PUBLICATIONS2018-02-12T15:48:26+00:00

Publications

2017

Zacharatou, E. T., Doraiswamy, H., Ailamaki, A., Silva, C., Freire, J. GPU Rasterization for Real-Time Spatial Aggregation over Arbitrary Polygons. In Proceedings of the VLDB Endowment. 11(3), 352-365. 2017.
doi: 10.14778/3157794.3157803

Rehman, N. A., Relia, K., Chunara, R. Using Sparse Digital Traces to Fill in Individual Level Mobility Timelines. 2017.

Kolawole, O., Oguntoye, M., Dam, T., Chunara, R. Etiology of Respiratory Tract Infections in the Community and Clinic in Ilorin, Nigeria. BioMed Central(BMC) Research Notes.  Ilorin, Nigeria. 2017
doi: 10.1186/s13104-017-3063-1

Baltrusaitis, K., Santillana, M., Crawley, A.W., Chunara, R. , Smolinski, M., Brownstein, J.S. Determinants of Participants’ Follow-Up and Characterization of Representativeness in Flu Near You, A Participatory Disease Surveillance SystemJMIR Public Health Surveill. 2017.
doi: 10.2196/publichealth.7304

Liu, E.R. Weitzman, R. Chunara. High-resolution Temporal Representations of Alcohol and Tobacco Behaviors from Social Media Data. Association of Computing Machinery Computer Supported Cooperative Work. pages-1320–1333. 2017.
doi: 10.1145/2998181.2998336

Felix, C., Franconeri, S., Bertini, E. Taking Word Clouds Apart: An Empirical Investigation of the Design Space for Keyword Summaries. In Proceedings of InfoVis, Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics, 2017. 52(4), 549-5532017.
doi: 10.1109/TVCG.2017.2746018

Krause, J., Dasgupta, A., Swartz, J., Aphinyanaphongs, Y., Bertini, E. A Workflow for Visual Diagnostics of Binary Classifiers using Instance-Level Explanations. In Proceedings of Institute of Electrical and Electronics Engineers Conference and Visual Analytics Science and Technology, 201752(4), 549-553. 2017.
doi:

Tamagnini, P., Krause, J., Dasgupta, A., Bertini, E. Interpreting Black-Box Classifiers Using Instance-Level Visual Explanations. In Proceedings of Special Interest Group on Management of Data Workshop on Human-In-the-Loop Data Analytics, 2017. 52(4), 549-553. 2017.
doi:

Boy, J., Satterthwaite, M., Pandey, A. V., Nov, O., Emerson, J., Bertini, E. Showing People Behind Data: Does Anthropomorphizing Visualizations Elicit More Empathy for Human Rights Data? In Proceedings of Association of Computing Machinery Computer Human Interation Conference on Human Factors in Computing Systems, 2017. Denver, CO, USA.
doi: 10.1145/3025453.3025512

Yushkevich,P. A., Gerig, G. ITK-SNAP: An Intractive Medical Image Segmentation Tool to Meet the Need for Expert-Guided Segmentation of Complex Medical Images. Institute of Electrical and Electronics Engineers Pulse. 2017. 8(4), 54-57.
doi: 10.1109/MPUL.2017.2701493

Krause, J., Dasgupta, A., Fekete, J. D., Bertini, E. SeekAView: An Intelligent Dimensionality Reduction Strategy for Navigating HD Data Spaces In Proceedings of Institute of Electrical and Electronics Engineers Symposium on Large Data Analysis and Visualization, 2016. Baltimore, MD, USA.
doi: 10.1109/LDAV.2016.7874305

Shen, M. D., Kim, S. H., McKinstry, R. C., Gu, H., Hazlett, H. C., Nordahl, C. W., Emerson, R. E., Shaw, D., Elison, J. T., Swanson, M. R., Fonov, V. S., Gerig, G., Dager, S. R., Botteron, K. N., Paterson, S., Schultz, R. T., Evans, A. C., Estes, A. M., Zwaigenbaum, L., Styner, M. A., Amaral, D. G., Piven, J., IBIS Network. Increased Extra-axial Cerebrospinal Fluid in High-Risk Infants who Later Develop Autism. Biol Psychiatry, 2017. 82(3), 186-193.
doi: 10.1016/j.biopsych.2017.02.1095

