Activity-Centered Domain Characterization for Problem-Driven Scientific Visualization

DITTO: A Visual Digital Twin for Interventions and Temporal Treatment Outcomes in Head and Neck Cancer

Digital twin models are of high interest to Head and Neck Cancer (HNC) oncologists, who have to navigate a series of complex treatment decisions that weigh the efficacy of tumor control against toxicity and mortality risks. Evaluating individual risk profiles necessitates a deeper understanding of the interplay between different factors such as patient health, spatial tumor location and spread, and risk of subsequent toxicities that can not be adequately captured through simple heuristics. To support clinicians in better understanding tradeoffs when deciding on treatment courses, we developed DITTO, a digital-twin and visual computing system that allows clinicians to analyze detailed risk profiles for each patient, and decide on a treatment plan. DITTO relies on a sequential Deep Reinforcement Learning digital twin (DT) to deliver personalized risk of both long-term and short-term disease outcome and toxicity risk for HNC patients. Based on a participatory collaborative design alongside oncologists, we also implement several visual explainability methods to promote clinical trust and encourage healthy skepticism when using our system. We evaluate the efficacy of DITTO through quantitative evaluation of performance and case studies with qualitative feedback. Finally, we discuss design lessons for developing clinical visual XAI applications for clinical end users.

Empowering Communities: Tailored Pandemic Data Visualization for Varied Tasks and Users

Data visualization methodologies were intensively leveraged during the COVID-19 pandemic. We review our design experience working on a set of interdisciplinary COVID-19 pandemic projects. We describe the challenges we met in these projects, characterize the respective user communities, the goals and tasks we supported, and the data types and visual media we worked with. Furthermore, we instantiate these characterizations in a series of case studies. Finally, we describe the visual analysis lessons we learned, considering future pandemics.

Roses Have Thorns: Understanding the Downside of Oncological Care Delivery Through Visual Analytics and Sequential Rule Mining

Personalized head and neck cancer therapeutics have greatly improved survival rates for patients, but are often leading to understudied long-lasting symptoms which affect quality of life. Sequential rule mining (SRM) is a promising unsupervised machine learning method for predicting longitudinal patterns in temporal data which, however, can output many repetitive patterns that are difficult to interpret without the assistance of visual analytics. We present a data-driven, human-machine analysis visual system developed in collaboration with SRM model builders in cancer symptom research, which facilitates mechanistic knowledge discovery in large scale, multivariate cohort symptom data. Our system supports multivariate predictive modeling of post-treatment symptoms based on during-treatment symptoms. It supports this goal through an SRM, clustering, and aggregation back end, and a custom front end to help develop and tune the predictive models. The system also explains the resulting predictions in the context of therapeutic decisions typical in personalized care delivery. We evaluate the resulting models and system with an interdisciplinary group of modelers and head and neck oncology researchers. The results demonstrate that our system effectively supports clinical and symptom research.

DASS Good: Explainable Data Mining of Spatial Cohort Data

Developing applicable clinical machine learning models is a difficult task when the data includes spatial information, for example, radiation dose distributions across adjacent organs at risk. We describe the co-design of a modeling system, DASS, to support the hybrid human-machine development and validation of predictive models for estimating long-term toxicities related to radiotherapy doses in head and neck cancer patients. Developed in collaboration with domain experts in oncology and data mining, DASS incorporates human-in-the-loop visual steering, spatial data, and explainable AI to augment domain knowledge with automatic data mining. We demonstrate DASS with the development of two practical clinical stratification models and report feedback from domain experts. Finally, we describe the design lessons learned from this collaborative experience.

Communicating Uncertainty in Digital Humanities Visualization Research

Due to their historical nature, humanistic data encompass multiple sources of uncertainty. While humanists are accustomed to handling such uncertainty with their established methods, they are cautious of visualizations that appear overly objective and fail to communicate this uncertainty. To design more trustworthy visualizations for humanistic research, therefore, a deeper understanding of its relation to uncertainty is needed. We systematically reviewed 126 publications from digital humanities literature that use visualization as part of their research process, and examined how uncertainty was handled and represented in their visualizations. Crossing these dimensions with the visualization type and use, we identified that uncertainty originated from multiple steps in the research process from the source artifacts to their datafication. We also noted how besides known uncertainty coping strategies, such as excluding data and evaluating its effects, humanists also embraced uncertainty as a separate dimension important to retain. By mapping how the visualizations encoded uncertainty, we identified four approaches that varied in terms of explicitness and customization. This work contributes with two empirical taxonomies of uncertainty and it's corresponding coping strategies, as well as with the foundation of a research agenda for uncertainty visualization in the digital humanities. Our findings further the synergy among humanists and visualization researchers, and ultimately contribute to the development of more trustworthy, uncertainty-aware visualizations.

