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Articles 241 - 270 of 1772
Full-Text Articles in Other Computer Sciences
Weed Seed Wizard Case Study - An Early Harvest Versus A Late Harvest, Department Of Primary Industries And Regional Development, Western Australia
Weed Seed Wizard Case Study - An Early Harvest Versus A Late Harvest, Department Of Primary Industries And Regional Development, Western Australia
Biosecurity research reports
The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.
The Weed Seed Wizard is a computer simulation tool that:
- applies to all Australian grain growing areas
- helps growers understand and manage weed seedbanks on their farms
- uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields
- uses farm-specific management and site-specific weather
- is multi-species
See www.dpird.wa.gov.au for further information on Weed Seed Wizard.
This case …
Weed Seed Wizard Scenario - Herbicide Resistance In Wild Radish In Moora, Western Australia, Department Of Primary Industries And Regional Development, Western Australia
Weed Seed Wizard Scenario - Herbicide Resistance In Wild Radish In Moora, Western Australia, Department Of Primary Industries And Regional Development, Western Australia
Biosecurity research reports
The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.
The Weed Seed Wizard is a computer simulation tool that:
- applies to all Australian grain growing areas
- helps growers understand and manage weed seedbanks on their farms
- uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields
- uses farm-specific management and site-specific weather
- is multi-species
See www.dpird.wa.gov.au for further information on Weed Seed Wizard.
This Western …
Using Ai For Qualitative Labeling: Consistency And Comparisons, James Mcintyre
Using Ai For Qualitative Labeling: Consistency And Comparisons, James Mcintyre
Honors Program Theses
This paper details a research study evaluating AI's ability to perform qualitative deductive coding. Multiple AI models were utilized and compared against three human coders and one expert coder. A series of 107 statements were sourced from a group discussion for a qualitative impact assessment of an organization. The AI models were provided these statements and directed to code them using the Community Capitals Framework. Two generations of AI models were evaluated. Overall, the AI achieved a fair level of agreement with the human annotators, but the alignment was far from perfect. Newer AI models did not increase agreement with …
Automated In Situ Segmentation Of Sugarcane Roots, Joseph Salas-Leon
Automated In Situ Segmentation Of Sugarcane Roots, Joseph Salas-Leon
Computer Science and Engineering Theses - Archive
Sugarcane roots are not understood and previous methods of collecting and processing data have proved to be laborious and time consuming. Using Minirhizotrons, Researchers observe and photograph roots without disturbing the soil and are useful for studying root growth over time. Software such as Rhyzovision exists to allow quick processing of root images. These software tools require clean or well annotated images of only the roots to provide accurate information. Current annotations of the images are done manually and requires a Scientist with domain knowledge of roots to accurately annotate the root images. We are employing the use of CNN …
Understanding Social Dynamics In Toxic Conversations And Public Health Intervention Acceptance On Social Media, Ana Aleksandric
Understanding Social Dynamics In Toxic Conversations And Public Health Intervention Acceptance On Social Media, Ana Aleksandric
Computer Science and Engineering Dissertations - Archive
Social media is now central to daily life, offering users a space to share content and opinions. However, these platforms also facilitate the spread of hate speech and misinformation, which can negatively impact public health. This dissertation develops methodologies to analyze social media data for insights that could inform health interventions. The research first examines user responses to toxic content, focusing on behavioral and emotional reactions, as well as group dynamics and bystander effects in toxic interactions. Another key focus is public opinion toward health interventions, particularly COVID-19 vaccination, using geolocated posts and analyzing factors such as race, ethnicity, and …
Advancing Deep Learning With Graph-Based Structural Insights: From Graph Classification To Semantic Segmentation, Xin Ma
Computer Science and Engineering Dissertations - Archive
