Digital Commons Network^™

Contribution Of Different Frass Fertilizer Products On Enhanced Growth, Yield And Nutrient Quality Of Broccoli [Brassica Oleracea], Noella Kagehi, Dennis Beesigamukama, Chrysantus M. Tanga, Mathew P. Ngugi, Sevgan Subramanian, Fathiya M. Khamis

All Peer-Reviewed Publications

Vegetables are crucial for food security and income, but in developing countries their production is hindered by low soil fertility. Although the insect frass fertilizer is a potential solution, its use is constrained by limited product choices. Unlike conventional fertilizers, which are available in different forms, the insect frass fertilizer is mostly available in solid form. Here, we evaluated the effects of different black soldier fly frass fertilizer (BSFFF) products on broccoli [Brassica oleracea] growth, yield, and nutritional profiles. Solid, liquid BSFFF, chitin-fortified solid BSFFF, chitin-fortified liquid BSFFF, and commercial organic fertilizer (Safi) were applied at rates equivalent to 250 …

A Review On Knowledge And Information Extraction From Pdf Documents And Storage Approaches, Salvador D. Atagong, Henri Tonnang, Kennedy Senagi, Mark Wamalwa, Komi M. Agboka, John Odindi

All Peer-Reviewed Publications

Introduction: Automating the extraction of information from Portable Document Format (PDF) documents represents a major advancement in information extraction, with applications in various domains such as healthcare, law, or biochemistry. However, existing solutions face challenges related to accuracy, domain adaptability, and implementation complexity. Methods: A systematic review of the literature was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology to examine approaches and trends in PDF information extraction and storage approaches. Results: The review revealed three dominant methodological categories: rule-based systems, statistical learning models, and neural network-based approaches. Key limitations include the rigidity of rule-based …

The Effectiveness Of Tech Support Fraud In Damaging Older Individual’S Financial Security, Vanessa Perera

Theses : Honours

This study discovers the tactics employed to create detrimental effects upon older people impacted from fraudulent tech-support incidents. It examines social engineering, and financial confusion of older people. This is significant considering adaptations towards digital banking and payment management. This research looked at online and active over 65s. Using largely qualitative approaches over 65s were interviewed and responses validated against cyber-professionals’ responses. This identified three key findings: older adults feel confused and misunderstand tech support scams; threat actors build trust by pretending to offer technical help but use this to deceive their victims; and older adults face serious social and …

Swatting Flies: Biting Insects As Non-Invasive Samplers For Mammalian Population Genomics, Anubhab Khan, Ryan Carter, Chengetai D. Mpamhanga, Daniel Masiga, Manun Channumsin, Marc Ciosi, Oliva Manangwa, Furaha Mramba, Umer Zeeshan Ijaz, Harriet Auty, Barbara K. Mable

All Peer-Reviewed Publications

Advances in next-generation sequencing have allowed the use of DNA obtained from unusual sources for wildlife studies. However, these samples have been used predominantly to sequence mitochondrial DNA for species identification while population genetics analyses have been rare. Since next-generation sequencing allows indiscriminate detection of all DNA fragments in a sample, technically it should be possible to sequence whole genomes of animals from environmental samples. Here we used a blood-feeding insect, tsetse fly, to target whole genome sequences of wild animals. Using pools of flies, we compared the ability to recover genomic data from hosts using the short-read sequencing (Illumina) …

Attribute-Based Encryption With Searchable Encryption, Yang Yang

Research Collection School Of Computing and Information Systems

Attribute-based encryption (ABE) with searchable encryption is a notion that inherits the advantages of both ABE (Goyal et al., 2006) and searchable encryption (SE) (Boneh et al., 2004; Boneh and Waters, 2007) mechanisms to realize secure share and search for the outsourced data. ABE creates fine-grained access control system to prevent sensitive data from being accessed by unauthorized user or external attacker (Bethencourt et al., 2007). SE generates encrypted index for outsourced data such that it can be searched by a keyword trapdoor (or token) (Shi et al., 2007; Naveed et al., 2014), where the outsourced content and search keyword(s) …

