EVL SAGE3 developers Luc Renambot and Lance Long with collaborators from the University of Hawaii Manoa and Virginia Tech present the latest advances in SAGE3 at the <a href="https://www.agu.org/fall-meeting">American Geophysical Union (AGU) Fall Meeting 2023</a> held December 11-15, 2023 in San Francisco, CA. 
The AGU Fall Meeting convenes annually, attracting >25,000 attendees from 100+ countries to showcase their research and network among colleagues. Researchers, scientists, educators, students, policymakers, exhibitors, journalists and communicators attend AGU Fall Meeting to better understand our planet and environment, and our role in preserving its future. It is a results-oriented gathering, rooted in celebrating and advancing positive individual and collective outcomes. 
The SAGE3 team presented the latest version of the SAGE environment to the AGU 2023 attendees on the exhibition floor, focussing on data visualization, no-code dashboard building, and advanced collaboration, with examples using geoscience applications.

SAGE3 Developers and Colllaborators from EVL/UIC, University of Hawaii Manoa and Virginia Tech at AGU 2023 booth.

EVL Presents SAGE3 at AGU Fall Meeting 2023

PhD Student: Andrew Wentzel 
Committee members: 
Dr G.Elisabeta Marai (chair) 
Dr. Xinhua Zhang 
Dr. Fabio Miranda 
Dr. Guadalupe Canahuate (University of Iowa) 
Dr. Renata Raidou (Vienna University of Technology) 
Date Time: Wednesday, Dec 6th at 10 am CST 
Location: ERF 2068 
Zoom Details: 
<a href="https://uic.zoom.us/j/83499037419?pwd=MFhvVHg2aXNZWnZwZHBhM0RKUE5ZQT09">Join Zoom Meeting</a> 
Meeting ID: 834 9903 7419 
Passcode: L1fCBhu9 
One tap mobile 
+13126266799,,83499037419#,,,,*43232065# US (Chicago) 
+13092053325,,83499037419#,,,,*43232065# US 
Abstract: 
Research in visual computing (VC) focuses on integrating visual representations of datasets with computing systems, thus leveraging the complementary abilities of humans and machines. The resulting VC systems may include machine learning (ML) techniques, which have remarkable abilities in terms of processing vast amounts of data. However, creating VC+ML systems that can operate on spatio-temporal data is a largely unexplored, difficult topic. Challenges in this area include: capturing domain characterizations for spatial VC+ML problems, in particular when serving both ML model builders and ML model clients; creating explainable VC+ML models that can operate on spatial data, including measures that can capture spatial structure similarity; designing visual encodings for ML models that use spatial information and that enhance the modeler and client understanding of the model; and measuring the effect of deploying such VC+ML systems in practice. 
Based on several multi-year collaborations, I document several instances where spatial and explainable VC+ML solutions are required, and what role spatiality plays in these instances. Throughout this process, I extract and describe design requirements for explainable spatial VC+ML systems, and I identify necessary VC advances, including spatially-aware similarity measures and spatial visual explainability. I construct spatially-aware similarity measures to support ML problems in precision oncology, patient risk stratification in data mining, and explainable interactive regression modeling for hypothesis testing in social science. I introduce novel encodings for 3-dimensional and geospatial data and explore how to integrate such encodings with ML model explanations. I implement and evaluate several VC+ML systems and several resulting models that are explicitly designed to integrate domain-specific structural spatial information and unsupervised ML. Throughout this process, I also articulate design lessons related to model actionability. In my proposed work, I expand my focus to exploring the issue of spatial VC+ML explainability, this time in a supervised deep-learning setting.

Presentation Slides

PhD Prelim Announcement: Visual Computing Design for Explainable, Spatially-aware Machine Learning

&ldquo;MouseScholar: Evaluating an Image+Text Search System for Biocuration&rdquo;, Juan Trelles Trabucco, Carla Floricel, Cecilia Arighi, Hagit Shatkay, Daniela Raciti, Martin Ringwald, and G. Elisabeta Marai is an accepted paper at 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2023). Of the 1084 paper submissions submitted to BIBM this year, only 211 regular papers were accepted (acceptance rate: 19.5%). 
Project Description: 
In this work, we instantiate and evaluate a first-in-kind, hybrid image+text document search system for biocuration (the process of analyzing biological or biomedical articles to organize biological data into data repositories using taxonomies and ontologies). 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. 
Congratulations EVL research team on being accepted for publication with this prestigious Conference!

Biocuration taxonomy of figures in scientific publications, with examples.

EVLers Juan Trelles Trabucco, Carla Floricel and Professor Elisabeta Marai Biocuration Research Recognized by IEEE BIBM 2023

EVl graduate student Hal Brynteson&rtsquo;s research in fluid dynamics will be showcased in Washington, DC at the Gallery of Fluid Motion during the 76th Annual Meeting of the APS Division of Fluid Dynamics. The Gallery of Fluid Motion is a visual record of the aesthetic and science of contemporary fluid mechanics shared with researchers in the discipline, as well as the general public. Submissions are judged on an annual basis for their visual qualities and scientific interest. 
Brynteson&rsquo;s poster entitled &ldquo;Effects of employing liquid-liquid emulsions on heat transfer within a turbulent Rayleigh-Benard convection&rdquo; (Authors: H. Brynteson, A. Moradi Bilondi, N. Scapin, L. Brandt, P. Mirbod, M.E. Papka) will be presented November 20th.

EVL Researcher Hal Brynteson&rsquo;s Work Showcased at the Gallery of Fluid Motion

PhD student Ke Fan&rsquo;s research in profiling and visualizing performance data at scale is recognized with a best poster nomination at SC23. &ldquo;Two-phase IO Enabling Large-scale Performance Introspection&rdquo; focuses on developing an effective and interactive exploration of the profiles of large-scale parallel programs, which remain a challenge due to the high I/O overheads of profiles and the difficulties in scaling downstream visualization tools. 
The poster presents Viveka, a lightweight end-to-end system for profiling and visualizing the performance of MPI-based applications. 
- A simple data format for the generated logs that minimizes metadata, leading to a smaller storage footprint and faster load times. (on average 3x more lightweight than Caliper). 
- Development of a custom two-phase data aggregation system to scale parallel I/O (of performance data) to high core counts, ensuring minimal overhead. 
- A lightweight web-based visualization dashboard that is capable of performing interactive analysis of performance data collected at high process counts. 
- A case study on real parallel applications to demonstrate the efficacy of our profiling and visualization system. 
Funding in part by NSF RII Track-4 award 2132013, NSF PPoSS planning award 2217036, NSF PPoSS large award 2316157 and, NSF collaborative research award 2221811. Compute hours provided on Theta Supercomputer Argonne Leadership Computing Facility&rsquo;s Directors Discretionary (DD) program.

