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1.
IEEE Trans Vis Comput Graph ; 29(1): 504-514, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36155455

RESUMO

The trouble with data is that it frequently provides only an imperfect representation of a phenomenon of interest. Experts who are familiar with their datasets will often make implicit, mental corrections when analyzing a dataset, or will be cautious not to be overly confident about their findings if caveats are present. However, personal knowledge about the caveats of a dataset is typically not incorporated in a structured way, which is problematic if others who lack that knowledge interpret the data. In this work, we define such analysts' knowledge about datasets as data hunches. We differentiate data hunches from uncertainty and discuss types of hunches. We then explore ways of recording data hunches, and, based on a prototypical design, develop recommendations for designing visualizations that support data hunches. We conclude by discussing various challenges associated with data hunches, including the potential for harm and challenges for trust and privacy. We envision that data hunches will empower analysts to externalize their knowledge, facilitate collaboration and communication, and support the ability to learn from others' data hunches.

2.
IEEE Trans Vis Comput Graph ; 28(1): 248-258, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34587022

RESUMO

Which drug is most promising for a cancer patient? A new microscopy-based approach for measuring the mass of individual cancer cells treated with different drugs promises to answer this question in only a few hours. However, the analysis pipeline for extracting data from these images is still far from complete automation: human intervention is necessary for quality control for preprocessing steps such as segmentation, adjusting filters, removing noise, and analyzing the result. To address this workflow, we developed Loon, a visualization tool for analyzing drug screening data based on quantitative phase microscopy imaging. Loon visualizes both derived data such as growth rates and imaging data. Since the images are collected automatically at a large scale, manual inspection of images and segmentations is infeasible. However, reviewing representative samples of cells is essential, both for quality control and for data analysis. We introduce a new approach for choosing and visualizing representative exemplar cells that retain a close connection to the low-level data. By tightly integrating the derived data visualization capabilities with the novel exemplar visualization and providing selection and filtering capabilities, Loon is well suited for making decisions about which drugs are suitable for a specific patient.


Assuntos
Gráficos por Computador , Microscopia , Automação , Humanos , Processamento de Imagem Assistida por Computador
3.
IEEE Trans Vis Comput Graph ; 27(2): 1106-1116, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33048719

RESUMO

Design study is an established approach of conducting problem-driven visualization research. The academic visualization community has produced a large body of work for reporting on design studies, informed by a handful of theoretical frameworks, and applied to a broad range of application areas. The result is an abundance of reported insights into visualization design, with an emphasis on novel visualization techniques and systems as the primary contribution of these studies. In recent work we proposed a new, interpretivist perspective on design study and six companion criteria for rigor that highlight the opportunities for researchers to contribute knowledge that extends beyond visualization idioms and software. In this work we conducted a year-long collaboration with evolutionary biologists to develop an interactive tool for visual exploration of multivariate datasets and phylogenetic trees. During this design study we experimented with methods to support three of the rigor criteria: ABUNDANT, REFLEXIVE, and TRANSPARENT. As a result we contribute two novel visualization techniques for the analysis of multivariate phylogenetic datasets, three methodological recommendations for conducting design studies drawn from reflections over our process of experimentation, and two writing devices for reporting interpretivist design study. We offer this work as an example for implementing the rigor criteria to produce a diverse range of knowledge contributions.


Assuntos
Gráficos por Computador , Software , Filogenia , Projetos de Pesquisa
4.
IEEE Trans Big Data ; 7(3): 524-534, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35693692

RESUMO

The size of large, geo-located datasets has reached scales where visualization of all data points is inefficient. Random sampling is a method to reduce the size of a dataset, yet it can introduce unwanted errors. We describe a method for subsampling of spatial data suitable for creating kernel density estimates from very large data and demonstrate that it results in less error than random sampling. We also introduce a method to ensure that thresholding of low values based on sampled data does not omit any regions above the desired threshold when working with sampled data. We demonstrate the effectiveness of our approach using both, artificial and real-world large geospatial datasets.

