Comparison of late-onset and non-late-onset systemic lupus erythematosus individuals in a real-world electronic health record cohort

Objective: Late-onset systemic lupus erythematosus (LO-SLE) is defined as SLE diagnosed at age 50 years or later. Current studies on LO-SLE are small and have conflicting results.Methods: Using a large, electronic health record (EHR)-based cohort of SLE individuals, we compared demographics, disease characteristics, SLE-specific antibodies, and medication prescribing practices in LO (n = 123) vs. NLO-SLE (n = 402) individuals.Results: The median age (interquartile range) at SLE diagnosis was 60 (56-67) years for LO-SLE and 28 (20-38) years for NLO-SLE. Both groups were predominantly female (85% vs. 91%, p = 0.10). LO-SLE individuals were more likely to be White than NLO-SLE individuals (74% vs. 60%, p = 0.005) and less likely to have positive dsDNA (39% vs. 58%, p = 0.001) and RNP (17% vs. 32%, p = 0.02) with no differences in Smith, SSA, and SSB. Autoantibody positivity declined with increasing age at SLE diagnosis. LO-SLE individuals were less likely to develop SLE nephritis (9% vs. 29%, p < 0.001) and less likely to be prescribed multiple classes of SLE medications including antimalarials (90% vs. 95%, p = 0.04), azathioprine (17% vs. 31%, p = 0.002), mycophenolate mofetil (12% vs. 38%, p < 0.001), and belimumab (2% vs. 8%, p = 0.02).Conclusion: LO-SLE individuals may be less likely to fit an expected course for SLE with less frequent positive autoantibodies at diagnosis and lower rates of nephritis, even after adjusting for race. Understanding how age impacts SLE disease presentation could help reduce diagnostic delays in SLE.

Identifying antinuclear antibody positive individuals at risk for developing systemic autoimmune disease: development and validation of a real-time risk model

Objective

Positive antinuclear antibodies (ANAs) cause diagnostic dilemmas for clinicians. Currently, no tools exist to help clinicians interpret the significance of a positive ANA in individuals without diagnosed autoimmune diseases. We developed and validated a risk model to predict risk of developing autoimmune disease in positive ANA individuals.

Methods

Using a de-identified electronic health record (EHR), we randomly chart reviewed 2,000 positive ANA individuals to determine if a systemic autoimmune disease was diagnosed by a rheumatologist. A priori, we considered demographics, billing codes for autoimmune disease-related symptoms, and laboratory values as variables for the risk model. We performed logistic regression and machine learning models using training and validation samples.

Results

We assembled training (n = 1030) and validation (n = 449) sets. Positive ANA individuals who were younger, female, had a higher titer ANA, higher platelet count, disease-specific autoantibodies, and more billing codes related to symptoms of autoimmune diseases were all more likely to develop autoimmune diseases. The most important variables included having a disease-specific autoantibody, number of billing codes for autoimmune disease-related symptoms, and platelet count. In the logistic regression model, AUC was 0.83 (95% CI 0.79-0.86) in the training set and 0.75 (95% CI 0.68-0.81) in the validation set.

Conclusion

We developed and validated a risk model that predicts risk for developing systemic autoimmune diseases and can be deployed easily within the EHR. The model can risk stratify positive ANA individuals to ensure high-risk individuals receive urgent rheumatology referrals while reassuring low-risk individuals and reducing unnecessary referrals.

Knowledge Graphs in Practice: Characterizing their Users, Challenges, and Visualization Opportunities

This study presents insights from interviews with nineteen Knowledge Graph (KG) practitioners who work in both enterprise and academic settings on a wide variety of use cases. Through this study, we identify critical challenges experienced by KG practitioners when creating, exploring, and analyzing KGs that could be alleviated through visualization design. Our findings reveal three major personas among KG practitioners - KG Builders, Analysts, and Consumers - each of whom have their own distinct expertise and needs. We discover that KG Builders would benefit from schema enforcers, while KG Analysts need customizable query builders that provide interim query results. For KG Consumers, we identify a lack of efficacy for node-link diagrams, and the need for tailored domain-specific visualizations to promote KG adoption and comprehension. Lastly, we find that implementing KGs effectively in practice requires both technical and social solutions that are not addressed with current tools, technologies, and collaborative workflows. From the analysis of our interviews, we distill several visualization research directions to improve KG usability, including knowledge cards that balance digestibility and discoverability, timeline views to track temporal changes, interfaces that support organic discovery, and semantic explanations for AI and machine learning predictions.

Preliminary Guidelines For Combining Data Integration and Visual Data Analysis

Data integration is often performed to consolidate information from multiple disparate data sources during visual data analysis. However, integration operations are usually separate from visual analytics operations such as encode and filter in both interface design and empirical research. We conducted a preliminary user study to investigate whether and how data integration should be incorporated directly into the visual analytics process. We used two interface alternatives featuring contrasting approaches to the data preparation and analysis workflow: manual file-based ex-situ integration as a separate step from visual analytics operations; and automatic UI-based in-situ integration merged with visual analytics operations. Participants were asked to complete specific and free-form tasks with each interface, browsing for patterns, generating insights, and summarizing relationships between attributes distributed across multiple files. Analyzing participants' interactions and feedback, we found both task completion time and total interactions to be similar across interfaces and tasks, as well as unique integration strategies between interfaces and emergent behaviors related to satisficing and cognitive bias. Participants' time spent and interactions emergent strategies revealed that in-situ integration enabled users to spend more time on analysis tasks compared with ex-situ integration. Participants' integration strategies and analytical behaviors revealed differences in interface usage for generating and tracking hypotheses and insights , yet their emergent behaviors suggested that in-situ integration could negatively affect the ability to generate and track hypotheses and insights. With these results, we synthesized preliminary guidelines for designing future visual analytics interfaces that can support integrating attributes throughout an active analysis process.