Gnnsynergy: A Multi-View Graph Neural Network For Predicting Anti-Cancer Drug Synergy, Zhifeng Hao, Jianming Zhan, Yuan Fang, Min Wu, Ruichu Cai

Research Collection School Of Computing and Information Systems

Drug combinations play very important roles in cancer therapy, as they can enhance curative efficacy and overcome drug resistance. Due to the increasing size of combinatorial space, experimental screening for all the drug combinations becomes infeasible in practice. Therefore, there is a great need to develop accurate computational approaches that can predict potential drug combinations to direct the experimental screening. In this paper, we propose a novel method called GNNSynergy to learn drug embeddings for drug synergy prediction. Given a specific cancer cell line, we propose a multi-view graph neural network framework which considers the current cell line as main …

Governing Intelligence: Singapore’S Evolving Ai Governance Framework, Jason G. Allen, Jane Loo, Jose Luna

Research Collection Yong Pung How School Of Law

This paper provides an outline analysis of the evolving governance framework for Artificial Intelligence (AI) in Singapore. Across the Singapore government, AI solutions are being adopted in line with Singapore’s “Smart Nation Initiative” to leverage technology to make impactful changes to the nation and the economy. In tandem, Singaporean authorities have been assiduous to release a growing number of governance documents, which we analyse together to chart the city-state’s approach to AI governance in international comparison. Characteristics of Singapore’s AI governance approach include an emphasis on consensusbuilding between stakeholders (particularly government and industry but also citizens) andvoluntary or “quasi” regulation, …

Machine Learning For Computer-Aided Diagnostics From Complex Medical Images, Afsah Saleem

Theses: Doctorates and Masters

Machine learning has significantly transformed medical image analysis in the current age of artificial intelligence offering vast potential in improving disease diagnosis and management. Cardiovascular diseases (CVDs) are among the leading cause of global mortality, emphasizing the need for early detection for effective intervention and prevention. Abdominal Aortic Calcification (AAC) is an early indicator and contributor to Atherosclerotic Cardiovascular Diseases (ASCVDs) and is commonly assessed through imaging modalities such as computed tomography (CT), X-rays, and Dual-energy X-ray Absorptiometry (DXA). Among these, lateral spine DXA scans, commonly used for osteoporosis screening, offer a cost-effective and low-radiation opportunity for opportunistic CVD risk …

An Exploratory Attempt To Incorporate Social Criteria Into Spent Nuclear Fuel Site Screening And Relocation, Julie M. Sorfleet

Cal Poly Humboldt theses and projects

Spent nuclear fuel, also known as nuclear waste, is the byproduct of nuclear power generation. The need for safe and responsible long-term storage and disposal of radioactive fuel presents significant technical and social challenges. These challenges are compounded by several factors, including the emerging nuclear renaissance in the United States, climate and coastal hazards, and the lack of consolidated interim or permanent storage. This research explores perceptions of risk, relocation, and siting spent nuclear fuel, predominantly focusing on Humboldt County, California. I used online surveys, the Analytic Hierarchy Process, and geographic information systems (GIS) analysis to inform how social and …

Groundwater Pumping Impacts On Stream Depletion In Humboldt County, Ca: Integrating Analytical Models And Field Data, Andy Hans Heise

Cal Poly Humboldt theses and projects

This study addresses the significant concern of stream depletion from groundwater pumping in Humboldt County, CA. The objective of this study is to develop an analytical model for estimating stream depletion and integrating field data into model parameters.

