Modelling patient trajectories using multimodal information.

BACKGROUND: Electronic Health Records (EHRs) aggregate diverse information at the patient level, holding a trajectory representative of the evolution of the patient health status throughout time. Although this information provides context and can be leveraged by physicians to monitor patient health and make more accurate prognoses/diagnoses, patient records can contain information from very long time spans, which combined with the rapid generation rate of medical data makes clinical decision making more complex. Patient trajectory modelling can assist by exploring existing information in a scalable manner, and can contribute in augmenting health care quality by fostering preventive medicine practices (e.g. earlier disease diagnosis). METHODS: We propose a solution to model patient trajectories that combines different types of information (e.g. clinical text, standard codes) and considers the temporal aspect of clinical data. This solution leverages two different architectures: one supporting flexible sets of input features, to convert patient admissions into dense representations; and a second exploring extracted admission representations in a recurrent-based architecture, where patient trajectories are processed in sub-sequences using a sliding window mechanism. RESULTS: The developed solution was evaluated on two different clinical outcomes, unexpected patient readmission and disease progression, using the publicly available Medical Information Mart for Intensive Care (MIMIC)-III clinical database. The results obtained demonstrate the potential of the first architecture to model readmission and diagnoses prediction using single patient admissions. While information from clinical text did not show the discriminative power observed in other existing works, this may be explained by the need to fine-tune the clinicalBERT model. Finally, we demonstrate the potential of the sequence-based architecture using a sliding window mechanism to represent the input data, attaining comparable performances to other existing solutions. CONCLUSION: Herein, we explored DL-based techniques to model patient trajectories and propose two flexible architectures that explore patient admissions on an individual and sequence basis. The combination of clinical text with other types of information led to positive results, which can be further improved by including a fine-tuned version of clinicalBERT in the architectures. The proposed solution can be publicly accessed at https://github.com/bioinformatics-ua/PatientTM.

A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases.

BACKGROUND: The content of the clinical notes that have been continuously collected along patients' health history has the potential to provide relevant information about treatments and diseases, and to increase the value of structured data available in Electronic Health Records (EHR) databases. EHR databases are currently being used in observational studies which lead to important findings in medical and biomedical sciences. However, the information present in clinical notes is not being used in those studies, since the computational analysis of this unstructured data is much complex in comparison to structured data. METHODS: We propose a two-stage workflow for solving an existing gap in Extraction, Transformation and Loading (ETL) procedures regarding observational databases. The first stage of the workflow extracts prescriptions present in patient's clinical notes, while the second stage harmonises the extracted information into their standard definition and stores the resulting information in a common database schema used in observational studies. RESULTS: We validated this methodology using two distinct data sets, in which the goal was to extract and store drug related information in a new Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) database. We analysed the performance of the used annotator as well as its limitations. Finally, we described some practical examples of how users can explore these datasets once migrated to OMOP CDM databases. CONCLUSION: With this methodology, we were able to show a strategy for using the information extracted from the clinical notes in business intelligence tools, or for other applications such as data exploration through the use of SQL queries. Besides, the extracted information complements the data present in OMOP CDM databases which was not directly available in the EHR database.

A Recommender System to Help Refining Clinical Research Studies.

The process of refining the research question in a medical study depends greatly on the current background of the investigated subject. The information found in prior works can directly impact several stages of the study, namely the cohort definition stage. Besides previous published methods, researchers could also leverage on other materials, such as the output of cohort selection tools, to enrich and to accelerate their own work. However, this kind of information is not always captured by search engines. In this paper, we present a methodology, based on a combination of content-based retrieval and text annotation techniques, to identify relevant scientific publications related to a research question and to the selected data sources.

Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach.

