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Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested.Database URL: http://www.biocreative.org

The introduction of pre-trained language models in natural language processing (NLP) based on deep learning and the availability of electronic health records (EHRs) presents a great opportunity to transfer the “knowledge” learned from data in the general domain to enable the analysis of unstructured textual data in clinical domains. This study explored the feasibility of applying NLP to a small EHR dataset to investigate the power of transfer learning to facilitate the process of patient screening in psychiatry. A total of 500 patients were randomly selected from a medical center database. Three annotators with clinical experience reviewed the notes to make diagnoses for major/minor depression, bipolar disorder, schizophrenia, and dementia to form a small and highly imbalanced corpus. Several state-of-the-art NLP methods based on deep learning along with pre-trained models based on shallow or deep transfer learning were adapted to develop models to classify the aforementioned diseases. We hypothesized that the models that rely on transferred knowledge would be expected to outperform the models learned from scratch. The experimental results demonstrated that the models with the pre-trained techniques outperformed the models without transferred knowledge by micro-avg. and macro-avg. F-scores of 0.11 and 0.28, respectively. Our results also suggested that the use of the feature dependency strategy to build multi-labeling models instead of problem transformation is superior considering its higher performance and simplicity in the training process.

Objective An adverse drug event (ADE) refers to an injury resulting from medical intervention related to a drug including harm caused by drugs or from the usage of drugs. Extracting ADEs from clinical records can help physicians associate adverse events to targeted drugs. Materials and Methods We proposed a cascading architecture to recognize medical concepts including ADEs, drug names, and entities related to drugs. The architecture includes a preprocessing method and an ensemble of conditional random fields (CRFs) and neural network–based models to respectively address the challenges of surrogate string and overlapping annotation boundaries observed in the employed ADEs and medication extraction (ADME) corpus. The effectiveness of applying different pretrained and postprocessed word embeddings for the ADME task was also studied. Results The empirical results showed that both CRFs and neural network–based models provide promising solution for the ADME task. The neural network–based models particularly outperformed CRFs in concept types involving narrative descriptions. Our best run achieved an overall micro F-score of 0.919 on the employed corpus. Our results also suggested that the Global Vectors for word representation embedding in general domain provides a very strong baseline, which can be further improved by applying the principal component analysis to generate more isotropic vectors. Conclusions We have demonstrated that the proposed cascading architecture can handle the problem of overlapped annotations and further improve the overall recall and F-scores because the architecture enables the developed models to exploit more context information and forms an ensemble for creating a stronger recognizer.

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Electronic health records (EHRs) at medical institutions provide valuable sources for research in both clinical and biomedical domains. However, before such records can be used for research purposes, protected health information (PHI) mentioned in the unstructured text must be removed. In Taiwan’s EHR systems the unstructured EHR texts are usually represented in the mixing of English and Chinese languages, which brings challenges for de-identification. This paper presented the first study, to the best of our knowledge, of the construction of a code-mixed EHR de-identification corpus and the evaluation of different mature entity recognition methods applied for the code-mixed PHI recognition task.

Code-mixing is a phenomenon when at least two languages combined in a hybrid way in the context of a single conversation. The use of mixed language is widespread in multilingual and multicultural countries and poses significant challenges for the development of automated language processing tools. In Taiwan's electronic health record (EHR) systems, the unstructured EHR texts are usually represented in the mixing of English and Chinese languages resulting in the difficulty for de-identification and synthetization of protected health information (PHI). We explored this problem by applied several state-of-the-art pretrained mono-and multilingual language models and proposed to apply the principle-based approach (PBA) for the tasks of PHI recognition and resynthesis on a code-mixed EHR corpus, which was annotated with 6 main categories and 25 subcategories of PHIs. In PBA, a hierarchical principle slot schema is defined to encode knowledge of code-mixed PHIs and the defined slots were learned from the training set to assemble into principles for recognizing PHI mentions and synthesizing surrogates at the same time. A semantic disambiguation process is developed used to disambiguate ambiguous PHI categories in the de-identification process and to dynamically extend the knowledge encoded in PBA during the knowledge augmentation process. The experimental results demonstrate that the proposed method can achieve the best micro-and macro-F-scores performance in comparison with the other mono-and multilingual language models finetuned on our code-mixed corpus.