Visual Analysis and Detection of Contrails in Aircraft Engine Simulations

Contrails are condensation trails generated from emitted particles by aircraft engines, which perturb Earth's radiation budget. Simulation modeling is used to interpret the formation and development of contrails. These simulations are computationally intensive and rely on high-performance computing solutions, and the contrail structures are not well defined. We propose a visual computing system to assist in defining contrails and their characteristics, as well as in the analysis of parameters for computer-generated aircraft engine simulations. The back-end of our system leverages a contrail-formation criterion and clustering methods to detect contrails' shape and evolution and identify similar simulation runs. The front-end system helps analyze contrails and their parameters across multiple simulation runs. The evaluation with domain experts shows this approach successfully aids in contrail data investigation.

Alveolus analysis: a web browser-based tool to analyze lung intravital microscopy

BACKGROUND

Acute lung injury and the acute respiratory distress syndrome are characterized by pulmonary inflammation, reduced endothelial barrier integrity and filling of the alveolar space with protein rich edema fluid and infiltrating leukocytes. Animal models are critical to uncovering the pathologic mechanisms of this devastating syndrome. Intravital imaging of the intact lung via two-photon intravital microscopy has proven a valuable method to investigate lung injury in small rodent models through characterization of inflammatory cells and vascular changes in real time. However, respiratory motion complicates the analysis of these time series images and requires selective data extraction to stabilize the image. Consequently, analysis of individual alveoli may not provide a complete picture of the integrated mechanical, vascular and inflammatory processes occurring simultaneously in the intact lung. To address these challenges, we developed a web browser-based visualization application named Alveolus Analysis to process, analyze and graphically display intravital lung microscopy data.

RESULTS

The designed tool takes raw temporal image data as input, performs image preprocessing and feature extraction offline, and visualizes the extracted information in a web browser-based interface. The interface allows users to explore multiple experiments in three panels corresponding to different levels of detail: summary statistics of alveolar/neutrophil behavior, characterization of alveolar dynamics including lung edema and inflammatory cells at specific time points, and cross-experiment analysis. We performed a case study on the utility of the visualization with two members or our research team and they found the tool useful because of its ability to preprocess data consistently and visualize information in a digestible and informative format.

CONCLUSIONS

Application of our software tool, Alveolus Analysis, to intravital lung microscopy data has the potential to enhance the information gained from these experiments and provide new insights into the pathologic mechanisms of inflammatory lung injury.

A Tale of Two Centers: Visual Exploration of Health Disparities in Cancer Care

The annual incidence of head and neck cancers (HNC) worldwide is more than 550,000 cases, with around 300,000 deaths each year. However, the incidence rates and disease-characteristics of HNC differ between treatment centers and different populations, due to undetermined reasons, which may or not include socioeconomic factors. The multi-faceted and multi-variate nature of the data in the context of the emerging field of health disparities research makes automated analysis impractical. Hence, we present a visual analysis approach to explore the health disparities in the data of HNC patients from two different cohorts at two cancer care centers. Our approach integrates data from multiple sources, including census data and city data, with custom visual encodings and with a nearest neighbor approach. Our design, created in collaboration with oncology experts, makes it possible to analyze the patients' demographic, disease characteristics, treatments and outcomes, and to make significant comparisons of these two cohorts and of individual patients. We evaluate this approach through two case studies performed with domain experts. The results demonstrate that this visual analysis approach successfully accomplishes the goal of comparing two cohorts in terms of different significant factors, and can provide insights into the main source of health disparities between the two centers.

THALIS: Human-Machine Analysis of Longitudinal Symptoms in Cancer Therapy

Although cancer patients survive years after oncologic therapy, they are plagued with long-lasting or permanent residual symptoms, whose severity, rate of development, and resolution after treatment vary largely between survivors. The analysis and interpretation of symptoms is complicated by their partial co-occurrence, variability across populations and across time, and, in the case of cancers that use radiotherapy, by further symptom dependency on the tumor location and prescribed treatment. We describe THALIS, an environment for visual analysis and knowledge discovery from cancer therapy symptom data, developed in close collaboration with oncology experts. Our approach leverages unsupervised machine learning methodology over cohorts of patients, and, in conjunction with custom visual encodings and interactions, provides context for new patients based on patients with similar diagnostic features and symptom evolution. We evaluate this approach on data collected from a cohort of head and neck cancer patients. Feedback from our clinician collaborators indicates that THALIS supports knowledge discovery beyond the limits of machines or humans alone, and that it serves as a valuable tool in both the clinic and symptom research.

