BERT Based Clinical Knowledge Extraction for Biomedical Knowledge Graph Construction and Analysis

Background : Knowledge is evolving over time, often as a result of new discoveries or changes in the adopted methods of reasoning. Also, new facts or evidence may become available, leading to new understandings of complex phenomena. This is particularly true in the biomedical field, where scientists and physicians are constantly striving to find new methods of diagnosis, treatment and eventually cure. Knowledge Graphs (KGs) offer a real way of organizing and retrieving the massive and growing amount of biomedical knowledge. Objective : We propose an end-to-end approach for knowledge extraction and analysis from biomedical clinical notes using the Bidirectional Encoder Representations from Transformers (BERT) model and Conditional Random Field (CRF) layer. Methods : The approach is based on knowledge graphs, which can effectively process abstract biomedical concepts such as relationships and interactions between medical entities. Besides offering an intuitive way to visualize these concepts, KGs can solve more complex knowledge retrieval problems by simplifying them into simpler representations or by transforming the problems into representations from different perspectives. We created a biomedical Knowledge Graph using using Natural Language Processing models for named entity recognition and relation extraction. The generated biomedical knowledge graphs (KGs) are then used for question answering. Results : The proposed framework can successfully extract relevant structured information with high accuracy (90.7% for Named-entity recognition (NER), 88% for relation extraction (RE)), according to experimental findings based on real-world 505 patient biomedical unstructured clinical notes. Conclusions : In this paper, we propose a novel end-to-end system for the construction of a biomedical knowledge graph from clinical textual using a variation of BERT models

Ensemble Transfer Learning for Multilingual Coreference Resolution

Entity coreference resolution is an important research problem with many applications, including information extraction and question answering. Coreference resolution for English has been studied extensively. However, there is relatively little work for other languages. A problem that frequently occurs when working with a non-English language is the scarcity of annotated training data. To overcome this challenge, we design a simple but effective ensemble-based framework that combines various transfer learning (TL) techniques. We first train several models using different TL methods. Then, during inference, we compute the unweighted average scores of the models' predictions to extract the final set of predicted clusters. Furthermore, we also propose a low-cost TL method that bootstraps coreference resolution models by utilizing Wikipedia anchor texts. Leveraging the idea that the coreferential links naturally exist between anchor texts pointing to the same article, our method builds a sizeable distantly-supervised dataset for the target language that consists of tens of thousands of documents. We can pre-train a model on the pseudo-labeled dataset before finetuning it on the final target dataset. Experimental results on two benchmark datasets, OntoNotes and SemEval, confirm the effectiveness of our methods. Our best ensembles consistently outperform the baseline approach of simple training by up to 7.68% in the F1 score. These ensembles also achieve new state-of-the-art results for three languages: Arabic, Dutch, and Spanish

A Survey on Semantic Processing Techniques

Semantic processing is a fundamental research domain in computational linguistics. In the era of powerful pre-trained language models and large language models, the advancement of research in this domain appears to be decelerating. However, the study of semantics is multi-dimensional in linguistics. The research depth and breadth of computational semantic processing can be largely improved with new technologies. In this survey, we analyzed five semantic processing tasks, e.g., word sense disambiguation, anaphora resolution, named entity recognition, concept extraction, and subjectivity detection. We study relevant theoretical research in these fields, advanced methods, and downstream applications. We connect the surveyed tasks with downstream applications because this may inspire future scholars to fuse these low-level semantic processing tasks with high-level natural language processing tasks. The review of theoretical research may also inspire new tasks and technologies in the semantic processing domain. Finally, we compare the different semantic processing techniques and summarize their technical trends, application trends, and future directions.Comment: Published at Information Fusion, Volume 101, 2024, 101988, ISSN 1566-2535. The equal contribution mark is missed in the published version due to the publication policies. Please contact Prof. Erik Cambria for detail

Stress Testing BERT Anaphora Resolution Models for Reaction Extraction in Chemical Patents

The high volume of published chemical patents and the importance of a timely acquisition of their information gives rise to automating information extraction from chemical patents. Anaphora resolution is an important component of comprehensive information extraction, and is critical for extracting reactions. In chemical patents, there are five anaphoric relations of interest: co-reference, transformed, reaction associated, work up, and contained. Our goal is to investigate how the performance of anaphora resolution models for reaction texts in chemical patents differs in a noise-free and noisy environment and to what extent we can improve the robustness against noise of the model