Computer Sciences Commons^™

Understaning Low Vision Graphical Perception Of Bar Charts, Yash Prakash, Akshay Kolgar Nayak, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok

Computer Science Faculty Publications

Bar charts are widely used for their simplicity in data representation, prompting numerous studies to explore and model how users interact with and perceive bar chart information. However, these studies have predominantly focused on sighted users, with a few also targeting blind screen-reader users, whereas the graphical perception of low-vision screen magnifier users is still an uncharted research territory. We fill this knowledge gap in this paper by designing four experiments for a laboratory study with 25 low-vision participants to examine their graphical perception while interacting with bar charts. For our investigation, we built a custom screen magnifier-based logger that …

Enhanced Skin Cancer Diagnosis Through Grid Search Algorithm-Optimized Deep Learning Models For Skin Lesion Analysis, Rudresh Pillai, Neha Sharma, Sheifali Gupta, Deepali Gupta, Sapna Juneja, Saurav Malik, Hong Qin, Mohammed S. Alqahtani, Amel Ksibi

Computer Science Faculty Publications

Skin cancer is a widespread and perilous disease that necessitates prompt and precise detection for successful treatment. This research introduces a thorough method for identifying skin lesions by utilizing sophisticated deep learning (DL) techniques. The study utilizes three convolutional neural networks (CNNs)-CNN1, CNN2, and CNN3-each assigned to a distinct categorization job. Task 1 involves binary classification to determine whether skin lesions are present or absent. Task 2 involves distinguishing between benign and malignant lesions. Task 3 involves multiclass classification of skin lesion images to identify the precise type of skin lesion from a set of seven categories. The most optimal …

The Combined Focal Loss And Dice Loss Function Improves The Segmentation Of Beta-Sheets In Medium-Resolution Cryo-Electron-Microscopy Density Maps, Yongcheng Mu, Thu Nguyen, Bryan Hawickhorst, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Although multiple neural networks have been proposed for detecting secondary structures from medium-resolution (5–10 Å) cryo-electron microscopy (cryo-EM) maps, the loss functions used in the existing deep learning networks are primarily based on cross-entropy loss, which is known to be sensitive to class imbalances. To monitor and tune the performance of various loss functions for the secondary structure detection problem, we investigated five loss functions: cross-entropy, Focal loss, Dice loss, and two combined loss functions. Using a U-Net architecture in our DeepSSETracer method and a dataset composed of 1,355 box-cropped atomic-structure/density-map pairs, we found that a newly designed loss function …

Retrogressive Document Manipulation Of Us Federal Environmental Websites, Lesley Frew, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

Changes made to webpages can affect their retrievability. Often this is done with the intention of increasing the page's search engine ranking to improve overall access to information on the page. The Environmental Data and Governance Initiative (EDGI) created a dataset that describes changes on US federal environmental webpages between 2016 and 2020. EDGI noted that many environmental terms were deleted from the pages, but without user data, claims that page retrievability and public information access were lowered are only anecdotal. The Open Resource for Click Analysis in Search (ORCAS) dataset was created during the same time frame, from 2017 …

Evaluating Social Media Reach Via Mainstream Media Discourse, Himarsha R. Jayanetti

Computer Science Faculty Publications

This study examines the intersection between social media and mainstream television (TV) news with an aim to understand how social media content amplifies its impact through TV broadcasts. While many studies emphasize social media as a primary platform for information dissemination, they often underestimate its total influence by focusing solely on interactions within the platform. This research examines instances where social media posts gain prominence on TV broadcasts, reaching new audiences and prompting public discourse. By using TV news closed captions, on-screen text recognition, and social media logo detection, we analyze how social media is referenced in TV news. Our …

Towards Trust And Reputation As A Service In Society 5.0, Stephan Olariu, Ravi Mukkamala, Meshari Aljohani

Computer Science Faculty Publications

Our paper was inspired by the recent Society 5.0 initiative of the Japanese Government which seeks to create a sustainable human-centric society by putting to work recent advances in technology. One of the key challenges in implementing Society 5.0 is providing trusted and secure services for everyone to use. Motivated by this challenge, this paper makes three contributions that we summarize as follows: Our first main contribution is to propose a novel blockchain and smart contract-based trust and reputation service design to reduce the uncertainty associated with buyer feedback in marketplaces that we expect to see in Society 5.0. Our …

Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers

Computer Science Faculty Publications

Motivation: This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results: We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 …

Improving Usability Of Data Charts In Multimodal Documents For Low Vision Users, Yash Prakash, Akshay Kolgar Nayak, Shoaib Mohammed Alyaan, Pathan Aseef Khan, Hae-Na Lee, Vikas Ashok

Computer Science Faculty Publications

Data chart visualizations and text are often paired in news articles, online blogs, and academic publications to present complex data. While chart visualizations offer graphical summaries of the data, the accompanying text provides essential context and explanation. Associating information from text and charts is straightforward for sighted users but presents significant challenges for individuals with low vision, especially on small-screen devices such as smartphones. The visual nature of charts coupled with the layout of the text inherently makes it difficult for low vision users to mentally associate chart data with text and comprehend the content due to their dependence on …

Exacfs - A Cil Method To Mitigate Catastrophic Forgetting, S. Balasubramanian, Sai Subramaniam M., Sai Sriram Talasu, Manepalli Pranav Phanindra Sai, Yedu P. Krishna, Darshan Gera, Ravi Mukkamala

Computer Science Faculty Publications

Deep neural networks (DNNs) excel at learning from static datasets but struggle with continual learning, where data arrives sequentially. Catastrophic forgetting, the phenomenon of forgetting previously learned knowledge, is a primary challenge. This paper introduces EXponentially Averaged Class-wise Feature Significance (EXACFS) to mitigate this issue in the class incremental learning (CIL) setting. By estimating the significance of model features for each learned class using loss gradients, gradually aging the significance through the incremental tasks and preserving the significant features through a distillation loss, EXACFS effectively balances remembering old knowledge (stability) and learning new knowledge (plasticity). Extensive experiments on CIFAR-100 and …

Sccad: Cluster Decomposition-Based Anomaly Detection For Rare Cell Identification In Single-Cell Expression Data, Yunpei Xu, Shaokai Wang, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li, Jianxin Wang

Computer Science Faculty Publications

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate …

Retrogressive Document Manipulation Of Us Federal Environmental Websites, Lesley Frew, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

Changes made to webpages can affect their retrievability. Often this is done with the intention of increasing the page's search engine ranking to improve overall access to information on the page. The Environmental Data and Governance Initiative (EDGI) created a dataset that describes changes on US federal environmental webpages between 2016 and 2020. EDGI noted that many environmental terms were deleted from the pages, but without user data, claims that page retrievability and public information access were lowered are only anecdotal. The Open Resource for Click Analysis in Search (ORCAS) dataset was created during the same time frame, from 2017 …

Dilf: Differentiable Rendering-Based Multi-View Image-Language Fusion For Zero-Shot 3d Shape Understanding, Xin Ning, Zaiyang Yu, Lusi Li, Weijun Li, Prayag Tiwari

Computer Science Faculty Publications

Zero-shot 3D shape understanding aims to recognize “unseen” 3D categories that are not present in training data. Recently, Contrastive Language–Image Pre-training (CLIP) has shown promising open-world performance in zero-shot 3D shape understanding tasks by information fusion among language and 3D modality. It first renders 3D objects into multiple 2D image views and then learns to understand the semantic relationships between the textual descriptions and images, enabling the model to generalize to new and unseen categories. However, existing studies in zero-shot 3D shape understanding rely on predefined rendering parameters, resulting in repetitive, redundant, and low-quality views. This limitation hinders the model’s …

A Survey On Few-Shot Class-Incremental Learning, Songsong Tian, Lusi Li, Weijun Li, Hang Ran, Xin Ning, Prayag Tiwari

Computer Science Faculty Publications

Large deep learning models are impressive, but they struggle when real-time data is not available. Few-shot class-incremental learning (FSCIL) poses a significant challenge for deep neural networks to learn new tasks from just a few labeled samples without forgetting the previously learned ones. This setup can easily leads to catastrophic forgetting and overfitting problems, severely affecting model performance. Studying FSCIL helps overcome deep learning model limitations on data volume and acquisition time, while improving practicality and adaptability of machine learning models. This paper provides a comprehensive survey on FSCIL. Unlike previous surveys, we aim to synthesize few-shot learning and incremental …

