F1 score improvements ranging from 1% to 2% over state-of-the-art methods with a simple but elegant formulation. Ablation studies justify the importance of various components built into the proposed architecture.
Temporal information extraction from unstructured text is essential for contextualizing events and deriving actionable insights, particularly in the medical domain. We address the task of extracting clinical events and their temporal relations using the well-studied I2B2 2012 Temporal Relations Challenge corpus. This task is inherently challenging due to complex clinical language, long documents, and sparse annotations. We introduce GRAPHTREX, a novel method integrating span-based entity-relation extraction, clinical large pre-trained language models (LPLMs), and Heterogeneous Graph Transformers (HGT) to capture local and global dependencies. Our HGT component facilitates information propagation across the document through innovative global landmarks that bridge distant entities. Our method improves the state-of-the-art with 5.5% improvement in the tempeval $F_1$ score over the previous best and up to 8.9% improvement on long-range relations, which presents a formidable challenge. This work not only advances temporal information extraction but also lays the groundwork for improved diagnostic and prognostic models through enhanced temporal reasoning.
Assertion status detection is a critical yet often overlooked component of clinical NLP, essential for accurately attributing extracted medical facts. Past studies have narrowly focused on negation detection, leading to underperforming commercial solutions such as AWS Medical Comprehend, Azure AI Text Analytics, and GPT-4o due to their limited domain adaptation. To address this gap, we developed state-of-the-art assertion detection models, including fine-tuned LLMs, transformer-based classifiers, few-shot classifiers, and deep learning (DL) approaches. We evaluated these models against cloud-based commercial API solutions, the legacy rule-based NegEx approach, and GPT-4o. Our fine-tuned LLM achieves the highest overall accuracy (0.962), outperforming GPT-4o (0.901) and commercial APIs by a notable margin, particularly excelling in Present (+4.2%), Absent (+8.4%), and Hypothetical (+23.4%) assertions. Our DL-based models surpass commercial solutions in Conditional (+5.3%) and Associated-with-Someone-Else (+10.1%) categories, while the few-shot classifier offers a lightweight yet highly competitive alternative (0.929), making it ideal for resource-constrained environments. Integrated within Spark NLP, our models consistently outperform black-box commercial solutions while enabling scalable inference and seamless integration with medical NER, Relation Extraction, and Terminology Resolution. These results reinforce the importance of domain-adapted, transparent, and customizable clinical NLP solutions over general-purpose LLMs and proprietary APIs.
Document-level relation extraction (DocRE) is the process of identifying and extracting relations between entities that span multiple sentences within a document. Due to its realistic settings, DocRE has garnered increasing research attention in recent years. Previous research has mostly focused on developing sophisticated encoding models to better capture the intricate patterns between entity pairs. While these advancements are undoubtedly crucial, an even more foundational challenge lies in the data itself. The complexity inherent in DocRE makes the labeling process prone to errors, compounded by the extreme sparsity of positive relation samples, which is driven by both the limited availability of positive instances and the broad diversity of positive relation types. These factors can lead to biased optimization processes, further complicating the task of accurate relation extraction. Recognizing these challenges, we have developed a robust framework called \textit{\textbf{COMM}} to better solve DocRE. \textit{\textbf{COMM}} operates by initially employing an instance-aware reasoning method to dynamically capture pertinent information of entity pairs within the document and extract relational features. Following this, \textit{\textbf{COMM}} takes into account the distribution of relations and the difficulty of samples to dynamically adjust the margins between prediction logits and the decision threshold, a process we call Concentrated Margin Maximization. In this way, \textit{\textbf{COMM}} not only enhances the extraction of relevant relational features but also boosts DocRE performance by addressing the specific challenges posed by the data. Extensive experiments and analysis demonstrate the versatility and effectiveness of \textit{\textbf{COMM}}, especially its robustness when trained on low-quality data (achieves \textgreater 10\% performance gains).