Two-phase IO Enabling Large-scale Performance Introspection

The challenges of profiling and visualizing large-scale parallel programs

EVL Affiliated Faculty Sidharth Kumar&rsquo;s Advisee Recognized with Best Poster Nomination at SC23

A team led by researchers at the Argonne Leadership Computing Facility (ALCF) including EVL Professor Mike Papka was recognized with the Best Paper Award for an innovative scientific visualization study presented at the 2023 In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization (ISAV) at the SC23 conference in Denver, Colorado. 
The paper, &ldquo;Scaling Computational Fluid Dynamics: In Situ Visualization of NekRS using SENSEI,&rdquo; (Mateevitsi, V.A., Bode, M., Ferrier, N., Fischer, P., Göbbert, J.H., Insley, J.A., Lan, Y., Min, M., Papka, M.E., Patel, S., Rizzi, S., Windgassen, J.) details the team&rsquo;s efforts to equip the NekRS computational fluid dynamics (CFD) code with in situ analysis and visualization capabilities. The winning paper explores the benefits of instrumenting the NekRS code with SENSEI, an open-source in situ interface developed with support from DOE&rsquo;s Exascale Computing Project. The researchers demonstrated the capabilities and scalability of their approach by running two real scientific use cases on the ALCF&rsquo;s Polaris supercomputer and JSC&rsquo;s JUWELS Booster supercomputer. They found that the ability to &ldquo;see&rdquo; the data in real-time significantly augmented their analytical capacities.

Visualization of the pb146 use case simulation, illustrating flow dynamics within a pebble-bed nuclear reactor.

ALCF Team Including EVL Professor Michael Papka Wins Best Paper at SC23 ISAV 2023 Workshop

EVL&rsquo;s professor Marai is part of UIC&rsquo;s brain research now funded by a $5 million grant from the National Institutes of Health. The project incorporates brain tissue research at UIC, Northwestern University, Lurie Children’s Hospital, Rush University, and the University of Chicago, utilizing the INTUITION data platform that combines tissue data with clinical, functional, genetic, and 3D imaging information. The goal of the project is to assist clinicians in treating patients and help researchers better understand the mechanisms of brain disorders by developing a new resource for clinical care and research on epilepsy, brain tumors, and neurological disorders. 
The project is led by Dr. Jeffrey Loeb, the John S. Garvin Endowed Chair in Neurology at UIC, professor, and head of neurology and rehabilitation in the College of Medicine. INTUITION was initially supported by funding from the Discovery Partners Institute to create I-BRAIN, an initiative exploring commercialization opportunities around brain tissue data and research. Other UIC researchers include Dr. Anna Serafini, Biswajit Maharathi, Fozia Mir and Dr. Ahmad Daher from the Department of Neurology and Rehabilitation; Dr. Francesco Pucci from the Department of Neurosurgery; and Dr. Tibor Valyi-Nagy from the Department of Pathology. 
For the full article see <a href="https://today.uic.edu/nih-grant-expands-uic-brain-bank-into-citywide-effort-to-study-epilepsy-brain-cancer/?utm_source=mailpoet&utm_medium=email&utm_campaign=today%2B02.14.23">UIC today</a>.

The Percival Bailey Brain Collection, located in UIC&rsquo;s Neuropsychiatric Institute.

EVL Professor G. Elisabeta Marai Part of Research Team Awarded NIH Funding to Expand UIC&rsquo;s Brain Bank

EVL Research Associate Professor Luc Renambot joins collaborators from the University of Hawaii Manoa and Virginia Tech to present the latest advances in SAGE3 with a tutorial session at the <a href="https://iss2023.acm.org/">ACM ISS 2023</a>. 
SAGE3, the newest and most advanced generation of the Smart Amplified Group Environment, is an open-source software designed to facilitate collaboration among scientists, researchers, students, and professionals across various fields. This tutorial aims to introduce attendees to the capabilities of SAGE3, demonstrating its ability to enhance collaboration and productivity in diverse settings, from co-located office collaboration to remote collaboration to both at once, with diverse displays, from personal laptops to large-scale display walls. Participants will learn how to effectively use SAGE3 for brainstorming, data analysis, and presentation purposes, as well as installation of private collaboration servers and development of custom applications. 
Presenters: 
Jesse Harden, Virginia Tech 
Nurit Kirshenbaum, University of Hawaii at Manoa 
Roderick S. Tabalba Jr., University of Hawaii at Manoa 
Jason Leigh, University of Hawaii at Manoa 
Luc Renambot, University of Illinois Chicago, EVL 
Chris North, Virginia Tech 
In-person and on-line Sunday Nov 5, 3 to 4:30PM, and Wed. Nov 8 1PM to 2:30 PM.