A Chinese Power Text Classification Algorithm Based On Deep Active Learning, Song Deng, Qianliang Li, Renjie Dai, Siming Wei, Di Wu, Yi He, Xindong Wu

Computer Science Faculty Publications

The construction of knowledge graph is beneficial for grid production, electrical safety protection, fault diagnosis and traceability in an observable and controllable way. Highly-precision text classification algorithm is crucial to build a professional knowledge graph in power system. Unfortunately, there are a large number of poorly described and specialized texts in the power business system, and the amount of data containing valid labels in these texts is low. This will bring great challenges to improve the precision of text classification models. To offset the gap, we propose a classification algorithm for Chinese text in the power system based on deep …

Building Datasets To Support Information Extraction And Structure Parsing From Electronic Theses And Dissertations, William A. Ingram, Jian Wu, Sampanna Yashwant Kahu, Javaid Akbar Manzoor, Bipasha Banerjee, Aman Ahuja, Muntabir Hasan Choudhury, Lamia Salsabil, Winston Shields, Edward A. Fox

Computer Science Faculty Publications

Despite the millions of electronic theses and dissertations (ETDs) publicly available online, digital library services for ETDs have not evolved past simple search and browse at the metadata level. We need better digital library services that allow users to discover and explore the content buried in these long documents. Recent advances in machine learning have shown promising results for decomposing documents into their constituent parts, but these models and techniques require data for training and evaluation. In this article, we present high-quality datasets to train, evaluate, and compare machine learning methods in tasks that are specifically suited to identify and …

Identifying Patterns For Neurological Disabilities By Integrating Discrete Wavelet Transform And Visualization, Soo Yeon Ji, Sampath Jayarathna, Anne M. Perrotti, Katrina Kardiasmenos, Dong Hyun Jeong

Computer Science Faculty Publications

Neurological disabilities cause diverse health and mental challenges, impacting quality of life and imposing financial burdens on both the individuals diagnosed with these conditions and their caregivers. Abnormal brain activity, stemming from malfunctions in the human nervous system, characterizes neurological disorders. Therefore, the early identification of these abnormalities is crucial for devising suitable treatments and interventions aimed at promoting and sustaining quality of life. Electroencephalogram (EEG), a non-invasive method for monitoring brain activity, is frequently employed to detect abnormal brain activity in neurological and mental disorders. This study introduces an approach that extends the understanding and identification of neurological disabilities …

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Learning Optimal Inter-Class Margin Adaptively For Few-Shot Class-Incremental Learning Via Neural Collapse-Based Meta-Learning, Hang Ran, Weijun Li, Lusi Li, Songsong Tian, Xin Ning, Prayag Tiwari

Computer Science Faculty Publications

Few-Shot Class-Incremental Learning (FSCIL) aims to learn new classes incrementally with a limited number of samples per class. It faces issues of forgetting previously learned classes and overfitting on few-shot classes. An efficient strategy is to learn features that are discriminative in both base and incremental sessions. Current methods improve discriminability by manually designing inter-class margins based on empirical observations, which can be suboptimal. The emerging Neural Collapse (NC) theory provides a theoretically optimal inter-class margin for classification, serving as a basis for adaptively computing the margin. Yet, it is designed for closed, balanced data, not for sequential or few-shot …

Robots Still Outnumber Humans In Web Archives In 2019, But Less Than In 2015 And 2012, Himarsha R. Jayanetti, Kritika Garg, Sawood Alam, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

The significance of the web and the crucial role of web archives in its preservation highlight the necessity of understanding how users, both human and robot, access web archive content, and how best to satisfy this disparate needs of both types of users. To identify robots and humans in web archives and analyze their respective access patterns, we used the Internet Archive’s (IA) Wayback Machine access logs from 2012, 2015, and 2019, as well as Arquivo.pt’s (Portuguese Web Archive) access logs from 2019. We identified user sessions in the access logs and classified those sessions as human or robot based …

Osfs-Vague: Online Streaming Feature Selection Algorithm Based On A Vague Set, Jie Yang, Zhijun Wang, Guoyin Wang, Yanmin Liu, Yi He, Di Wu