Previous work on clinical relation extraction from free-text sentences leveraged information about semantic types from clinical knowledge bases as a part of entity representations. In this paper, we exploit additional evidence by also making use of domain-specific semantic type dependencies. We encode the relation between a span of tokens matching a Unified Medical Language System (UMLS) concept and other tokens in the sentence. We implement our method and compare against different named entity recognition (NER) architectures (i.e., BiLSTM-CRF and BiLSTM-GCN-CRF) using different pre-trained clinical embeddings (i.e., BERT, BioBERT, UMLSBert). Our experimental results on clinical datasets show that in some cases NER effectiveness can be significantly improved by making use of domain-specific semantic type dependencies. Our work is also the first study generating a matrix encoding to make use of more than three dependencies in one pass for the NER task.
We conduct an empirical analysis of neural network architectures and data transfer strategies for causal relation extraction. By conducting experiments with various contextual embedding layers and architectural components, we show that a relatively straightforward BioBERT-BiGRU relation extraction model generalizes better than other architectures across varying web-based sources and annotation strategies. Furthermore, we introduce a metric for evaluating transfer performance, $F1_{phrase}$ that emphasizes noun phrase localization rather than directly matching target tags. Using this metric, we can conduct data transfer experiments, ultimately revealing that augmentation with data with varying domains and annotation styles can improve performance. Data augmentation is especially beneficial when an adequate proportion of implicitly and explicitly causal sentences are included.
Extracting causal relationships from a medical case report is essential for comprehending the case, particularly its diagnostic process. Since the diagnostic process is regarded as a bottom-up inference, causal relationships in cases naturally form a multi-layered tree structure. The existing tasks, such as medical relation extraction, are insufficient for capturing the causal relationships of an entire case, as they treat all relations equally without considering the hierarchical structure inherent in the diagnostic process. Thus, we propose a novel task, Causal Tree Extraction (CTE), which receives a case report and generates a causal tree with the primary disease as the root, providing an intuitive understanding of a case's diagnostic process. Subsequently, we construct a Japanese case report CTE dataset, J-Casemap, propose a generation-based CTE method that outperforms the baseline by 20.2 points in the human evaluation, and introduce evaluation metrics that reflect clinician preferences. Further experiments also show that J-Casemap enhances the performance of solving other medical tasks, such as question answering.
In this article, we present the BTransformer18 model, a deep learning architecture designed for multi-label relation extraction in French texts. Our approach combines the contextual representation capabilities of pre-trained language models from the BERT family - such as BERT, RoBERTa, and their French counterparts CamemBERT and FlauBERT - with the power of Transformer encoders to capture long-term dependencies between tokens. Experiments conducted on the dataset from the TextMine'25 challenge show that our model achieves superior performance, particularly when using CamemBERT-Large, with a macro F1 score of 0.654, surpassing the results obtained with FlauBERT-Large. These results demonstrate the effectiveness of our approach for the automatic extraction of complex relations in intelligence reports.
Typically, Few-shot Continual Relation Extraction (FCRE) models must balance retaining prior knowledge while adapting to new tasks with extremely limited data. However, real-world scenarios may also involve unseen or undetermined relations that existing methods still struggle to handle. To address these challenges, we propose a novel approach that leverages the Open Information Extraction concept of Knowledge Graph Construction (KGC). Our method not only exposes models to all possible pairs of relations, including determined and undetermined labels not available in the training set, but also enriches model knowledge with diverse relation descriptions, thereby enhancing knowledge retention and adaptability in this challenging scenario. In the perspective of KGC, this is the first work explored in the setting of Continual Learning, allowing efficient expansion of the graph as the data evolves. Experimental results demonstrate our superior performance compared to other state-of-the-art FCRE baselines, as well as the efficiency in handling dynamic graph construction in this setting.
