Digital Commons Network^™

Advancing Data Usability, Activity Modeling, And Stability Optimization In Computational Enzyme Design, Spencer Gardiner

Theses and Dissertations

A grand challenge of computational biology is to computationally design, in a single pass, a protein sequence that catalyzes an arbitrary chemical reaction at a high rate under specified conditions [1]. This work details advances in three essential areas on the path to that goal: data quality, activity prediction and modeling, and stability optimization. The structure and implementation of the Allotrope Simple Model (a FAIR data format for many scientific instruments) was examined in [2], setting the stage for training deep learning models on high-quality experimental datasets from diverse sources. In [3], the limits of physics-based and deep learning tools …

Beyond Single Images: A Comprehensive Benchmark For Album-Level Vision-Language Understanding, Shawn Huang

Theses and Dissertations

Automatic album organization has been studied extensively over the past decades due to significant progress in digital photography. Recent Vision-Language Models (VLMs) have shown strong performance on multi-image understanding, making them natural candidates for automating album organization workflows. While VLMs’ abilities in multi-image understanding have been widely studied, their performance on album organization remains underexplored. To bridge this gap, we introduce AlbumBench, the first comprehensive benchmark for automatic album organization. Specifically, we (1) define album organization tasks as photo selection for album-specific user objectives, photo rating according to how well user intents are fulfilled, and album-specific photo grouping given a …

Long-Term Monitoring Of The Optical Performance Of The Primary Mirrors At The Coihueco And Loma Amarilla Sites Of The Pierre Auger Observatory, A. Abdul Halim, P. Abreu, M. Aglietta, M. Ahmed, I. Allekotte, K. Almeida Cheminant, B. Fick, K. Nguyen, D. Nitz, Et Al.

Michigan Tech Publications

This paper presents the results of an optical performance monitoring campaign for the primary mirrors installed in fluorescence telescopes at the Coihueco and Loma Amarilla sites at the Pierre Auger Observatory in Argentina. Since the end of 2003, this effort has developed into a unique long-term dataset that addresses the performance of the primary mirrors. We have focused on the scattering characteristics and specular reflectance of mirror segments, as well as their evolution over several years of operation. Despite being housed in climate-controlled buildings, dust accumulation, impurities, and natural aging — such as oxidation or other chemical or physical degradation …

Generation Of Khz-Rate Complex-Structured Liquid Targets For Relativistic Laser–Plasma Interactions, Michael L. Dexter, Stephen J. Hageman, Gregory Ngirmang, Kyle D. Frische, Joseph Snyder, John T. Morrison, Enam A. Chowdury, Anil K. Patnaik

Faculty Publications

With the rise of high repetition rate ultra-intense laser systems, there is a need for solid density targets to study relativistic laser–plasma interactions that can operate at the same repetition rate. Flowing liquid targets are attractive because they are self-replenished, debris free, cost effective and easy to use. Liquid targets have been used for high-repetition rate (up to kHz rate) generation of electrons, protons, x rays, and neutrons by our group and elsewhere. In this Letter, we demonstrate a kHz-rate generation of a variety of dynamically shaped complex-structured targets from the interaction of a 10¹⁶ W/cm² focused laser …

Using Galex Uv Excess To Search For Metal-Poor Halo Stars, Chase L. Smith, Maxwell Moe, Megan Frank, Raven Cilley, Javier Fregoso, Alexander Gleason, Grace Nelson, Et Al.

Michigan Tech Publications

Metal-poor solar-type stars display a significant reduction in metal-line blanketing at short wavelengths, leading to an excess of near-ultraviolet (NUV) flux compared to their metal-rich counterparts. We utilize Galaxy Evolution Explorer Satellite (GALEX) NUV and Gaia DR3 photometry along with ground-based spectroscopy to establish a correlation between NUV excess and [Fe/H]. We construct a sample of 492 solar-type (F5-G9) halo stars with NUV excess and measured metallicities. We perform our own observations with the KOSMOS spectrograph at Apache Point Observatory’s 3.5 m telescope to measure the abundances of 13 halo stars, 11 of which did not have previous metallicity measurements. …

