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Articles 91 - 120 of 928
Full-Text Articles in Computer Sciences
A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh
A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh
Computer Science Faculty Publications
Conventional drug discovery is expensive, time-consuming, and prone to failure. Artificial intelligence has become a potent substitute over the last decade, providing strong answers to challenging biological issues in this field. Among these difficulties, drug-target binding (DTB) is a key component of drug discovery techniques. In this context, drug-target affinity and drug–target interaction are complementary and essential frameworks that work together to improve our comprehension of DTB dynamics. In this work, we thoroughly analyze the most recent deep learning models, popular benchmark datasets, and assessment metrics for DTB prediction. We look at the paradigm shift in the development of drug …
Geometric Gnns For Charged Particle Tracking At Gluex, Ahmed Hossam Mohammed, Kishansingh Rajput, Simon Taylor, Denis Furletov, Sergey Furletov, Malachi Schram
Geometric Gnns For Charged Particle Tracking At Gluex, Ahmed Hossam Mohammed, Kishansingh Rajput, Simon Taylor, Denis Furletov, Sergey Furletov, Malachi Schram
Computer Science Faculty Publications
Nuclear physics experiments are aimed at uncovering the fundamental building blocks of matter. The experiments involve high-energy collisions that produce complex events with many particle trajectories. Tracking charged particles resulting from collisions in the presence of a strong magnetic field is critical to enable the reconstruction of particle trajectories and precise determination of interactions. It is traditionally achieved through combinatorial approaches that scale worse than linearly as the number of hits grows. Since particle hit data naturally form a point cloud and can be structured as graphs, graph neural networks (GNNs) emerge as an intuitive and effective choice for this …
A Bibliographic And Topic Modeling Analysis Of The P-Adic Theory Literature Using Latent Dirichlet Allocation, Humberto Llinás, Ismael Gutiérrez, Anselmo Torresblanca, Javier De La Hoz, Brian Llinás
A Bibliographic And Topic Modeling Analysis Of The P-Adic Theory Literature Using Latent Dirichlet Allocation, Humberto Llinás, Ismael Gutiérrez, Anselmo Torresblanca, Javier De La Hoz, Brian Llinás
Computer Science Faculty Publications
P-adic analysis, introduced by Kurt Hensel in the early 20th century, has developed into a fundamental area of mathematical research with broad applications in number theory, algebraic geometry, and mathematical physics. This study aims to examine the thematic evolution and scholarly impact of p-adic research through a comprehensive topic modeling and bibliometric analysis. Using classical bibliometric techniques (e.g., performance analysis, co-authorship, and co-citation networks) combined with Latent Dirichlet Allocation (LDA), we analyzed 7388 peer-reviewed documents published between 1965 and 2024. The computational workflow was conducted using R (version 4.4.1) and VOSviewer (version 1.6.20), which enabled the identification of 20 distinct …
From Philosophy To Nlu: Evolving Definitions With Research Hypotheses, Jian Wu, Sarah Rajtmajer
From Philosophy To Nlu: Evolving Definitions With Research Hypotheses, Jian Wu, Sarah Rajtmajer
Computer Science Faculty Publications
Over the past decades, alongside advancements in natural language processing, significant attention has been paid to training models to automatically extract, understand, test, and generate hypotheses in open and scientific domains. However, interpretations of the term hypothesis for various natural language understanding (NLU) tasks have migrated from traditional definitions in the natural, social, and formal sciences. Even within NLU, we observe differences defining hypotheses across literature. In this paper, we overview and delineate various definitions of hypothesis. Especially, we discern the nuances of definitions across recently published NLU tasks. We highlight the importance of well-structured and well-defined hypotheses, particularly as …
Quickque: Enabling Quick Access To Information In User Reviews For Screen Reader Users, Mohan Sunkara, Akshay Kolgar Nayak, Sandeep Kalari, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok
Quickque: Enabling Quick Access To Information In User Reviews For Screen Reader Users, Mohan Sunkara, Akshay Kolgar Nayak, Sandeep Kalari, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok
Computer Science Faculty Publications
