The visualization and analysis of street and pedestrian networks are important to various domain experts, including urban planners, climate researchers, and health experts. This has led to the development of new techniques for street and pedestrian network visualization, expanding possibilities for effective data presentation and interpretation. Despite their increasing adoption, there is no established design framework to guide the creation of these visualizations while addressing the diverse requirements of various domains. When exploring a feature of interest, domain experts often need to transform, integrate, and visualize a combination of thematic data (e.g., demographic, socioeconomic, pollution) and physical data (e.g., zip codes, street networks), often spanning multiple spatial and temporal scales. This not only complicates the process of visual data exploration and system implementation for developers but also creates significant entry barriers for experts who lack a background in programming. With this in mind, in this paper, we reviewed 45 studies utilizing street-overlaid visualizations to understand how they are applied in practice. Through qualitative coding of these visualizations, we analyzed three key aspects of street and pedestrian network visualization usage: their analytical purposes, the visualization approaches employed, and the data sources used in their creation. Building on this design space, we introduce StreetWeave, a declarative grammar for designing custom visualizations of multivariate spatial network data across multiple resolutions. We demonstrate how StreetWeave can be used to create various street-overlaid visualizations, enabling effective exploration and analysis of spatial data. StreetWeave is available at urbantk.org/streetweave.

Abstract In the biomedical domain, taxonomies organize the acquisition modalities of scientific images in hierarchical structures. Such taxonomies leverage large sets of correct image labels and provide essential information about the importance of a scientific publication, which could then be used in biocuration tasks. However, the hierarchical nature of the labels, the overhead of processing images, the absence or incompleteness of labelled data and the expertise required to label this type of data impede the creation of useful datasets for biocuration. From a multi‐year collaboration with biocurators and text‐mining researchers, we derive an iterative visual analytics and active learning (AL) strategy to address these challenges. We implement this strategy in a system called BI‐LAVA—Biocuration with Hierarchical Image Labelling through Active Learning and Visual Analytics. BI‐LAVA leverages a small set of image labels, a hierarchical set of image classifiers and AL to help model builders deal with incomplete ground‐truth labels, target a hierarchical taxonomy of image modalities and classify a large pool of unlabelled images. BI‐LAVA's front end uses custom encodings to represent data distributions, taxonomies, image projections and neighbourhoods of image thumbnails, which help model builders explore an unfamiliar image dataset and taxonomy and correct and generate labels. An evaluation with machine learning practitioners shows that our mixed human–machine approach successfully supports domain experts in understanding the characteristics of classes within the taxonomy, as well as validating and improving data quality in labelled and unlabelled collections.

Patient-Reported Outcomes (PRO) consist of information provided directly by the patients about their health status including symptom ratings. PROs are commonly used in clinical practice to support clinical decision-making and have recently been incorporated into machine learning models to improve risk prediction. In this work, we aim to evaluate whether the inclusion of a patient stratification based on 12-month post-treatment predicted Patient Reported Outcomes improves risk prediction of radiation-induced toxicity and overall survival for head and neck cancer patients. A bidirectional long-short term memory (Bi-LSTM) recurrent neural network was used to model the longitudinal PRO data and to predict symptom ratings 12 months post-treatment. Patients were stratified using hierarchical clustering over the LSTM-predicted data. A logistic regression model was trained to predict Xerostomia at 12 months and a Cox regression model to predict overall survival. Results show that the inclusion of symptom burden clusters derived from the predicted Patient Reported Outcomes improves radiation-induced toxicity and overall survival prediction for head and neck cancer patients.

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.

Abstract We present a visual computing framework for analysing moral rhetoric on social media around controversial topics. Using Moral Foundation Theory, we propose a methodology for deconstructing and visualizing the when, where and who behind each of these moral dimensions as expressed in microblog data. We characterize the design of this framework, developed in collaboration with experts from language processing, communications and causal inference. Our approach integrates microblog data with multiple sources of geospatial and temporal data, and leverages unsupervised machine learning (generalized additive models) to support collaborative hypothesis discovery and testing. We implement this approach in a system named MOTIV. We illustrate this approach on two problems, one related to Stay‐at‐home policies during the COVID‐19 pandemic, and the other related to the Black Lives Matter movement. Through detailed case studies and discussions with collaborators, we identify several insights discovered regarding the different drivers of moral sentiment in social media. Our results indicate that this visual approach supports rapid, collaborative hypothesis testing, and can help give insights into the underlying moral values behind controversial political issues. Supplemental Material: https://osf.io/ygkzn/?view_only=6310c0886938415391d977b8aae8b749

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.

