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1.
IEEE Trans Vis Comput Graph ; 28(1): 1106-1116, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34587072

RESUMO

Table2Text systems generate textual output based on structured data utilizing machine learning. These systems are essential for fluent natural language interfaces in tools such as virtual assistants; however, left to generate freely these ML systems often produce misleading or unexpected outputs. GenNI (Generation Negotiation Interface) is an interactive visual system for high-level human-AI collaboration in producing descriptive text. The tool utilizes a deep learning model designed with explicit control states. These controls allow users to globally constrain model generations, without sacrificing the representation power of the deep learning models. The visual interface makes it possible for users to interact with AI systems following a Refine-Forecast paradigm to ensure that the generation system acts in a manner human users find suitable. We report multiple use cases on two experiments that improve over uncontrolled generation approaches, while at the same time providing fine-grained control. A demo and source code are available at https://genni.vizhub.ai.

2.
IEEE Trans Vis Comput Graph ; 28(2): 1222-1236, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-32746284

RESUMO

Classifiers are among the most widely used supervised machine learning algorithms. Many classification models exist, and choosing the right one for a given task is difficult. During model selection and debugging, data scientists need to assess classifiers' performances, evaluate their learning behavior over time, and compare different models. Typically, this analysis is based on single-number performance measures such as accuracy. A more detailed evaluation of classifiers is possible by inspecting class errors. The confusion matrix is an established way for visualizing these class errors, but it was not designed with temporal or comparative analysis in mind. More generally, established performance analysis systems do not allow a combined temporal and comparative analysis of class-level information. To address this issue, we propose ConfusionFlow, an interactive, comparative visualization tool that combines the benefits of class confusion matrices with the visualization of performance characteristics over time. ConfusionFlow is model-agnostic and can be used to compare performances for different model types, model architectures, and/or training and test datasets. We demonstrate the usefulness of ConfusionFlow in a case study on instance selection strategies in active learning. We further assess the scalability of ConfusionFlow and present a use case in the context of neural network pruning.

3.
IEEE Comput Graph Appl ; 41(6): 7-12, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34890313

RESUMO

The increasing use of artificial intelligence (AI) technologies across application domains has prompted our society to pay closer attention to AI's trustworthiness, fairness, interpretability, and accountability. In order to foster trust in AI, it is important to consider the potential of interactive visualization, and how such visualizations help build trust in AI systems. This manifesto discusses the relevance of interactive visualizations and makes the following four claims: i) trust is not a technical problem, ii) trust is dynamic, iii) visualization cannot address all aspects of trust, and iv) visualization is crucial for human agency in AI.


Assuntos
Inteligência Artificial , Confiança , Humanos , Responsabilidade Social
4.
PLoS Comput Biol ; 17(10): e1009360, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34710090

RESUMO

The spread of infectious diseases such as COVID-19 presents many challenges to healthcare systems and infrastructures across the world, exacerbating inequalities and leaving the world's most vulnerable populations most affected. Given their density and available infrastructure, refugee and internally displaced person (IDP) settlements can be particularly susceptible to disease spread. In this paper we present an agent-based modeling approach to simulating the spread of disease in refugee and IDP settlements under various non-pharmaceutical intervention strategies. The model, based on the June open-source framework, is informed by data on geography, demographics, comorbidities, physical infrastructure and other parameters obtained from real-world observations and previous literature. The development and testing of this approach focuses on the Cox's Bazar refugee settlement in Bangladesh, although our model is designed to be generalizable to other informal settings. Our findings suggest the encouraging self-isolation at home of mild to severe symptomatic patients, as opposed to the isolation of all positive cases in purpose-built isolation and treatment centers, does not increase the risk of secondary infection meaning the centers can be used to provide hospital support to the most intense cases of COVID-19. Secondly we find that mask wearing in all indoor communal areas can be effective at dampening viral spread, even with low mask efficacy and compliance rates. Finally, we model the effects of reopening learning centers in the settlement under various mitigation strategies. For example, a combination of mask wearing in the classroom, halving attendance regularity to enable physical distancing, and better ventilation can almost completely mitigate the increased risk of infection which keeping the learning centers open may cause. These modeling efforts are being incorporated into decision making processes to inform future planning, and further exercises should be carried out in similar geographies to help protect those most vulnerable.