To What Extent Could Quantum Computing Pose A Threat To Global Modern Data Security?, Aniket Maheshwari

Journal of Cybersecurity Education, Research and Practice

Quantum computing has emerged as a transformative technology with the potential to fundamentally disrupt modern cryptographic systems that underpin global data security. This paper examines the extent to which quantum computing could pose a threat to modern global data security by synthesising existing technical, institutional, and policy-oriented literature. Drawing on a narrative review of scholarly research, industry reports, and government frameworks, the analysis focuses on the implications of quantum algorithms such as Shor’s and Grover’s, which challenge the mathematical foundations of widely used cryptographic schemes. The findings suggest that while quantum computing presents a credible long-term threat to asymmetric encryption …

Editorial: Plant Responses To Abiotic Stress: Unraveling Complex Mechanisms Through Genomics And Physiology, Mizanur Rahman, Takashi Asaeda, Md Harun Rashid

School of Earth, Environmental, & Marine Sciences Faculty Publications

No abstract provided.

Label-Flip Attack Detection Via Trust-Weighted Aggregation In Federated Learning For Underground Mine Security, Md Sazedur Rahman, Sanjay Madria, Samuel Frimpong

Computer Science Faculty Research & Creative Works

Underground mining operations are increasingly dependent on autonomous vehicles, robotic drilling systems, and intelligent inspection platforms operating in confined, GPS-denied tunnel environments. These systems rely on distributed perception models to interpret navigation cues, hazard warnings, and environmental signals in real time. While centralized deep learning can enhance model performance, transferring raw operational data across mining sites introduces serious confidentiality and security risks. Federated Learning (FL) offers a privacy-preserving alternative by enabling collaborative model training without sharing local datasets. However, deploying FL in underground mining introduces several critical challenges: (i) Training labels may be modified either maliciously by compromised clients or …

Van Der Waals Interactions Through The Lens Of 2d Materials With Emphasis On Many-Body Effects, Thi Xuan Diem Dang

USF Tampa Graduate Theses and Dissertations

This dissertation addresses the long-standing challenge of accurately and efficiently modeling long-range electron correlations, with a particular focus on van der Waals (vdW) interactions. These interactions play an essential role in predicting the structure, stability, and functionality of molecular systems and condensed matter materials. Although Density Functional Theory (DFT) has become a robust cornerstone of computational materials science, traditional formulations of the theory frequently fail to capture dispersive interactions, leading to significant errors in determining interlayer distances, binding energies, and stacking configurations. These limitations become particularly pronounced in layered materials and vdW heterostructures (HSTs), where weak long-range correlations are sensitive …

Re: Conditional Approval Letter For The Butte Priority Soils Operable Unit (Bpsou) Clark Tailings Consolidated Waste Management Area (Ctcwma) Site Investigation Quality Assurance Project Plan (Qapp) (Dated June 1, 2026), Emma Rott

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Potential For Lunar Interior Science By The Gravitational-Wave Detector Lila, Mark P. Panning, Philippe Lognonné, Teviet Creighton, James Trippe, Volker Quetschke, Josipa Majstorović, Karan Jani

Physics & Astronomy Faculty Publications

The laser interferometer lunar antenna (LILA), a concept for measuring sub-Hz gravitational waves on the Moon, would use laser strainmeters to obtain extremely sensitive strain measurements from 1 mHz to 1 Hz. With proposed strain sensitivities, LILA would also be able to measure the normal modes of the Moon from 1–10 mHz at high signal-to-noise ratio. Such measurements would enable significant advances in our understanding of both the spherically symmetric and even 3D deep internal structure of the Moon. Strainmeter measurements may even be able to detect the translational mode of the solid inner core of the Moon at frequencies …

Where Evidence-Based Medicine Meets Ai: Promise, Pitfalls, And Practice, Sangil Lee, Joshua Davis, Ken Milne, Christina Shenvi, Lars K. Beattie, Martin Wegman, Laura Melville, Richard D. Shih, Bryan Kane

Department of Emergency Medicine Faculty Papers

No abstract provided.