Biocuration is the process of analyzing biological or biomedical articles to organize biological data into data repositories using taxonomies and ontologies. Due to the expanding number of articles and the relatively small number of biocurators, automation is desired to improve the workflow of assessing articles worth curating. As figures convey essential information, automatically integrating images may improve curation. In this work, we instantiate and evaluate a first-in-kind, hybrid image+text document search system for biocuration. The system, MouseScholar, leverages an image modality taxonomy derived in collaboration with biocurators, in addition to figure segmentation, and classifiers components as a back-end and a streamlined front-end interface to search and present document results. We formally evaluated the system with ten biocurators on a mouse genome informatics biocuration dataset and collected feedback. The results demonstrate the benefits of blending text and image information when presenting scientific articles for biocuration.

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.

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.

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.

With the onset of the COVID-19 pandemic, a number of public policy measures have been developed to curb the spread of the virus. However, little is known about the attitudes towards stay-at-home orders expressed on social media despite the fact that social media are central platforms for expressing and debating personal attitudes. To address this gap, we analyze the prevalence and framing of attitudes towards stay-at-home policies, as expressed on Twitter in the early months of the pandemic. We focus on three aspects of tweets: whether they contain an attitude towards stay-at-home measures, whether the attitude was for or against, and the moral justification for the attitude, if any. We collect and annotate a dataset of stay-at-home tweets and create classifiers that enable large-scale analysis of the relationship between moral frames and stay-at-home attitudes and their temporal evolution. Our findings suggest that frames of care are correlated with a supportive stance, whereas freedom and oppression signify an attitude against stay-at-home directives. There was widespread support for stay-at-home orders in the early weeks of lockdowns, followed by increased resistance toward the end of May and the beginning of June 2020. The resistance was associated with moral judgment that mapped to political divisions.

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.

Figures within biomedical articles present essential evidence of the relevance of a publication in a curation workflow. In particular, visual cues of the image modality or experimental methods can help expert curators identify relevant papers from an increasing number of publications. Automating the identification of these content-bearing images can thus be helpful in computer-assisted curation. However, the paucity of labeled datasets and the specialized training required to label such images hinder the development of such tools. To address this problem, we present the design of ANIMO, a labeling system that integrates extraction and segmentation tools to ease the annotation burden. We first introduce two taxonomies of image modalities and experimental methods, derived in collaboration with curators. On the back-end of the system, we process batches of documents and create a labeling task per document. At the front-end, expert curators can access these tasks through a web interface and access the article of interest. We describe the evaluation of this system by a group of biocurators, and the human factor lessons learned from this interdisciplinary experience.

Patient-Reported Outcome (PRO) surveys are used to monitor patients' symptoms during and after cancer treatment. Acute symptoms refer to those experienced during treatment and late symptoms refer to those experienced after treatment. While most patients experience severe symptoms during treatment, these usually subside in the late stage. However, for some patients, late toxicities persist negatively affecting the patient's quality of life (QoL). In the case of head and neck cancer patients, PRO surveys are recorded every week during the patient's visit to the clinic and at different follow-up times after the treatment has concluded. In this paper, we model the PRO data as a time-series and apply Long-Short Term Memory (LSTM) neural networks for predicting symptom severity in the late stage. The PRO data used in this project corresponds to MD Anderson Symptom Inventory (MDASI) questionnaires collected from head and neck cancer patients treated at the MD Anderson Cancer Center. We show that the LSTM model is effective in predicting symptom ratings under the RMSE and NRMSE metrics. Our experiments show that the LSTM model also outperforms other machine learning models and time-series prediction models for these data.

