The disease coding task involves assigning a unique identifier from a controlled vocabulary to each disease mentioned in a clinical document. This task is relevant since it allows information extraction from unstructured data to perform, for example, epidemiological studies about the incidence and prevalence of diseases in a determined context. However, the manual coding process is subject to errors as it requires medical personnel to be competent in coding rules and terminology. In addition, this process consumes a lot of time and energy, which could be allocated to more clinically relevant tasks. These difficulties can be addressed by developing computational systems that automatically assign codes to diseases. In this way, we propose a two-step system for automatically coding diseases in referrals from the Chilean public healthcare system. Specifically, our model uses a state-of-the-art NER model for recognizing disease mentions and a search engine system based on Elasticsearch for assigning the most relevant codes associated with these disease mentions. The system’s performance was evaluated on referrals manually coded by clinical experts. Our system obtained a MAP score of 0.63 for the subcategory level and 0.83 for the category level, close to the best-performing models in the literature. This system could be a support tool for health professionals, optimizing the coding and management process. Finally, to guarantee reproducibility, we publicly release the code of our models and experiments.

Word embeddings have been widely used in Natural Language Processing (NLP) tasks. Although these representations can capture the semantic information of words, they cannot learn the sequence-level semantics. This problem can be handled using contextual word embeddings derived from pre-trained language models, which have contributed to significant improvements in several NLP tasks. Further improvements are achieved when pre-training these models on domain-specific corpora. In this paper, we introduce Clinical Flair, a domain-specific language model trained on Spanish clinical narratives. To validate the quality of the contextual representations retrieved from our model, we tested them on four named entity recognition datasets belonging to the clinical and biomedical domains. Our experiments confirm that incorporating domain-specific embeddings into classical sequence labeling architectures improves model performance dramatically compared to general-domain embeddings, demonstrating the importance of having these resources available.

Nested Named Entity Recognition (NER) is an information extraction task that aims to identify entities that may be nested within other entity mentions. Despite the availability of several corpora with nested entities in the Spanish clinical domain, most previous work has overlooked them due to the lack of models and a clear annotation scheme for dealing with the task. To fill this gap, this paper provides an empirical study of straightforward methods for tackling the nested NER task on two Spanish clinical datasets, Clinical Trials, and the Chilean Waiting List. We assess the advantages and limitations of two sequence labeling approaches; one based on Multiple LSTM-CRF architectures and another on Joint labeling models. To better understand the differences between these models, we compute task-specific metrics that adequately measure the ability of models to detect nested entities and perform a fine-grained comparison across models. Our experimental results show that employing domain-specific language models trained from scratch significantly improves the performance obtained with strong domain-specific and general-domain baselines, achieving state-of-the-art results in both datasets. Specifically, we obtained F1 scores of 89.21 and 83.16 in Clinical Trials and the Chilean Waiting List, respectively. Interestingly enough, we observe that the task-specific metrics and analysis properly reflect the limitations of the models when recognizing nested entities. Finally, we perform a case study on an aggregated NER dataset created from several clinical corpora in Spanish. We highlight how entity length and the simultaneous recognition of inner and outer entities are the most critical variables for the nested NER task.

Clinical coding is the task of transforming medical documents into structured codes following a standard ontology. Since these terminologies are composed of hundreds of codes, this problem can be considered an Extreme Multi-label Classification task. This paper proposes a novel neural network-based architecture for clinical coding. First, we take full advantage of the hierarchical nature of ontologies to create clusters based on semantic relations. Then, we use a Matcher module to assign the probability of documents belonging to each cluster. Finally, the Ranker calculates the probability of each code considering only the documents in the cluster. This division allows a fine-grained differentiation within the cluster, which cannot be addressed using a single classifier. In addition, since most of the previous work has focused on solving this task in English, we conducted our experiments on three clinical coding corpora in Spanish. The experimental results demonstrate the effectiveness of our model, achieving state-of-the-art results on two of the three datasets. Specifically, we outperformed previous models on two subtasks of the CodiEsp shared task: CodiEsp-D (diseases) and CodiEsp-P (procedures). Automatic coding can profoundly impact healthcare by structuring critical information written in free text in electronic health records.

Using language models created from large data sources has improved the performance of several deep learning-based architectures, obtaining state-of-the-art results in several NLP extrinsic tasks. However, little research is related to creating intrinsic tests that allow us to compare the quality of different language models when obtaining contextualized embeddings. This gap increases even more when working on specific domains in languages other than English. This paper proposes a novel graph-based intrinsic test that allows us to measure the quality of different language models in clinical and biomedical domains in Spanish. Our results show that our intrinsic test performs better for clinical and biomedical language models than a general one. Also, it correlates with better outcomes for a NER task using a probing model over contextualized embeddings. We hope our work will help the clinical NLP research community to evaluate and compare new language models in other languages and find the most suitable models for solving downstream tasks.

Named Entity Recognition (NER) is an important task in Natural Language Processing that aims to identify text spans belonging to predefined categories. Traditional NER systems ignore nested entities, which are entities contained in other entity mentions. Although several methods have been proposed to address this case, most of them rely on complex task-specific structures and ignore potentially useful baselines for the task. We argue that this creates an overly optimistic impression of their performance. This paper revisits the Multiple LSTM-CRF (MLC) model, a simple, overlooked, yet powerful approach based on training independent sequence labeling models for each entity type. Extensive experiments with three nested NER corpora show that, regardless of the simplicity of this model, its performance is better or at least as well as more sophisticated methods. Furthermore, we show that the MLC architecture achieves state-of-the-art results in the Chilean Waiting List corpus by including pre-trained language models. In addition, we implemented an open-source library that computes task-specific metrics for nested NER. The results suggest that metrics used in previous work do not measure well the ability of a model to detect nested entities, while our metrics provide new evidence on how existing approaches handle the task.

This paper describes our approaches used to solve the SocialDisNER task, which belongs to the Social Media Mining for Health Applications (SMM4H) shared task. This task aims to identify disease mentions in tweets written in Spanish. The proposed model is an architecture based on the FLERT approach. It consists of fine-tuning a language model that creates an input representation of a sentence based on its neighboring sentences, thus obtaining the document-level context. The best result was obtained using an ensemble of six language models using the FLERT approach. The system achieved an F1 score of 0.862, significantly surpassing the average performance among competitor models of 0.680 on the test partition.

In this work we describe the Waiting List Corpus consisting of de-identified referrals for several specialty consultations from the waiting list in Chilean public hospitals. A subset of 900 referrals was manually annotated with 9,029 entities, 385 attributes, and 284 pairs of relations with clinical relevance. A trained medical doctor annotated these referrals, and then together with other three researchers, consolidated each of the annotations. The annotated corpus has nested entities, with 32.2% of entities embedded in other entities. We use this annotated corpus to obtain preliminary results for Named Entity Recognition (NER). The best results were achieved by using a biLSTM-CRF architecture using word embeddings trained over Spanish Wikipedia together with clinical embeddings computed by the group. NER models applied to this corpus can leverage statistics of diseases and pending procedures within this waiting list. This work constitutes the first annotated corpus using clinical narratives from Chile, and one of the few for the Spanish language. The annotated corpus, the clinical word embeddings, and the annotation guidelines are freely released to the research community.