Assuntos
COVID-19/epidemiologia , COVID-19/transmissão , Epidemias , Refugiados , SARS-CoV-2 , Bangladesh/epidemiologia , COVID-19/prevenção & controle , Comorbidade , Biologia Computacional , Simulação por Computador , Visualização de Dados , Progressão da Doença , Humanos , Máscaras , Distanciamento Físico , Refugiados/estatística & dados numéricos , Instituições Acadêmicas , Análise de Sistemas
6.
Sci Adv ; 7(15)2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33827815

RESUMO

Humans use different domain languages to represent, explore, and communicate scientific concepts. During the last few hundred years, chemists compiled the language of chemical synthesis inferring a series of "reaction rules" from knowing how atoms rearrange during a chemical transformation, a process called atom-mapping. Atom-mapping is a laborious experimental task and, when tackled with computational methods, requires continuous annotation of chemical reactions and the extension of logically consistent directives. Here, we demonstrate that Transformer Neural Networks learn atom-mapping information between products and reactants without supervision or human labeling. Using the Transformer attention weights, we build a chemically agnostic, attention-guided reaction mapper and extract coherent chemical grammar from unannotated sets of reactions. Our method shows remarkable performance in terms of accuracy and speed, even for strongly imbalanced and chemically complex reactions with nontrivial atom-mapping. It provides the missing link between data-driven and rule-based approaches for numerous chemical reaction tasks.

7.
Nat Biomed Eng ; 5(6): 613-623, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33707779

RESUMO

The de novo design of antimicrobial therapeutics involves the exploration of a vast chemical repertoire to find compounds with broad-spectrum potency and low toxicity. Here, we report an efficient computational method for the generation of antimicrobials with desired attributes. The method leverages guidance from classifiers trained on an informative latent space of molecules modelled using a deep generative autoencoder, and screens the generated molecules using deep-learning classifiers as well as physicochemical features derived from high-throughput molecular dynamics simulations. Within 48 days, we identified, synthesized and experimentally tested 20 candidate antimicrobial peptides, of which two displayed high potency against diverse Gram-positive and Gram-negative pathogens (including multidrug-resistant Klebsiella pneumoniae) and a low propensity to induce drug resistance in Escherichia coli. Both peptides have low toxicity, as validated in vitro and in mice. We also show using live-cell confocal imaging that the bactericidal mode of action of the peptides involves the formation of membrane pores. The combination of deep learning and molecular dynamics may accelerate the discovery of potent and selective broad-spectrum antimicrobials.


Assuntos
Antibacterianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/farmacologia , Aprendizado Profundo , Desenho de Fármacos , Descoberta de Drogas/métodos , Farmacorresistência Bacteriana/efeitos dos fármacos , Acinetobacter baumannii/efeitos dos fármacos , Acinetobacter baumannii/crescimento & desenvolvimento , Acinetobacter baumannii/ultraestrutura , Sequência de Aminoácidos , Animais , Antibacterianos/síntese química , Peptídeos Catiônicos Antimicrobianos/síntese química , Escherichia coli/efeitos dos fármacos , Escherichia coli/crescimento & desenvolvimento , Escherichia coli/ultraestrutura , Feminino , Infecções por Klebsiella/tratamento farmacológico , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/crescimento & desenvolvimento , Klebsiella pneumoniae/ultraestrutura , Camundongos , Camundongos Endogâmicos BALB C , Testes de Sensibilidade Microbiana , Simulação de Dinâmica Molecular , Pseudomonas aeruginosa/efeitos dos fármacos , Pseudomonas aeruginosa/crescimento & desenvolvimento , Pseudomonas aeruginosa/ultraestrutura , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/crescimento & desenvolvimento , Staphylococcus aureus/ultraestrutura , Relação Estrutura-Atividade
8.
Proc Natl Acad Sci U S A ; 117(48): 30071-30078, 2020 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873639

RESUMO

Deep neural networks excel at finding hierarchical representations that solve complex tasks over large datasets. How can we humans understand these learned representations? In this work, we present network dissection, an analytic framework to systematically identify the semantics of individual hidden units within image classification and image generation networks. First, we analyze a convolutional neural network (CNN) trained on scene classification and discover units that match a diverse set of object concepts. We find evidence that the network has learned many object classes that play crucial roles in classifying scene classes. Second, we use a similar analytic method to analyze a generative adversarial network (GAN) model trained to generate scenes. By analyzing changes made when small sets of units are activated or deactivated, we find that objects can be added and removed from the output scenes while adapting to the context. Finally, we apply our analytic framework to understanding adversarial attacks and to semantic image editing.

9.
IEEE Trans Vis Comput Graph ; 26(1): 863-873, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31502978

RESUMO

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

10.
IEEE Trans Vis Comput Graph ; 26(1): 884-894, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31425116

RESUMO

Automation of tasks can have critical consequences when humans lose agency over decision processes. Deep learning models are particularly susceptible since current black-box approaches lack explainable reasoning. We argue that both the visual interface and model structure of deep learning systems need to take into account interaction design. We propose a framework of collaborative semantic inference (CSI) for the co-design of interactions and models to enable visual collaboration between humans and algorithms. The approach exposes the intermediate reasoning process of models which allows semantic interactions with the visual metaphors of a problem, which means that a user can both understand and control parts of the model reasoning process. We demonstrate the feasibility of CSI with a co-designed case study of a document summarization system.