Discrete Fracture Network Application To Rock Slope Stability In An Open Pit Mine, Elvis Karikari Mensah, Erzah Ackah, Reginald Hammah, Hani Mitri

Journal of Sustainable Mining

The stability of rock slopes in open pit mines is crucial for the safety and efficiency of the mining operation. Conventional stability analysis methods, such as kinematic and limit equilibrium analyses, primarily focus on identifying structural failure mechanisms and evaluating their factors of safety. Although insightful, these approaches do not accurately estimate failure volumes and block locations due to their limited consideration of joint frequency and persistence, which are key parameters in understanding block geometries. Discrete fracture network (DFN) modelling addresses these limitations by explicitly simulating rock mass discontinuities in 3D, which automatically incorporates joint spacing and persistence.

This paper …

Integration Of Intraoperative Data In Interpretable Machine Learning Models To Predict Postoperative Aki In Noncardiac Surgery Patients, Justin Do, Karan H. Shah, Melissa Xu, Andrew Hyunwoo Kim, Vivaswat Suresh, Nidhir Guggilla, Michael Li, Rishi Kothari

Department of Anesthesiology Faculty Papers

OBJECTIVES: We aimed to (1) quantify changes in discrimination when adding intraoperative data to preoperative data and (2) compare tabular machine learning with feature engineering against a time-aware LSTM-based model.

MATERIALS AND METHODS: Retrospective cohort of 46 204 adults undergoing 57 055 eligible noncardiac surgery in the INSPIRE database. We extracted 38 preoperative and 49 intraoperative variables; acute kidney injury (AKI) was defined by KDIGO serum creatinine criteria and modeled as stage 2/3 postoperative AKI. Models were trained on preoperative-only and combined pre- and intraoperative data. Intraoperative series were summarized using eight statistical features for tabular models or integrated directly …

Artificial Intelligence Empowers Particle Physics And Nuclear Physics: From Fundamental Research To Major Applications, Yifang Wang, Yuan He, Yao Huang, Wanbing He, Yi Jiao, Congqiao Li, Ke Li, Beijiang Liu, Yingqi Ma, Yugang Ma, Longgang Pang, Fazhi Qi, Sichao Tan, Chunpeng Wang, Meng Wang, Xiaoheng Xu, Xing Xu, Zhentang Zhao, Yingxun Zhang, Zhengde Zhang, Hongwei Zhao, Lina Zhao

Bulletin of Chinese Academy of Sciences (Chinese Version)

Particle physics and nuclear physics are core foundational disciplines for exploring the fundamental structure of matter and the origin of the universe. The deep integration of artificial intelligence (AI) technology is providing entirely new pathways to address systemic challenges such as the processing of massive amounts of multimodal data, the realization of extreme experimental conditions, bottlenecks in theoretical calculations, and the intelligent control of large-scale scientific facilities. The article systematically elaborates on how AI deeply empowers particle physics and nuclear physics, particularly in major application scenarios such as research on the fundamental structure and origin of mass of matter, the …

Consolidating Chemical Substance Creation Capability Through Ai For Science-Enabled Innovation Equity, Mengchu Jin, Wandong Wang, Jun Zhang, Yi Luo, Zaiku Xie, Jinlong Yang, Jun Jiang

Bulletin of Chinese Academy of Sciences (Chinese Version)

AI for Science (hereinafter referred to as AI4S) is driving profound changes in the paradigm of scientific research. Chemistry, as a central discipline for creating new substances and supporting major national strategic needs such as energy, health, dual carbon goals, advanced manufacturing, and ecological governance, is an important application scenario of AI4S. At present, innovation in the discipline of chemistry by young researchers still faces knowledge silos, capability silos, and resource silos: the accumulation of professional knowledge requires years of effort, frontier knowledge is highly differentiated, experimental capabilities are difficult to reuse, and high-end resources are difficult to coordinate, which …