Computer Science Faculty Publications

Online streaming feature selection (OSFS), as an online learning manner to handle streaming features, is critical in addressing high-dimensional data. In real big data-related applications, the patterns and distributions of streaming features constantly change over time due to dynamic data generation environments. However, existing OSFS methods rely on presented and fixed hyperparameters, which undoubtedly lead to poor selection performance when encountering dynamic features. To make up for the existing shortcomings, the authors propose a novel OSFS algorithm based on vague set, named OSFS-Vague. Its main idea is to combine uncertainty and three-way decision theories to improve feature selection from the …

A-Disetrac Advanced Analytic Dashboard For Distributed Eye Tracking, Yasasi Abeysinghe, Bhanuka Mahanama, Gavindya Jayawardena, Yasith Jayawardena, Mohan Sunkara, Andrew T. Duchowski, Vikas Ashok, Sampath Jayarathna

Computer Science Faculty Publications

Understanding how individuals focus and perform visual searches during collaborative tasks can help improve user engagement. Eye tracking measures provide informative cues for such understanding. This article presents A-DisETrac, an advanced analytic dashboard for distributed eye tracking. It uses off-the-shelf eye trackers to monitor multiple users in parallel, compute both traditional and advanced gaze measures in real-time, and display them on an interactive dashboard. Using two pilot studies, the system was evaluated in terms of user experience and utility, and compared with existing work. Moreover, the system was used to study how advanced gaze measures such as ambient-focal coefficient K …

Autonomous Strike Uavs In Support Of Homeland Security Missions: Challenges And Preliminary Solutions, Meshari Aljohani, Ravi Mukkamala, Stephan Olariu

Computer Science Faculty Publications

Unmanned Aerial Vehicles (UAVs) are becoming crucial tools in modern homeland security applications, primarily because of their cost-effectiveness, risk reduction, and ability to perform a wider range of activities. This study focuses on the use of autonomous UAVs to conduct, as part of homeland security applications, strike missions against high-value terrorist targets. Owing to developments in ledger technology, smart contracts, and machine learning, activities formerly carried out by professionals or remotely flown UAVs are now feasible. Our study provides the first in-depth analysis of the challenges and preliminary solutions for the successful implementation of an autonomous UAV mission. Specifically, we …

Mosaic: A Prune-And-Assemble Approach For Efficient Model Pruning In Privacy-Preserving Deep Learning, Yifei Cai, Qiao Zhang, Rui Ning, Chunsheng Xin, Hongyi Wu

Computer Science Faculty Publications

To enable common users to capitalize on the power of deep learning, Machine Learning as a Service (MLaaS) has been proposed in the literature, which opens powerful deep learning models of service providers to the public. To protect the data privacy of end users, as well as the model privacy of the server, several state-of-the-art privacy-preserving MLaaS frameworks have also been proposed. Nevertheless, despite the exquisite design of these frameworks to enhance computation efficiency, the computational cost remains expensive for practical applications. To improve the computation efficiency of deep learning (DL) models, model pruning has been adopted as a strategic …

Speculative Anisotropic Mesh Adaptation On Shared Memory For Cfd Applications, Christos Tsolakis, Nikos Chrisochoides

Computer Science Faculty Publications

Efficient and robust anisotropic mesh adaptation is crucial for Computational Fluid Dynamics (CFD) simulations. The CFD Vision 2030 Study highlights the pressing need for this technology, particularly for simulations targeting supercomputers. This work applies a fine-grained speculative approach to anisotropic mesh operations. Our implementation exhibits more than 90% parallel efficiency on a multi-core node. Additionally, we evaluate our method within an adaptive pipeline for a spectrum of publicly available test-cases that includes both analytically derived and error-based fields. For all test-cases, our results are in accordance with published results in the literature. Support for CAD-based data is introduced, and its …

Charged Track Reconstruction With Artificial Intelligence For Clas12, Gagik Gavalian, Polykarpos Thomadakis, Angelos Angelopoulos, Nikos Chrisochoides

