The rapid expansion of medical literature presents growing challenges for structuring and integrating domain knowledge at scale. Knowledge Graphs (KGs) offer a promising solution by enabling efficient retrieval, automated reasoning, and knowledge discovery. However, current KG construction methods often rely on supervised pipelines with limited generalizability or naively aggregate outputs from Large Language Models (LLMs), treating biomedical corpora as static and ignoring the temporal dynamics and contextual uncertainty of evolving knowledge. To address these limitations, we introduce MedKGent, a LLM agent framework for constructing temporally evolving medical KGs. Leveraging over 10 million PubMed abstracts published between 1975 and 2023, we simulate the emergence of biomedical knowledge via a fine-grained daily time series. MedKGent incrementally builds the KG in a day-by-day manner using two specialized agents powered by the Qwen2.5-32B-Instruct model. The Extractor Agent identifies knowledge triples and assigns confidence scores via sampling-based estimation, which are used to filter low-confidence extractions and inform downstream processing. The Constructor Agent incrementally integrates the retained triples into a temporally evolving graph, guided by confidence scores and timestamps to reinforce recurring knowledge and resolve conflicts. The resulting KG contains 156,275 entities and 2,971,384 relational triples. Quality assessments by two SOTA LLMs and three domain experts demonstrate an accuracy approaching 90%, with strong inter-rater agreement. To evaluate downstream utility, we conduct RAG across seven medical question answering benchmarks using five leading LLMs, consistently observing significant improvements over non-augmented baselines. Case studies further demonstrate the KG's value in literature-based drug repurposing via confidence-aware causal inference.

Relational Triple Extraction (RTE) is a fundamental task in Natural Language Processing (NLP). However, prior research has primarily focused on optimizing model performance, with limited efforts to understand the internal mechanisms driving these models. Many existing methods rely on complex preprocessing to induce specific interactions, often resulting in opaque systems that may not fully align with their theoretical foundations. To address these limitations, we propose SMARTe: a Slot-based Method for Accountable Relational Triple extraction. SMARTe introduces intrinsic interpretability through a slot attention mechanism and frames the task as a set prediction problem. Slot attention consolidates relevant information into distinct slots, ensuring all predictions can be explicitly traced to learned slot representations and the tokens contributing to each predicted relational triple. While emphasizing interpretability, SMARTe achieves performance comparable to state-of-the-art models. Evaluations on the NYT and WebNLG datasets demonstrate that adding interpretability does not compromise performance. Furthermore, we conducted qualitative assessments to showcase the explanations provided by SMARTe, using attention heatmaps that map to their respective tokens. We conclude with a discussion of our findings and propose directions for future research. Our code is available at https://github.com/Chen-XueWen/SMARTe.

Link Prediction (LP) is an essential task over Knowledge Graphs (KGs), traditionally focussed on using and predicting the relations between entities. Textual entity descriptions have already been shown to be valuable, but models that incorporate numerical literals have shown minor improvements on existing benchmark datasets. It is unclear whether a model is actually better in using numerical literals, or better capable of utilizing the graph structure. This raises doubts about the effectiveness of these methods and about the suitability of the existing benchmark datasets. We propose a methodology to evaluate LP models that incorporate numerical literals. We propose i) a new synthetic dataset to better understand how well these models use numerical literals and ii) dataset ablations strategies to investigate potential difficulties with the existing datasets. We identify a prevalent trend: many models underutilize literal information and potentially rely on additional parameters for performance gains. Our investigation highlights the need for more extensive evaluations when releasing new models and datasets.

Relational triple extraction is crucial work for the automatic construction of knowledge graphs. Existing methods only construct shallow representations from a token or token pair-level. However, previous works ignore local spatial dependencies of relational triples, resulting in a weakness of entity pair boundary detection. To tackle this problem, we propose a novel Region-based Table Filling method (RTF). We devise a novel region-based tagging scheme and bi-directional decoding strategy, which regard each relational triple as a region on the relation-specific table, and identifies triples by determining two endpoints of each region. We also introduce convolution to construct region-level table representations from a spatial perspective which makes triples easier to be captured. In addition, we share partial tagging scores among different relations to improve learning efficiency of relation classifier. Experimental results show that our method achieves state-of-the-art with better generalization capability on three variants of two widely used benchmark datasets.