5.
Gigascience ; 9(1)2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31972021

RESUMO

BACKGROUND: Metabolic networks represent all chemical reactions that occur between molecular metabolites in an organism's cells. They offer biological context in which to integrate, analyze, and interpret omic measurements, but their large scale and extensive connectivity present unique challenges. While it is practical to simplify these networks by placing constraints on compartments and hubs, it is unclear how these simplifications alter the structure of metabolic networks and the interpretation of metabolomic experiments. RESULTS: We curated and adapted the latest systemic model of human metabolism and developed customizable tools to define metabolic networks with and without compartmentalization in subcellular organelles and with or without inclusion of prolific metabolite hubs. Compartmentalization made networks larger, less dense, and more modular, whereas hubs made networks larger, more dense, and less modular. When present, these hubs also dominated shortest paths in the network, yet their exclusion exposed the subtler prominence of other metabolites that are typically more relevant to metabolomic experiments. We applied the non-compartmental network without metabolite hubs in a retrospective, exploratory analysis of metabolomic measurements from 5 studies on human tissues. Network clusters identified individual reactions that might experience differential regulation between experimental conditions, several of which were not apparent in the original publications. CONCLUSIONS: Exclusion of specific metabolite hubs exposes modularity in both compartmental and non-compartmental metabolic networks, improving detection of relevant clusters in omic measurements. Better computational detection of metabolic network clusters in large data sets has potential to identify differential regulation of individual genes, transcripts, and proteins.


Assuntos
Biologia Computacional , Metabolismo Energético , Redes e Vias Metabólicas , Metabolômica , Modelos Biológicos , Biologia Computacional/métodos , Humanos , Metabolômica/métodos , Software , Interface Usuário-Computador , Navegador
6.
PLoS Comput Biol ; 15(9): e1007244, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31557157

RESUMO

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.


Assuntos
Biologia Computacional/métodos , Gráficos por Computador , Atenção , Cor , Humanos , Mapas de Interação de Proteínas/fisiologia , Transdução de Sinais/fisiologia , Percepção Visual
7.
Appl Clin Inform ; 10(2): 278-285, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-31018234

RESUMO

OBJECTIVE: Visual cohort analysis utilizing electronic health record data has become an important tool in clinical assessment of patient outcomes. In this article, we introduce Composer, a visual analysis tool for orthopedic surgeons to compare changes in physical functions of a patient cohort following various spinal procedures. The goal of our project is to help researchers analyze outcomes of procedures and facilitate informed decision-making about treatment options between patient and clinician. METHODS: In collaboration with orthopedic surgeons and researchers, we defined domain-specific user requirements to inform the design. We developed the tool in an iterative process with our collaborators to develop and refine functionality. With Composer, analysts can dynamically define a patient cohort using demographic information, clinical parameters, and events in patient medical histories and then analyze patient-reported outcome scores for the cohort over time, as well as compare it to other cohorts. Using Composer's current iteration, we provide a usage scenario for use of the tool in a clinical setting. CONCLUSION: We have developed a prototype cohort analysis tool to help clinicians assess patient treatment options by analyzing prior cases with similar characteristics. Although Composer was designed using patient data specific to orthopedic research, we believe the tool is generalizable to other healthcare domains. A long-term goal for Composer is to develop the application into a shared decision-making tool that allows translation of comparison and analysis from a clinician-facing interface into visual representations to communicate treatment options to patients.


Assuntos
Estudos de Coortes , Registros Eletrônicos de Saúde , Interface Usuário-Computador , Humanos , Resultado do Tratamento
8.
IEEE Trans Vis Comput Graph ; 25(3): 1543-1558, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-29993603

RESUMO

The majority of diseases that are a significant challenge for public and individual heath are caused by a combination of hereditary and environmental factors. In this paper we introduce Lineage, a novel visual analysis tool designed to support domain experts who study such multifactorial diseases in the context of genealogies. Incorporating familial relationships between cases with other data can provide insights into shared genomic variants and shared environmental exposures that may be implicated in such diseases. We introduce a data and task abstraction, and argue that the problem of analyzing such diseases based on genealogical, clinical, and genetic data can be mapped to a multivariate graph visualization problem. The main contribution of our design study is a novel visual representation for tree-like, multivariate graphs, which we apply to genealogies and clinical data about the individuals in these families. We introduce data-driven aggregation methods to scale to multiple families. By designing the genealogy graph layout to align with a tabular view, we are able to incorporate extensive, multivariate attributes in the analysis of the genealogy without cluttering the graph. We validate our designs by conducting case studies with our domain collaborators.