Deep learning has profoundly transformed machine learning by offering sophisticated data representations, yet effectively incorporating structural information remains a challenge. Structural data, whether explicit or implicit, has the potential to significantly enhance the performance of deep learning tasks. This research investigates the benefits of structural information across three crucial tasks: classification, clustering, and segmentation. For explicit structural data, where inputs are directly represented as graphs, we investigate graph-level classification in brain connectivity networks. We introduce the Multi-resolution Edge Network (MENET), a novel framework designed to identify disease-specific connectomic benchmarks with high discriminatory power across diagnostic categories. MENET leverages graph-level representations …
Investigating Efficiency Of Free-For-All Models In A Matchmaking Context, Emil Gensby, Bryan S. Weber, Anders H. Christiansen
Investigating Efficiency Of Free-For-All Models In A Matchmaking Context, Emil Gensby, Bryan S. Weber, Anders H. Christiansen
Publications and Research
We explore several popular (and unpopular) systems for matchmaking and ranking in free-for-all (FFA) environments. The commonplace existing methods involve the reinterpretation of established two-player ranking systems (ie. Elo/Glicko) and decomposing multiplayer games into a set of multiple one-vs-one pairings. This decomposition, while commonplace, is not part of the intended use-case of these two-player ranking systems. We are the first to formally explore this ad-hoc usage and reassuringly find evidence that it converges to correct values. Second, we identify a method that appears to dominate what appears to be the most common publicly used method. At the same time, this …
The Impact Of Dissolved Organic Matter On Photodegradation Rates, Byproduct Formations, And Degradation Pathways For Two Neonicotinoid Insecticides In Simulated River Waters, Josephus F. Borsuah, Tiffany L. Messer, Daniel D. Snow, Steven D. Comfort, Shannon Bartelt-Hunt
The Impact Of Dissolved Organic Matter On Photodegradation Rates, Byproduct Formations, And Degradation Pathways For Two Neonicotinoid Insecticides In Simulated River Waters, Josephus F. Borsuah, Tiffany L. Messer, Daniel D. Snow, Steven D. Comfort, Shannon Bartelt-Hunt
UK CARES Faculty Publications
The influences of dissolved organic matter (DOM) on neonicotinoid photochemical degradation and product formation in natural waters remain unclear, potentially impacting the sustainability of river systems. Therefore, our overall objective was to investigate the photodegradation mechanisms and phototransformation byproducts of two neonicotinoid pesticides, imidacloprid and thiamethoxam, under simulated sunlight at the microcosm scale, to assess the implications of DOM for insecticide degradation in rivers. Direct and indirect photolysis were investigated using twelve water matrices to identify possible reaction pathways with two DOM sources and three quenching agents. Imidacloprid, thiamethoxam, and potential degradants were measured, and reaction pathways identified. The photodegradation …
Stealthy Control Logic Attacks And Defense In Industrial Control Systems, Adeen Ayub
Stealthy Control Logic Attacks And Defense In Industrial Control Systems, Adeen Ayub
Theses and Dissertations
Industrial control systems (ICS) play a crucial role in monitoring and managing critical infrastructure, including nuclear plants, oil and gas pipelines, and power grid stations. Programmable logic controllers (PLCs) are a fundamental component of ICS, directly interfacing with physical processes and implementing control logic programs that govern operations. Due to their significance in controlling critical infrastructure, PLCs often become prime targets for attackers seeking to disrupt these systems. Exploitable vulnerabilities in PLCs render them susceptible to such attacks. While many attacks on PLCs leave a large footprint in network traffic and are detectable by intrusion detection systems (IDS), this dissertation …
Adaptable And Trustworthy Machine Learning For Human Activity Recognition From Bioelectric Signals, Morgan S. Stuart
Adaptable And Trustworthy Machine Learning For Human Activity Recognition From Bioelectric Signals, Morgan S. Stuart
Theses and Dissertations
Enabling machines to learn measures of human activity from bioelectric signals has many applications in human-machine interaction and healthcare. However, labeled activity recognition datasets are costly to collect and highly varied, which challenges machine learning techniques that rely on large datasets. Furthermore, activity recognition in practice needs to account for user trust - models are motivated to enable interpretability, usability, and information privacy. The objective of this dissertation is to improve adaptability and trustworthiness of machine learning models for human activity recognition from bioelectric signals. We improve adaptability by developing pretraining techniques that initialize models for later specialization to unseen …
Predicting An Optimal Medication/Prescription Regimen For Patient Discordant Chronic Comorbidities Using Multi-Output Models, Ichchha Pradeep Sharma, Tam Nguyen, Shruti Ajay Singh, Tom Ongwere