Bioinformatics (2021), Volume 37(Suppl1), i468–i476, doi:10.1093/bioinformatics/btab331 The error is thus only in mis-typing the formulae themselves; not in the actual calculations of the precision and the recall used throughout the paper. As such, the other parts of the manuscript – specifically the experimental results reported, all stand as they appear in the original publication, and are not impacted by this correction.

MOTIVATION: Biomedical research findings are typically disseminated through publications. To simplify access to domain-specific knowledge while supporting the research community, several biomedical databases devote significant effort to manual curation of the literature-a labor intensive process. The first step toward biocuration requires identifying articles relevant to the specific area on which the database focuses. Thus, automatically identifying publications relevant to a specific topic within a large volume of publications is an important task toward expediting the biocuration process and, in turn, biomedical research. Current methods focus on textual contents, typically extracted from the title-and-abstract. Notably, images and captions are often used in publications to convey pivotal evidence about processes, experiments and results. RESULTS: We present a new document classification scheme, using both image and caption information, in addition to titles-and-abstracts. To use the image information, we introduce a new image representation, namely Figure-word, based on class labels of subfigures. We use word embeddings for representing captions and titles-and-abstracts. To utilize all three types of information, we introduce two information integration methods. The first combines Figure-words and textual features obtained from captions and titles-and-abstracts into a single larger vector for document representation; the second employs a meta-classification scheme. Our experiments and results demonstrate the usefulness of the newly proposed Figure-words for representing images. Moreover, the results showcase the value of Figure-words, captions and titles-and-abstracts in providing complementary information for document classification; these three sources of information when combined, lead to an overall improved classification performance. AVAILABILITY AND IMPLEMENTATION: Source code and the list of PMIDs of the publications in our datasets are available upon request.

Microscopy images are pervasive in biomedical research publications, where images obtained through various microscopy modalities (light, fluorescence, scanning, transmission) are often used to describe and summarize experiments and contributions. Hence, there is growing interest in automatically identifying these microscopy images' modality and utilizing this knowledge in automated search tools. However, identifying microscopy images poses challenges due to a lack of extensive collections of labeled images. We describe and evaluate two alternative approaches to microscopy image classification. In the first approach, we progressively fine-tuned layers of ResNet models. The second approach uses shallow variants of ResNet networks, where we leverage the outputs from previous convolutional blocks. We compare these results against a Support Vector Machine (SVM)-based baseline. Our results show that fine-tuning specific layers yields better results than fine-tuning the whole model. Furthermore, shallower variants produce competitive results when compared to the entire fine-tuned model.

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.

Biological network figures are ubiquitous in the biology and medical literature. On the one hand, a good network figure can quickly provide information about the nature and degree of interactions between items and enable inferences about the reason for those interactions. On the other hand, good network figures are difficult to create. In this paper, we outline 10 simple rules for creating biological network figures for communication, from choosing layouts, to applying color or other channels to show attributes, to the use of layering and separation. These rules are accompanied by illustrative examples. We also provide a concise set of references and additional resources for each rule.

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.

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.

Although visualization design models exist in the literature in the form of higher-level methodological frameworks, these models do not present a clear methodological prescription for the domain characterization step. This work presents a framework and end-to-end model for requirements engineering in problem-driven visualization application design. The framework and model are based on the activity-centered design paradigm, which is an enhancement of human-centered design. The proposed activity-centered approach focuses on user tasks and activities, and allows an explicit link between the requirements engineering process with the abstraction stage-and its evaluation-of existing, higher-level visualization design models. In a departure from existing visualization design models, the resulting model: assigns value to a visualization based on user activities; ranks user tasks before the user data; partitions requirements in activity-related capabilities and nonfunctional characteristics and constraints; and explicitly incorporates the user workflows into the requirements process. A further merit of this model is its explicit integration of functional specifications, a concept this work adapts from the software engineering literature, into the visualization design nested model. A quantitative evaluation using two sets of interdisciplinary projects supports the merits of the activity-centered model. The result is a practical roadmap to the domain characterization step of visualization design for problem-driven data visualization. Following this domain characterization model can help remove a number of pitfalls that have been identified multiple times in the visualization design literature.