Assuntos
Gráficos por Computador , Doença/genética , Genômica/métodos , Linhagem , Algoritmos , Bases de Dados Genéticas , Feminino , Genealogia e Heráldica , Humanos , Masculino
9.
Artigo em Inglês | MEDLINE | ID: mdl-30188828

RESUMO

Analyzing large, multivariate graphs is an important problem in many domains, yet such graphs are challenging to visualize. In this paper, we introduce a novel, scalable, tree+table multivariate graph visualization technique, which makes many tasks related to multivariate graph analysis easier to achieve. The core principle we follow is to selectively query for nodes or subgraphs of interest and visualize these subgraphs as a spanning tree of the graph. The tree is laid out linearly, which enables us to juxtapose the nodes with a table visualization where diverse attributes can be shown. We also use this table as an adjacency matrix, so that the resulting technique is a hybrid node-link/adjacency matrix technique. We implement this concept in Juniper and complement it with a set of interaction techniques that enable analysts to dynamically grow, restructure, and aggregate the tree, as well as change the layout or show paths between nodes. We demonstrate the utility of our tool in usage scenarios for different multivariate networks: a bipartite network of scholars, papers, and citation metrics and a multitype network of story characters, places, books, etc.

10.
BMC Bioinformatics ; 18(1): 406, 2017 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-28899361

RESUMO

BACKGROUND: With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data. RESULTS: In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes. CONCLUSIONS: Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.


Assuntos
Algoritmos , Interface Usuário-Computador , Análise por Conglomerados , Genótipo , Humanos , Internet , Neoplasias/classificação , Neoplasias/genética , Neoplasias/patologia , Fenótipo
11.
Bioinformatics ; 33(18): 2938-2940, 2017 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-28645171

RESUMO

MOTIVATION: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. RESULTS: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. AVAILABILITY AND IMPLEMENTATION: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/ . CONTACT: nils@hms.harvard.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Biologia Computacional/métodos , Software , Técnicas de Genotipagem/métodos , Análise de Sequência de DNA/métodos
12.
IEEE Trans Vis Comput Graph ; 22(1): 399-408, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26529712

RESUMO

Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets.


Assuntos
Processamento Alternativo/genética , Gráficos por Computador , Genômica/métodos , Modelos Genéticos
13.
Nat Methods ; 12(4): 281, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25825831
14.
Proc SIGCHI Conf Hum Factor Comput Syst ; CHI -apos14: 3705-3714, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25325078

RESUMO

Content on computer screens is often inaccessible to users because it is hidden, e.g., occluded by other windows, outside the viewport, or overlooked. In search tasks, the efficient retrieval of sought content is important. Current software, however, only provides limited support to visualize hidden occurrences and rarely supports search synchronization crossing application boundaries. To remedy this situation, we introduce two novel visualization methods to guide users to hidden content. Our first method generates awareness for occluded or out-of-viewport content using see-through visualization. For content that is either outside the screen's viewport or for data sources not opened at all, our second method shows off-screen indicators and an on-demand smart preview. To reduce the chances of overlooking content, we use visual links, i.e., visible edges, to connect the visible content or the visible representations of the hidden content. We show the validity of our methods in a user study, which demonstrates that our technique enables a faster localization of hidden content compared to traditional search functionality and thereby assists users in information retrieval tasks.

15.
BMC Proc ; 8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica): S5, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25237392

RESUMO

BACKGROUND: A complete understanding of the relationship between the amino acid sequence and resulting protein function remains an open problem in the biophysical sciences. Current approaches often rely on diagnosing functionally relevant mutations by determining whether an amino acid frequently occurs at a specific position within the protein family. However, these methods do not account for the biophysical properties and the 3D structure of the protein. We have developed an interactive visualization technique, Mu-8, that provides researchers with a holistic view of the differences of a selected protein with respect to a family of homologous proteins. Mu-8 helps to identify areas of the protein that exhibit: (1) significantly different bio-chemical characteristics, (2) relative conservation in the family, and (3) proximity to other regions that have suspect behavior in the folded protein. METHODS: Our approach quantifies and communicates the difference between a reference protein and its family based on amino acid indices or principal components of amino acid index classes, while accounting for conservation, proximity amongst residues, and overall 3D structure. RESULTS: We demonstrate Mu-8 in a case study with data provided by the 2013 BioVis contest. When comparing the sequence of a dysfunctional protein to its functional family, Mu-8 reveals several candidate regions that may cause function to break down.

