An open repository of real-time COVID-19 indicators.

The COVID-19 pandemic presented enormous data challenges in the United States. Policy makers, epidemiological modelers, and health researchers all require up-to-date data on the pandemic and relevant public behavior, ideally at fine spatial and temporal resolution. The COVIDcast API is our attempt to fill this need: Operational since April 2020, it provides open access to both traditional public health surveillance signals (cases, deaths, and hospitalizations) and many auxiliary indicators of COVID-19 activity, such as signals extracted from deidentified medical claims data, massive online surveys, cell phone mobility data, and internet search trends. These are available at a fine geographic resolution (mostly at the county level) and are updated daily. The COVIDcast API also tracks all revisions to historical data, allowing modelers to account for the frequent revisions and backfill that are common for many public health data sources. All of the data are available in a common format through the API and accompanying R and Python software packages. This paper describes the data sources and signals, and provides examples demonstrating that the auxiliary signals in the COVIDcast API present information relevant to tracking COVID activity, augmenting traditional public health reporting and empowering research and decision-making.

Mining and exploring care pathways from electronic medical records with visual analytics.

OBJECTIVE: In order to derive data-driven insights, we develop Care Pathway Explorer, a system that mines and visualizes a set of frequent event sequences from patient EMR data. The goal is to utilize historical EMR data to extract common sequences of medical events such as diagnoses and treatments, and investigate how these sequences correlate with patient outcome. MATERIALS AND METHODS: The Care Pathway Explorer uses a frequent sequence mining algorithm adapted to handle the real-world properties of EMR data, including techniques for handling event concurrency, multiple levels-of-detail, temporal context, and outcome. The mined patterns are then visualized in an interactive user interface consisting of novel overview and flow visualizations. RESULTS: We use the proposed system to analyze the diagnoses and treatments of a cohort of hyperlipidemic patients with hypertension and diabetes pre-conditions, and demonstrate the clinical relevance of patterns mined from EMR data. The patterns that were identified corresponded to clinical and published knowledge, some of it unknown to the physician at the time of discovery. CONCLUSION: Care Pathway Explorer, which combines frequent sequence mining techniques with advanced visualizations supports the integration of data-driven insights into care pathway discovery.

A methodology for interactive mining and visual analysis of clinical event patterns using electronic health record data.

Patients' medical conditions often evolve in complex and seemingly unpredictable ways. Even within a relatively narrow and well-defined episode of care, variations between patients in both their progression and eventual outcome can be dramatic. Understanding the patterns of events observed within a population that most correlate with differences in outcome is therefore an important task in many types of studies using retrospective electronic health data. In this paper, we present a method for interactive pattern mining and analysis that supports ad hoc visual exploration of patterns mined from retrospective clinical patient data. Our approach combines (1) visual query capabilities to interactively specify episode definitions, (2) pattern mining techniques to help discover important intermediate events within an episode, and (3) interactive visualization techniques that help uncover event patterns that most impact outcome and how those associations change over time. In addition to presenting our methodology, we describe a prototype implementation and present use cases highlighting the types of insights or hypotheses that our approach can help uncover.

Dead or Alive: Continuous Data Profiling for Interactive Data Science.

Profiling data by plotting distributions and analyzing summary statistics is a critical step throughout data analysis. Currently, this process is manual and tedious since analysts must write extra code to examine their data after every transformation. This inefficiency may lead to data scientists profiling their data infrequently, rather than after each transformation, making it easy for them to miss important errors or insights. We propose continuous data profiling as a process that allows analysts to immediately see interactive visual summaries of their data throughout their data analysis to facilitate fast and thorough analysis. Our system, AutoProfiler, presents three ways to support continuous data profiling: (1) it automatically displays data distributions and summary statistics to facilitate data comprehension; (2) it is live, so visualizations are always accessible and update automatically as the data updates; (3) it supports follow up analysis and documentation by authoring code for the user in the notebook. In a user study with 16 participants, we evaluate two versions of our system that integrate different levels of automation: both automatically show data profiles and facilitate code authoring, however, one version updates reactively ("live") and the other updates only on demand ("dead"). We find that both tools, dead or alive, facilitate insight discovery with 91% of user-generated insights originating from the tools rather than manual profiling code written by users. Participants found live updates intuitive and felt it helped them verify their transformations while those with on-demand profiles liked the ability to look at past visualizations. We also present a longitudinal case study on how AutoProfiler helped domain scientists find serendipitous insights about their data through automatic, live data profiles. Our results have implications for the design of future tools that offer automated data analysis support.

MedSyn: Text-guided Anatomy-aware Synthesis of High-Fidelity 3D CT Images.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. Algorithmic comparative assessments and blind evaluations conducted by 10 board-certified radiologists indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines and airways. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Patient and Provider Perspectives on Symptom Monitoring During Outpatient Chemotherapy: Interview Study.