Lewis, J. D., Evans, A. C., Pruett, J. R., Botteron, K. N., McKinstry, R. C., Zwaigenbaum, L., Estes, A., Collins, D. L., Kostopoulos, P., Gerig, G., Dager, S., Paterson, S., Schultz, R. T., Styner, M., Hazlett, H., Piven, J., IBIS Network. The Emergence of Network Inefficiencies in Infants with Autism Spectrum Disorder. Biol Psychiatry, 2017. 82(3), 176-185.
doi: 10.1016/j.biopsych.2017.03.006

Fishbaugh, J., Durrleman, S., Prastawa, M., Gerig, G. Geodesic Shape Regression with Multiple Geometries and Sparse Parameters. Med. Image Anal., Elsevier, 2017. (39), 1-17.
doi: 10.1016/j.media.2017.03.008

Emerson, R. W., Adams, C., Nishino, T., Hazlett, H. C., Wolff, J. J., Zwaigenbaum, L., Constantino, Shen, M. D., Swanson, M. R., Elison, J. T., Kandala, S., Estes, A. M., Botteron, K. N., Collins, L., Dager, S. R., Evans, A. C., Gerig, G., Gu, H., McKinstry, R. C., Paterson, S., Schultz, R. T., Styner, M., IBIS Network, Schlaggar, B. L., Pruett Jr, J. R., Piven, J. Functional Neuroimaging of High-risk 6-Month-old Infants Predicts a Diagnosis of Autism at 24 Months of Age. Science Translational Medicine, 9(393). 2017.
doi: 10.1126/scitranslmed.aag2882

Girot C., Ishikawa H., Fishbaugh J., Wollstein G., Schuman J., Gerig G.. Spatiotemporal Analysis of Structural Changes of the Lamina Cribrosa. Infant and Ophthalmic Medical Image Analysis. FIFI 2017, OMIA 2017.
doi: 10.1007/978-3-319-67561-9_21

Fishbaugh J., Prastawa M., Wang B., Reynolds P., Aylward S., Gerig G. Data-Driven Rank Aggregation with Application to Grand Challenges. Medical Image Computing and Computer-Assisted Intervention, 2017.
doi:

Vardhan A., Fishbaugh J., Vachet C., Gerig G. Longitudinal Modeling of Multi-modal Image Contrast Reveals Patterns of Early Brain Growth. Medical Image Computing and Computer-Assisted Intervention, 2017. (10433). 2017.
doi:

Dey, N. S., Hong, S., Tong, Y., Mohammed, T., Heintzmann, R., Hammer, M., Gerig, G. et al. Consistent Automatic Spectral Signature Recovery of Human retinal pigment epithelium (RPE) Lipofuscin Components and Drusen in Donors with Age-related Macular Degeneration (AMD) using Multi-Excitation Hyperspectral Autofluorescence (AF) Imaging. Investigative Ophthalmology & Visual Science, 58(8), 399. 2017.
doi:

Tong, Y., Agee, J. M., Mohammed, T., Dey, N. S., Hong, S., Heintzmann, R., Hammer M., et al. Hyperspectral Autofluorescence (AF) and Mechanisms of Retinal Pigment Epithelium (RPE) Lipofuscin Loss in Age-Related Macular Degeneration (AMD). Investigative Ophthalmology & Visual Science, 58(8), 404. 2017.
doi:

Ach, T., Hong, S., Heintzmann, R., Hillenkamp, J., Sloan, K. R., Dey, N. S., Gerig, G., Smith, T., Curcio, C., Bermond, K. High-resolution and multispectral imaging of autofluorescent retinal pigment epithelium (RPE) granules. Investigative Ophthalmology & Visual Science, 58(8), 3382. 2017.
doi:

Liu, E., Chunara R. Assessing Behavioral Stages From Social Media Data . Association of Computing Machinery Conference on Computer-Supported Cooperative Work and Social Computing at Portland, OR, USA. 1320-1333. 2017.
doi: 10.1145/2998181.2998336

2016

B. Ray, Chunara, R. Predicting Acute Respiratory Infections from Participatory Data. International Society for Disease Surveillance Conference. Atlanta, USA. 2016.
doi: 10.5210/ojphi.v9i1.7650
Second Prize Award for Outstanding Student or Post-Degree Abstract

