Neural negated entity recognition in Spanish electronic health records

This work deals with negation detection in the context of clinical texts. Negation detection is a key for decision support systems since negated events (detection of absence of some events) help ascertain current medical conditions. For artificial intelligence, negation detection is a valuable point as it can revert the meaning of a part of a text and, accordingly, influence other tasks such as medical dosage adjustment, the detection of adverse drug reactions or hospital acquired diseases. We focus on negated medical events such as disorders, findings and allergies. From Natural Language Processing (NLP) background, we refer to them as negated medical entities. A novelty of this work is that we approached this task as Named Entity Recognition (NER) with the restriction that just negated medical entities must be recognized (in an attempt to help distinguish them from non-negated ones). Our study is driven with Electronic Health Records (EHRs) written in Spanish. A challenge to cope with is the lexical variability (alternative medical forms, abbreviations, etc.). To this end, we employed an approach based on deep learning. Specifically, the system combines character embeddings to cope with out-of-vocabulary (OOV) words, Long Short-Term Memory (LSTM) networks to model contextual representations and it makes use of Conditional Random Fields (CRF) to classify each medical entity as either negated or not given the contextual dense representation. Moreover, we explored both embeddings created from words and embeddings created from lemmas. The best results were obtained with the lemmatized embeddings. Apparently, this approach reinforced the capability of the LSTMs to cope with the high lexical variability. The f-measure for exact-match was 65.1 and 82.4 for the partial-match.

Smoothing dense spaces for improved relation extraction between drugs and adverse reactions

BACKGROUND AND OBJECTIVE

This work aims at extracting Adverse Drug Reactions (ADRs), i.e. a harm directly caused by a drug at normal doses, from Electronic Health Records (EHRs). The lack of readily available EHRs because of confidentiality issues and their lexical variability make the ADR extraction challenging. Furthermore, ADRs are rare events. Therefore, efficient representations against data sparsity are needed.

METHODS

Embedding-based characterizations are able to group semantically related words. However, dense spaces suffer from data sparsity. We employed context-aware continuous representations to enhance the modelling of infrequent events through their context and we turned to simple smoothing techniques to increase the proximity between similar words (e.g. direction cosines, truncation, Principal Component Analysis (PCA) and clustering) in an attempt to cope with data sparsity.

RESULTS

An F-measure of 0.639 for the ADR classification was achieved, obtaining an improvement of approximately 0.300 in comparison with the results obtained by a word-based characterization.

CONCLUSION

The embbeding-based representation together with the smoothing techniques increased the robustness of the ADR characterization. It was proven particularly appropriate to cope with lexical variability and data sparsity.

The class imbalance problem detecting adverse drug reactions in electronic health records

This work focuses on adverse drug reaction extraction tackling the class imbalance problem. Adverse drug reactions are infrequent events in electronic health records, nevertheless, it is compulsory to get them documented. Text mining techniques can help to retrieve this kind of valuable information from text. The class imbalance was tackled using different sampling methods, cost-sensitive learning, ensemble learning and one-class classification and the Random Forest classifier was used. The adverse drug reaction extraction model was inferred from a dataset that comprises real electronic health records with an imbalance ratio of 1:222, this means that for each drug–disease pair that is an adverse drug reaction, there are approximately 222 that are not adverse drug reactions. The application of a sampling technique before using cost-sensitive learning offered the best result. On the test set, the f-measure was 0.121 for the minority class and 0.996 for the majority class.