SAGE3 Tutorial Sessions at ACM Interactive Surfaces and Spaces Conference (ACM ISS 2023)

EVL alumnus Khairi Reda presents his research at EVL tech meeting: 
Friday, November 3, 2023, 12PM - 1PM 
EVL Continuum, Room 2068 ERF 
Towards Trustworthy Visual Analytics 
Abstract: Interactive visualization tools, such as Tableau, Jupyter notebooks, and R with ggplot, have become vital instruments in the data science ecosystem. These systems empower users to explore data and search for new patterns that might lead to insights. However, these tools can also expose analysts to noise and random data fluctuations. Analysts can frequently misinterpret these spurious patterns and mistake them for reliable effects. This phenomenon has led to a &ldquo;replication crisis,&rdquo; with many previously published results failing to replicate, eroding trust in the scientific process. 
In this talk, Reda will discuss his research on reducing the risk of spurious visualizations and describe techniques we have developed to operationalize analyst hypotheses and beliefs in the visual analytics process. Empirical results showing that these unobtrusive interactions can promote good analytical practices and reduce the incidence of false discoveries will be discussed. Finally, Reda will show how using visual inference as a benchmark can provide a complementary account of visualization utility, leading to new insights into visualization design beyond what can be learned from traditional &ldquo;graphical perception&rdquo; studies. 
Bio: Khairi Reda is an Associate Professor in the Luddy School of Informatics & Computing at Indiana University Indianapolis. He is an alumnus of EVL, having earned a PhD in CS from the University of Illinois at Chicago. His research employs a variety of methods, weaving together techniques from human-computer interaction, machine learning, and design thinking to investigate new approaches for visualizing and interacting with data.

EVL Alumnus Khairi Reda Presents his Research &ldquo;Towards Trustworthy Visual Analytics&rdquo;

EVL researchers M. Mantovani, A. Wentzel, J. Trelles, J. Michaelis, G.E. Marai have an image of their visualization research featured on the cover of the Journal of Imaging Science and Technology, Vol 67 No 6, Nov/Dec 2023 issue. &ldquo;Kiviat Defense: An Empirical Evaluation of Visual Encoding Effectiveness in Multivariate Data Similarity Detection&rdquo; was presented in January 2024 at the Electronic Imaging Conference in Burlingame, CA. 
Congratulations EVL student and faculty researchers!

EVL Research Team&rsquo;s Visualization Featured on the Journal of Imaging Science and Technology

EVL alumni Tommy Marrinan, Victor Mateevitsi and Mike Papka (also EVL Professor) are recognized at <a href="https://sciviscontest2023.github.io/">2023 IEEE VIS SciVis Contest</a> for their research in the visualization of neuronal network simulations of plasticity changes in the human brain. 
The first award was for Best Workflow; enabling a scientific workflow was identified as one of the 4 main tasks for this year&rsquo;s contest. The goal of this component was to combine the functionality of the other tasks into a combined framework and interface that enables experts to explore the data and investigate several questions interactively. Which tools help the users to mark, select, and analyze the data on different levels of complexity and transfer information among these levels? 
The second award was for 1st Place Overall; judges took into account how the submission addressed all 4 main tasks, as well as any additional features. The judging was based on a short paper description of the visualization system and an 8-minute video demo. 
Congratulations, Tommy, Victor, and Mike! 
See <a href="https://insidehpc.com/2023/11/alcf-team-wins-first-place-and-best-workflow-at-2023-ieee-scivis-contest/">Inside HPC</a>, &ldquo;ALCF Team Wins First Place and Best Workflow at 2023 IEEE SciVis Contest&rdquo;

EVL Alumni Win Best Workflow and 1st Place Overall at 2023 IEEE SciVis Contest

EVL affiliated faculty member and Computer Science Assistant Professor Sidharth Kumar and his graduate students Landon Dyken and Will Usher are recognized with the Best Paper Award at the 13th IEEE Symposium on Large Data Analysis and Visualization. This year&rsquo;s LDAV 2023 focus is on Big Data Analysis and Visualization, specifically targeting methodological innovation, algorithmic foundations, and possible end-to-end solutions. 
&ldquo;Speculative Progressive Raycasting for Memory Constrained Isosurface Visualization of Massive Volumes&rdquo; (Usher, W., Dyken, L., Kumar, S.) proposes a new GPU algorithm for implicit isosurface rendering that progressively traverses rays through the volume and decompresses data on-demand to minimize its memory footprint. Up to 5.7× reductions in overall memory use and 8.4× reductions in data decompressed compared to the state of the art in memory constrained isosurface extraction is acheived, without sacrificing interactivity. At 1280×720, the Richtmyer-Meshkov averages 264ms per-pass and 1.2s total on an RTX 3080. 
Congratulations team!

EVL Affiliated Faculty Sidharth Kumar&rsquo;s Advisees Recognized with Best Paper Award at LDAV 2023

The EVL research team lead by Professor Liz Marai and graduate research assistants Carla Floricel and Andrew Wentzel has their visual analytics work published at the IEEE Transactions on Visualization and Computer Graphics session at the IEEE Vis 2023 Conference held in Melbourne, Australia, October 22- 27, 2023. &ldquo;Roses Have Thorns: Understanding the Downside of Oncological Care Delivery Through Visual Analytics and Sequential Rule Mining&rdquo; (authors: Carla Gabriela Floricel, Andrew Wentzel, Abdallah Mohamed, Clifton David Fuller, Guadalupe Canahuate, G. Elisabeta Marai) is an interactive analysis system to support sequential rule mining (SRM) model builders who work in cancer symptom research. 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. Our system facilitates mechanistic knowledge discovery of treatment-related toxicities (i.e., &ldquo;roses have thorns&rdquo;) in large-scale cohort data. 
This work was developed by visual computing researchers at EVL in collaboration with data mining specialists at the University of Iowa, and clinicians at the MD Anderson Cancer Center in Texas, and it is supported by funding from the US National Institutes of Health (NIH awards NCI-R01-CA258827 and NLM-R01-LM012527), and US National Science Foundation (NSF awards CDSE-1854815 and CNS-1828265).

Visual representation of treatment comparison.