The methodology involved conducting a field study near three operating wells by a stream, installing stream gages upstream and downstream of the wells, and recording pumping rates and schedules for two of the wells. The third well’s pumping data was synthetically generated, for privacy concerns of the well owner. The StreamDepletR package was used for estimating depletion rates in a stream in …

Oriented Surface Immobilization Of Antibodies Using Enzyme-Mediated Site-Specific Biotinylation For Enhanced Antigen-Binding Capacity, Emily Beitello, Kwame Osei, Trent Kobulnicky, Faith Breausche, Jon A. Friesen, Jeremy D. Driskell

Faculty Publications – Chemistry

The effectiveness of surface-immobilized antibodies is often diminished by improper antibody orientation and limited stability, impeding the analytical performance of biosensors. Here, we report a novel enzyme-mediated strategy to biotinylate the Fc region of an anti-horseradish peroxidase (anti-HRP) antibody with site-specificity that enables oriented immobilization on a streptavidin-functionalized surface. Microbial transglutaminase (mTG) catalyzes the covalent coupling between the amine functional group on a biotin analogue (NH₂-PEG₄-biotin) and the side chain of a privileged glutamine residue (Q295) located on the heavy chain Fc region of IgG antibodies. For comparison, an anti-HRP antibody was biotinylated using an amine-reactive …

Revised Final Multi-Pathway Residential Metals Abatement Program Plan, Atlantic Richfield Company, Butte Silver Bow

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Heterogeneous Clustering Of Multiomics Data For Breast Cancer Subgroup Classification And Detection, Joseph Pateras, Musaddiq Lodi, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

The rapid growth of diverse -omics datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation–maximization routine for the joint latent variable modeling of multiomics patient profiles. By combining this approach with traditional biological feature selection methods, this study optimizes latent distribution, enabling efficient patient clustering from well-studied cancer types with reduced computational expense. The proposed optimization subroutines enhance survival analysis and improve runtime performance. This article presents a framework for distinguishing cancer subtypes and identifying potential biomarkers for breast cancer. Key insights into individual subtype expression and function were obtained through differentially expressed gene …

A Data-Driven Sliding-Window Pairwise Comparative Approach For The Estimation Of Transmission Fitness Of Sars-Cov-2 Variants And The Construction Of The Evolution Fitness Landscape, Md Jubair Pantho, Richard Annan, Landen Alexander Bauder, Sophia Huang, Letu Qingge, Hong Qin

Computer Science Faculty Publications

Estimating the transmission fitness of SARS-CoV-2 variants and understanding their evolutionary fitness trends are important for epidemiological forecasting. Existing methods are often constrained by their parametric natures and do not satisfactorily align with the observations during COVID-19. Here, we introduce a sliding-window data-driven pairwise comparison method, the differential population growth rate (DPGR) that uses viral strains as internal controls to mitigate sampling biases. DPGR is applicable in time windows in which the logarithmic ratio of two variant subpopulations is approximately linear. We apply DPGR to genomic surveillance data and focus on variants of concern (VOCs) in multiple countries and regions. …

The Invisible Influencer In Information Infrastructure, Herbert Van De Sompel, Michael L. Nelson

Computer Science Faculty Publications

The UPS Prototype was a proof-of-concept web portal built in preparation for the Universal Preprint Service Meeting held in October 1999 in Santa Fe, New Mexico. The portal provided search functionality for a set of metadata records that had been aggregated from a range of repositories that hosted preprints, working papers, and technical reports. Every search result was overlaid with a dynamically generated menu, called an SFX-menu, that provided a selection of value-adding links for the described scholarly work. The meeting eventually led to the Open Archives Initiative and its Protocol for Metadata Harvesting (OAI-PMH), which remains widely used in …

Coldstartcpi: Induced-Fit Theory-Guided Dti Predictive Model With Improved Generalization Performance, Qichang Zhao, Haochen Zhao, Linyuan Gao, Kai Zheng, Yajie Li, Qiao Ling, Jing Tang, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Predicting compound-protein interactions (CPIs) plays a crucial role in drug discovery. Traditional methods, based on the key-lock theory and rigid docking, often fail with novel compounds and proteins due to their inability to account for molecular flexibility and the high sparsity of CPI data. Here, we introduce ColdstartCPI, a framework inspired by induced-fit theory, which leverages unsupervised pre-training features and a Transformer module to learn both compound and protein characteristics. ColdstartCPI treats proteins and compounds as flexible molecules during inference, aligning with biological insights. It outperforms state-of-the-art sequence-based models, particularly for unseen compounds and proteins, and shows strong generalization capability …

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.