BACKGROUND: Fluctuating symptoms and side effects are common during outpatient cancer treatment, and approaches to monitoring symptoms vary widely across providers, patients, and clinical settings. To design a remote symptom monitoring system that patients and providers find to be useful, it may be helpful to understand current clinical approaches to monitoring and managing chemotherapy-related symptoms among patients and providers and assess how more frequent and systematic assessment and sharing of data could improve patient and provider experiences. OBJECTIVE: The goals of this study were to learn about patient and provider perspectives on monitoring symptoms during chemotherapy, understand barriers and challenges to effective symptom monitoring at one institution, and explore the potential value of remote symptom monitoring between provider visits. METHODS: A total of 15 patients who were currently undergoing or had recently completed chemotherapy and 7 oncology providers participated in semistructured interviews. Interviews were transcribed and coded using an iterative thematic analysis approach. The study was conducted at a National Cancer Institute-Designated Comprehensive Cancer Center. RESULTS: Four main themes were discussed by patients and providers: (1) asynchronous nature of current methods for tracking and managing symptoms, (2) variability in reported symptoms due to patient factors, (3) limitations of existing communication channels, and (4) potential value of real-time remote symptom monitoring during chemotherapy. Current asynchronous methods and existing communication channels resulted in a disconnect between when symptoms are most severe and when conversations about symptoms happen, a situation further complicated by memory impairments during chemotherapy. Patients and providers both highlighted improvements in patient-provider communication as a potential benefit of remote real-time symptom monitoring. Providers also emphasized the value of temporal data regarding when symptoms first emerge and how they progress over time, as well as the potential value of concurrent activity or other data about daily activities and functioning. Patients noted that symptom monitoring could result in better preparation for subsequent treatment cycles. CONCLUSIONS: Both patients and providers highlighted significant challenges of asynchronous, patient-initiated, phone-dependent symptom monitoring and management. Oncology patients and providers reported that more routine remote monitoring of symptoms between visits could improve patient-provider communication, prepare patients for subsequent chemotherapy cycles, and facilitate provider insight and clinical decision-making with regard to symptom management.

TextEssence: A Tool for Interactive Analysis of Semantic Shifts Between Corpora.

Embeddings of words and concepts capture syntactic and semantic regularities of language; however, they have seen limited use as tools to study characteristics of different corpora and how they relate to one another. We introduce TextEssence, an interactive system designed to enable comparative analysis of corpora using embeddings. TextEssence includes visual, neighbor-based, and similarity-based modes of embedding analysis in a lightweight, web-based interface. We further propose a new measure of embedding confidence based on nearest neighborhood overlap, to assist in identifying high-quality embeddings for corpus analysis. A case study on COVID-19 scientific literature illustrates the utility of the system. TextEssence can be found at https://textessence.github.io.

Ablate, Variate, and Contemplate: Visual Analytics for Discovering Neural Architectures.

The performance of deep learning models is dependent on the precise configuration of many layers and parameters. However, there are currently few systematic guidelines for how to configure a successful model. This means model builders often have to experiment with different configurations by manually programming different architectures (which is tedious and time consuming) or rely on purely automated approaches to generate and train the architectures (which is expensive). In this paper, we present Rapid Exploration of Model Architectures and Parameters, or REMAP, a visual analytics tool that allows a model builder to discover a deep learning model quickly via exploration and rapid experimentation of neural network architectures. In REMAP, the user explores the large and complex parameter space for neural network architectures using a combination of global inspection and local experimentation. Through a visual overview of a set of models, the user identifies interesting clusters of architectures. Based on their findings, the user can run ablation and variation experiments to identify the effects of adding, removing, or replacing layers in a given architecture and generate new models accordingly. They can also handcraft new models using a simple graphical interface. As a result, a model builder can build deep learning models quickly, efficiently, and without manual programming. We inform the design of REMAP through a design study with four deep learning model builders. Through a use case, we demonstrate that REMAP allows users to discover performant neural network architectures efficiently using visual exploration and user-defined semi-automated searches through the model space.

"Search, show context, expand on demand": supporting large graph exploration with degree-of-interest.

A common goal in graph visualization research is the design of novel techniques for displaying an overview of an entire graph. However, there are many situations where such an overview is not relevant or practical for users, as analyzing the global structure may not be related to the main task of the users that have semi-specific information needs. Furthermore, users accessing large graph databases through an online connection or users running on less powerful (mobile) hardware simply do not have the resources needed to compute these overviews. In this paper, we advocate an interaction model that allows users to remotely browse the immediate context graph around a specific node of interest. We show how Furnas' original degree of interest function can be adapted from trees to graphs and how we can use this metric to extract useful contextual subgraphs, control the complexity of the generated visualization and direct users to interesting datapoints in the context. We demonstrate the effectiveness of our approach with an exploration of a dense online database containing over 3 million legal citations.