EVL Research Team Publishes Their Visual Analytics Research for Oncological Care

The National Science Foundation has awarded EVL a Major Research Instrumentation (MRI) grant to build the Data Observation and Computation Collaboratory (DOCC) in the new Computer Design Research and Learning Center (CDRBC) building. The Data Observation and Computation Collaboratory (DOCC, &rsquo;the dock&rsquo;) is a much-needed visual data science instrument for UIC science and engineering research and research training. DOCC provides high-performance computing, advanced networking, high-speed data storage, interactive high-resolution displays and software and services for Artificial Intelligence / Machine Learning (AI/ML), data analytics, data simulations, visualization, and virtual-reality requirements. Given how varied modern data-science application requirements can be, DOCC is designed as a configurable, heterogeneous computing environment that prioritizes real-time, interactive, collaborative applications and remote data streaming, but can be scheduled off-hours for large, batch-mode processing. 
DOCC will empower users to work with their data and their colleagues in real-time, test codes, view a &rsquo;window in the oven&rsquo;to watch large simulations run, and simultaneously view results along with related data and ensemble runs on large display walls. DOCC has a visual front end that enables users to easily access familiar collaboration tools, scientific notebooks, AI/ML workflows, and popular visualization software. 
Alternatively, users can add new AI/ML models or create them from scratch. And because DOCC will be connected to the campus research network, data and/or computer codes can be ported to remote computer and cloud resources located on campus, regionally, nationally, or internationally. 
A room-sized instrument, DOCC will be located in the high-trafficked atrium of the new CDRLC, home to the UIC Computer Science Department, part of the College of Engineering, situated across from an auditorium and multi-purpose event space. This location will promote UIC data-science research initiatives and the instrument&rsquo;s collaboration potential. DOCC will also be used to conduct campus research meetings, programs and training initiatives. 
Award Number (FAIN): 2320261 
Period of Performance: 10/01/2023 - 09/30/2026 
Project Title: Research Infrastructure: MRI: Track 2 Acquisition of Data Observation and Computation Collaboratory (DOCC)

EVL Awarded NSF MRI Support to Build the Data Observation and Computation Collaboratory (DOCC)

Carla Gabriela Floricel has been awarded funding by the UI Health Cancer Center to offset the cost of travel and registration to present her cancer-related work at the IEEE VIS 2023 Conference held in Melbourne, Australia October 22-27, 2023. Floricel, a fifth-year Computer Science PhD student and research assistant at EVL. Her advisor is CS Professor and EVL faculty Liz Marai, who is also a Cancer Center member, part of the Cancer Center&rdquo;s Cancer Prevention and Control research program. 
Floricel&rsquo;s research is in visual data science, primarily medical data visualization. Her work is a collaboration with Marai and clinical oncologists from MD Anderson at the University of Texas and data scientists from the University of Iowa. The goal of their work is to better understand symptoms that head and neck cancer patients undergoing radiotherapy are facing during and after cancer treatment. 
Congratulations, Carla!

EVLer Carla Floricel Awarded UI Health Cancer Center <a href="https://cancer.uillinois.edu/fall-travel-award-recipients/">Fall 2023 Travel Award</a>

Roberto Cesar Jr., professor/department head of Computer Science at the University of Sao Paolo and director of eScience Research Center presents his research in computer vision and image processing for urban visualization. Dr. Cesar&rsquo; invited talk will be held: 
EVL&rsquo;s Continuum 
Engineering Research Facility, Room 2068 
Friday, September 29th, noon 
&ldquo;Computer vision and physical models for urban informatics&rdquo; 
Computer vision techniques have played an important role in urban data analysis. Such techniques are useful for capturing and analyzing visual information about cities&rsquo; infrastructure, social manifestations and mobility, to name just a few. However, the adoption of computer vision techniques in urban environments faces important challenges, such as the restricted heterogeneous hardware typically involved, outdoor image variations, and other uncontrolled aspects. In this talk, we present some recent results to overcome these limitations. Specifically, we discuss computer vision techniques for rain scenes, pedestrian mobility analysis, and physical models for urban green regions and graffiti distributions. 
Bio: 
Roberto is a professor at the University of Sao Paulo (USP) since 1998 (BSc in Computer Science - UNESP - 1991; MSc in Electrical Engineering - UNICAMP - 1993; Ph.D. in Physics - USP/Brazil, IPT-UCL/Belgium - 1997). He is currently a full professor in the Department of Computer Science - IME - USP working in the Data Science Research Group. He is currently a special advisor for Physical Sciences and Engineering at the Sao Paulo Research Foundation - FAPESP. He served as the Director of the eScience Research Center at USP and as the head of the Computer Science Department. He was a member of the Image and Vision Computing and the Signal, Image and Video Processing editorial boards, chair and invited speaker of conferences and workshops (Sibgrapi 2003, CIARP 2010, Sibgrapi 2011; SHAPES 2.0 - 2012, eSon - IEEE eScience 2013, IEEE eScience 2014). He has experience in computer science, with an emphasis on computer vision, machine learning, and artificial intelligence. 
<a href="https://www.ime.usp.br/~cesar/">https://www.ime.usp.br/~cesar/</a>

Roberto Cesar Jr. Invited to Present &ldquo;Computer vision and physical models for urban informatics&rdquo;

EVL assistant professor Fabio Miranda&rsquo;s IEEE VIS2023 paper entitled <a href="https://www.evl.uic.edu/pubs/2744">&ldquo;ProWis: A visual approach for building, managing, and analyzing weather simulation ensembles in runtime&rdquo;</a> is recognized among the Best Papers Honorable Mention. A dedicated committee of experienced community members selects <a href="https://ieeevis.org/year/2023/info/awards/best-paper-awards">best paper and honorable mention awards</a> as outstanding work from the pool of accepted papers. 
ProWis is an interactive and provenance-oriented system to help weather experts build, manage, and analyze simulation ensembles at runtime. The system follows a human-in-the-loop approach to enable the exploration of multiple atmospheric variables and weather scenarios.

Overview of the PROWIS components.