BACKGROUND: Visualizing the complex probability landscape of stochastic gene regulatory networks can further biologists' understanding of phenotypic behavior associated with specific genes. RESULTS: We present PRODIGEN (PRObability DIstribution of GEne Networks), a web-based visual analysis tool for the systematic exploration of probability distributions over simulation time and state space in such networks. PRODIGEN was designed in collaboration with bioinformaticians who research stochastic gene networks. The analysis tool combines in a novel way existing, expanded, and new visual encodings to capture the time-varying characteristics of probability distributions: spaghetti plots over one dimensional projection, heatmaps of distributions over 2D projections, enhanced with overlaid time curves to display temporal changes, and novel individual glyphs of state information corresponding to particular peaks. CONCLUSIONS: We demonstrate the effectiveness of the tool through two case studies on the computed probabilistic landscape of a gene regulatory network and of a toggle-switch network. Domain expert feedback indicates that our visual approach can help biologists: 1) visualize probabilities of stable states, 2) explore the temporal probability distributions, and 3) discover small peaks in the probability landscape that have potential relation to specific diseases.

High-throughput and high-resolution experimental methods in biology pose enormous challenges for current biological data visualization approaches. To address these challenges, researchers in the visualization and bioinformatics communities need to engage in the design, implementation, application, and evaluation of novel visualization techniques and tools that provide insight into large and highly complex data sets. BioVis 2015 - the fifth Symposium on Biological Data Visualization - brought together researchers from the visualization, bioinformatics, and biology communities to establish an interdisciplinary dialogue and promote the sharing of expertise between both meeting participants and the communities at large. The meeting educated, inspired, and engaged visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. The symposium serves as a platform for researchers from these fields to increase the impact of data visualization approaches in biology. The BioVis 2015 symposium is affiliated with ISMB, the Intelligent Systems for Molecular Biology conference, as a Special Interest Group (SIG) and was colocated with ISMB in Dublin, Ireland, July 10-11 2015. Each paper was reviewed by researchers from both the bioinformatics and visualization fields and was evaluated for improvements over state-of-the-art and for scientific soundness. The review process was organized in two review cycles. In the first review cycle, each paper was reviewed by three to four reviewers. In the second review cycle, the primary reviewers checked whether the required revisions for conditionally accepted papers were successfully included. Based on the reviewers' scores, reviews, and recommendations, the BioVis 2015 Paper and Publication Chairs and the BMC Bioinformatics Section Editor together selected those that would be published as a BMC Bioinformatics supplement. The papers from BioVis 2015 appear in two different proceedings: As of the 5th Symposium on Biological Data Visualization: Part 1 in this BMC Bioinformatics supplement and as of the 5th Symposium on Biological Data Visualization: Part 2 in BMC Proceedings (http://www.biomedcentral.com/bmcproc/supplements/9/S6). From the 21 papers submitted to BioVis 2015, 9 papers are published in this BMC Bioinformatics supplement and 5 papers are published in BMC Proceedings. The articles in this supplement cover a wide spectrum of challenging problems in biological data visualization and their solutions. Overall, three main themes arise from the BioVis 2015 articles: omics, proteins, and imaging. In the omics field, Younesy et al. [1] describe VisRseq: a user-friendly interface for biologists to use libraries in R that provides a method for linking R-apps with interactive components. Chelaru et al. [2] expand on the design behind Epiviz, another tool for bringing genome visualization and computational environments together. Hennig et al. [3] describe Pan-Tetris and Aurisano et al. [4] describe BactoGeNIE: both systems are designed for comparing different genomes. The XCluSim tool by L'Yi et al. [5] has a more general application field and aims to provide insight into how different clustering results relate to each other. In the protein field, Stolte et al. [6] give an overview of the design decisions that underlie Aquaria, a visual analytics tool for exploring protein-related data. Finally, three papers are included from the imaging field. Topics range from image generation, as discussed by Abdellah et al. [7], to a method for parameter optimization in image processing by Pretorius et al. [9] (e.g. for cell nuclei detection and colour deconvolution for histology), and all the way to graph-based exploration of histology images in the GRAPHIE system proposed by Ding et al. [8]. The diversity of topics covered in this issue highlights the wide range of challenges in applying existing visualization techniques to biological data. With this analysis and formalization of our collective experiences, we hope to motivate visualization researchers to think about new problems and new approaches to pressing problems in biology.