Artificial Intelligence-Enabled Materials Innovation: Implementation Levels And Strategic Layout, Ziwei Zhao, Fengxiang Zhou, Yanglili Zhou, Can Wang, Pei Zhang, Weihua Wang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Materials innovation has long been constrained by vast design spaces, complex processing routes, lengthy validation cycles, and difficulties in engineering translation. Traditional research and development models, which mainly rely on accumulated experience, theoretical deduction, and experimental trial and error, have become increasingly insufficient to meet the demand for rapid breakthroughs in critical materials. In recent years, artificial intelligence has been increasingly integrated into materials design, synthesis, and processing, characterization, evaluation, optimization, and application feedback, promoting the transformation of materials innovation from experience-driven exploration to data-driven development and from discrete trial and error to closed-loop optimization. Based on an analysis of …

Artificial Intelligence For Cybersecurity: Opportunities, Challenges, And Approaches, Kai Chen, Ding Li, Guozhu Meng, Shouling Ji, Changjiang Li, Yi Yang, Dengguo Feng

Bulletin of Chinese Academy of Sciences (Chinese Version)

Cybersecurity research, institutional structures, and governance policies are undergoing profound transformations. Currently, increasingly covert and rapidly evolving intelligent attacks, coupled with the national urgent expectations for high-level security, are driving significant shifts in the roles and interactions of governments, research institutions, and enterprises. Consequently, this study, based on analyzing the challenges and opportunities of the AI era, explores core application scenarios such as critical information infrastructure protection, national data security, and the maintenance of cyberspace sovereignty. It provides an analysis of artificial intelligence in dimensions such as correlation and causality, and proposes a governance framework, aiming to provide insights for …

Artificial Intelligence For Astronomy: Strategic Opportunities, Policy Challenges And Development Strategies, Jin Chang, Yihan Song, Bing Du, Kefei Wu, Ali Luo, Jifeng Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

To alleviate the bottlenecks hindering the integrated development of artificial intelligence and astronomy in China and to reinforce the country’s strategic edge in science and technology, this study uses systematic analysis and path-comparison approaches to examine the policy requirements for their deep integration. The findings indicate that this topic is closely tied to global competition in science and technology, strategic security, and industrial upgrading. At present, the world has entered a new “astronomy + AI” paradigm, with the United States and the European Union already having taken the lead in establishing corresponding strategic frameworks. Leveraging major scientific infrastructures such as …

Artificial Intelligence Empowering Remote Sensing: Challenges, Paradigms And Strategic Layout, Jiayuan Shen, Peirui Cheng, Zhirui Wang, Wei Liang, Xian Sun, Yirong Wu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Remote sensing science and technology, as a key discipline for Earth observation and global change research, faces systemic challenges in processing massive multi-source data, accurately extracting complex information, and delivering high-timeliness application services. The rapid advances in artificial intelligence (AI) provide a new opportunity to address the deep-seated dilemma in remote sensing of being “data-rich but insufficient in effective information mining”. Guided by a problem-oriented approach, this study first systematically analyzes the core challenges facing the development of remote sensing across four dimensions: data understanding, technical methods, scientific mechanisms, and application ecosystems. It then reviews the technical evolution of AI-empowered …

Artificial Intelligence For Deep Earth Science: Key Challenges, Major Application Scenarios And Development Pathways, Qingyun Di, Liang Zhao, Yikang Zheng, Zhi Geng, Zhichao Yu, Xiaocai Shan, Chao Li, Zhiyao Xu, Pengfei Lv

Bulletin of Chinese Academy of Sciences (Chinese Version)

Deep Earth science is central to understanding Earth’s internal architecture and the coupled evolution of its major spheres, while also underpinning energy security, the supply of critical mineral resources, and resilience to major geohazards. Nevertheless, the advancement of deep Earth science is currently hindered by insufficient in situ observations under extreme conditions, the difficulty of integrating multi-source heterogeneous data, and the limited capability to model complex multiphysics coupling processes. Recent advances in artificial intelligence offer a potential route beyond these limitations. By integrating data-driven learning with physical and geological understanding, AI is reshaping deep Earth science from empirical interpretation to …