&ldquo;ProWis&rdquo; Awarded IEEE VIS2023 Best Paper Honorable Mention

Candidate: Juan Trelles Trabucco 
Committee members: 
- Dr. Liz Marai 
- Dr. Andy Johnson 
- Dr. Wei Tang 
- Dr. Cecilia Arighi (University of Delaware) 
- Dr. Steven Drucker (Microsoft Research) 
Date/time: Aug 24th, 11 am CT 
Location: ERF 3036 and Zoom 
https://uic.zoom.us/j/84392472211?pwd=RTVwQjZaSlVBcERHcUloc1N6THQ0QT09
Meeting ID: 843 9247 2211 Passcode: UA6mfGMR 
Abstract: 
Images in scientific publications communicate essential information, such as experiments performed and results obtained, that researchers can use as a proxy for the publication'&rsquo;s relevance to their research interests. Domains like biocuration, where biomedical experts analyze the literature to extract and organize information for future retrieval and analysis, can benefit from computationally leveraging these images in their workflows. Prior work in biomedical document classification for biocuration has shown that combining features from images (e.g., acquisition modality) with text features can improve precision and recall. However, the considerations and benefits obtained from computationally integrating such image-based features in biocuration workflows are less clear. 
Based on a multi-year collaboration with text-mining researchers and biocurators, this dissertation identifies and tackles several challenges to computationally using image-data in the biocuration process. These challenges include the scarcity of labeled datasets for training image classifiers, the lack of characterization for the needed modality classes in biocuration, the lack of available labeling systems to label extensive collections of images, and the lack of support for image-based features in academic search engines. This dissertation addresses these issues by proposing two taxonomies for image modalities found in biomedical publications; introducing training strategies using shallower neural networks and hierarchical organization of classifiers; describing two labeling systems, one for domain experts and one for model builders who require support for data understanding; and concludes by merging several building blocks into document search systems that successfully leverage image-based data.

PhD Dissertation Announcement: &ldquo;Integrating Image Features to Support the Biocuration Workflow&rdquo;

Starting Academic Year 23/24 visiting professor Zhiling Lan joins as faculty in the Department of Computer Science and EVL. Dr. Lan comes with significant expertise in high-performance computing and parallel/distributed systems. Prior to her tenure at UIC, she was a professor of Computer Science, at the Illinois Institute of Technology between 2002 and 2023. She is also a guest research faculty at Argonne National Laboratory. 
Dr. Lan also heads the <a href="https://spear.lab.uic.edu/">SPEAR (Systems for Performance, Energy, And Resiliency) lab</a>, which conducts research spanning various areas of parallel and distributed systems including cluster management, interconnection networking, performance modeling and simulation, power and energy efficiency, and fault tolerance. SPEAR&rsquo;smission is to unify systems and AI, where we are committed to creating software systems to expedite AI applications and exploring advanced AI technologies to tackle critical research challenges in computer systems.

EVL Welcomes Professor Zhiling Lan to High Performance Computing Faculty Team

Assistant Professor Sidhart Kumar joins the Computer Science and EVL faculty with expertise in High-Performance Computing.  Kumar&rsquo;s research goal is to provide a comprehensive framework for high-performance data management, critical in extracting meaningful insights from large and complex computational systems. More broadly his interest is in developing scalable algorithms and data structures that can inject interactivity and performance into data- and compute-intensive applications. Kumar's overall research relies on the effective use of techniques from a variety of domains including databases, topology, visualization, and machine learning.

Sidharth Kumar Joins EVL Affiliated Faculty - Assistant Professor, Computer Science

The 2023-2024 University Scholar Program has selected EVL professor G. Elisabeta Marai among its awarded and honored candidates. Dr. Marai is among two other designees within the College of Engineering - Professor Natasha Devroye with the Department of Electrical and Computer Engineering Department, and Professor Karl Rockne with Civil, Materials, and Environmental Engineering. Sponsored by the Office of the President, the program rewards outstanding faculty who have been recognized for their superior performance in research, teaching, and scholarly activities. 
Join us in congratulating professor Liz! 
<a href="https://emails.uofi.uic.edu/newsletter/25/464513625.html">See the full article.</a>

EVL Professor G. Elisabeta Marai Awarded 2023-2024 University Scholar

EVL professor Mike Papka and his research students have been awarded an Honorable Mention in the EuroVis Best Paper Category for &ldquo;ChemoGraph: Interactive Visual Exploration of the Chemical Space&rdquo;. Co-authored by collaborators Bharat Kale, Austin Clyde, Maoyuan Sun, Arvind Ramanathan, Rick Stevens, and Michael E. Papka, ChemoGraph is a novel visual analytics technique for interactively exploring related chemicals. A chemical space is formalized as a hypergraph with novel machine-learning models to compute related chemical compounds applied. It uses a database to find related compounds from an available space and a machine learning model to generate new ones, which helps enlarge the known space. Moreover, ChemoGraph highlights interactive features that support users in viewing, comparing, and organizing computationally identified related chemicals. 
<a href="https://youtu.be/kVpz6TDjQMw ">See a video teaser on EVLTube.</a>

&ldquo;ChemoGraph: Interactive Visual Exploration of the Chemical Space&rdquo; Awarded with Honorable Mention in the EuroVis Best Paper Category

The annual &ldquo;SAGE3: Smart Amplified Group Environment for Harnessing the Data Revolution&rdquo; all hands meeting was held this year at the University of Hawaii at Manoa, in Oahu, Hawaii, June 26 - 30 2023. UIC&rsquo; PI Andrew Johnson, CoPI Luc Renambot, and senior research staff member Lance Long attended the meeting with collaborators from Virginia Tech and the University of Hawaii to discuss the future of the project, achieved milestones, and current challenges. These face-to-face meetings have proven critical to the advancement of the overall project objectives, as developers are able to exchange success stories and lessons learned from their collaborative work. The intensive brainstorming has helped crystalize future directions and potential project expansion. 
Funded by NSF, SAGE3 puts the &ldquo;human in the loop&rdquo; by providing scientists with an intuitive framework that integrates state-of-the-art AI technologies with applications, workflows, smart visualizations and collaboration services to help them access, share, explore and analyze their data, come to conclusions, and make decisions with greater speed, accuracy, comprehension and confidence. The project is scheduled to conclude in 2025.