BACKGROUND: Electronic health records store large amounts of patient clinical data. Despite efforts to structure patient data, clinical notes containing rich patient information remain stored as free text, greatly limiting its exploitation. This includes family history, which is highly relevant for applications such as diagnosis and prognosis. OBJECTIVE: This study aims to develop automatic strategies for annotating family history information in clinical notes, focusing not only on the extraction of relevant entities such as family members and disease mentions but also on the extraction of relations between the identified entities. METHODS: This study extends a previous contribution for the 2019 track on family history extraction from national natural language processing clinical challenges by improving a previously developed rule-based engine, using deep learning (DL) approaches for the extraction of entities from clinical notes, and combining both approaches in a hybrid end-to-end system capable of successfully extracting family member and observation entities and the relations between those entities. Furthermore, this study analyzes the impact of factors such as the use of external resources and different types of embeddings in the performance of DL models. RESULTS: The approaches developed were evaluated in a first task regarding entity extraction and in a second task concerning relation extraction. The proposed DL approach improved observation extraction, obtaining F1 scores of 0.8688 and 0.7907 in the training and test sets, respectively. However, DL approaches have limitations in the extraction of family members. The rule-based engine was adjusted to have higher generalizing capability and achieved family member extraction F1 scores of 0.8823 and 0.8092 in the training and test sets, respectively. The resulting hybrid system obtained F1 scores of 0.8743 and 0.7979 in the training and test sets, respectively. For the second task, the original evaluator was adjusted to perform a more exact evaluation than the original one, and the hybrid system obtained F1 scores of 0.6480 and 0.5082 in the training and test sets, respectively. CONCLUSIONS: We evaluated the impact of several factors on the performance of DL models, and we present an end-to-end system for extracting family history information from clinical notes, which can help in the structuring and reuse of this type of information. The final hybrid solution is provided in a publicly available code repository.

Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics.

Electronic health records contain valuable information on patients' clinical history in the form of free text. Manually analyzing millions of these documents is unfeasible and automatic natural language processing methods are essential for efficiently exploiting these data. Within this, normalization of clinical entities, where the aim is to link entity mentions to reference vocabularies, is of utmost importance to successfully extract knowledge from clinical narratives. In this paper we present sieve-based models combined with heuristics and word embeddings and present results of our participation in the 2019 n2c2 (National NLP Clinical Challenges) shared-task on clinical concept normalization.

SCREEN-DR: Collaborative platform for diabetic retinopathy.

BACKGROUND AND OBJECTIVE: Diabetic retinopathy (DR) is the most prevalent microvascular complication of diabetes mellitus and can lead to irreversible visual loss. Screening programs, based on retinal imaging techniques, are fundamental to detect the disease since the initial stages are asymptomatic. Most of these examinations reflect negative cases and many have poor image quality, representing an important inefficiency factor. The SCREEN-DR project aims to tackle this limitation, by researching and developing computer-aided methods for diabetic retinopathy detection. This article presents a multidisciplinary collaborative platform that was created to meet the needs of physicians and researchers, aiming at the creation of machine learning algorithms to facilitate the screening process. METHODS: Our proposal is a collaborative platform for textual and visual annotation of image datasets. The architecture and layout were optimized for annotating DR images by gathering feedback from several physicians during the design and conceptualization of the platform. It allows the aggregation and indexing of imagiology studies from diverse sources, and supports the creation and annotation of phenotype-specific datasets to feed artificial intelligence algorithms. The platform makes use of an anonymization pipeline and role-based access control for securing personal data. RESULTS: The SCREEN-DR platform has been deployed in the production environment of the SCREEN-DR project at http://demo.dicoogle.com/screen-dr, and the source code of the project is publicly available. We provide a description of the platform's interface and use cases it supports. At the time of publication, four physicians have created a total of 1826 annotations for 701 distinct images, and the annotated data has been used for training classification models.

Controlled searching in reversibly de-identified medical imaging archives.

Nowadays, digital medical imaging in healthcare has become a fundamental tool for medical diagnosis. This growth has been accompanied by the development of technologies and standards, such as the DICOM standard and PACS. This environment led to the creation of collaborative projects where there is a need to share medical data between different institutions for research and educational purposes. In this context, it is necessary to maintain patient data privacy and provide an easy and secure mechanism for authorized personnel access. This paper presents a solution that fully de-identifies standard medical imaging objects, including metadata and pixel data, providing at the same time a reversible de-identifier mechanism that retains search capabilities from the original data. The last feature is important in some scenarios, for instance, in collaborative platforms where data is anonymized when shared with the community but searchable for data custodians or authorized entities. The solution was integrated into an open source PACS archive and validated in a multidisciplinary collaborative scenario.