Generative pre-trained transformer (GPT) models have shown promise in clinical entity and relation extraction tasks because of their precise extraction and contextual understanding capability. In this work, we further leverage the Unified Medical Language System (UMLS) knowledge base to accurately identify medical concepts and improve clinical entity and relation extraction at the document level. Our framework selects UMLS concepts relevant to the text and combines them with prompts to guide language models in extracting entities. Our experiments demonstrate that this initial concept mapping and the inclusion of these mapped concepts in the prompts improves extraction results compared to few-shot extraction tasks on generic language models that do not leverage UMLS. Further, our results show that this approach is more effective than the standard Retrieval Augmented Generation (RAG) technique, where retrieved data is compared with prompt embeddings to generate results. Overall, we find that integrating UMLS concepts with GPT models significantly improves entity and relation identification, outperforming the baseline and RAG models. By combining the precise concept mapping capability of knowledge-based approaches like UMLS with the contextual understanding capability of GPT, our method highlights the potential of these approaches in specialized domains like healthcare.

Antonyms vs synonyms distinction is a core challenge in lexico-semantic analysis and automated lexical resource construction. These pairs share a similar distributional context which makes it harder to distinguish them. Leading research in this regard attempts to capture the properties of the relation pairs, i.e., symmetry, transitivity, and trans-transitivity. However, the inability of existing research to appropriately model the relation-specific properties limits their end performance. In this paper, we propose InterlaCed Encoder NETworks (i.e., ICE-NET) for antonym vs synonym distinction, that aim to capture and model the relation-specific properties of the antonyms and synonyms pairs in order to perform the classification task in a performance-enhanced manner. Experimental evaluation using the benchmark datasets shows that ICE-NET outperforms the existing research by a relative score of upto 1.8% in F1-measure. We release the codes for ICE-NET at https://github.com/asif6827/ICENET.

Biomedical relation extraction (RE) is the task of automatically identifying and characterizing relations between biomedical concepts from free text. RE is a central task in biomedical natural language processing (NLP) research and plays a critical role in many downstream applications, such as literature-based discovery and knowledge graph construction. State-of-the-art methods were used primarily to train machine learning models on individual RE datasets, such as protein-protein interaction and chemical-induced disease relation. Manual dataset annotation, however, is highly expensive and time-consuming, as it requires domain knowledge. Existing RE datasets are usually domain-specific or small, which limits the development of generalized and high-performing RE models. In this work, we present a novel framework for systematically addressing the data heterogeneity of individual datasets and combining them into a large dataset. Based on the framework and dataset, we report on BioREx, a data-centric approach for extracting relations. Our evaluation shows that BioREx achieves significantly higher performance than the benchmark system trained on the individual dataset, setting a new SOTA from 74.4% to 79.6% in F-1 measure on the recently released BioRED corpus. We further demonstrate that the combined dataset can improve performance for five different RE tasks. In addition, we show that on average BioREx compares favorably to current best-performing methods such as transfer learning and multi-task learning. Finally, we demonstrate BioREx's robustness and generalizability in two independent RE tasks not previously seen in training data: drug-drug N-ary combination and document-level gene-disease RE. The integrated dataset and optimized method have been packaged as a stand-alone tool available at https://github.com/ncbi/BioREx.

Analogical reasoning is a fundamental cognitive ability of humans. However, current language models (LMs) still struggle to achieve human-like performance in analogical reasoning tasks due to a lack of resources for model training. In this work, we address this gap by proposing ANALOGYKB, a million-scale analogy knowledge base (KB) derived from existing knowledge graphs (KGs). ANALOGYKB identifies two types of analogies from the KGs: 1) analogies of the same relations, which can be directly extracted from the KGs, and 2) analogies of analogous relations, which are identified with a selection and filtering pipeline enabled by large LMs (InstructGPT), followed by minor human efforts for data quality control. Evaluations on a series of datasets of two analogical reasoning tasks (analogy recognition and generation) demonstrate that ANALOGYKB successfully enables LMs to achieve much better results than previous state-of-the-art methods.

Argumentation is a type of discourse where speakers try to persuade their audience about the reasonableness of a claim by presenting supportive arguments. Most work in argument mining has focused on modeling arguments in monologues. We propose a computational model for argument mining in online persuasive discussion forums that brings together the micro-level (argument as product) and macro-level (argument as process) models of argumentation. Fundamentally, this approach relies on identifying relations between components of arguments in a discussion thread. Our approach for relation prediction uses contextual information in terms of fine-tuning a pre-trained language model and leveraging discourse relations based on Rhetorical Structure Theory. We additionally propose a candidate selection method to automatically predict what parts of one's argument will be targeted by other participants in the discussion. Our models obtain significant improvements compared to recent state-of-the-art approaches using pointer networks and a pre-trained language model.