Efficiently perusing online customer reviews is presently challenging for blind users, who rely on a screen reader that supports predominantly one-dimensional narration of content via keyboard shortcuts. To address this, with restaurant reviews as seminal case study, we developed QuickCue, a browser extension prototype that enables screen reader users to quickly obtain the positives and negatives regarding different aspects of a restaurant (e.g., food quality, hygiene, ambiance), without having to sift through numerous reviews containing redundant information. At its core, QuickCue utilizes a large language model to perform aspect and sentiment-based joint classification of reviews to group them based on …
Can Llms Beat Humans On Discerning Human-Written And Llm-Generated Science News, Dominik Soós, Meng Jiang, Jian Wu
Can Llms Beat Humans On Discerning Human-Written And Llm-Generated Science News, Dominik Soós, Meng Jiang, Jian Wu
Computer Science Faculty Publications
Science news is increasingly important in connecting scientists and the public by sharing discoveries and innovations. With the rise of large language models (LLMs), there is potential to automate science news creation, but concerns exist about the quality of LLM-generated news versus human-written news. This paper explores whether LLMs can outperform humans in distinguishing between human-written and LLM-generated news. Inspired by the Chain-of-Thought prompting method, we designed a simple yet effective variant called Guided Few-shot (GFS), which encodes the characteristics of news of two types with examples. Our experiments indicated that GFS with just a single example effectively boosted the …
Accessmenu: Enhancing Usability Of Online Restaurant Menus For Screen Reader Users, Nithiya Venkatraman, Akshay Kolgar Nayak, Suyog Dahal, Yash Prakash, Hae-Na Lee, Vikas Ashok
Accessmenu: Enhancing Usability Of Online Restaurant Menus For Screen Reader Users, Nithiya Venkatraman, Akshay Kolgar Nayak, Suyog Dahal, Yash Prakash, Hae-Na Lee, Vikas Ashok
Computer Science Faculty Publications
Online food ordering has become commonplace due to its convenience. The wide variety of culinary choices, combined with fast and economical door-delivery services, encourages more people to order food online. To facilitate this process, food vendors, including restaurants, often provide full menus on their websites, typically in visual formats such as images or PDFs. While this is convenient for sighted users, blind and visually impaired (BVI) individuals face significant challenges accessing these visual menus with their screen reader assistive technology. An interview study with 12 BVI screen reader users revealed that present assistive tools do not adequately satisfy the needs …
Neural Topic Modeling Via Contextual And Graph Information Fusion, Jiyuan Liu, Jiaxing Yan, Chunjiang Zhu, Xingyu Liu, Qing Li, Yanghui Rao
Neural Topic Modeling Via Contextual And Graph Information Fusion, Jiyuan Liu, Jiaxing Yan, Chunjiang Zhu, Xingyu Liu, Qing Li, Yanghui Rao
Computer Science Faculty Publications
Topic modeling is a powerful unsupervised tool for knowledge discovery. However, existing work struggles with generating limited-quality topics that are uninformative and incoherent, which hindering interpretable insights from managing textual data. In this paper, we improve the original variational autoencoder framework by incorporating contextual and graph information to address the above issues. First, the encoder utilizes topic fusion techniques to combine contextual and bag-of-words information well, and meanwhile exploits the constraints of topic alignment and topic sharpening to generate informative topics. Second, we develop a simple word co-occurrence graph information fusion strategy that efficiently increases topic coherence. On three benchmark …
Coming Back Differently: An Exploratory Case Study Of Near Death Experiences Of Webpages, Lesley Frew, Michael L. Nelson, Michele Weigle
Coming Back Differently: An Exploratory Case Study Of Near Death Experiences Of Webpages, Lesley Frew, Michael L. Nelson, Michele Weigle
Computer Science Faculty Publications
In this case study, we use web archives to analyze 8,824 webpages that were taken offline and subsequently put back online, thus experiencing a “near death experience.” We enumerate the stages of a webpage’s near death experience, including the change from a successful HTTP status code to non-successful and back, the intermediate stage with markers such as an under construction banner, and an analysis of how the pages came back differently.