Predicting An Optimal Medication/Prescription Regimen For Patient Discordant Chronic Comorbidities Using Multi-Output Models, Ichchha Pradeep Sharma, Tam Nguyen, Shruti Ajay Singh, Tom Ongwere
Computer Science Faculty Publications
This paper focuses on addressing the complex healthcare needs of patients struggling with discordant chronic comorbidities (DCCs). Managing these patients within the current healthcare system often proves to be a challenging process, characterized by evolving treatment needs necessitating multiple medical appointments and coordination among different clinical specialists. This makes it difficult for both patients and healthcare providers to set and prioritize medications and understand potential drug interactions. The primary motivation of this research is the need to reduce medication conflict and optimize medication regimens for individuals with DCCs. To achieve this, we allowed patients to specify their health conditions and …
(Meta-)Physical Artworks: Digital Augmentation In Art Observation, Macy A. Toppan
(Meta-)Physical Artworks: Digital Augmentation In Art Observation, Macy A. Toppan
Dartmouth College Master’s Theses
Augmented art— the subgenre of art that incorporates physical and digital artwork— is a rapidly growing field driven by advancing technology and a new generation for whom that tech is a given. Yet the presence of media like augmented and virtual reality in exhibition remains a controversial subject. Rather than focusing on the many theoretical debates about whether digital pieces can qualify as "good" art, we study it in practice through the eyes of the casual art observer. This paper highlights the audience in a within-participant study that asked viewers to take in a physical sculpture intentionally built with virtual …
A Virtual Time Driven Simulator For Devs Models, Ronald R. Stempien
A Virtual Time Driven Simulator For Devs Models, Ronald R. Stempien
Dissertations, Master's Theses and Master's Reports
When simulating a system that includes some software component, simulation authors are faced with the problem of how to appropriately model the software within the simulation. While many formal methods for modeling software exist, in some contexts these may not be appropriate or viable for a given simulation. Instead, simulation authors may model a computer within the simulation, and run the software in question “as is” on the modeled machine. In this work, we introduce a theoretical framework to allow for the use of hardware virtualization technologies as a hardware accelerator for CPU models in Discrete Event System Specification (DEVS) …
A Self-Supervised Knowledge Distillation Approach To Anomaly Detection In X-Ray Imagery, Kaden Quinn Mceldowney
A Self-Supervised Knowledge Distillation Approach To Anomaly Detection In X-Ray Imagery, Kaden Quinn Mceldowney
Graduate Theses, Dissertations, and Problem Reports (ETD)
Many cargo containers enter the United States every day by truck, rail, and sea. As a result of the large number of cargo containers entering the United States, not all of them can be thoroughly inspected. Most of these containers contain properly documented and legal cargo, but some people take advantage of this situation by hiding illicit items in the cargo containers such as drugs. To more efficiently and thoroughly inspect cargo containers, Customs and Border Protection (CBP) uses X-ray imaging machines to obtain images that reveal the interior of cargo containers. These X-ray images must be inspected to ensure …
Detecting And Recovering From Player Preference Shifts In A Player Modeled Experience Management Environment, Anton Vinogradov
Detecting And Recovering From Player Preference Shifts In A Player Modeled Experience Management Environment, Anton Vinogradov
Theses and Dissertations--Computer Science
An important challenge in game design is understanding and maintaining player engagement. This is particularly crucial in both entertainment and educational games, where the player's commitment to the game directly impacts their experience and learning outcomes. However, quantifying engagement proves challenging due to the diverse interests of players. This dilemma is addressed through adaptive game design techniques where the game world is personalized to suit player preferences. In computer games, this personalization is facilitated through Experience Management and Player Modeling, where an intelligent agent gathers information on the player, including their preferences and actions, and takes actions to modify the …
Weed Seed Wizard Scenario - Glyphosate Resistance In Barnyard Grass In Goondiwindi, Queensland, Department Of Primary Industries And Regional Development, Western Australia
Weed Seed Wizard Scenario - Glyphosate Resistance In Barnyard Grass In Goondiwindi, Queensland, Department Of Primary Industries And Regional Development, Western Australia
Biosecurity research reports
The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.