SAGE3 2023 All Hands Meeting

EVL hosted ChicagoCHI&rsquo;s June presentation &rlquo;Making Design Sense of Hearing&rdquo;, June 22, 2023. Guest Speaker Greg Olsen, Portfolio Scientist Lead in the GN Advanced Science group presented his research augmented hearing, along with design insights and considerations from compensating for age-related hearing loss to enhancing one of the 5 senses beyond the current human capability. The event was organized by EVL alumn and ChicagoCHI chair Victor Mateevisti. 
<a href="https://www.chicagochi.org/2023/06/02/making-design-sense-of-hearing/">For more information.</a>

EVL Hosts ChicagoCHI Presentation

Ph.D. Student: Ashwini G. Naik 
Committee Members: 
Dr. Nikita Soni 
Dr. Debaleena Chattopadhyay 
Dr. Steve Jones (External Member) 
Dr. Robert Kenyon (Co-Advisor) 
Dr. Andrew Johnson (Advisor and Chair) 
Date and Time: May 23, 2023, 9 AM-11 AM Chicago Time 
Location: ERF 2068 
Zoom Link: <a href="https://uic.zoom.us/j/7898336493">https://uic.zoom.us/j/7898336493</a> 
Abstract: 
Strategizing and sensemaking in immersive environments have predominantly been explored for training, learning, and recreational tasks. The ability to embed these concepts into the data analysis pipeline is recently emerging and has seen limited research. In our work, we present Personal Situated Analytics (PSA) that provides individuals the ability to embed themselves in recorded events in multiple degrees of immersion on the Reality-Virtuality spectrum, evaluate the benefits, and study their exploration patterns. With the increasing availability of sensors and capturing devices, we can now actively record and leverage data from our daily activities to gain valuable insights and make informed decisions. PSA at its core formulates a combination of embodied cognition, situated analytics, and conversation analysis while exploiting the benefits of strategic immersion and sensemaking in immersive environments. To that end, we first developed a framework for embedding the individuals in the environment where the conversation originally occurred. Secondly, we conducted a pilot user study (n=12, protocol #STUDY2023-0018), to compare user experiences while exploring recorded conversations in Mixed Reality through the HoloLens2 device, and in Virtual Reality through the Quest2 device. Our proposed framework encompasses various stages such as tracking, data capturing, data cleaning, data synchronization, prototype building, and deploying the final product to end-user hardware. In the first part of the experiment, we used datasets consisting of seated participants (protocol #2022-0354). In the future, we will record and analyze datasets with standing and non-stationary participants (protocol #STUDY2023-0509) in two settings that would employ various collaboration profiles among the participants. Drawing from our experience during the preliminary user study and the feedback we received from the participants, we catalog our lessons learned and insights which can potentially drive advancements in embodied situated analytics and thereby enhance the conversation analysis pipeline.

PSA is an immersive MR/VR framework for experiencing and analyzing recorded conversations and events. We see two participants represented as virtual avatars engaged in a conversation.

PhD Prelim Announcement: Improving Conversation Analysis Pipeline through Personal Situated Analytics in Extended Reality

EVl Professor Liz Marai&rsquo;s research in visual analytics and visualization, along with her advisees has been cited in the book &ldquo;Visualization, Visual Analytics and Virtual Reality in Medicine&rdquo; published by Elsevier and authored by Bernhard Preim, Renata Raidou, Noeska Smit, Kai Lawonn. In Chapter 11 - ﻿﻿﻿Visual analytics in clinical medicine and Visual analytics for prediction Marai&rsquo;s and EVLers Andrew Wentzel, Peter Hanula, Carla Floricel, Nafiul Nipu visualization applications T-SSIM and THALIS are featured. 
&ldquo;Visualization, Visual Analytics and Virtual Reality in Medicine: State-of-the-art Techniques and Applications describes important techniques and applications that show an understanding of actual user needs as well as technological possibilities. The book includes user research, for example, task and requirement analysis, visualization design and algorithmic ideas without going into the details of implementation. This reference will be suitable for researchers and students in visualization and visual analytics in medicine and healthcare, medical image analysis scientists and biomedical engineers in general. 
Visualization and visual analytics have become prevalent in public health and clinical medicine, medical flow visualization, multimodal medical visualization and virtual reality in medical education and rehabilitation. Relevant applications now include digital pathology, virtual anatomy and computer-assisted radiation treatment planning.&rdquo; 
<a href="https://shop.elsevier.com/books/visualization-visual-analytics-and-virtual-reality-in-medicine/preim/978-0-12-822962-0">Purchase a copy of the book.</a>

Cohort-based radiation therapy prediction using T-SSIM, where a stylized 3D view of the predicted radiation plan of the current patient is used.  Additional RT views show the most similar patients who contribute to the prediction.

EVL Professor G. Elisabeta Marai&rsquo;s Research and Students&rsquo; Work Cited in &ldquo;Visualization, Visual Analytics and Virtual Reality in Medicine&rdquo;

Master of Design graduate student Quentin Bu presents her virtual reality performance piece &ldquo;An Elegy for the Departed - an Interactive Virtual Reality+Physical Computing Typographic Performance&rdquo; in EVL&rsquo;s CAVE2. 
Friday, May 5, 2023 
11:15 - 11:45 AM 
Room 2036 ERF 
Elegy is a highly experimental virtual reality work, merging the artist&rsquo;s original poetry and audio composition, graphic design, 3D typography and physical computing activated through participant movement and gestures. In the artist&rsquo;s own words &ldquo;The Elegy is my poetic, perhaps futile attempt to consolidate and immortalize the transitory states of life.&rdquo;

Elegy in EVL&rsquo;s CAVE2

MDES Thesis Presentation &ldquo;The Elegy&rdquo;