BACKGROUND: The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. RESULTS: In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. CONCLUSIONS: BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.

BACKGROUND: Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presents significant challenges that range from identifying structural similarities and differences between models to understanding how these differences affect system dynamics. RESULTS: We present the development and features of an interactive model exploration system, MOSBIE, which provides utilities for identifying similarities and differences between models within a family. Models are clustered using a custom similarity metric, and a visual interface is provided that allows a researcher to interactively compare the structures of pairs of models as well as view simulation results. CONCLUSIONS: We illustrate the usefulness of MOSBIE via two case studies in the cell signaling domain. We also present feedback provided by domain experts and discuss the benefits, as well as the limitations, of the approach.

We introduce a web-based computing infrastructure to assist the visual integration, mining and interactive navigation of large-scale astronomy observations. Following an analysis of the application domain, we design a client-server architecture to fetch distributed image data and to partition local data into a spatial index structure that allows prefix-matching of spatial objects. In conjunction with hardware-accelerated pixel-based overlays and an online cross-registration pipeline, this approach allows the fetching, displaying, panning and zooming of gigabit panoramas of the sky in real time. To further facilitate the integration and mining of spatial and non-spatial data, we introduce interactive trend images-compact visual representations for identifying outlier objects and for studying trends within large collections of spatial objects of a given class. In a demonstration, images from three sky surveys (SDSS, FIRST and simulated LSST results) are cross-registered and integrated as overlays, allowing cross-spectrum analysis of astronomy observations. Trend images are interactively generated from catalog data and used to visually mine astronomy observations of similar type. The front-end of the infrastructure uses the web technologies WebGL and HTML5 to enable cross-platform, web-based functionality. Our approach attains interactive rendering framerates; its power and flexibility enables it to serve the needs of the astronomy community. Evaluation on three case studies, as well as feedback from domain experts emphasize the benefits of this visual approach to the observational astronomy field; and its potential benefits to large scale geospatial visualization in general.

We present the design of a novel framework for the visual integration, comparison, and exploration of correlations in spatial and non-spatial geriatric research data. These data are in general high-dimensional and span both the spatial, volumetric domain--through magnetic resonance imaging volumes--and the non-spatial domain, through variables such as age, gender, or walking speed. The visual analysis framework blends medical imaging, mathematical analysis and interactive visualization techniques, and includes the adaptation of Sparse Partial Least Squares and iterated Tikhonov Regularization algorithms to quantify potential neurologymobility connections. A linked-view design geared specifically at interactive visual comparison integrates spatial and abstract visual representations to enable the users to effectively generate and refine hypotheses in a large, multidimensional, and fragmented space. In addition to the domain analysis and design description, we demonstrate the usefulness of this approach on two case studies. Last, we report the lessons learned through the iterative design and evaluation of our approach, in particular those relevant to the design of comparative visualization of spatial and non-spatial data.

Students usually do not study individually; instead, they tend to study collaboratively. The “power of known peers” can be embraced to provide implicit navigation support for collaborative social e-learning environments. In this paper, we present a novel approach to collaborative e-learning through

This demo presents AstroShelf, our on-going effort to enable astrophysicists to collaboratively investigate celestial objects using data originating from multiple sky surveys, hosted at different sites. The AstroShelf platform combines database and data stream, workflow and visualization technologies to provide a means for querying and displaying telescope images (in a Google Sky manner), visualizations of spectrum data, and for managing annotations. In addition to the user interface, AstroShelf supports a programmatic interface (available as a web service), which allows astrophysicists to incorporate functionality from AstroShelf in their own programs. A key feature is Live Annotations which is the detection and delivery of events or annotations to users in real-time, based on their profiles. We demonstrate the capabilities of AstroShelf through real end-user exploration scenarios (with participation from "stargazers" in the audience), in the presence of simulated annotation workloads executed through web services.

BACKGROUND: Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, to make specification of models less error prone, and to improve workflows. RESULTS: We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry. We present the user requirements, visual paradigms, algorithms and design decisions behind RuleBender, with emphasis on visual global/local model exploration and integrated execution of simulations. The support of RBM creation, debugging, and interactive visualization expedites the RBM learning process and reduces model construction time; while built-in model simulation and results with multiple linked views streamline the execution and analysis of newly created models and generated networks. CONCLUSION: RuleBender has been adopted as both an educational and a research tool and is available as a free open source tool at http://www.rulebender.org. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community.