Adapting Online Customer Reviews For Blind Users: A Case Study Of Restaurant Reviews, Mohan Sunkara, Akshay Kolgar Nayak, Sandeep Kalari, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok
Adapting Online Customer Reviews For Blind Users: A Case Study Of Restaurant Reviews, Mohan Sunkara, Akshay Kolgar Nayak, Sandeep Kalari, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok
Computer Science Faculty Publications
Online reviews have become an integral aspect of consumer decision-making on e-commerce websites, especially in the restaurant industry. Unlike sighted users who can visually skim through the reviews, perusing reviews remains challenging for blind users, who rely on screen reader assistive technology that supports predominantly one-dimensional narration of content via keyboard shortcuts. In an interview study, we uncovered numerous pain points of blind screen reader users with online restaurant reviews, notably, the listening fatigue and frustration after going through only the first few reviews. To address these issues, we developed QuickCue assistive tool that performs aspect-focused sentiment-driven summarization to reorganize …
Adversarially Attacking Graph Properties And Sparsification In Graph Learning, Chunjiang Zhu, Blake Gaines, Jing Deng, Jinbo Bi
Adversarially Attacking Graph Properties And Sparsification In Graph Learning, Chunjiang Zhu, Blake Gaines, Jing Deng, Jinbo Bi
Computer Science Faculty Publications
Graph neural networks and graph transformers explicitly or implicitly rely on fundamental properties of the underlying graph, such as spectral properties and shortest-path distances. However, it is still not clear how these graph properties are vulnerable to adversarial attacks and what impacts this has on the downstream graph learning. Moreover, while graph sparsification has been used to improve computational cost of learning over graphs, its susceptibility to adversarial attacks has not been studied. In this paper, we study adversarial attacks on graph properties and graph sparsification and their impacts on downstream graph learning, paving the way for how to protect …
Decode The Workload: Training Deep Learning Models For Efficient Compute Cluster Representation, Ahmed Hossam Mohammed, Mark Jones, Diana Mcspadden, Malachi Schram, Bryan Hess, Kishansingh Rajput
Decode The Workload: Training Deep Learning Models For Efficient Compute Cluster Representation, Ahmed Hossam Mohammed, Mark Jones, Diana Mcspadden, Malachi Schram, Bryan Hess, Kishansingh Rajput
Computer Science Faculty Publications
In this study, we address the mounting challenge of monitoring high throughput computing clusters running computationally intensive jobs, which increasingly strains system administrators. We develop autoencoders that analyze traces of Linux kernel CPU metrics to capture salient system features by producing robust compressed embeddings for various downstream tasks. In addition, we employ graph neural networks to incorporate contextual information from surrounding CPUs and assess their performance. We also demonstrate the enhanced job differentiation achieved by increasing the sampling rate of these traces. Our models are evaluated based on their ability to generate meaningful latent representations, detect anomalies, and distinguish between …
From Philosophy To Nlu: Evolving Definitions Of Research Hypotheses, Jian Wu, Sarah Rajtmajer
From Philosophy To Nlu: Evolving Definitions Of Research Hypotheses, Jian Wu, Sarah Rajtmajer
Computer Science Faculty Publications
Over the past decades, alongside advancements in natural language processing, significant attention has been paid to training models to automatically extract, understand, test, and generate hypotheses in open and scientific domains. However, interpretations of the term hypothesis for various natural language understanding (NLU) tasks have migrated from traditional definitions in the natural, social, and formal sciences. Even within NLU, we observe differences defining hypotheses across literature. In this paper, we overview and delineate various definitions of hypothesis. Especially, we discern the nuances of definitions across recently published NLU tasks. We highlight the importance of well-structured and well-defined hypotheses, particularly as …