EVL alumna and Associate Professor in Interactive Systems at the Department of Informatics & Telecommunications, National and Kapodistrian University of Athens, Maria Roussou presents her research in immersive eXtended Reality (XR): 
Wednesday, May 3, 2023, 1:30PM 
EVL Continuum Room 2068 ERF 
Dr. Roussou&rsquo;s talk entitled &ldquo:Extending the virtual: the museum as a hybrid experience&rdquo; will discuss the use of advanced digital technologies, such as Virtual Reality, in the GLAM sector (e.g., galleries, libraries, archives, museums, etc.) to create immersive experiences for visitors has come of age. However, to date, the emphasis has been on reconstructing the real to transgress the built environment's limitations. Nowadays, the focus turns to integrating the physical and the virtual. The physical space is highlighted, complemented, and expanded through close coupling with the digital. Tangible objects are integrated and play a leading role in the digital experiences of visitors, creating a hybrid reality. Drawing from a range of high-end immersive eXtended Reality (XR) applications but also lower-end mobile tours created for cultural or informal educational purposes, this talk will explore how the future’s hybrid nature is shifting immersive presentation from the mainly didactic walkthroughs to experiences that are playful, emotive, social and shared, meaningfully interactive, and, ultimately, relevant and resonant to those they are designed for. 
Specifically, Roussou will present aspects of the BRIDGES project, a multi-user, multisensory XR experience set in informal learning contexts, and the EMOTIVE project, which aims to leverage interactive, social, and participatory capabilities. Both combine historical accuracy in representation with dramatic storytelling to enhance knowledge about the past, historical empathy, and resonance. 
--- 
The <a href="https://www.bridges-horizon.eu">BRIDGES project</a> and the <a href="https://www.emotiveproject.eu/">EMOTIVE project</a> have received funding from the European Union’s Horizon 2020 research and innovation program. 
Bio: 
Maria Roussou is an Associate Professor in Interactive Systems at the Department of Informatics & Telecommunications, National and Kapodistrian University of Athens. In 2003 she founded and co-directed <a href="http://www.makebelieve.gr/mroussou
">makebelieve</a>, an experience design and consulting company. Previously, she established (in 1998) and directed (until 2003) the Virtual Reality Department at the Foundation of the Hellenic World, where she was responsible for setting up the immersive projection-based VR exhibits and managing the research, design and development of the VR programs and related visitor experiences. She holds a PhD in Computer Science (VR/HCI) from the University of London (UCL), a Master in Fine Arts (MFA) degree in Electronic Visualization from the School of Art and Design, University of Illinois at Chicago, a Master of Science (M.Sc) in Electrical Engineering & Computer Science from the same university, and an undergraduate degree in Applied Informatics from the Athens University of Economics and Business. Maria is a Senior Member of the ACM, and Vice-chair of the Greek ACM SIGCHI Chapter and the Greek ACM-W Chapter.

Extending the virtual: the museum as a hybrid experience

Standing in front of Argonne National Laboratory&rsquo;s Aurora supercomputer, EVL and computer science department professor
Michael E. Papka is the Featured Photo of the Spring 2023 RISE publication. Papka holds a joint appointment with UIC and is also Deputy Associate Laboratory Director, Computing, Environment, and Life Sciences, Argonne National Laboratory. Among his charge is the new Aurora supercomputer, which once fully online, will be among the United States&rsquo; most powerful exascale machines used for research. Sponsored by the Department of Energy and designed by Intel and Hewlett Packard Enterprise, Aurora will provide scientists a new and extremely powerful tool for a host of research initiatives. 
<a href="https://engineering.uic.edu/about/coe-news/rise/rise-spring-2023/">See the RISE: Spring 2023 feature</a>.

EVL Professor Papka is the Featured Photo in UIC Engineering&rsquo;s RISE 2023

EVL graduate student Hal Brynteson in collaboration with Dr. Parisa Mirbod and PhD student Abbas Moradi Bilondi (Mechanical and Industrial Engineering) has been awarded an honorable mention for this year's <a href="https://grad.uic.edu/funding-awards/the-image-of-research/">Image of Research Competition</a>. The Image of Research is an annual interdisciplinary exhibit competition organized by the Graduate College and University Library to showcase the breadth and diversity of research at UIC. 
Brynteson&rsquo;s visualization was created using Blender/ParaView, and represents The Rayleigh Bénard convection. As Bilondi explains, &ldquo;The Rayleigh Bénard convection, where a fluid is heated from below and cooled from above, is an important mechanism of mass and heat transfer in nature and in numerous industrial applications. One can cite geophysics, astrophysics, meteorology, heat exchangers, multilayer walls in buildings, and cooling of electronic components for example. In the present work, by considering bubbles inside the fluid flow, we aim to investigate the effects of the presence of bubbles on the heat transfer rate.&rdquo; 
A celebration of the 2023 Image of Research awardees on Friday, April 28, at 3 p.m., in the Richard J. Daley Library, 801 S. Morgan St., Chicago, IL 60607.

The Rayleigh Bénard Convection

EVL Graduate Student Awarded with 2023 UIC Image of Research Honorable Mention

EVL-affiliated faculty and Computer Science Assistant Professor Nikita Soni&rsquo;s research in human-computer interaction (HCI), along with three other researchers working in this area: Assistant Professor Debaleena Chattopadhyay, Professor Andruid Kerne, and Assistant Professor Joseph E. Michaelis is featured in the Spring 2023 issue of UIC Engineering RISE.
Soni&rsquo;s research focuses on user interface design honed for teaching and learning in support of greater creativity allowing users to interact using natural input methods such as touch and speech. Her work includes multi-touch spherical displays for Earth Science education in museums and classrooms. Her multi-touch spherical display uses familiar smartphone-like gestures for interaction with earth science and climate data displayed on a globe. In addition to working on user interfaces for novel display technologies, Soni also creates mobile interfaces for creative uses, such as photographic editing. 
<a href="https://engineering.uic.edu/about/coe-news/rise/rise-spring-2023/putting-humans-first-in-computer-design/">Read the full article &ldquo;Putting humans first in computer design&rdquo; featuring HCI research at UIC.</a>

Nikita Soni with Spherical Display

EVL Affiliate Faculty Nikita Soni Featured in UIC Engineering RISE Spring 2023 Issue

Candidate: Arthur Nishimoto 
Committee: 
Andrew Johnson, Chair and Advisor 
Debaleena Chattopadhyay 
Steve Jones 
Wei Tang 
Jason Leigh (University of Hawaiʻi at Manoa) 
Date: Thursday, April 20, 2023 
Time: 4-5 PM 
Location: EVL Continuum, Room 2068 ERF 
Abstract: 
Given the adoption of many variations of virtual and augmented reality devices such as CAVE/CAVE2, large virtual reality (VR) capable displays walls/domes, and a growing set of increasingly capable and affordable head mounted displays (HMD) in both commercial and industrial applications, it has become apparent that not one platform will be appropriate for every use case scenario. HMDs are becoming increasingly more lightweight and powerful, but in collaborative settings there always will be a need for a shared display or environment to bring discussions together. 
The goal of this dissertation is to leverage the best of current augmented reality (AR) head mounted display technologies: 360 degree field of regard visuals, rendering of graphics over the real world, and personalized views with the best of large display wall environments: high resolution and contrast, shared visual environment, and more accurate tracking. 
A collaborative user study was conducted to evaluate how two participants wearing AR HMDs (HoloLens 1 and 2) in CAVE2 work with each other and the combination of visuals on the CAVE2 shared display and the AR HMD in completing a building network wiring task in 3D spatial AR.