Named Entity Recognition and Relation Extraction are two crucial and challenging subtasks in the field of Information Extraction. Despite the successes achieved by the traditional approaches, fundamental research questions remain open. First, most recent studies use parameter sharing for a single subtask or shared features for both two subtasks, ignoring their semantic differences. Second, information interaction mainly focuses on the two subtasks, leaving the fine-grained informtion interaction among the subtask-specific features of encoding subjects, relations, and objects unexplored. Motivated by the aforementioned limitations, we propose a novel model to jointly extract entities and relations. The main novelties are as follows: (1) We propose to decouple the feature encoding process into three parts, namely encoding subjects, encoding objects, and encoding relations. Thanks to this, we are able to use fine-grained subtask-specific features. The experimental results demonstrate that our model outperforms several previous state-of-the-art models. Extensive additional experiments further confirm the effectiveness of our model. A Decoupling and Aggregating Framework for Joint Extraction of Entities and Relations Introduction Named Entity Recognition (NER) and Relation Extraction (RE), as two essential subtasks in information extraction, aim to extract entities and relations from semi-structured and unstructured texts. They are used in many downstream applications in different domains, such as knowledge graph construction [38, 39], Question-Answering [36, 37], and knowledge graph-based recommendation system [40, 41]. Most traditional models and some methods used in specialized areas [9,35,43,46] construct separate models for NER and RE to extract entities and relations in a pipelined manner. This type of method suffers from error propagation and unilateral information interaction.

The in-context learning (ICL) for relational triple extraction (RTE) has achieved promising performance, but still encounters two key challenges: (1) how to design effective prompts and (2) how to select proper demonstrations. Existing methods, however, fail to address these challenges appropriately. On the one hand, they usually recast RTE task to text-to-text prompting formats, which is unnatural and results in a mismatch between the output format at the pre-training time and the inference time for large language models (LLMs). On the other hand, they only utilize surface natural language features and lack consideration of triple semantics in sample selection. These issues are blocking improved performance in ICL for RTE, thus we aim to tackle prompt designing and sample selection challenges simultaneously. To this end, we devise a tabular prompting for RTE (\textsc{TableIE}) which frames RTE task into a table generation task to incorporate explicit structured information into ICL, facilitating conversion of outputs to RTE structures. Then we propose instructive in-context learning (I$^2$CL) which only selects and annotates a few samples considering internal triple semantics in massive unlabeled samples.

Extracting relational triples from text is a crucial task for constructing knowledge bases. Recent advancements in joint entity and relation extraction models have demonstrated remarkable F1 scores ($\ge 90\%$) in accurately extracting relational triples from free text. However, these models have been evaluated under restrictive experimental settings and unrealistic datasets. They overlook sentences with zero triples (zero-cardinality), thereby simplifying the task. In this paper, we present a benchmark study of state-of-the-art joint entity and relation extraction models under a more realistic setting. We include sentences that lack any triples in our experiments, providing a comprehensive evaluation. Our findings reveal a significant decline (approximately 10-15\% in one dataset and 6-14\% in another dataset) in the models' F1 scores within this realistic experimental setup. Furthermore, we propose a two-step modeling approach that utilizes a simple BERT-based classifier. This approach leads to overall performance improvement in these models within the realistic experimental setting.

Two distinct approaches have been proposed for relational triple extraction - pipeline and joint. Joint models, which capture interactions across triples, are the more recent development, and have been shown to outperform pipeline models for sentence-level extraction tasks. Document-level extraction is a more challenging setting where interactions across triples can be long-range, and individual triples can also span across sentences. Joint models have not been applied for document-level tasks so far. In this paper, we benchmark state-of-the-art pipeline and joint extraction models on sentence-level as well as document-level datasets. Our experiments show that while joint models outperform pipeline models significantly for sentence-level extraction, their performance drops sharply below that of pipeline models for the document-level dataset.

Joint entity and relation extraction has been a core task in the field of information extraction. Recent approaches usually consider the extraction of relational triples from a stereoscopic perspective, either learning a relation-specific tagger or separate classifiers for each relation type. However, they still suffer from error propagation, relation redundancy and lack of high-level connections between triples. To address these issues, we propose a novel query-based approach to construct instance-level representations for relational triples. By metric-based comparison between query embeddings and token embeddings, we can extract all types of triples in one step, thus eliminating the error propagation problem. In addition, we learn the instance-level representation of relational triples via contrastive learning. In this way, relational triples can not only enclose rich class-level semantics but also access to high-order global connections. Experimental results show that our proposed method achieves the state of the art on five widely used benchmarks.

Existing research studies on cross-sentence relation extraction in long-form multi-party conversations aim to improve relation extraction without considering the explainability of such methods. This work addresses that gap by focusing on extracting explanations that indicate that a relation exists while using only partially labeled data. We propose our model-agnostic framework, D-REX, a policy-guided semi-supervised algorithm that explains and ranks relations. We frame relation extraction as a re-ranking task and include relation- and entity-specific explanations as an intermediate step of the inference process. We find that about 90% of the time, human annotators prefer D-REX's explanations over a strong BERT-based joint relation extraction and explanation model. Finally, our evaluations on a dialogue relation extraction dataset show that our method is simple yet effective and achieves a state-of-the-art F1 score on relation extraction, improving upon existing methods by 13.5%.