Objective: To optimize in-context learning in biomedical natural language processing by improving example selection. Methods: We introduce a novel multi-mode retrieval-augmented generation (MMRAG) framework, which integrates four retrieval strategies: (1) Random Mode, selecting examples arbitrarily; (2) Top Mode, retrieving the most relevant examples based on similarity; (3) Diversity Mode, ensuring variation in selected examples; and (4) Class Mode, selecting category-representative examples. This study evaluates MMRAG on three core biomedical NLP tasks: Named Entity Recognition (NER), Relation Extraction (RE), and Text Classification (TC). The datasets used include BC2GM for gene and protein mention recognition (NER), DDI for drug-drug interaction extraction (RE), GIT for general biomedical information extraction (RE), and HealthAdvice for health-related text classification (TC). The framework is tested with two large language models (Llama2-7B, Llama3-8B) and three retrievers (Contriever, MedCPT, BGE-Large) to assess performance across different retrieval strategies. Results: The results from the Random mode indicate that providing more examples in the prompt improves the model's generation performance. Meanwhile, Top mode and Diversity mode significantly outperform Random mode on the RE (DDI) task, achieving an F1 score of 0.9669, a 26.4% improvement. Among the three retrievers tested, Contriever outperformed the other two in a greater number of experiments. Additionally, Llama 2 and Llama 3 demonstrated varying capabilities across different tasks, with Llama 3 showing a clear advantage in handling NER tasks. Conclusion: MMRAG effectively enhances biomedical in-context learning by refining example selection, mitigating data scarcity issues, and demonstrating superior adaptability for NLP-driven healthcare applications.
Universal Information Extraction (UIE) has garnered significant attention due to its ability to address model explosion problems effectively. Extractive UIE can achieve strong performance using a relatively small model, making it widely adopted. Extractive UIEs generally rely on task instructions for different tasks, including single-target instructions and multiple-target instructions. Single-target instruction UIE enables the extraction of only one type of relation at a time, limiting its ability to model correlations between relations and thus restricting its capability to extract complex relations. While multiple-target instruction UIE allows for the extraction of multiple relations simultaneously, the inclusion of irrelevant relations introduces decision complexity and impacts extraction accuracy. Therefore, for multi-relation extraction, we propose LDNet, which incorporates multi-aspect relation modeling and a label drop mechanism. By assigning different relations to different levels for understanding and decision-making, we reduce decision confusion. Additionally, the label drop mechanism effectively mitigates the impact of irrelevant relations. Experiments show that LDNet outperforms or achieves competitive performance with state-of-the-art systems on 9 tasks, 33 datasets, in both single-modal and multi-modal, few-shot and zero-shot settings.\footnote{https://github.com/Lu-Yang666/LDNet}
Temporal relation extraction (TRE) is a fundamental task in natural language processing (NLP) that involves identifying the temporal relationships between events in a document. Despite the advances in large language models (LLMs), their application to TRE remains limited. Most existing approaches rely on pairwise classification, where event pairs are classified in isolation, leading to computational inefficiency and a lack of global consistency in the resulting temporal graph. In this work, we propose a novel zero-shot method for TRE that generates a document's complete temporal graph in a single step, followed by temporal constraint optimization to refine predictions and enforce temporal consistency across relations. Additionally, we introduce OmniTemp, a new dataset with complete annotations for all pairs of targeted events within a document. Through experiments and analyses, we demonstrate that our method outperforms existing zero-shot approaches and offers a competitive alternative to supervised TRE models.
Current research highlights the great potential of Large Language Models (LLMs) for constructing Scholarly Knowledge Graphs (SKGs). One particularly complex step in this process is relation extraction, aimed at identifying suitable properties to describe the content of research. This study builds directly on previous research of three Open Research Knowledge Graph (ORKG) team members who assessed the readiness of LLMs such as GPT-3.5, Llama 2, and Mistral for property extraction in scientific literature. Given the moderate performance observed, the previous work concluded that fine-tuning is needed to improve these models' alignment with scientific tasks and their emulation of human expertise. Expanding on this prior experiment, this study evaluates the impact of advanced prompt engineering techniques and demonstrates that these techniques can highly significantly enhance the results. Additionally, this study extends the property extraction process to include property matching to existing ORKG properties, which are retrieved via the API. The evaluation reveals that results generated through advanced prompt engineering achieve a higher proportion of matches with ORKG properties, further emphasizing the enhanced alignment achieved. Moreover, this lays the groundwork for addressing challenges such as the inconsistency of ORKG properties, an issue highlighted in prior studies. By assigning unique URIs and using standardized terminology, this work increases the consistency of the properties, fulfilling a crucial aspect of Linked Data and FAIR principles - core commitments of ORKG. This, in turn, significantly enhances the applicability of ORKG content for subsequent tasks such as comparisons of research publications. Finally, the study concludes with recommendations for future improvements in the overall property extraction process.