Confronting data sparsity to identify potential sources of Zika virus spillover infection among primates.

The recent Zika virus (ZIKV) epidemic in the Americas ranks among the largest outbreaks in modern times. Like other mosquito-borne flaviviruses, ZIKV circulates in sylvatic cycles among primates that can serve as reservoirs of spillover infection to humans. Identifying sylvatic reservoirs is critical to mitigating spillover risk, but relevant surveillance and biological data remain limited for this and most other zoonoses. We confronted this data sparsity by combining a machine learning method, Bayesian multi-label learning, with a multiple imputation method on primate traits. The resulting models distinguished flavivirus-positive primates with 82% accuracy and suggest that species posing the greatest spillover risk are also among the best adapted to human habitations. Given pervasive data sparsity describing animal hosts, and the virtual guarantee of data sparsity in scenarios involving novel or emerging zoonoses, we show that computational methods can be useful in extracting actionable inference from available data to support improved epidemiological response and prevention.

SEQ2SEQ-VIS : A Visual Debugging Tool for Sequence-to-Sequence Models.

Neural sequence-to-sequence models have proven to be accurate and robust for many sequence prediction tasks, and have become the standard approach for automatic translation of text. The models work with a five-stage blackbox pipeline that begins with encoding a source sequence to a vector space and then decoding out to a new target sequence. This process is now standard, but like many deep learning methods remains quite difficult to understand or debug. In this work, we present a visual analysis tool that allows interaction and "what if"-style exploration of trained sequence-to-sequence models through each stage of the translation process. The aim is to identify which patterns have been learned, to detect model errors, and to probe the model with counterfactual scenario. We demonstrate the utility of our tool through several real-world sequence-to-sequence use cases on large-scale models.

Clustervision: Visual Supervision of Unsupervised Clustering.

Clustering, the process of grouping together similar items into distinct partitions, is a common type of unsupervised machine learning that can be useful for summarizing and aggregating complex multi-dimensional data. However, data can be clustered in many ways, and there exist a large body of algorithms designed to reveal different patterns. While having access to a wide variety of algorithms is helpful, in practice, it is quite difficult for data scientists to choose and parameterize algorithms to get the clustering results relevant for their dataset and analytical tasks. To alleviate this problem, we built Clustervision, a visual analytics tool that helps ensure data scientists find the right clustering among the large amount of techniques and parameters available. Our system clusters data using a variety of clustering techniques and parameters and then ranks clustering results utilizing five quality metrics. In addition, users can guide the system to produce more relevant results by providing task-relevant constraints on the data. Our visual user interface allows users to find high quality clustering results, explore the clusters using several coordinated visualization techniques, and select the cluster result that best suits their task. We demonstrate this novel approach using a case study with a team of researchers in the medical domain and showcase that our system empowers users to choose an effective representation of their complex data.

Coping with Volume and Variety in Temporal Event Sequences: Strategies for Sharpening Analytic Focus.

The growing volume and variety of data presents both opportunities and challenges for visual analytics. Addressing these challenges is needed for big data to provide valuable insights and novel solutions for business, security, social media, and healthcare. In the case of temporal event sequence analytics it is the number of events in the data and variety of temporal sequence patterns that challenges users of visual analytic tools. This paper describes 15 strategies for sharpening analytic focus that analysts can use to reduce the data volume and pattern variety. Four groups of strategies are proposed: (1) extraction strategies, (2) temporal folding, (3) pattern simplification strategies, and (4) iterative strategies. For each strategy, we provide examples of the use and impact of this strategy on volume and/or variety. Examples are selected from 20 case studies gathered from either our own work, the literature, or based on email interviews with individuals who conducted the analyses and developers who observed analysts using the tools. Finally, we discuss how these strategies might be combined and report on the feedback from 10 senior event sequence analysts.

Balancing systematic and flexible exploration of social networks.

Social network analysis (SNA) has emerged as a powerful method for understanding the importance of relationships in networks. However, interactive exploration of networks is currently challenging because: (1) it is difficult to find patterns and comprehend the structure of networks with many nodes and links, and (2) current systems are often a medley of statistical methods and overwhelming visual output which leaves many analysts uncertain about how to explore in an orderly manner. This results in exploration that is largely opportunistic. Our contributions are techniques to help structural analysts understand social networks more effectively. We present SocialAction, a system that uses attribute ranking and coordinated views to help users systematically examine numerous SNA measures. Users can (1) flexibly iterate through visualizations of measures to gain an overview, filter nodes, and find outliers, (2) aggregate networks using link structure, find cohesive subgroups, and focus on communities of interest, and (3) untangle networks by viewing different link types separately, or find patterns across different link types using a matrix overview. For each operation, a stable node layout is maintained in the network visualization so users can make comparisons. SocialAction offers analysts a strategy beyond opportunism, as it provides systematic, yet flexible, techniques for exploring social networks.