S²Il: Structurally Stable Incremental Learning, S. Balasubramanian, P. Yedu Krishna, Talasu Sai Sriram, M. Sai Subramaniam, Manepalli Pranav Phanindra Sai, Ravi Mukkamala
S²Il: Structurally Stable Incremental Learning, S. Balasubramanian, P. Yedu Krishna, Talasu Sai Sriram, M. Sai Subramaniam, Manepalli Pranav Phanindra Sai, Ravi Mukkamala
Computer Science Faculty Publications
Feature Distillation (FD) strategies are proven to be effective in mitigating Catastrophic Forgetting (CF) seen in Class Incremental Learning (CIL). However, current FD approaches enforce strict alignment of feature magnitudes and directions across incremental steps, limiting the model’s ability to adapt to new knowledge. In this paper, we propose Structurally Stable Incremental Learning (S²IL), a FD method for CIL that mitigates forgetting by focusing on preserving the overall spatial patterns of features which promote flexible (plasticity) yet stable representations that preserve old knowledge (stability). We also demonstrate that our proposed method S²IL achieves strong incremental accuracy and outperforms other FD …
Benchmarking And Improving Foundation Model Dietary Estimates From Meal Images, Yongcheng Mu, Jiangwen Sun, Jing He
Benchmarking And Improving Foundation Model Dietary Estimates From Meal Images, Yongcheng Mu, Jiangwen Sun, Jing He
Computer Science Faculty Publications
Accurate quantifying dietary contents, such as calories, proteins, carbohydrates, and fats, from an image of a meal plate is vital for managing diabetes. Recently, Large Multimodal Models (LMMs) have excelled in complex vision-language tasks due to their use of very large, highly diverse data. This study benchmarked the use of seven LMMs that include full and lightweight models of GPT, Gemini, and Llama for nutrition estimation based on Google's Nutrition5k dataset and our own phone-collected DonateAndLearn dataset. We analyzed the performance of LMMs and the RGB-D fusion model, in which the RGB-D model was specifically trained using Nutrition5k data. On …
Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He
Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He
Computer Science Faculty Publications
DeepSSETracer is a method for segmenting protein secondary structure from medium-resolution (5-10Å) cryogenic electron microscopy (cryo-EM) density maps. We conducted experiments and ablation studies to examine the effects of normalization methods, max-pooling, activation functions, and loss calculation region on DeepSSETracer. By combining multiple technical improvements, the performance of the new version, DeepSSETracer 2.0, was significantly enhanced compared to DeepSSETracer 1.1. On a set of 77 test cases, the weighted average per-voxel F1 score increased from 62.1% to 70.3% for helix detection, and from 47.8% to 62.5% for β-sheet detection. While each of the five modifications in the network enhanced the …
Effective Pii Extraction From Llms Through Augmented Few-Shot Learning, Shuai Cheng, Shu Meng, Haitao Xu, Haoran Zhang, Shuai Hao, Chuan Yue, Wenrui Ma, Meng Han, Fang Zhang, Zhao Li
Effective Pii Extraction From Llms Through Augmented Few-Shot Learning, Shuai Cheng, Shu Meng, Haitao Xu, Haoran Zhang, Shuai Hao, Chuan Yue, Wenrui Ma, Meng Han, Fang Zhang, Zhao Li
Computer Science Faculty Publications
Large Language Models (LLMs) exhibit strong natural language processing capabilities but also pose significant privacy risks, particularly regarding the leakage of Personally Identifiable Information (PII) embedded in their training data. Existing PII extraction methods suffer from the limitations of low success rates or impracticality for large-scale PII extraction. In this study, we propose a novel PII extraction approach based on enhanced few-shot learning techniques, which achieves efficient and cost-effective PII retrieval without relying on fine-tuning or jailbreaking. We evaluated our approach on both open-source and closed-source LLMs. The experimental results demonstrate that, for non-targeted PII extraction, the attack success rate …
An Optimized Generalized Multi-Color Point Implicit Solver For Intel Gpus Using Oneapi Esimd, Joseph Wassell, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Timothée Ewart