Computer Science Faculty Publications

In this paper, we present the results of charged particle track reconstruction in CLAS12 using artificial intelligence. In our approach, we use neural networks working together to identify tracks based on the raw signals in the Drift Chambers. A Convolutional Auto-Encoder is used to de-noise raw data by removing the hits that do not satisfy the patterns for tracks, and second Multi-Layer Perceptron is used to identify tracks from combinations of clusters in the drift chambers. Our method increases the tracking efficiency by 50% for multi-particle final states already conducted experiments. The de-noising results indicate that future experiments can run …

Multitasking Scheduling With Shared Processing, Bin Fu, Yumei Huo, Hairong Zhao

Computer Science Faculty Publications

Recently, the problem of multitasking scheduling has raised a lot of interest in the service industries. Hall et al. (Discrete Applied Mathematics, 2016) proposed a shared processing multitasking scheduling model which allows a team to continue to work on the primary tasks while processing the routinely scheduled activities as they occur. With a team being modeled as a single machine, the processing sharing of the machine is achieved by allocating a fraction of the processing capacity to routine jobs and the remaining fraction, which we denote as sharing ratio, to the primary jobs. In this paper, we generalize this model …

Building Squares With Optimal State Complexity In Restricted Active Self-Assembly, Robert M. Alaniz, David Caballero, Sonya C. Cirlos, Timothy Gomez, Elize Grizzell, Andrew Rodriguez, Robert Schweller, Armando Tenorio, Tim Wylie

Computer Science Faculty Publications

Tile Automata is a recently defined model of self-assembly that borrows many concepts from cellular automata to create active self-assembling systems where changes may be occurring within an assembly without requiring attachment. This model has been shown to be powerful even with limited assembly size, but many fundamental questions have yet to be explored. Here, we study the state complexity of assembling n×n squares in seeded Tile Automata systems where growth starts from a seed and tiles attach one at a time, similar to the abstract Tile Assembly Model. We provide optimal bounds for three classes of seeded Tile Automata …

Spectrum-Enhanced Trca (Se-Trca): A Novel Approach For Direction Detection In Ssvep-Based Bci, Amirmohammad Mijani, Mohammad Norizadeh Cherloo, Haoteng Tang, Liang Zhan

Computer Science Faculty Publications

The Steady State Visual Evoked Potential (SSVEP) is a widely used component in BCIs due to its high noise resistance and low equipment requirements. Recently, a novel SSVEP-based paradigm has been introduced for direction detection, in which, unlike the common SSVEP paradigms that use several frequency stimuli, only one flickering stimulus is used and it makes direction detection very challenging. So far, only the CCA method has been used for direction detection using SSVEP component analysis. Since Canonical Correlation Analysis (CCA) has some limitations, a Task-Related Component Analysis (TRCA) based method has been introduced for feature extraction to improve the …

A Fast And Responsive Web-Based Framework For Visualizing Hpc Application Usage, Ved Arora, Nayeli Gurrola, Amiya K. Maji, Guangzhen Jin

Computer Science Faculty Publications

Insights about applications and user environments can help HPC center staff make data-driven decisions about cluster operations. In this paper, we present a fast and responsive web-based visualization framework for analyzing HPC application usage. By leveraging XALT, a powerful tool for tracking application and library usage, we collected tens of millions of data points on a national supercomputer. The portable visualization framework created with Plotly Dash can be easily launched as a container and accessed from a web browser. The presented visualizations take a deep dive into the XALT data, analyzing application use, compiler usage, library usage, and even user-specific …

A Comprehensive Survey Of Complex Brain Network Representation, Haoteng Tang, Guixiang Ma, Yanfu Zhang, Kai Ye, Lei Guo, Guodong Liu, Qi Huang, Yalin Wang, Olusola Ajilore, Alex D. Leow

Computer Science Faculty Publications

Highlights

• Major traditional and deep learning methods on brain network representation are overviewed.

• Brain network datasets and algorithm implementation tools are summarized.

• Promising research directions in brain network analysis are discussed.

Abstract

Recent years have shown great merits in utilizing neuroimaging data to understand brain structural and functional changes, as well as its relationship to different neurodegenerative diseases and other clinical phenotypes. Brain networks, derived from different neuroimaging modalities, have attracted increasing attention due to their potential to gain system-level insights to characterize brain dynamics and abnormalities in neurological conditions. Traditional methods aim to pre-define multiple topological features of brain …