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 …

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 …

Optiselect And Enshap: Integrating Machine Learning And Game Theory For Ischemic Stroke Prediction, Pritam Chakraborty, Anjan Bandyopadhyay, Sricheta Parul, Sujata Swain, Partha Sarathy Banerjee, Tapas Si, Hong Qin, Saurav Mallik

Computer Science Faculty Publications

Stroke analysis using game theory and machine learning techniques. The study investigates the use of the Shapley value in predictive ischemic brain stroke analysis. Initially, preference algorithms identify the most important features in various machine learning models, including logistic regression, K-nearest neighbor, decision tree, support vector machine (linear kernel), support vector machine ( RBF kernel), neural networks, etc. For each sample, the top 3, 4, and 5 features are evaluated and selected to evaluate their performance. The Shapley value method was used to rank the models using their best four features based on their predictive capabilities. As a result, better-performing …

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 …

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 …

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 …

Draft Final Silver Bow Creek Conservation Area Repository Data Gap Data Summary Report (Dsr), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

This Silver Bow Creek Conservation Area (SBCCA) Repository Data Gap Data Summary Report (DSR) presents the results from the soil sampling activities conducted as specified in the SBCCA Repository Data Gap Quality Assurance Project Plan (QAPP) (referred to herein as the SBCCA Repository Data Gap QAPP; Atlantic Richfield Company, 2024). The information presented in this DSR includes laboratory analytical results from subsurface soil sampling collected from Buffalo Gulch (BG), Butte Reduction Works (BRW), Diggings East (DE), and Northside Tailings (NST) within the SBCCA. This DSR was prepared by Pioneer Technical Services, Inc. (Pioneer), 1101 S. Montana Street, Butte, Montana 59701 …

Draft Final Butte Priority Soils Operable Unit (Bpsou) Unreclaimed Sites: Ur-03 Site Remedial Action Work Plan (Rawp), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Final Horseshoe Bend Effluent Line (Hbel) Discharge Structure Surface Enhancements Work Plan, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Benchmarking Batch-Effect Correction Methods Towards The Construction Of A Triple-Negative Breast Cancer Cell Atlas, Peter Scheible, Amy H. Tang, Jing He, Jiangwen Sun

Computer Science Faculty Publications

Triple-negative breast cancer (TNBC) requires detailed cellular mapping given its aggressive nature, immense tumor heterogeneity and genetic diversity. We integrated 156,794 cells from six scRNA-seq datasets—including tumors, metastases, and cell lines—to build a TNBC scRNA cell atlas, focusing on batch effect mitigation while maintaining biological and molecular details. Preprocessing f ilters noise, normalizes data, and leverages PCA for integration readiness. We utilized scANVI, a semi-supervised tool, to align datasets, preserving TNBC’s complex tumor heterogeneity via marker annotations [1]. UMAPs demonstrate biological clustering in integrated data, contrasted with datasetdriven unintegrated patterns. Assessments verifying effective batch correction. This method aligns with NASA’s …

Multi-Modal Mri Based Segmentation Of Brain Metastases Using Adaptive Self-Attention, Evan Savaria

Computer Science Faculty Publications

Brain metastases (BMs) are the most common adult central nervous system malignancy, affecting 20–40% of cancer patients. Accurate segmentation of metastatic lesions in multi-modal MRI is essential for treatment planning and prognosis however, manual delineation is time consuming and prone to variability. Traditional deep learning models such as U-Net, have improved segmentation accuracy but capture limited long-range dependencies and struggle with variations in metastasis size, shape, and distribution. This study introduces the Adaptive Integrated Multi-modal Segmentation (AIMS) model, an adaptive self-attention framework within a hybrid U-Net and Transformer architecture to enhance BM segmentation by leveraging multi-modal MRI integration. The proposed …

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 …

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 …