Recent advances in Swedish and Spanish medical entity recognition in clinical texts using deep neural approaches

Named entity recognition for de-identifying Spanish electronic health records

BACKGROUND AND OBJECTIVES

There is an increasing and renewed interest in Electronic Health Records (EHRs) as a substantial information source for clinical decision making. Consequently, automatic de-identification of EHRs is an indispensable task, since their dissociation from personal data is a necessary prerequisite for their dissemination. Nevertheless, the bulk of prior research in this domain has been conducted using English EHRs, given the limited availability of annotated corpora in other languages, including Spanish.

METHODS

In this study, the automatic de-identification of medical documents in Spanish was explored. A private corpus comprising 599 genuine clinical cases was annotated with eight different categories of protected health information. The prediction problem was approached as a named entity recognition task and two deep learning-based methodologies were developed. The first strategy was based on recurrent neural networks (RNN) and the second, an end-to-end approach, was based on Transformers. In addition, we have implemented a procedure to expand the amount of texts employed for model training.

RESULTS

Our findings demonstrate that Transformers surpass RNNs in the de-identification of clinical data in Spanish. Particularly noteworthy is the excellent performance of the XLM-RoBERTa large Transformer, achieving a rigorous strict-match micro-average of 0.946 for precision, 0.954 for recall, and an F1 score of 0.95 when applied to the amplified version of the corpus. Furthermore, a web-based application has been created to assist specialized clinicians in de-identifying EHRs through the aid of the implemented models.

CONCLUSION

The study's conclusions showcase the practical applicability of the state-of-the-art Transformers models for precise de-identification of clinical notes in real-world medical settings in Spanish, with the potential to improve performance if continual pre-training strategies are implemented.

Named Entity Recognition in Electronic Health Records: A Methodological Review

OBJECTIVES

A substantial portion of the data contained in Electronic Health Records (EHR) is unstructured, often appearing as free text. This format restricts its potential utility in clinical decision-making. Named entity recognition (NER) methods address the challenge of extracting pertinent information from unstructured text. The aim of this study was to outline the current NER methods and trace their evolution from 2011 to 2022.

METHODS

We conducted a methodological literature review of NER methods, with a focus on distinguishing the classification models, the types of tagging systems, and the languages employed in various corpora.

RESULTS

Several methods have been documented for automatically extracting relevant information from EHRs using natural language processing techniques such as NER and relation extraction (RE). These methods can automatically extract concepts, events, attributes, and other data, as well as the relationships between them. Most NER studies conducted thus far have utilized corpora in English or Chinese. Additionally, the bidirectional encoder representation from transformers using the BIO tagging system architecture is the most frequently reported classification scheme. We discovered a limited number of papers on the implementation of NER or RE tasks in EHRs within a specific clinical domain.

CONCLUSIONS

EHRs play a pivotal role in gathering clinical information and could serve as the primary source for automated clinical decision support systems. However, the creation of new corpora from EHRs in specific clinical domains is essential to facilitate the swift development of NER and RE models applied to EHRs for use in clinical practice.

Advances in monolingual and crosslingual automatic disability annotation in Spanish

BACKGROUND

Unlike diseases, automatic recognition of disabilities has not received the same attention in the area of medical NLP. Progress in this direction is hampered by obstacles like the lack of annotated corpus. Neural architectures learn to translate sequences from spontaneous representations into their corresponding standard representations given a set of samples. The aim of this paper is to present the last advances in monolingual (Spanish) and crosslingual (from English to Spanish and vice versa) automatic disability annotation. The task consists of identifying disability mentions in medical texts written in Spanish within a collection of abstracts from journal papers related to the biomedical domain.

RESULTS

In order to carry out the task, we have combined deep learning models that use different embedding granularities for sequence to sequence tagging with a simple acronym and abbreviation detection module to boost the coverage.

CONCLUSIONS

Our monolingual experiments demonstrate that a good combination of different word embedding representations provide better results than single representations, significantly outperforming the state of the art in disability annotation in Spanish. Additionally, we have experimented crosslingual transfer (zero-shot) for disability annotation between English and Spanish with interesting results that might help overcoming the data scarcity bottleneck, specially significant for the disabilities.

A Survey on Recent Named Entity Recognition and Relationship Extraction Techniques on Clinical Texts

Significant growth in Electronic Health Records (EHR) over the last decade has provided an abundance of clinical text that is mostly unstructured and untapped. This huge amount of clinical text data has motivated the development of new information extraction and text mining techniques. Named Entity Recognition (NER) and Relationship Extraction (RE) are key components of information extraction tasks in the clinical domain. In this paper, we highlight the present status of clinical NER and RE techniques in detail by discussing the existing proposed NLP models for the two tasks and their performances and discuss the current challenges. Our comprehensive survey on clinical NER and RE encompass current challenges, state-of-the-art practices, and future directions in information extraction from clinical text. This is the first attempt to discuss both of these interrelated topics together in the clinical context. We identified many research articles published based on different approaches and looked at applications of these tasks. We also discuss the evaluation metrics that are used in the literature to measure the effectiveness of the two these NLP methods and future research directions.

Automated Coding of Under-Studied Medical Concept Domains: Linking Physical Activity Reports to the International Classification of Functioning, Disability, and Health

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts, such as functional outcomes and social determinants of health, lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of medical information in under-studied domains, and demonstrate its applicability through a case study on physical mobility function. Mobility function is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is represented as one domain of human activity in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in the medical informatics literature, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility status to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro-averaged F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This research has implications for continued development of language technologies to analyze functional status information, and the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

Using machine learning for predicting cervical cancer from Swedish electronic health records by mining hierarchical representations

Electronic health records (EHRs) contain rich documentation regarding disease symptoms and progression, but EHR data is challenging to use for diagnosis prediction due to its high dimensionality, relative scarcity, and substantial level of noise. We investigated how to best represent EHR data for predicting cervical cancer, a serious disease where early detection is beneficial for the outcome of treatment. A case group of 1321 patients with cervical cancer were matched to ten times as many controls, and for both groups several types of events were extracted from their EHRs. These events included clinical codes, lab results, and contents of free text notes retrieved using a LSTM neural network. Clinical events are described with great variation in EHR texts, leading to a very large feature space. Therefore, an event hierarchy inferred from the textual events was created to represent the clinical texts. Overall, the events extracted from free text notes contributed the most to the final prediction, and the hierarchy of textual events further improved performance. Four classifiers were evaluated for predicting a future cancer diagnosis where Random Forest achieved the best results with an AUC of 0.70 from a year before diagnosis up to 0.97 one day before diagnosis. We conclude that our approach is sound and had excellent discrimination at diagnosis, but only modest discrimination capacity before this point. Since our study objective was earlier disease prediction than such, we propose further work should consider extending patient histories through e.g. the integration of primary health records preceding referral to hospital.