Are Metrics Enough? Guidelines for Communicating and Visualizing Predictive Models to Subject Matter Experts

Presenting a predictive model's performance is a communication bottleneck that threatens collaborations between data scientists and subject matter experts. Accuracy and error metrics alone fail to tell the whole story of a model - its risks, strengths, and limitations - making it difficult for subject matter experts to feel confident in their decision to use a model. As a result, models may fail in unexpected ways or go entirely unused, as subject matter experts disregard poorly presented models in favor of familiar, yet arguably substandard methods. In this paper, we describe an iterative study conducted with both subject matter experts and data scientists to understand the gaps in communication between these two groups. We find that, while the two groups share common goals of understanding the data and predictions of the model, friction can stem from unfamiliar terms, metrics, and visualizations - limiting the transfer of knowledge to SMEs and discouraging clarifying questions being asked during presentations. Based on our findings, we derive a set of communication guidelines that use visualization as a common medium for communicating the strengths and weaknesses of a model. We provide a demonstration of our guidelines in a regression modeling scenario and elicit feedback on their use from subject matter experts. From our demonstration, subject matter experts were more comfortable discussing a model's performance, more aware of the trade-offs for the presented model, and better equipped to assess the model's risks - ultimately informing and contextualizing the model's use beyond text and numbers.

UnProjection: Leveraging Inverse-Projections for Visual Analytics of High-Dimensional Data

Projection techniques are often used to visualize high-dimensional data, allowing users to better understand the overall structure of multi-dimensional spaces on a 2D screen. Although many such methods exist, comparably little work has been done on generalizable methods of inverse-projection - the process of mapping the projected points, or more generally, the projection space back to the original high-dimensional space. In this article we present NNInv, a deep learning technique with the ability to approximate the inverse of any projection or mapping. NNInv learns to reconstruct high-dimensional data from any arbitrary point on a 2D projection space, giving users the ability to interact with the learned high-dimensional representation in a visual analytics system. We provide an analysis of the parameter space of NNInv, and offer guidance in selecting these parameters. We extend validation of the effectiveness of NNInv through a series of quantitative and qualitative analyses. We then demonstrate the method's utility by applying it to three visualization tasks: interactive instance interpolation, classifier agreement, and gradient visualization.

Identifying problematic opioid use in electronic health record data: Are we looking in the right place?

OBJECTIVE

To examine the value of data obtained outside of regular healthcare visits (clinical communications) to detect problematic opioid use in electronic health records (EHRs).

DESIGN

A retrospective cohort study.

PARTICIPANTS

Chronic pain patient records in a large academic medical center.

INTERVENTIONS

We compared evidence for problematic opioid use in (1) clinic notes, (2) clinical communications, and (3) full EHR data. We analyzed keyword counts and calculated concordance and Cohen's κ between data sources.

MAIN OUTCOME MEASURE

Evidence of problematic opioid use in EHR defined as none, some, or high.

RESULTS

Twenty-six percent of records were discordant in determination of problematic opioid use between clinical communications and clinic notes. Of these, 54 percent detected more evidence in clinical communications, and 46 percent in clinic notes. Compared to full EHR review, clinic notes exhibited higher concordance (78 percent; κ = 0.619) than clinical communications (60 percent; κ = 0.290).

CONCLUSION

Clinical communications are a valuable addition to opioid EHR research.

Persistent Homology Guided Force-Directed Graph Layouts

Graphs are commonly used to encode relationships among entities, yet their abstractness makes them difficult to analyze. Node-link diagrams are popular for drawing graphs, and force-directed layouts provide a flexible method for node arrangements that use local relationships in an attempt to reveal the global shape of the graph. However, clutter and overlap of unrelated structures can lead to confusing graph visualizations. This paper leverages the persistent homology features of an undirected graph as derived information for interactive manipulation of force-directed layouts. We first discuss how to efficiently extract 0-dimensional persistent homology features from both weighted and unweighted undirected graphs. We then introduce the interactive persistence barcode used to manipulate the force-directed graph layout. In particular, the user adds and removes contracting and repulsing forces generated by the persistent homology features, eventually selecting the set of persistent homology features that most improve the layout. Finally, we demonstrate the utility of our approach across a variety of synthetic and real datasets.

Molecular and biochemical approaches in the identification of heterozygotes for homocystinuria

We compared biochemical and molecular methods for the identification of heterozygous carriers of mutations in the cystathionine beta-synthase (CBS) gene. Eleven relatives of seven unrelated patients with homocystinuria due to homozygous CBS deficiency and controls were studied with respect to total homocysteine concentrations before and after methionine loading. In addition, we determined CBS activity in cultured skin fibroblasts and tested for the presence of five known mutations by a PCR-based method in these seven patients, their relatives and controls. The results demonstrate that measurement of homocysteine after methionine loading and assay of CBS enzyme activity in cultured fibroblasts identify most but not all heterozygotes. There was significant correlation between homocysteine concentrations and CBS activities only after methionine loading (r = 0.12, 0.48, 0.48 and 0.50 at 0, 4, 6 and 8 h, respectively). Among the homozygous patients, molecular approaches identified five T833C and two G919A mutations out of 14 independent alleles, confirming the studies of others that these represent the two most prevalent mutations. In addition, we found that three of six heterozygotes with the T833 C allele had post-methionine loading homocysteine levels which overlapped with controls and of the other three, one (as well as an obligate heterozygote who did not carry any of the five mutant alleles tested) had CBS activity comparable to that of controls. These findings demonstrate that genotyping is useful as an adjunctive method for the diagnosis of the heterozygous carrier state of CBS deficiency.