A User-Centered Design Study in Scientific Visualization Targeting Domain Experts

The development of usable visualization solutions is essential for ensuring both their adoption and effectiveness. User-centered design principles, which involve users throughout the entire development process, have been shown to be effective in numerous information visualization endeavors. We describe how we applied these principles in scientific visualization over a two year collaboration to develop a hybrid in situ/post hoc solution tailored towards combustion researcher needs. Furthermore, we examine the importance of user-centered design and lessons learned over the design process in an effort to aid others seeking to develop effective scientific visualization solutions.

A spatial neighborhood methodology for computing and analyzing lymph node carcinoma similarity in precision medicine

Precision medicine seeks to tailor therapy to the individual patient, based on statistical correlates from patients who are similar to the one under consideration. These correlates can and should go beyond genetics, and in general, beyond tabular or array data that can be easily represented computationally and compared. For example, in many types of cancer, cancer treatment and toxicity depend in large measure on the spatial disease spread-e.g., metastasizes to regional lymph nodes in head and neck cancer. However, there is currently a lack of methodology for integrating spatial information when considering patient similarity. We present a novel modeling methodology for the comparison of cancer patients within a cohort, based on the spatial spread of the lymph nodes affected in each patient. The method uses a topological map, bigrams, and hierarchical clustering to group patients based on their similarity. We compare this approach against a nonspatial (categorical) similarity approach where patients are binned solely by their affected nodes. We present similarity results on a 582 head and neck cancer patient cohort, along with two visual abstractions for analysis of the results, and we present clinician feedback. Our novel methodology partitions a patient cohort into clinically meaningful groups more susceptible to treatment side-effects. Such spatially-aware similarity approaches can help maximize the effectiveness of each patient's treatment.

Visual Analytics for Electromagnetic Situation Awareness in Radio Monitoring and Management

Traditional radio monitoring and management largely depend on radio spectrum data analysis, which requires considerable domain experience and heavy cognition effort and frequently results in incorrect signal judgment and incomprehensive situation awareness. Faced with increasingly complicated electromagnetic environments, radio supervisors urgently need additional data sources and advanced analytical technologies to enhance their situation awareness ability. This paper introduces a visual analytics approach for electromagnetic situation awareness. Guided by a detailed scenario and requirement analysis, we first propose a signal clustering method to process radio signal data and a situation assessment model to obtain qualitative and quantitative descriptions of the electromagnetic situations. We then design a two-module interface with a set of visualization views and interactions to help radio supervisors perceive and understand the electromagnetic situations by a joint analysis of radio signal data and radio spectrum data. Evaluations on real-world data sets and an interview with actual users demonstrate the effectiveness of our prototype system. Finally, we discuss the limitations of the proposed approach and provide future work directions.

Cohort-based T-SSIM Visual Computing for Radiation Therapy Prediction and Exploration

We describe a visual computing approach to radiation therapy (RT) planning, based on spatial similarity within a patient cohort. In radiotherapy for head and neck cancer treatment, dosage to organs at risk surrounding a tumor is a large cause of treatment toxicity. Along with the availability of patient repositories, this situation has lead to clinician interest in understanding and predicting RT outcomes based on previously treated similar patients. To enable this type of analysis, we introduce a novel topology-based spatial similarity measure, T-SSIM, and a predictive algorithm based on this similarity measure. We couple the algorithm with a visual steering interface that intertwines visual encodings for the spatial data and statistical results, including a novel parallel-marker encoding that is spatially aware. We report quantitative results on a cohort of 165 patients, as well as a qualitative evaluation with domain experts in radiation oncology, data management, biostatistics, and medical imaging, who are collaborating remotely.

Visual Analysis of a Smart City’s Energy Consumption

Through the use of open data portals, cities, districts and countries are increasingly making available energy consumption data. These data have the potential to inform both policymakers and local communities. At the same time, however, these datasets are large and complicated to analyze. We present the activity-centered-design, from requirements to evaluation, of a web-based visual analysis tool to explore energy consumption in Chicago. The resulting application integrates energy consumption data and census data, making it possible for both amateurs and experts to analyze disaggregated datasets at multiple levels of spatial aggregation and to compare temporal and spatial differences. An evaluation through case studies and qualitative feedback demonstrates that this visual analysis application successfully meets the goals of integrating large, disaggregated urban energy consumption datasets and of supporting analysis by both lay users and experts.