Rheological Protocol To Assess And Optimize Latex Coagulation Dynamics For The Thin Glove Coagulant Dipping Process, Monday U. Okoronkwo, Kok Kong Ng, Wolfram Franke, Gaurav Sant

Chemical and Biochemical Engineering Faculty Research & Creative Works

Many products that directly impact the quality of human life today — gloves, catheters, condoms, and baby bottle teats — are made through the latex-dipping technology. While a variety of methods have been developed – e.g., particle counting, turbidimetry, microscopy, and light scattering – which are suitable for studying the coagulation of latex at very low concentrations, much less work has focused on methods suitable for in-situ characterization of latex coagulation in concentrated solutions (e.g., as relevant to the dipping process). This paper presents a process-relevant rheological protocol for assessing and optimizing latex coagulation dynamics for the thin glove coagulant …

Artificial Intelligence Empowered Biological Research: Paradigm Shifts, Application Scenarios, And Strategic Layout, Xinguang Zhu, Yiming Bao, Zhenong Jin, Xin Li, Sijia Wang, Yueming Wang, Yungui Yang, Cao Xu, Yan Xiong, Bin Han

Bulletin of Chinese Academy of Sciences (Chinese Version)

Life related processes are characterized by high dimensionality and multi-scale properties. Understanding mechanisms underpinning life processes helps promote national healthcare, agricultural development, sustainable ecological civilization, and national security. Current life science research is confronted with an enormous challenge of dimensionality stemming from data explosion and data fragmentation, for which the recent rapid advancement of artificial intelligence (AI) provides novel solutions. AI will catalyze a paradigm shift in life science research from the current experiment based empirical induction to a new closed-loop knowledge acquisition including large scale data collection, model building, model prediction, experimental validation, and iterative of these procedures. Life …

Artificial Intelligence–Driven Paradigm Transformation In Biopharmaceutical R&D: Applications And Emerging Scenarios, Lili Liu, Mingyue Zheng, Ye Yuan, Xutong Li, Rong Fan, Wei Wei, Jinxin Zhao, Guobin Qi, Hua Yue, Likun Gong, Songping Zhang, Jiachen Li, Yuchen Sun, Xiaoyan Chen, Yao Chen, Xin Liu, Xiao Zhang, Yuehong Gao, Jianfeng Li, Kaixian Chen, Guanghui Ma, Jianmin Yue

Bulletin of Chinese Academy of Sciences (Chinese Version)

The biopharmaceutical industry is a critical domain underpinning national scientific and technological innovation development and public health. With the rapid advancement of artificial intelligence (AI) and its deep integration with the life sciences, biomedicine research is undergoing a paradigm shift from traditional experience-driven trial-and-error approaches to data-driven and predictive validation-based models. This study systematically examines the pathways for reshaping research in biomedicine paradigms under the convergence of data-driven, mechanism-driven, and intelligence-driven approaches. It focuses on recent advances in the application of AI across key stages, including drug discovery and design, druggability evaluation, delivery system design and optimization, nonclinical and clinical …

Artificial Intelligence For Science: Connotations, Characteristics, And System, Kaihua Chen, Heyang Li, Hongxin Liu, Binbin Zhao, Shuo Yang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Artificial intelligence is profoundly transforming the fundamental nature of scientific research, reshaping its modes of knowledge production and organizational operation, driving the emergence of a new artificial intelligence for science (AI4S) research paradigm, and accelerating full-chain innovation paradigm transformation. This study defines the basic connotations of AI4S across three dimensions, namely, enabling applications, tools and methods, and epistemic knowledge, and systematically identifies five core characteristics: human-machine symbiosis, autonomous evolution, interdisciplinary integration, resource intensity, and open ecosystems. It further constructs a supporting system and operational architecture encompassing layers of infrastructure, data resources, model tools, task execution, and application scenarios. Building on …