PhD Dissertation Announcement: &ldquo;Collaborative Augmented Reality for Virtual Reality Display Wall Environments&rdquo;

&ldquo;Hummingbird&rdquo; is coming to the Chicago Children&rsquo;s Theater March 24-26th. Written by Jo Catell and developed by Daria Tsoupikova, Sai Priya Jyothula, Andrew Johnson, Arthur Nishimoto and Lance Long at EVL, this experience is described as collaborative Virtual Reality (VR) for tele-Immersive interactive theater. &ldquo;Hummingbird&rdquo; performances provide the opportunity for people to experience the show in two different ways: as a VR participant wearing a head-mounted display and interacting with the environment, or as an observer watching participants perform! 
A gutsy teen has to outsmart her mother&rsquo;s narcissistic boss and survive dangerous new technology in hummingbird: a live, immersive adventure that transforms theatrical storytelling utilizing cutting-edge, virtual reality technology1 
Free Performances: Fri 3/24 @ 6:30pm, Sat 3/25 @ 2:30pm & 4pm, Sun 3/26 @ 2:30pm & 4pm 
Recommended For Ages 10 & Up 
Run Time:50 minutes 
See the Chicago Children&rsquo;s Theater <a href="https://chicagochildrenstheatre.org/event/hummingbird/">web posting</a> for more information. 
&ldquo;Hummingbird&rdquo; performances are made possible with the support from the National Endowment for the Arts grant for art projects, Illinois Arts Council, Electronic Visualization Laboratory (EVL), and the University of Illinois Presidential Initiative to Celebrate the Impact of the Arts. 
See <a href="https://hummingbirdvr.com/"> https://hummingbirdvr.com/</a>

&ldquo;Hummingbird&rdquo; Performances Scheduled at the Chicago Children&rsquo;s Theater

The First Environmental Justice Workshop, entitled &ldquo;Generating a Discussion Between Communities and Industries: Data Collection, Analytics, Policy, and Tools&rdquo; was held at the Electronic Visualization Laboratory's Continuum environment on March 15, 2023. In many cities across the United States, many communities are located close to an excessive number of environmentally polluting industrial facilities. From an environmental justice viewpoint, the fact that the environmental burden is not shared across all populations living in a city is unfair. The aim of the environmental justice workshop is to bring together different stakeholders such as industries and southwest Chicago communities to get their perspective, identify and discuss pressing environmental justice challenges across Chicago, share current work across disciplines, and brainstorm solutions. 
Among topics for discussion were posing questions to participants such as - What are the fundamental concepts of environmental justice? How do environmental issues disproportionately impact certain communities? What environmental injustices exist in different communities? Are there any organizations working to create awareness about environmental justice? How can we use interactive visualization to access environmental justice issues? 
Workshop organizers include: 
Apostolis Sambanis, Health Policy and Administration, University of Illinois, Chicago 
Fabio Miranda, Computer Science, University of Illinois, Chicago 
Federica Fusi, Urban Planning and Public Affairs, University of Illinois, Chicago 
Marisol Becerra, Urban Planning and Public Affairs, University of Illinois, Chicago 
Michael Cailas, Environmental and Occupational Health Sciences, University of Illinois, Chicago 
Michael D Siciliano, Public Policy, Management, and Analytics, University of Illinois, Chicago 
Phillip A. Boda, Special Education, University of Illinois, Chicago 
Sanjana Srabanti, Computer Science, University of Illinois, Chicago 
Sybil Derrible, Civil, Materials, and Environmental Engineering, University of Illinois, Chicago

The First Environmental Justice Workshop Held at EVL

&ldquo;Where the sidewalk ends&rdquo; in <a href="https://news.mit.edu/2023/open-source-tool-mapping-sidewalks-0315">MIT News</a> discusses how Miranda along with researchers from MIT, University of Sao Paulo, and New York University have built an open-source tool that uses aerial imagery and image-recognition to create complete maps of sidewalks and crosswalks. The tool, called TILE2NET can help planners, policymakers, and urbanists who want to expand pedestrian infrastructure. 
The research team used computerized image-recognition techniques to build a tool that will visually recognize sidewalks, crosswalks, and footpaths. To do that, the researchers first used 20,000 aerial images from Boston, Cambridge, New York City, and Washington - places where comprehensive pedestrian maps already existed. By training the image-recognition model on such clearly defined objects and using portions of those cities as a starting point, they were able to see how well TILE2NET would work elsewhere in those cities. 
<a href="https://news.mit.edu/2023/open-source-tool-mapping-sidewalks-0315">Read the full MIT News article.</a> 
For additional information regarding this research see the Computers, Environment and Urban Systems publication <a href="https://www2.evl.uic.edu/entry.php?id=2703">&ldquo;Mapping the walk: A scalable computer vision approach for generating sidewalk network datasets from aerial imagery&rdquo;</a>.

Boston Commons: a) Aerial image, b) Detected sidewalk and footpath polygons (in orange) and detected crosswalks (in red), c) Fitted sidewalk, crosswalk, and footpath centerlines superimposed on the aerial image.

Events - 2023

EVL Presents SAGE3 at AGU Fall Meeting 2023

PhD Prelim Announcement: Visual Computing Design for Explainable, Spatially-aware Machine Learning

EVLers Juan Trelles Trabucco, Carla Floricel and Professor Elisabeta Marai Biocuration Research Recognized by IEEE BIBM 2023

EVL Researcher Hal Brynteson’s Work Showcased at the Gallery of Fluid Motion

EVL Affiliated Faculty Sidharth Kumar’s Advisee Recognized with Best Poster Nomination at SC23

ALCF Team Including EVL Professor Michael Papka Wins Best Paper at SC23 ISAV 2023 Workshop

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