Abstract Summary: Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling intracellular biochemistry. Current interfaces for RBM are predominantly text-based and command-line driven. Better visual tools are needed to make RBM accessible to a broad range of users, to make specification of models less error prone and to improve workflows. We present RULEBENDER, an open-source visual interface that facilitates interactive debugging, simulation and analysis of RBMs. Availability: RULEBENDER is freely available for Mac, Windows and Linux at http://rulebender.org. Contact: [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract We present The Chinese Room, a visualization interface that allows users to explore and interact with a multitude of linguistic resources in order to decode and correct poor machine translations. The target users of The Chinese Room are not bilingual and are not familiar with machine translation technologies. We investigate the ability of our system to assist such users in decoding and correcting faulty machine translations. We found that by collaborating with our application, end‐users can overcome many difficult translation errors and disambiguate translated passages that were otherwise baffling. We also examine the utility of our system to machine translation researchers. Anecdotal evidence suggests that The Chinese Room can help such researchers develop better machine translation systems.

Abstract-Orthopedists invest significant amounts of effort and time trying to understand the biomechanics of arthrodial (gliding) joints. Although new image acquisition and processing methods currently generate richer-than-ever geometry and kinematic data sets that are individual specific, the computational and visualization tools needed to enable the comparative analysis and exploration of these data sets lag behind. In this paper, we present a framework that enables the cross-data-set visual exploration and analysis of arthrodial joint biomechanics. Central to our approach is a computer-vision-inspired markerless method for establishing pairwise correspondences between individual-specific geometry. Manifold models are subsequently defined and deformed from one individual-specific geometry to another such that the markerless correspondences are preserved while minimizing model distortion. The resulting mutually consistent parameterization and visualization allow the users to explore the similarities and differences between two data sets and to define meaningful quantitative measures. We present two applications of this framework to human-wrist data: articular cartilage transfer from cadaver data to in vivo data and cross-data-set kinematics analysis. The method allows our users to combine complementary geometries acquired through different modalities and thus overcome current imaging limitations. The results demonstrate that the technique is useful in the study of normal and injured anatomy and kinematics of arthrodial joints. In principle, the pairwise cross-parameterization method applies to all spherical topology data from the same class and should be particularly beneficial in instances where identifying salient object features is a nontrivial task.

We present a method for registering the position and orientation of bones across multiple computed-tomography (CT) volumes of the same subject. The method is subvoxel accurate, can operate on multiple bones within a set of volumes, and registers bones that have features commensurate in size to the voxel dimension. First, a geometric object model is extracted from a reference volume image. We use then unsupervised tissue classification to generate from each volume to be registered a super-resolution distance field--a scalar field that specifies, at each point, the signed distance from the point to a material boundary. The distance fields and the geometric bone model are finally used to register an object through the sequence of CT images. In the case of multiobject structures, we infer a motion-directed hierarchy from the distance-field information that allows us to register objects that are not within each other's capture region. We describe a validation framework and evaluate the new technique in contrast with grey-value registration. Results on human wrist data show average accuracy improvements of 74% over grey-value registration. The method is of interest to any intrasubject, same-modality registration applications where subvoxel accuracy is desired.

We present JointViewer, a software tool to aid orthopedics researchers in exploring complex, in-vivo joint kinematics. Given bone-geometry data and bone-motion information, JointViewer models and visualizes bone inter-spacing in the joint. Next, it proposes and displays plausible ligament paths which connect bones together. Both types of models are constructed through a distancefield approach. Users can maneuver the bones in a joint for better viewing, see motion relative to a specific bone, or remove bones from a joint. We demonstrate JointViewer’s effectiveness in three applications: examining normal human wrist kinematics, capturing the effect of injury on forearm kinematics, and exploring the kinematic constraints imposed by ligaments in a pigeon shoulder. In all applications, the system effectively highlights subtle yet important relationships among bones and soft-tissue that in previous standard joint visualizations had gone unnoticed.