Ray, E., Chunara R. Network Inference from Multimodal data: A Review of Approaches from Infectious Disease Transmission. Journal of Biomedical Informatics. 2016.
doi: 10.1016/j.jbi.2016.09.004

Rehman N., Liu J., Chunara R. Using Propensity Score Matching to Understand the Relationship Between Online Health Information Sources and Vaccination Sentiment. Association for the advancement of Artificial Intelligence Spring Symposium at Stanford University Palo Alto, CA, USA. 52(4), 549-553. 2016.
doi: 10.1109/jbhi.2015.2404829

Felix C., Pey C., Bertini E. TextTile: An Interactive Visualization Tool for Seamless Exploratory Analysis of Structured Data and Unstructured Text. In Proceedings of Visual Analytics Science and Technology Institute of Electrical and Electronics Engineers, Transactions on Visualization and Computer Graphics, 23(1), 161-170. 2016.
doi: 10.1109/TVCG.2016.2598447

Krause J., Perer A., Bertini E. Using Visual Analytics to Interpret Predictive Machine Learning Models. Workshop on Human Interpretability in Machine Learning (WHI). 2016.
doi:

Rall, K., Satterthwaite, M. L., Pey, A. V., Emerson, J., Boy, J., Nov, O., Bertini E. Data Visualization for Human Rights Advocacy. Journal of Human Rights Practice, 8(2) 171–197. 2016.
doi: 10.1093/jhuman/huw011

Pey, A. V., Krause, J., Felix, C., Boy, J., Bertini, E. Towards Understanding Human Similarity Perception in the Analysis of Large Sets of Scatter Plots. In Proceedings of Proceedings of Association for Computing Machinery Conference on Human Factors in Computing Systems. 2016.
doi: 10.1145/2858036.2858155
Best Paper Award: Honorable Mention

Gerig, G., Fishbaugh, J., Sadeghi, N., Elsevier. Longitudinal Modeling of Appearance and Shape and its Potential for Clinical Use, Medical Image Analysis. Med. Image Anal., In Press. 2016.
doi: 10.1016/j.media.2016.06.014

Tong, Y., Ami, T. B., Hong, S., Heintzmann, R., Gerig, G., Ablonczy, Z., Curcio, Z. A., Ach, T., Smith, R. T. Hyperspectral Autofluorescence Imaging of Drusen and Retinal Pigment Epithelium in Donor. RETINA The Journal of Retinal and Vitreous Diseases. 2016.
doi: 10.1097/IAE.0000000000001325

Kim, S. H., Lyu I., Fonov, V. S., Vachet,C., Hazlett, H. C., Smith R. G., Piven J., Dager, S. R., McKinstry, R. C., Pruett Jr, J. R., Evans, A., C., Collins, L. D., Botteron, K. N., Schultz, R. T., Gerig, G., Styner, M. A., The IBIS Network. Development of Cortical Shape in the Human Brain from 6 to 24 Months of Age via a Novel Measure of Shape Complexity. Neuroimage. 2016.
doi:  10.1016/j.neuroimage.2016.04.053

Wang, B., Prastawa, M., Irimia, A., Saha, A., Liu, W., Goh, S. Y. M., Vespa, P. M., Horn, J. D. V., Gerig, G. Modeling 4D Pathological Changes by Leveraging Normative Models, Computer Vision and Image Understanding. Computer Vision and Image Understanding. 3-13. 2016.
doi: 10.1016/j.cviu.2016.01.007

Yushkevich, P. A., Gao, Y., Gerig, G. Itk-snap: An Interactive Tool for Semi-Automatic Segmentation of Multi-Modality Biomedical Images. In Proceedings of Institute of Electrical and Electronics Engineers Engineering in Medicine and Biology Society (EMBS) at Orlando, FL, USA. 2016.
doi: 10.1109/EMBC.2016.7591443

Elhabian, S., Vachet, C., Piven, J., Styner, M., Gerig, G.. Compressive Sensing based Q-space Resampling for handling fast bulk motion in HARDI acquisitions. In Proceedings of Institute of Electrical and Electronics Engineers International Symposium of Biomedical Imaging at Prague, Czech Republic2016.
doi: 10.1109/ISBI.2016.7493412

Gao, Y., Zhang, M., Fletcher, P. T., Gerig, G. Image Registration And Segmentation In Longitudinal MRI Using Temporal Appearance Modeling. In Proceedings of Institute of Electrical and Electronics Engineers International Symposium of Biomedical Imaging at Prague, Czech Republic2016.
doi: 10.1109/ISBI.2016.7493346