Joint entity-relation extraction is a critical task in transforming unstructured or semi-structured text into triplets, facilitating the construction of large-scale knowledge graphs, and supporting various downstream applications. Despite its importance, research on Chinese text, particularly with complex semantics in specialized domains like medicine, remains limited. To address this gap, we introduce the CH-DDI, a Chinese drug-drug interactions dataset designed to capture the intricacies of medical text. Leveraging the strengths of attention mechanisms in capturing long-range dependencies, we propose the SEA module, which enhances the extraction of complex contextual semantic information, thereby improving entity recognition and relation extraction. Additionally, to address the inefficiencies of existing methods in facilitating information exchange between entity recognition and relation extraction, we present an interactive fusion representation module. This module employs Cross Attention for bidirectional information exchange between the tasks and further refines feature extraction through BiLSTM. Experimental results on both our CH-DDI dataset and public CoNLL04 dataset demonstrate that our model exhibits strong generalization capabilities. On the CH-DDI dataset, our model achieves an F1-score of 96.73% for entity recognition and 78.43% for relation extraction. On the CoNLL04 dataset, it attains an entity recognition precision of 89.54% and a relation extraction accuracy of 71.64%.
Maintaining comprehensive and up-to-date knowledge graphs (KGs) is critical for modern AI systems, but manual curation struggles to scale with the rapid growth of scientific literature. This paper presents KARMA, a novel framework employing multi-agent large language models (LLMs) to automate KG enrichment through structured analysis of unstructured text. Our approach employs nine collaborative agents, spanning entity discovery, relation extraction, schema alignment, and conflict resolution that iteratively parse documents, verify extracted knowledge, and integrate it into existing graph structures while adhering to domain-specific schema. Experiments on 1,200 PubMed articles from three different domains demonstrate the effectiveness of KARMA in knowledge graph enrichment, with the identification of up to 38,230 new entities while achieving 83.1\% LLM-verified correctness and reducing conflict edges by 18.6\% through multi-layer assessments.
Extracting event relations that deviate from known schemas has proven challenging for previous methods based on multi-class classification, MASK prediction, or prototype matching. Recent advancements in large language models have shown impressive performance through instruction tuning. Nevertheless, in the task of event relation extraction, instruction-based methods face several challenges: there are a vast number of inference samples, and the relations between events are non-sequential. To tackle these challenges, we present an improved instruction-based event relation extraction framework named MAQInstruct. Firstly, we transform the task from extracting event relations using given event-event instructions to selecting events using given event-relation instructions, which reduces the number of samples required for inference. Then, by incorporating a bipartite matching loss, we reduce the dependency of the instruction-based method on the generation sequence. Our experimental results demonstrate that MAQInstruct significantly improves the performance of event relation extraction across multiple LLMs.
In this work, we reimagine classical probing to evaluate knowledge transfer from simple source to more complex target tasks. Instead of probing frozen representations from a complex source task on diverse simple target probing tasks (as usually done in probing), we explore the effectiveness of embeddings from multiple simple source tasks on a single target task. We select coreference resolution, a linguistically complex problem requiring contextual understanding, as focus target task, and test the usefulness of embeddings from comparably simpler tasks tasks such as paraphrase detection, named entity recognition, and relation extraction. Through systematic experiments, we evaluate the impact of individual and combined task embeddings. Our findings reveal that task embeddings vary significantly in utility for coreference resolution, with semantic similarity tasks (e.g., paraphrase detection) proving most beneficial. Additionally, representations from intermediate layers of fine-tuned models often outperform those from final layers. Combining embeddings from multiple tasks consistently improves performance, with attention-based aggregation yielding substantial gains. These insights shed light on relationships between task-specific representations and their adaptability to complex downstream tasks, encouraging further exploration of embedding-level task transfer.