The Weed Seed Wizard is a computer simulation tool that:
- applies to all Australian grain growing areas
- helps growers understand and manage weed seedbanks on their farms
- uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields
- uses farm-specific management and site-specific weather
- is multi-species
See www.dpird.wa.gov.au for further information on Weed Seed Wizard.
This Queensland …
Adaptive Neh With Constrained Nearest Neighbor Subtours For The Electric Vehicle Routing Problem With Time Windows, Andrew Struthers
Adaptive Neh With Constrained Nearest Neighbor Subtours For The Electric Vehicle Routing Problem With Time Windows, Andrew Struthers
All Master's Theses
The development of electric vehicles is currently considered one of the most innovative areas in manufacturing. Largely driven by the desire to reduce greenhouse emissions, electric vehicles are seen as a viable alternative to internal combustion engine cars. Starting from consumer cars, a dedicated effort is being made to translate this into commercial vehicles for freight and delivery. This research introduces a novel adaptive Nawaz, Enscore, Ham (NEH) algorithm with constrained nearest neighbor subtour (NEH-NN). This algorithm is tested on the standard benchmark problems in literature and used as a seed solution for the Genetic Algorithm (GA). The performance and …
Examining Information Systems Use To Facilitate The Workplace Accommodation Process, Shiya Cao
Examining Information Systems Use To Facilitate The Workplace Accommodation Process, Shiya Cao
Statistical and Data Sciences: Faculty Publications
BACKGROUND: The workplace accommodation process is often affected by ineffective and inefficient communications and information exchanges among disabled employees and other stakeholders. Information systems (IS) can play a key role in facilitating a more effective and efficient accommodation process since IS has been shown to facilitate business processes and effect positive organizational changes.
OBJECTIVE: Since there is little to no research that exists on IS use to facilitate the workplace accommodation process, this paper, as a critical first step, examines how IS have been used in the accommodation process.
METHODS: Thirty-six interviews were conducted with disabled employees from various organizations. …
Questions (And Answers) For Incorporating Nontraditional Grading In Your Statistics Courses, Brenna Curley
Questions (And Answers) For Incorporating Nontraditional Grading In Your Statistics Courses, Brenna Curley
Statistical and Data Sciences: Faculty Publications
Nontraditional grading methods have recently become more common, and as with any large pedagogical shift, there are a number of questions to consider when applying a new grading scheme to a course. This article summarizes four types of nontraditional grading and shares experiences from the authors who have applied them to a variety of courses in statistics. This article is structured as a set of questions and answers, seeking to address many of the concerns and considerations that one may face as they transition a course’s grading structure. Supplementary materials for this article are available online.
Weed Seed Wizard Scenario - Dormancy Shift In Barley Grass In Balaklava, South Australia, Department Of Primary Industries And Regional Development, Western Australia
Weed Seed Wizard Scenario - Dormancy Shift In Barley Grass In Balaklava, South Australia, Department Of Primary Industries And Regional Development, Western Australia
Biosecurity research reports
The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.
