Automated Feature Selection from Medical Literature.

We propose an automated approach to rank the most salient variables related to a certain clinical phenomenon from scientific literature. Our solution is an automated approach to improve the efficiency of the collection of different health-related measures from a population, and to accelerate the discovery of novel associations and dependencies between health-related concepts.

Automatic Mapping of Terminology Items with Transformers.

Biomedical ontologies are a key component in many systems for the analysis of textual clinical data. They are employed to organize information about a certain domain relying on a hierarchy of different classes. Each class maps a concept to items in a terminology developed by domain experts. These mappings are then leveraged to organize the information extracted by Natural Language Processing (NLP) models to build knowledge graphs for inferences. The creation of these associations, however, requires extensive manual review. In this paper, we present an automated approach and repeatable framework to learn a mapping between ontology classes and terminology terms derived from vocabularies in the Unified Medical Language System (UMLS) metathesaurus. According to our evaluation, the proposed system achieves a performance close to humans and provides a substantial improvement over existing systems developed by the National Library of Medicine to assist researchers through this process.

Subtyping Gastrointestinal Surgical Outcomes from Real World Data: A Comprehensive Analysis of UK Biobank.

Chronic gastrointestinal (GI) conditions, such as inflammatory bowel diseases (IBD), offer a promising opportunity to create classification systems that can enhance the accuracy of predicting the most effective therapies and prognosis for each patient. Here, we present a novel methodology to explore disease subtypes using our open-sourced BiomedSciAI toolkit. Applying methods available in this toolkit on the UK Biobank, including subpopulation-based feature selection and multi-dimensional subset scanning, we aimed to discover unique subgroups from GI surgery cohorts. Of a 12,073-patient cohort, a subgroup of 440 IBD patients was discovered with an increased risk of a subsequent GI surgery (OR: 2.21, 95% CI [1.81-2.69]). We iteratively demonstrate the discovery process using an additional cohort (with a narrower definition of GI surgery). Our results show that the iterative process can refine the subgroup discovery process and generate novel hypotheses to investigate determinants of treatment response.

Encoding Health Records into Pathway Representations for Deep Learning.

There is a growing trend in building deep learning patient representations from health records to obtain a comprehensive view of a patient's data for machine learning tasks. This paper proposes a reproducible approach to generate patient pathways from health records and to transform them into a machine-processable image-like structure useful for deep learning tasks. Based on this approach, we generated over a million pathways from FAIR synthetic health records and used them to train a convolutional neural network. Our initial experiments show the accuracy of the CNN on a prediction task is comparable or better than other autoencoders trained on the same data, while requiring significantly less computational resources for training. We also assess the impact of the size of the training dataset on autoencoders performances. The source code for generating pathways from health records is provided as open source.

Deep EHR Spotlight: a Framework and Mechanism to Highlight Events in Electronic Health Records for Explainable Predictions.

The wide adoption of Electronic Health Records (EHR) has resulted in large amounts of clinical data becoming available, which promises to support service delivery and advance clinical and informatics research. Deep learning techniques have demonstrated performance in predictive analytic tasks using EHRs yet they typically lack model result transparency or explainability functionalities and require cumbersome pre-processing tasks. Moreover, EHRs contain heterogeneous and multi-modal data points such as text, numbers and time series which further hinder visualisation and interpretability. This paper proposes a deep learning framework to: 1) encode patient pathways from EHRs into images, 2) highlight important events within pathway images, and 3) enable more complex predictions with additional intelligibility. The proposed method relies on a deep attention mechanism for visualisation of the predictions and allows predicting multiple sequential outcomes.

Social Determinant Trends of COVID-19: An Analysis Using Knowledge Graphs from Published Evidence and Online Trends.

This paper presents the results of a new approach to discover related health and social factors during the COVID-19 pandemic. The approach leverages a knowledge graph of related concepts mined from a corpus of published evidence (PubMed) prior to the pandemic. Population trends from online searches were used to identify social determinants of health (SDoH) concepts that trended high at the outset of the pandemic from a list of SDoH topics from the World Health Organization (WHO). The trending concepts were then mapped to the knowledge graph and a subsequent analysis of the derived insights, spanning two years, was conducted. This paper suggests an approach to derive new related health and social factors that may have either played a role in, or been affected by, the onset of the global COVID-19 pandemic. In particular, our results show how, from a list of SDoH topics, Food Security, Unemployment trended the highest at the start of the pandemic. Further work is needed to continue to ascertain the validity of the derived relations in a population health context and to improve mining insights from published evidence.

Discovering Associations between Social Determinants and Health Outcomes: Merging Knowledge Graphs from Literature and Electronic Health Data.

Social Determinants of Health (SDoH) are an increasingly important part of the broader research and public health efforts in understanding individuals' physical and mental well-being. Despite this, non-clinical factors affecting health are poorly recorded in electronic health databases and techniques to study how SDoH might relate to population outcomes are lacking. This paper proposes an approach to systematically identify and quantify associations between SDoH and health-related outcomes in a specific cohort of people by (1) leveraging published evidence from literature to build a knowledge graph of health and social factor associations and (2) analysing a large dataset of claims and medical records where those associations may be found. This work demonstrates how the proposed approach could be used to generate hypotheses and inform further research on SDoH in a data-driven manner.

Exploring the Social Drivers of Health During a Pandemic: Leveraging Knowledge Graphs and Population Trends in COVID-19.

Social determinants of health (SDoH) are the factors which lie outside of the traditional health system, such as employment or access to nutritious foods, that influence health outcomes. Some efforts have focused on identifying vulnerable populations during the COVID-19 pandemic, however, both the short- and long-term social impacts of the pandemic on individuals and populations are not well understood. This paper presents a pipeline to discover health outcomes and related social factors based on trending SDoH at population-level using Google Trends. A knowledge graph was built from a corpus of research literature (PubMed) and the social determinants that trended high at the start of the pandemic were examined. This paper reports on related social and health concepts which may be impacted by the COVID-19 outbreak and may be important to monitor as the pandemic evolves. The proposed pipeline should have wider applicability in surfacing related social or clinical characteristics of interest, outbreak surveillance, or to mine relations between social and health concepts that can, in turn, help inform and support citizen-centred services.

Bridging Clinical and Social Determinants of Health Using Unstructured Data.

There is a growing interest in identifying, weighing and accounting for the impact of health determinants that lie outside of the traditional healthcare system, yet there is a remarkable paucity of data and sources to sustain these efforts. Decision support systems would greatly benefit from leveraging models which are able to extend and use such cross-domain knowledge. This paper describes an approach to identify and explore related social and clinical terms based on large corpora of unstructured data. Using word embedding techniques on relevant sources of knowledge, we have identified terms that appear close together in the high-dimensional space. In particular, having created a model with cross-domain knowledge on the social determinants of health, we have been able to demonstrate that it is possible to surface terms in this domain when querying for related clinical terms, thereby creating a bridge between the social and clinical determinants of health. This is a promising approach with significant applicability in decision support efforts in healthcare.

Using Semantic Technologies to Extract Highlights from Care Notes.

We propose a cognitive system for patient-centric care that leverages and combines natural language processing, semantics, and learning from users over time to support care professionals working with large volumes of patient notes. The proposed methods highlight the entities embedded in the unstructured data to provide a holistic semantic view of an individual. A user-based evaluation is presented, showing consensus between the users and the system.