Assuntos
Gráficos por Computador , Aprendizado Profundo , Semântica , Simulação por Computador , Humanos , Interface Usuário-Computador , Redação
11.
Artigo em Inglês | MEDLINE | ID: mdl-30334796

RESUMO

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

12.
Genome Biol ; 19(1): 125, 2018 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-30143029

RESUMO

We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform.


Assuntos
Mapeamento Cromossômico , Genoma , Internet , Interface Usuário-Computador
14.
Bioinformatics ; 34(20): 3557-3565, 2018 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-29741573

RESUMO

Motivation: Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the Saccharomyces cerevisiae and Escherichia coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. Results: We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S.cerevisiae and E.coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution. Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (P-value < 10-10) and -0.46 (P-value < 10-10) for S.cerevisiae and E.coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant. Availability and implementation: ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Proteoma/análise , Software , Sequência de Aminoácidos , Proteínas de Transporte/análise , Escherichia coli/química , Proteínas de Escherichia coli/análise , Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/análise
15.
SLAS Discov ; 23(2): 218-223, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-28937848

RESUMO

Screening is a methodology widely used in biological and biomedical research. There are numerous visualization methods to validate screening data quality but very few visualization applications capable of hit selection. Here, we present MightyScreen ( mightyscreen.net ), a novel web-based application designed for visual data evaluation as well as visual hit selection. We believe MightyScreen is an intuitive and interactive addition to conventional hit selection methods. We also provide study cases showing how MightyScreen is used to visually explore screening data and make hit selections.


Assuntos
Ensaios de Triagem em Larga Escala/métodos , Computadores , Análise de Dados , Internet , Software , Interface Usuário-Computador
16.
IEEE Trans Vis Comput Graph ; 24(1): 667-676, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28866526

RESUMO

Recurrent neural networks, and in particular long short-term memory (LSTM) networks, are a remarkably effective tool for sequence modeling that learn a dense black-box hidden representation of their sequential input. Researchers interested in better understanding these models have studied the changes in hidden state representations over time and noticed some interpretable patterns but also significant noise. In this work, we present LSTMVis, a visual analysis tool for recurrent neural networks with a focus on understanding these hidden state dynamics. The tool allows users to select a hypothesis input range to focus on local state changes, to match these states changes to similar patterns in a large data set, and to align these results with structural annotations from their domain. We show several use cases of the tool for analyzing specific hidden state properties on dataset containing nesting, phrase structure, and chord progressions, and demonstrate how the tool can be used to isolate patterns for further statistical analysis. We characterize the domain, the different stakeholders, and their goals and tasks. Long-term usage data after putting the tool online revealed great interest in the machine learning community.


Assuntos
Gráficos por Computador , Redes Neurais de Computação , Reconhecimento Automatizado de Padrão/métodos , Interface Usuário-Computador , Aprendizado de Máquina
17.
IEEE Trans Vis Comput Graph ; 23(1): 571-580, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27875172

RESUMO

Information hierarchies are difficult to express when real-world space or time constraints force traversing the hierarchy in linear presentations, such as in educational books and classroom courses. We present booc.io, which allows linear and non-linear presentation and navigation of educational concepts and material. To support a breadth of material for each concept, booc.io is Web based, which allows adding material such as lecture slides, book chapters, videos, and LTIs. A visual interface assists the creation of the needed hierarchical structures. The goals of our system were formed in expert interviews, and we explain how our design meets these goals. We adapt a real-world course into booc.io, and perform introductory qualitative evaluation with students.

18.
IEEE Trans Vis Comput Graph ; 23(1): 591-600, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27875174

RESUMO

High-throughput and high-content screening enables large scale, cost-effective experiments in which cell cultures are exposed to a wide spectrum of drugs. The resulting multivariate data sets have a large but shallow hierarchical structure. The deepest level of this structure describes cells in terms of numeric features that are derived from image data. The subsequent level describes enveloping cell cultures in terms of imposed experiment conditions (exposure to drugs). We present Screenit, a visual analysis approach designed in close collaboration with screening experts. Screenit enables the navigation and analysis of multivariate data at multiple hierarchy levels and at multiple levels of detail. Screenit integrates the interactive modeling of cell physical states (phenotypes) and the effects of drugs on cell cultures (hits). In addition, quality control is enabled via the detection of anomalies that indicate low-quality data, while providing an interface that is designed to match workflows of screening experts. We demonstrate analyses for a real-world data set, CellMorph, with 6 million cells across 20,000 cell cultures.

19.
IEEE Trans Vis Comput Graph ; 22(5): 1637, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-27045918

RESUMO

Presents corrections for the paper, "Guidelines for effective usage of text highlighting techniques," (Strobelt, H., et al), IEEE Trans. Vis. Comput.Graph., vol. 22, no. 1, pp. 489-498, Jan. 2016.

20.
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
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