The Weed Seed Wizard is a computer simulation tool that:
- applies to all Australian grain growing areas
- helps growers understand and manage weed seedbanks on their farms
- uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields
- uses farm-specific management and site-specific weather
- is multi-species
See www.dpird.wa.gov.au for further information on Weed Seed Wizard.
This South …
Weed Seed Wizard Case Study - Grower From Western Australia’S Central Wheatbelt, Department Of Primary Industries And Regional Development, Western Australia
Weed Seed Wizard Case Study - Grower From Western Australia’S Central Wheatbelt, Department Of Primary Industries And Regional Development, Western Australia
Biosecurity research reports
The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.
The Weed Seed Wizard is a computer simulation tool that:
- applies to all Australian grain growing areas
- helps growers understand and manage weed seedbanks on their farms
- uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields
- uses farm-specific management and site-specific weather
- is multi-species
See www.dpird.wa.gov.au for further information on Weed Seed Wizard.
This case …
Weed Seed Wizard Scenario - Herbicide Resistance In Wild Oats In Wagga Wagga, New South Wales, Department Of Primary Industries And Regional Development, Western Australia
Weed Seed Wizard Scenario - Herbicide Resistance In Wild Oats In Wagga Wagga, New South Wales, Department Of Primary Industries And Regional Development, Western Australia
Biosecurity research reports
The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.
The Weed Seed Wizard is a computer simulation tool that:
- applies to all Australian grain growing areas
- helps growers understand and manage weed seedbanks on their farms
- uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields
- uses farm-specific management and site-specific weather
- is multi-species
See www.dpird.wa.gov.au for further information on Weed Seed Wizard.
This New …
Bias-Aware Gaze Uniformity Assessment In Group Images, Omkar Kulkarni
Bias-Aware Gaze Uniformity Assessment In Group Images, Omkar Kulkarni
Electronic Theses & Dissertations (2024 - present)
Today, more than 5 billion photos are captured every day, with smartphones generating over 94\% of these images. However, despite advancements in technology, achieving aesthetically pleasing group photos remains challenging, especially when it comes to aligning the direction of everyone’s gaze. While current methods focus on facial features, they often fail to ensure consistent gaze direction. The introduction of the iPhone's Live mode, which captures a 1.5-second video snippet along with still images, complicates the selection of the best key photo due to its subjective nature and a lack of publicly available data, especially during the pandemic.
To address these …
Machine-Learning-Assisted Design Of Deep Eutectic Solvents Based On Uncovered Hydrogen Bond Patterns, Usman Lame Abbas, Yuxuan Zhang, Joseph Tapia, Md Selim, Jin Chen, Jian Shi, Qing Shao
Machine-Learning-Assisted Design Of Deep Eutectic Solvents Based On Uncovered Hydrogen Bond Patterns, Usman Lame Abbas, Yuxuan Zhang, Joseph Tapia, Md Selim, Jin Chen, Jian Shi, Qing Shao
Markey Cancer Center Faculty Publications
Non-ionic deep eutectic solvents (DESs) are non-ionic designer solvents with various applications in catalysis, extraction, carbon capture, and pharmaceuticals. However, discovering new DES candidates is challenging due to a lack of efficient tools that accurately predict DES formation. The search for DES relies heavily on intuition or trial-and-error processes, leading to low success rates or missed opportuni- ties. Recognizing that hydrogen bonds (HBs) play a central role in DES formation, we aim to identify HB features that distinguish DES from non-DES systems and use them to develop machine learning (ML) models to discover new DES systems. We first analyze the …
Towards Dynamic Context Detection From Voice Commands And Conversations With Smart Assistants In Smart Homes, Jeniya Sultana
Towards Dynamic Context Detection From Voice Commands And Conversations With Smart Assistants In Smart Homes, Jeniya Sultana
Graduate Theses/Dissertations