An Optimized Generalized Multi-Color Point Implicit Solver For Intel Gpus Using Oneapi Esimd, Joseph Wassell, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Timothée Ewart
Computer Science Faculty Publications
This paper presents an efficient implementation of a linear-solver kernel relevant to FUN3D, a suite of computational fluid dynamics software developed at NASA’s Langley Research Center. The linear solver is optimized for a range of block sizes commonly used in FUN3D. The implementation targets Aurora, the Argonne Leadership Computing Facility’s (ALCF) exascale machine featuring Intel Data Center Max 1550 GPUs. The linear solver’s performance is memory bandwidth-bound due to its low arithmetic intensity. The primary performance challenges stem from variable matrix row lengths and indirect memory access patterns inherent in unstructured-grid applications. Variable block sizes introduce additional complexity through differing …
Understanding Pii Leakage In Large Language Models: A Systematic Survey, Shuai Cheng, Zhao Li, Shu Meng, Mengxia Ren, Haitao Xu, Shuai Hao, Chuan Yue, Fang Zhang
Understanding Pii Leakage In Large Language Models: A Systematic Survey, Shuai Cheng, Zhao Li, Shu Meng, Mengxia Ren, Haitao Xu, Shuai Hao, Chuan Yue, Fang Zhang
Computer Science Faculty Publications
Large Language Models (LLMs) have demonstrated exceptional success across a variety of tasks, particularly in natural language processing, leading to their growing integration into numerous facets of daily life. However, this widespread deployment has raised substantial privacy concerns, especially regarding personally identifiable information (PII), which can be directly associated with specific individuals. The leakage of such information presents significant real-world privacy threats. In this paper, we conduct a systematic investigation into existing research on PII leakage in LLMs, encompassing commonly utilized PII datasets, evaluation metrics, and current studies on both PII leakage attacks and defensive strategies. Finally, we identify unresolved …
Energy-Based Deep Incomplete Multi-View Clustering, Ziyu Wang, Yiming Du, Rui Ning, Lusi Li
Energy-Based Deep Incomplete Multi-View Clustering, Ziyu Wang, Yiming Du, Rui Ning, Lusi Li
Computer Science Faculty Publications
Incomplete multi-view clustering (IMVC) deals with real-world scenarios where certain views are partially missing, posing significant challenges to effective clustering. Most existing IMVC approaches face a trade-off: imputation-free methods suffer from information bias and imbalance, while full-imputation methods risk introducing and propagating noise. To overcome these limitations, we propose Energy-Based Deep Incomplete Multi-View Clustering (Energy-DIMC), a novel selective-imputation framework that leverages energy-based models (EBMs) to guide reliable imputations and robust clustering. EBMs assess data compatibility by assigning lower energy to more coherent structures, effectively modeling complex inter-view and inter-sample dependencies. Inspired by EBMs, Energy-DIMC integrates four key components: 1) a …
Icu-Length Of Stay Prediction On Electronic Health Records Using Graph Neural Networks And Homogeneous Similarity Graphs, Ahmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman Iv, Rishabh Kapoor, Preetam Ghosh
Icu-Length Of Stay Prediction On Electronic Health Records Using Graph Neural Networks And Homogeneous Similarity Graphs, Ahmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman Iv, Rishabh Kapoor, Preetam Ghosh
Computer Science Faculty Publications
Predicting the length of stay (LoS) is important for hospital administration, as it helps allocate proper resources, such as bed management and hospital staffing. Patients' Electronic Health Records (EHRs) contain highly relevant data for LoS prediction; however, their integration and effective use in predictive modeling for accurately estimating LoS remain challenging. To address this, we propose a homogeneous Graph Neural Network (GNN)-based framework for predicting LoS. This method employs a comprehensive data fusion strategy based on the hospital Visit-based Similarity Graph (VSG), which integrates diverse multi-modal clinical features into a coherent, homogeneous graph representation. Next, this VSG is fed into …