Supporting Iterative Cohort Construction with Visual Temporal Queries.

Many researchers across diverse disciplines aim to analyze the behavior of cohorts whose behaviors are recorded in large event databases. However, extracting cohorts from databases is a difficult yet important step, often overlooked in many analytical solutions. This is especially true when researchers wish to restrict their cohorts to exhibit a particular temporal pattern of interest. In order to fill this gap, we designed COQUITO, a visual interface that assists users defining cohorts with temporal constraints. COQUITO was designed to be comprehensible to domain experts with no preknowledge of database queries and also to encourage exploration. We then demonstrate the utility of COQUITO via two case studies, involving medical and social media researchers.

Synthesizing analytic evidence to refine care pathways.

Care pathways play significant roles in delivering evidence-based and coordinated care to patients with specific conditions. In order to put care pathways into practice, clinical institutions always need to adapt them based on local care settings so that the best local practices can be incorporated and used to develop refined pathways. However, it is knowledge-intensive and error-prone to incorporate various analytic insights from local data sets. In order to assist care pathway developers in working effectively and efficiently, we propose to automatically synthesize the analytical evidences derived from multiple analysis methods, and recommend modelling operations accordingly to derive a refined care pathway for a specific patient cohort. We validated our method by adapting a Congestive Heart Failure (CHF) Ambulatory Care Pathway for patients with additional condition of COPD through synthesizing the results of variation analysis and frequent pattern mining against patient records.

INFUSE: Interactive Feature Selection for Predictive Modeling of High Dimensional Data.

Predictive modeling techniques are increasingly being used by data scientists to understand the probability of predicted outcomes. However, for data that is high-dimensional, a critical step in predictive modeling is determining which features should be included in the models. Feature selection algorithms are often used to remove non-informative features from models. However, there are many different classes of feature selection algorithms. Deciding which one to use is problematic as the algorithmic output is often not amenable to user interpretation. This limits the ability for users to utilize their domain expertise during the modeling process. To improve on this limitation, we developed INFUSE, a novel visual analytics system designed to help analysts understand how predictive features are being ranked across feature selection algorithms, cross-validation folds, and classifiers. We demonstrate how our system can lead to important insights in a case study involving clinical researchers predicting patient outcomes from electronic medical records.

Progressive Visual Analytics: User-Driven Visual Exploration of In-Progress Analytics.

As datasets grow and analytic algorithms become more complex, the typical workflow of analysts launching an analytic, waiting for it to complete, inspecting the results, and then re-Iaunching the computation with adjusted parameters is not realistic for many real-world tasks. This paper presents an alternative workflow, progressive visual analytics, which enables an analyst to inspect partial results of an algorithm as they become available and interact with the algorithm to prioritize subspaces of interest. Progressive visual analytics depends on adapting analytical algorithms to produce meaningful partial results and enable analyst intervention without sacrificing computational speed. The paradigm also depends on adapting information visualization techniques to incorporate the constantly refining results without overwhelming analysts and provide interactions to support an analyst directing the analytic. The contributions of this paper include: a description of the progressive visual analytics paradigm; design goals for both the algorithms and visualizations in progressive visual analytics systems; an example progressive visual analytics system (Progressive Insights) for analyzing common patterns in a collection of event sequences; and an evaluation of Progressive Insights and the progressive visual analytics paradigm by clinical researchers analyzing electronic medical records.

Predicting changes in hypertension control using electronic health records from a chronic disease management program.

OBJECTIVE: Common chronic diseases such as hypertension are costly and difficult to manage. Our ultimate goal is to use data from electronic health records to predict the risk and timing of deterioration in hypertension control. Towards this goal, this work predicts the transition points at which hypertension is brought into, as well as pushed out of, control. METHOD: In a cohort of 1294 patients with hypertension enrolled in a chronic disease management program at the Vanderbilt University Medical Center, patients are modeled as an array of features derived from the clinical domain over time, which are distilled into a core set using an information gain criteria regarding their predictive performance. A model for transition point prediction was then computed using a random forest classifier. RESULTS: The most predictive features for transitions in hypertension control status included hypertension assessment patterns, comorbid diagnoses, procedures and medication history. The final random forest model achieved a c-statistic of 0.836 (95% CI 0.830 to 0.842) and an accuracy of 0.773 (95% CI 0.766 to 0.780). CONCLUSIONS: This study achieved accurate prediction of transition points of hypertension control status, an important first step in the long-term goal of developing personalized hypertension management plans.