Open Data From Ligo, Virgo, And Kagra Through The First Part Of The Fourth Observing Run, A. G. Abac, I. Abouelfettouh, Teviet Creighton, Mario C. Diaz, Raul Alberto Espinosa Perez, J. Lawrence, Francisco Llamas Villarreal, Soma Mukherjee, Volker Quetschke, Miriam Ramos Arevalo, Wenhui Wang

Physics & Astronomy Faculty Publications

LIGO, Virgo, and KAGRA form a network of gravitational-wave observatories. Data and analysis results from this network are made publicly available through the Gravitational Wave Open Science Center. This paper describes open data from this network, including the addition of data from the first part of the fourth observing run and selected periods from the preceding engineering run, collected from 2023 May to 2024 January. The public dataset includes calibrated strain time series for each instrument, data from additional channels used for noise subtraction and detector characterization, and analysis data products from version 4.0 of the Gravitational-Wave Transient Catalog.

Gwtc-4.0: Updating The Gravitational-Wave Transient Catalog With Observations From The First Part Of The Fourth Ligo–Virgo–Kagra Observing Run, A. G. Abac, I. Abouelfettouh, Teviet Creighton, Mario C. Diaz, Raul Alberto Espinosa Perez, J. Lawrence, Francisco Llamas Villarreal, Soma Mukherjee, Volker Quetschke, Miriam Ramos Arevalo, Wenhui Wang

Physics & Astronomy Faculty Publications

Version 4.0 of the Gravitational-Wave Transient Catalog (GWTC-4.0) adds new candidates detected by the LIGO, Virgo, and KAGRA observatories through the first part of the fourth observing run (O4a: 2023 May 24 15:00:00 to 2024 January 16 16:00:00 UTC) and a preceding engineering run. In these new data, we find 128 compact binary coalescence candidates that are identified by at least one of our search algorithms with a probability of astrophysical origin pastro ≥ 0.5 and that are not vetoed during event validation. We also provide detailed source property measurements for 86 of these that have a false-alarm rate …

Optimization Of Sea Transportation Services In The Kepulauan Seribu Using The Vehicle Routing Problem (Vrp) Model, Darmadi Darmadi, Sutanto Soehodho, Nahry Nahry

Smart City

The Kepulauan Seribu regency relies heavily on sea transportation for passenger mobility and goods distribution. However, current systems face efficiency challenges, high operational costs, and potential imbalances between demand and service capacity. This study proposes a framework to optimize sea transportation services in the Kepulauan Seribu using the Vehicle Routing Problem (VRP) method, especially the Capacitated Vehicle Routing Problem – Many Single Depot (CVRP–MSD) model with heterogeneous fleets and mixed cargo (passenger and goods). The main objective is to minimize total operating costs, which include fixed costs of using the vessel and variable travel costs, and unmet demand, both passenger …

Galaxy Morphology Classification Using Deep Learning, Dipanwita Kundu Roy

Master’s Dissertations

Galaxy morphology is the study of the shape and visual appearance of galaxies, such as spiral, smooth, edge-on, and other morphological types. Morphological classification plays an important role in understanding how galaxies form and evolve over cosmic time. Most existing machine learning approaches for galaxy morphology classification rely solely on RGB galaxy images, which primarily capture spatial information and lack the physical spectral context of galaxies. In contrast, astronomical spectral datacubes contain rich information across multiple wavelengths, providing insights into the internal and physical properties of galaxies. However, such spectral observations are available for only a limited number of objects. …

Relay Selection And User Scheduling In Reconfigurable Intelligent Surface Assisted Millimeter-Wave D2d Communication, Lakshmikanta Sau

Doctoral Theses

Reconfigurable intelligent surface (RIS) assisted millimeter wave (mmWave) device to device (D2D) communication has recently been proposed as a viable solution to support the overwhelming data traffic in fifth-generation (5G) and beyond wireless networks. However, due to the substantial propagation and penetration losses of mmWave, a direct line of sight (LoS) link between a pair of proximity devices is required for effective communication. Static obstacles like trees and buildings can easily obstruct the direct LoS connectivity between a device pair. In such cases, RISs help to establish an indirect LoS link between an obstructed device pair by reflecting the signals …