Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification, often fail to capture complex concepts not explicitly stated in the text. To overcome this limitation, we introduce MA-COIR, a framework that reformulates concept recognition as an indexing-recognition task. By assigning semantic search indexes (ssIDs) to concepts, MA-COIR resolves ambiguities in ontology entries and enhances recognition efficiency. Using a pretrained BART-based model fine-tuned on small datasets, our approach reduces computational requirements to facilitate adoption by domain experts. Furthermore, we incorporate large language models (LLMs)-generated queries and synthetic data to improve recognition in low-resource settings. Experimental results on three scenarios (CDR, HPO, and HOIP) highlight the effectiveness of MA-COIR in recognizing both explicit and implicit concepts without the need for mention-level annotations during inference, advancing ontology-driven concept recognition in biomedical domain applications. Our code and constructed data are available at https://github.com/sl-633/macoir-master.

Phenotype concept recognition (CR) is a fundamental task in biomedical text mining, enabling applications such as clinical diagnostics and knowledge graph construction. However, existing methods often require ontology-specific training and struggle to generalize across diverse text types and evolving biomedical terminology. We present AutoPCR, a prompt-based phenotype CR method that does not require ontology-specific training. AutoPCR performs CR in three stages: entity extraction using a hybrid of rule-based and neural tagging strategies, candidate retrieval via SapBERT, and entity linking through prompting a large language model. Experiments on four benchmark datasets show that AutoPCR achieves the best average and most robust performance across both mention-level and document-level evaluations, surpassing prior state-of-the-art methods. Further ablation and transfer studies demonstrate its inductive capability and generalizability to new ontologies.

Prior research in representation engineering has revealed that LLMs encode concepts within their representation spaces, predominantly centered around English. In this study, we extend this philosophy to a multilingual scenario, delving into multilingual human value concepts in LLMs. Through our comprehensive exploration covering 7 types of human values, 16 languages and 3 LLM series with distinct multilinguality, we empirically substantiate the existence of multilingual human values in LLMs. Further cross-lingual analysis on these concepts discloses 3 traits arising from language resource disparities: cross-lingual inconsistency, distorted linguistic relationships, and unidirectional cross-lingual transfer between high- and low-resource languages, all in terms of human value concepts. Additionally, we validate the feasibility of cross-lingual control over value alignment capabilities of LLMs, leveraging the dominant language as a source language. Drawing from our findings on multilingual value alignment, we prudently provide suggestions on the composition of multilingual data for LLMs pre-training: including a limited number of dominant languages for cross-lingual alignment transfer while avoiding their excessive prevalence, and keeping a balanced distribution of non-dominant languages. We aspire that our findings would contribute to enhancing the safety and utility of multilingual AI.

Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. Materials and Methods: The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. Results: Our results show that, with an appropriate setup, these models can achieve state of the art performance. The best run, using few-shot learning, achieved 0.58 macro F1 score on publication abstracts and 0.75 macro F1 score on clinical observations, the former being comparable with the state of the art, while the latter surpassing the current best in class tool. Conclusion: While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.

We hypothesize that large language models (LLMs) based on the transformer architecture can enable automated detection of clinical phenotype terms, including terms not documented in the HPO. In this study, we developed two types of models: PhenoBCBERT, a BERT-based model, utilizing Bio+Clinical BERT as its pre-trained model, and PhenoGPT, a GPT-based model that can be initialized from diverse GPT models, including open-source versions such as GPT-J, Falcon, and LLaMA, as well as closed-source versions such as GPT-3 and GPT-3.5. We compared our methods with PhenoTagger, a recently developed HPO recognition tool that combines rule-based and deep learning methods. We found that our methods can extract more phenotype concepts, including novel ones not characterized by HPO. We also performed case studies on biomedical literature to illustrate how new phenotype information can be recognized and extracted. We compared current BERT-based versus GPT-based models for phenotype tagging, in multiple aspects including model architecture, memory usage, speed, accuracy, and privacy protection. We also discussed the addition of a negation step and an HPO normalization layer to the transformer models for improved HPO term tagging. In conclusion, PhenoBCBERT and PhenoGPT enable the automated discovery of phenotype terms from clinical notes and biomedical literature, facilitating automated downstream tasks to derive new biological insights on human diseases.

We build a common-knowledge concept recognition system for a Systems Engineer's Virtual Assistant (SEVA) which can be used for downstream tasks such as relation extraction, knowledge graph construction, and question-answering. The problem is formulated as a token classification task similar to named entity extraction. With the help of a domain expert and text processing methods, we construct a dataset annotated at the word-level by carefully defining a labelling scheme to train a sequence model to recognize systems engineering concepts. We use a pre-trained language model and fine-tune it with the labeled dataset of concepts. In addition, we also create some essential datasets for information such as abbreviations and definitions from the systems engineering domain. Finally, we construct a simple knowledge graph using these extracted concepts along with some hyponym relations.

Background: Automatic recognition of medical concepts in unstructured text is an important component of many clinical and research applications, and its accuracy has a large impact on electronic health record analysis. The mining of medical concepts is complicated by the broad use of synonyms and nonstandard terms in medical documents. Objective: We present a machine learning model for concept recognition in large unstructured text, which optimizes the use of ontological structures and can identify previously unobserved synonyms for concepts in the ontology. Methods: We present a neural dictionary model that can be used to predict if a phrase is synonymous to a concept in a reference ontology. Our model, called the Neural Concept Recognizer (NCR), uses a convolutional neural network to encode input phrases and then rank medical concepts based on the similarity in that space.

With rapid growth of medical informatics technology, a large number of electronic health records (EHRs) have been available in recent years, including a huge mass of data, such as clinical narratives. They have been being used not only to support computerized clinical systems (e.g., computerized clinical decision support systems [1][2]), but also to help the development of clinical and translational research [3]. One of the challenges to use them is that much information is embedded in clinical notes, but cannot be directly accessible for computerized clinical systems which rely on structured information. Therefore, natural language processing (NLP) technologies, which can extract structured information from narrative text, have received great attention in medical domain [4], and many clinical NLP systems have been developed for different applications [5]. Clinical concept recognition (CCR) as a fundamental task of clinical NLP has also attracted great attention, and a large number of systems have been developed to recognize clinical concepts from various types of clinical notes in last two decades.