Bessa, A., Silva, F. D. M., Nogueira, R. F., Bertini, E., Freire J. RioBusData: Outlier Detection in Bus Routes of Rio de Janeiro. In Proceedings of Symposium on Visualization in Data Science, 9(393). 2016.
doi: doival

Chunara, R., Goldstein, E., Patterson-Lomba, O., & Brownstein, J. S. Estimating influenza attack rates in the United States using a participatory cohort. Scientific reports, 5-5940. 2016.
doi: 10.1038/srep09540

J., Rowe A., Brownstein J.S., Chunara R. Surveillance of Acute Respiratory Infections Using Community-Submitted Symptoms and Specimens for Molecular Diagnostic Testing. Public Library of Science(PLoS) Currents, 9(393). 2016.
doi: 10.1371/currents.outbreaks.0371243baa7f3810ba1279e30b96d3b6

Freire, J., Fuhr, N., Rauber A. Reproducibility of Data-Oriented Experiments in e-Science. Dagstuhl Reports, 6(1), 108–159. 2016.
doi: 10.4230/DagRep.6.1.108

Freire, J., Bessa, A., Chirigati, F., Vo, H., Zhao, K. Exploring What not to Clean in Urban Data: A Study Using New York City Taxi Trips. Institute of Electrical and Electronics Engineers, Data Engineering Bulletin, 2016. 39(2), 63-77. 2016.
doi: 10.1111/cgf.12628

Chirigati, F., Capone, R., Rampin, R., Freire, J., Shasha D. A collaborative approach to computational reproducibility. Information Systems, 59(3), 95-97. 2016.
doi: 10.1016/j.is.2016.03.002

Campen, M., Silva, C., Zorin D. Bijective Maps from Simplicial Foliations. Association of Computing Machinery Transactions on Graphics (Special Interest Group on Computer Graphics and Interactive Techniques),. 2016.
doi: 10.1145/2897824.2925890

Lage M. J., Ono, P., Cervone, D., Chiang, J., Dietrich, C., Silva, C. Statcast Dashboard: Exploration of Spatiotemporal Baseball Data. Institute of Electrical and Electronics Engineers Computer Graphics and Applications, 36(5), 28-37. 2016.
doi: 10.1109/MCG.2016.101

Oliveira, G., Sotomayor J., Torchelsen, R., Silva, C., Comba, J. Visual Analysis of Bike-Sharing Systems. Computers & Graphics, 9(393). 2016.
doi: 10.1016/j.cag.2016.08.005

Muralidharan P., Fishbaugh F., Kim E. Y., Paulsen J., Johnson H., Gerig, G., Fletcher, P. T. Bayesian Covariate Selection in Mixed-Effects Models For Longitudinal Shape Analysis. In Proceedings of Institute of Electrical and Electronics Engineers International Symposium of Biomedical Imaging at Prague, Czech Republic. 9(393). 2016.
doi: 10.1109/ISBI.2016.7493352

Vieira K., Barbosa L., Silva, A. S. D., Freire, J., Moura E. Finding seeds to bootstrap focused crawlers. World Wide Web, 19(3): 2016, 449-474. 2016.
doi: 10.1007/s11280-015-0331-7

Palomo, C., Guo, Z., Silva, C. T., Freire, J. Visually Exploring Transportation Schedules. Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics, 22(1): 2016, 170-179. 2016.
doi: 10.1109/TVCG.2015.2467592

Douriez, M., Doraiswamy, H., Silva, C. T., Freire, J.. Anonymizing NYC Taxi Data: Does It Matter? In Institute of Electrical and Electronics Engineers International Conference on Data Science and Advanced Analytics, 2016. 2016.
doi: 10.1109/DSAA.2016.21

Hoang-Vu, T., Vo, H., Freire, J. A Unified Index for Spatio-Temporal Keyword Queries. In Association of Computing Machinery Conference on Information and Knowledge Management, 2016. 135-144. 2016.
doi: 10.1145/2983323.2983751

Krishnamurthy Y., Pham, K., Santos, A., Freire, J. Interactive Exploration for Domain Discovery on the Web. In Association of Computing Machinery KDD Workshop on Interactive Data Exploration and Analytics, 2016, 64-71. 2016.
doi:

Pham, K., Santos, A. S. R., Freire, J. Understanding Website Behavior based on User Agent. In Association of Computing Machinery Special Interest Group on Information Retrieval, 2016, 1053-1056. 2016.
doi: 10.1145/2911451.2914757

Chirigati, F., Doraiswamy, H., Damoulas T., Freire, J. Data Polygamy: The Many-Many Relationships among Urban Spatio-Temporal Data Sets. In Association of Computing Machinery Special Interest Group Management of Data, 2016. 1011-1025. 2016.
doi: 10.1145/2882903.2915245

Chirigati, F., Rampin, R., Shasha, D., Freire, J. ReproZip: Computational Reproducibility With Ease.  In Association of Computing Machinery Special Interest Group Management of Data, 2016. 2085-2088. 2016.
doi: 10.1145/2882903.2899401

Freire, J., Glavic, B., Kennedy, O., Mueller H. The Exception that Improves the Rule. In Association of Computing Machinery Special Interest Group Management of Data Workshop on Human-In-the-Loop Data Analytics, 2016.. 2016.
doi: 10.1145/2939502.2939509

Doraiswamy, H., Huy T. Vo, Silva, C. T., Freire, J. A GPU-Based Index to Support Interactive Spatio-Temporal Queries over Historical Data. In Proceedings of Institute of Electrical and Electronics Engineers International Conference on Data Engineering, 2016 at Helsinki, Finland. 1086-1097. 2016.
doi: 10.1109/ICDE.2016.7498315

Chirigati, F., Simeon, J., Hirzel, M., Freire, J. Virtual Lightweight Snapshots for Consistent Analytics in NoSQL Stores. In Proceedings of Institute of Electrical and Electronics Engineers International Conference on Data Engineering, 2016, 1310-1321. 2016.
doi:  10.1109/ICDE.2016.7498334

Santos, A., Pasini B., Freire, J. A First Study on Temporal Dynamics of Topics on the Web. In Proceedings of the 25th International Conference Companion on World Wide Web at Montréal, Québec, Canada. 849-854. 2016.
doi: 10.1145/2872518.2889291

Kohwalter, T., Oliveira, T., Freire, J., Clua, E., Murta L. Prov Viewer: a graph-based visualization tool for interactive exploration of provenance data. In Proceedings of the International Provenance and Annotation Workshop, 2016. 71-82. 2016.
doi: 10.1007/978-3-319-40593-3_6

Pimentel, J. F. N., Freire, J., Braganholo, V., Murta, L. Tracking and Analyzing the Evolution of Provenance from Scripts. In Proceedings of the International Provenance and Annotation Workshop, 2016. 16-28. 2016.
doi: 10.1007/978-3-319-40593-3_2

Pimentel, J. F. N., Freire, J., Braganholo, V., Murta, L. Fine-Grained Provenance Collection over Scripts Through Program Slicing. In Proceedings of The International Provenance and Annotation Workshop, 2016 at McLean, VA, USA. 199-203 2016.
doi: 0.1007/978-3-319-40593-3_21

B. Yu Silva, C. T. VisFlow – Web-based Visualization Framework for Tabular Data with a Subset Flow Model. Publication, 9(393). 2016. Institute of Electrical and Electronics Engineers Transactions on Visualization and Computer Graphics (Visual Analytics Science and Technology 2016) at NJ, USA. 251-260. 2016.
doi:10.1109/TVCG.2016.2598497

Mira, F., Doraiswamy, H., Lage, M., Zhao, K., Goncalves, B., Wilson, L., Hsieh, M., Silva, C. T. Urban Pulse: Capturing the Rhythm of Cities. Publication, 9(393). 2016.
doi: 10.1109/TVCG.2016.2598585

Berger, M., Tagliasacchi, A., Seversky, L., Alliez, P., Guennebaud, G., Levine, J., Sharf, A., Silva, C. T. State of the Art in Surface Reconstruction from Point Clouds. Computer Graphics Forum. 2016.
doi:

Dasgupta, A., Poco, J., Bertini, E., Silva, C. T. Reducing the Analytical Bottleneck for Domain Scientists: Lessons from a Climate Data Visualization Case Study. Computing in Science and Engineering. 18(1), 92-100. 2016.
doi: 10.1109/MCSE.2016.7

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