17.
IEEE Comput Graph Appl ; 34(2): 38-47, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24808198

RESUMO

Dual analysis uses statistics to describe both the dimensions and rows of a high-dimensional dataset. Researchers have integrated it into StratomeX, a Caleydo view for cancer subtype analysis. In addition, significant-difference plots show the elements of a candidate subtype that differ significantly from other subtypes, thus letting analysts characterize subtypes. Analysts can also investigate how data samples relate to their assigned subtype and other groups. This approach lets them create well-defined subtypes based on statistical properties. Three case studies demonstrate the approach's utility, showing how it reproduced findings from a published subtype characterization.


Assuntos
Biologia Computacional/métodos , Gráficos por Computador , Perfilação da Expressão Gênica/métodos , Neoplasias/genética , Análise por Conglomerados , Humanos , Neoplasias/metabolismo
18.
IEEE Trans Vis Comput Graph ; 20(12): 1883-92, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26356902

RESUMO

Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets. At its core ConTour lists all items of each dataset in a column. Relationships between the columns are revealed through interaction: selecting one or multiple items in one column highlights and re-sorts the items in other columns. Filters based on relationships enable drilling down into the large data space. To identify interesting items in the first place, ConTour employs advanced sorting strategies, including strategies based on connectivity strength and uniqueness, as well as sorting based on item attributes. ConTour also introduces interactive nesting of columns, a powerful method to show the related items of a child column for each item in the parent column. Within the columns, ConTour shows rich attribute data about the items as well as information about the connection strengths to other datasets. Finally, ConTour provides a number of detail views, which can show items from multiple datasets and their associated data at the same time. We demonstrate the utility of our system in case studies conducted with a team of chemical biologists, who investigate the effects of chemical compounds on cells and need to understand the underlying mechanisms.


Assuntos
Biologia Computacional/métodos , Gráficos por Computador , Descoberta de Drogas/métodos , Interface Usuário-Computador , Algoritmos , Bases de Dados Factuais , Humanos
19.
IEEE Trans Vis Comput Graph ; 20(12): 1983-92, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26356912

RESUMO

Understanding relationships between sets is an important analysis task that has received widespread attention in the visualization community. The major challenge in this context is the combinatorial explosion of the number of set intersections if the number of sets exceeds a trivial threshold. In this paper we introduce UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. UpSet is focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersections, and a duality between the visualization of the elements in a dataset and their set membership. UpSet visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes. Sorting according to various measures enables a task-driven analysis of relevant intersections and aggregates. The elements represented in the sets and their associated attributes are visualized in a separate view. Queries based on containment in specific intersections, aggregates or driven by attribute filters are propagated between both views. We also introduce several advanced visual encodings and interaction methods to overcome the problems of varying scales and to address scalability. UpSet is web-based and open source. We demonstrate its general utility in multiple use cases from various domains.


Assuntos
Gráficos por Computador , Bases de Dados Factuais , Informática/métodos
20.
IEEE Trans Vis Comput Graph ; 20(12): 2023-32, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26356916

RESUMO

Answering questions about complex issues often requires analysts to take into account information contained in multiple interconnected datasets. A common strategy in analyzing and visualizing large and heterogeneous data is dividing it into meaningful subsets. Interesting subsets can then be selected and the associated data and the relationships between the subsets visualized. However, neither the extraction and manipulation nor the comparison of subsets is well supported by state-of-the-art techniques. In this paper we present Domino, a novel multiform visualization technique for effectively representing subsets and the relationships between them. By providing comprehensive tools to arrange, combine, and extract subsets, Domino allows users to create both common visualization techniques and advanced visualizations tailored to specific use cases. In addition to the novel technique, we present an implementation that enables analysts to manage the wide range of options that our approach offers. Innovative interactive features such as placeholders and live previews support rapid creation of complex analysis setups. We introduce the technique and the implementation using a simple example and demonstrate scalability and effectiveness in a use case from the field of cancer genomics.


Assuntos
Gráficos por Computador , Informática/métodos , Bases de Dados Factuais , Humanos
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