Precision Risk Analysis of Cancer Therapy with Interactive Nomograms and Survival Plots

We present the design and evaluation of an integrated problem solving environment for cancer therapy analysis. The environment intertwines a statistical martingale model and a K Nearest Neighbor approach with visual encodings, including novel interactive nomograms, in order to compute and explain a patient's probability of survival as a function of similar patient results. A coordinated views paradigm enables exploration of the multivariate, heterogeneous and few-valued data from a large head and neck cancer repository. A visual scaffolding approach further enables users to build from familiar representations to unfamiliar ones. Evaluation with domain experts show how this visualization approach and set of streamlined workflows enable the systematic and precise analysis of a patient prognosis in the context of cohorts of similar patients. We describe the design lessons learned from this successful, multi-site remote collaboration.

DarkSky Halos: Use-Based Exploration of Dark Matter Formation Data in a Hybrid Immersive Virtual Environment

Hybrid virtual reality environments allow analysts to choose how much of the screen real estate they want to use for Virtual Reality (VR) immersion, and how much they want to use for displaying different types of 2D data. We present the use-based design and evaluation of an immersive visual analytics application for cosmological data that uses such a 2D/3D hybrid environment. The applications is a first-in-kind immersive instantiation of the Activity-Centered-Design theoretical paradigm, as well as a first documented immersive instantiation of a details-first paradigm based on scientific workflow theory. Based on a rigorous analysis of the user activities and on a details-first paradigm, the application was designed to allow multiple domain experts to interactively analyze visual representations of spatial (3D) and nonspatial (2D) cosmology data pertaining to dark matter formation. These hybrid data are represented at multiple spatiotemporal scales as time-aligned merger trees, pixel-based heatmaps, GPU-accelerated point clouds and geometric primitives, which can further be animated according to simulation data and played back for analysis. We have demonstrated this multi-scale application to several groups of lay users and domain experts, as well as to two senior domain experts from the Adler Planetarium, who have significant experience in immersive environments. Their collective feedback shows that this hybrid, immersive application can assist researchers in the interactive visual analysis of large-scale cosmological simulation data while overcoming navigation limitations of desktop visualizations.

A Framework for Creative Visualization-Opportunities Workshops

Applied visualization researchers often work closely with domain collaborators to explore new and useful applications of visualization. The early stages of collaborations are typically time consuming for all stakeholders as researchers piece together an understanding of domain challenges from disparate discussions and meetings. A number of recent projects, however, report on the use of creative visualization-opportunities (CVO) workshops to accelerate the early stages of applied work, eliciting a wealth of requirements in a few days of focused work. Yet, there is no established guidance for how to use such workshops effectively. In this paper, we present the results of a 2-year collaboration in which we analyzed the use of 17 workshops in 10 visualization contexts. Its primary contribution is a framework for CVO workshops that: 1) identifies a process model for using workshops; 2) describes a structure of what happens within effective workshops; 3) recommends 25 actionable guidelines for future workshops; and 4) presents an example workshop and workshop methods. The creation of this framework exemplifies the use of critical reflection to learn about visualization in practice from diverse studies and experience.

Details-First, Show Context, Overview Last: Supporting Exploration of Viscous Fingers in Large-Scale Ensemble Simulations

Visualization research often seeks designs that first establish an overview of the data, in accordance to the information seeking mantra: "Overview first, zoom and filter, then details on demand". However, in computational fluid dynamics (CFD), as well as in other domains, there are many situations where such a spatial overview is not relevant or practical for users, for example when the experts already have a good mental overview of the data, or when an analysis of a large overall structure may not be related to the specific, information-driven tasks of users. Using scientific workflow theory and, as a vehicle, the problem of viscous finger evolution, we advocate an alternative model that allows domain experts to explore features of interest first, then explore the context around those features, and finally move to a potentially unfamiliar summarization overview. In a model instantiation, we show how a computational back-end can identify and track over time low-level, small features, then be used to filter the context of those features while controlling the complexity of the visualization, and finally to summarize and compare simulations. We demonstrate the effectiveness of this approach with an online web-based exploration of a total volume of data approaching half a billion seven-dimensional data points, and report supportive feedback provided by domain experts with respect to both the instantiation and the theoretical model.