Humans Vs. Llms On Open Domain Scientific Claim Verification: A Baseline Study, Benjamin Curtis, Stefania Dzhaman, Matthew Maisonave, Jian Wu
Humans Vs. Llms On Open Domain Scientific Claim Verification: A Baseline Study, Benjamin Curtis, Stefania Dzhaman, Matthew Maisonave, Jian Wu
Computer Science Faculty Publications
Verifying scientific claims is challenging for the general public because most people lack domain knowledge. Manual verification by subject domain experts is accurate, but it is obviously not scalable to meet the rising number of scientific claims on the Web. Whether the emerging large language models and large reasoning models can be used for scientific claim verification, and how their performances compare to humans, are still research questions. To this end, we developed a new benchmark MSVEC2 that consists of 138 claims from credible fact verification websites and science news outlets. Two tasks were given to both human and LLM …
Historical Review Of Variants Of Informal Semantics For Logic Programs Under Answer Set Semantics: Gl’88, Gl’91, Gk’14, D-V’12, Yuliya Lierler
Historical Review Of Variants Of Informal Semantics For Logic Programs Under Answer Set Semantics: Gl’88, Gl’91, Gk’14, D-V’12, Yuliya Lierler
Computer Science Faculty Publications
This note presents a historical survey of informal semantics that are associated with logic programming under answer set semantics. We review these in uniform terms and align them with two paradigms: Answer Set Programming and ASP-Prolog — two prominent Knowledge Representation and Reasoning Paradigms in Artificial Intelligence.
Data Quality Based Intelligent Instrument Selection With Security Integration, Sergei Chuprov, Raman Zatsarenko, Leon Reznik, Igor Khokhlov
Data Quality Based Intelligent Instrument Selection With Security Integration, Sergei Chuprov, Raman Zatsarenko, Leon Reznik, Igor Khokhlov
Computer Science Faculty Publications
We propose a novel Data Quality with Security (DQS) integrated instrumentation selection approach that facilitates aggregation of multi-modal data from heterogeneous sources. As our major contribution, we develop a framework that incorporates multiple levels of integration in finding the best DQS-based instrument selection: data fusion from multi-modal sensors embedded into heterogeneous platforms, using multiple quality and security metrics and knowledge integration. Our design addresses the security aspect in the instrumentation design, which is commonly overlooked in real applications, by aggregating it with other metrics into an integral DQS calculus. We develop DQS calculus that formalizes the problem of finding the …
Interpretable Spatio-Temporal Embedding For Brain Structural-Effective Network With Ordinary Differential Equation, Haoteng Tang, Guodong Liu, Siyuan Dai, Kai Ye, Kun Zhao, Wenlu Wang, Carl Yang, Lifang He, Alex D. Leow, Paul Thompson
Interpretable Spatio-Temporal Embedding For Brain Structural-Effective Network With Ordinary Differential Equation, Haoteng Tang, Guodong Liu, Siyuan Dai, Kai Ye, Kun Zhao, Wenlu Wang, Carl Yang, Lifang He, Alex D. Leow, Paul Thompson
Computer Science Faculty Publications
The MRI-derived brain network serves as a pivotal instrument in elucidating both the structural and functional aspects of the brain, encompassing the ramifications of diseases and developmental processes. However, prevailing methodologies, often focusing on synchronous BOLD signals from functional MRI (fMRI), may not capture directional influences among brain regions and rarely tackle temporal functional dynamics. In this study, we first construct the brain-effective network via the dynamic causal model. Subsequently, we introduce an interpretable graph learning framework termed Spatio-Temporal Embedding ODE (STE-ODE). This framework incorporates specifically designed directed node embedding layers, aiming at capturing the dynamic inter-play between structural and …
Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness And Parameterized Bounds, Erik D. Demaine, Elize Grizzell, Jayson Lynch, Ahmed Shalaby, Timothy Gomez, Markus Hecher, Robert Schweller, Damien Woods
Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness And Parameterized Bounds, Erik D. Demaine, Elize Grizzell, Jayson Lynch, Ahmed Shalaby, Timothy Gomez, Markus Hecher, Robert Schweller, Damien Woods
Computer Science Faculty Publications
Molecular programmers and nanostructure engineers use domain-level design to abstract away messy DNA/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded DNA/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, …
Transforming Computer Science Pedagogy: An Exploration Of Self-Recorded Videos (Srv) As A Teaching And Evaluation Tool, Hussam Ghunaim
Transforming Computer Science Pedagogy: An Exploration Of Self-Recorded Videos (Srv) As A Teaching And Evaluation Tool, Hussam Ghunaim
Computer Science Faculty Publications
This study aims to introduce Self-Recorded Videos (SRV) as a novel method to help improve students’ performance in coding assignments in computer science courses. To our best knowledge, this is the first time the SRV method is applied in the context of computer science classes. The study was conducted with a sample size of 41 students who were registered in the online CSCI 331 Operating Systems course at Fort Hays State University. These students were given specific instructions to create Self-Recorded Videos SRVs for every coding assignment they were tasked with. This approach was designed to encourage students to engage …
Tuning Pid Controller For Quadrotor Using Particle Swarm Optimization, Eric X. Rodriguez, Qi Lu
Tuning Pid Controller For Quadrotor Using Particle Swarm Optimization, Eric X. Rodriguez, Qi Lu
Computer Science Faculty Publications
Energy expenditure for quadrotor control has a likelihood of being costly given parameter-dependent controllers that are less than optimal. The cost can grow proportionally when applied to multiple quadrotors for tracking and collaborative navigation tasks. This research aims to establish a basic approach to tuning PID (Proportional-Integral-Derivative) parameters for a simulated quadrotor drone. A PID controller for autonomy provides a straightforward method for correcting robotic movement based on its current state. However, applying a PID system to a flight controller poses challenges with an inherently under-actuated system, which includes the likelihood of large overshoots and lengthy adjustment times. To address …
Detection And Mitigation Of Misleading Pheromone Trails In Foraging Robot Swarms, Ryan Luna, Qi Lu
Detection And Mitigation Of Misleading Pheromone Trails In Foraging Robot Swarms, Ryan Luna, Qi Lu
Computer Science Faculty Publications
This study addresses the overlooked aspect of security in swarm robotics by exploring the vulnerabilities of stigmergic communication in foraging robot swarms. More specifically, we study the swarm's susceptibility to attacks that introduce misleading pheromone trails. Simulated scenarios in which detractor robots lay misleading trails to deceive benign foraging robots effectively reduce the foraging performance of the swarm. We analyze the impact of the attack on the swarm and evaluate the reduction of foraging efficiency. We introduce a defense mechanism using distance-based clustering (DBSCAN) along with a cluster grouping method to isolate large batches of detractors early in the simulation. …
Controlling Adversarial Pheromone-Based Infections Via Quarantine Strategies In Foraging Robot Swarms, Ryan Luna, Qi Lu
Controlling Adversarial Pheromone-Based Infections Via Quarantine Strategies In Foraging Robot Swarms, Ryan Luna, Qi Lu
Computer Science Faculty Publications
Virtual pheromone trails that facilitate efficient and adaptable coordination among foraging robot swarms are vulnerable to threats that exploit stigmergic communication. This study investigates the impact of a fake resource attack on the performance of a pheromone-based foraging algorithm and demonstrates the effectiveness of a “quarantine strategy” in mitigating the attack. The study simulates the fake resources and examines the swarm's behavior as robots are attracted to these fake resource locations. To prevent access to fake resources, circular quarantine regions are deployed, and a distance-based merging algorithm is implemented to reduce storage require-ments. The experiments are conducted with varying numbers …