Voice-enabled interactions have become increasingly popular with the rise of voice assistants. Identifying contexts or meanings from voice commands and conversations with smart assistants can contribute to the autonomous control of smart home devices and appliances. To improve automation, there is a growing need for efficient context detection that eliminates the need to memorize voice commands. To address this need, I followed a two-step approach in my research. In the first step, I developed a unique context recognition model using a transformer, an attention mechanism, and a fully connected neural network. I trained this model on a conversational dataset of …
Gnss Software Defined Radio: History, Current Developments, And Standardization Efforts, Thomas Pany, Dennis Akos, Javier Arribas, M. Zahidul H. Bhuiyan, Pau Closas, Fabio Dovis, Ignacio Fernandez-Hernandez, Carles Fernandez-Prades, Sanjeev Gunawardena, Todd Humphreys, Zaher M. Kassas, Jose A. Lopez Salcedo, Mario Nicola, Mario L. Psiaki, Alexander Rugamer, Yong-Jin Song, Jong-Hoon Won
Gnss Software Defined Radio: History, Current Developments, And Standardization Efforts, Thomas Pany, Dennis Akos, Javier Arribas, M. Zahidul H. Bhuiyan, Pau Closas, Fabio Dovis, Ignacio Fernandez-Hernandez, Carles Fernandez-Prades, Sanjeev Gunawardena, Todd Humphreys, Zaher M. Kassas, Jose A. Lopez Salcedo, Mario Nicola, Mario L. Psiaki, Alexander Rugamer, Yong-Jin Song, Jong-Hoon Won
Faculty Publications
Taking the work conducted by the global navigation satellite system (GNSS) software-defined radio (SDR) working group during the last decade as a seed, this contribution summarizes, for the first time, the history of GNSS SDR development. This report highlights selected SDR implementations and achievements that are available to the public or that influenced the general development of SDR. Aspects related to the standardization process of intermediate-frequency sample data and metadata are discussed, and an update of the Institute of Navigation SDR Standard is proposed. This work focuses on GNSS SDR implementations in general-purpose processors and leaves aside developments conducted on …
Improving The Robustness Of Neural Networks To Adversarial Patch Attacks Using Masking And Attribution Analysis, Atandra Mahalder
Improving The Robustness Of Neural Networks To Adversarial Patch Attacks Using Masking And Attribution Analysis, Atandra Mahalder
Honors Undergraduate Theses
Computer vision algorithms, including image classifiers and object detectors, play a pivotal role in various cyber-physical systems, spanning from facial recognition to self-driving vehicles and security surveillance. However, the emergence of real-world adversarial patches, which can be as simple as stickers, poses a significant threat to the reliability of AI models utilized within these systems. To address this challenge, several defense mechanisms such as PatchGuard, Minority Report, and (De)Randomized Smoothing have been proposed to enhance the resilience of AI models against such attacks. In this thesis, we introduce a novel framework that integrates masking with attribution analysis to robustify AI …
Recovering Access Control Via Disk Forensics On Low-Level Flash Memory, Caleb J. Rother
Recovering Access Control Via Disk Forensics On Low-Level Flash Memory, Caleb J. Rother
Dissertations, Master's Theses and Master's Reports
In the history of access control, nearly every system designed has relied on the operating system (OS) to enforce the access control protocols. However, if the OS (and specifically root access) is compromised, there are few if any solutions that can get users back into their system efficiently. In this work, we have proposed a novel approach that allows secure and efficient rollback of file access control after an adversary compromises the OS and corrupts the access control metadata. Our key observation is that the underlying flash memory typically performs out-of-place updates. Taking advantage of this unique feature, we can …
Multi-Activity Student Knowledge And Behavior Modeling Via Transfer Learning, Siqian Zhao
Multi-Activity Student Knowledge And Behavior Modeling Via Transfer Learning, Siqian Zhao
Electronic Theses & Dissertations (2024 - present)
Online education systems have grown in popularity over the past few years, providing abundant opportunities for students to learn. As the number of students using these systems grows, it promotes the development of the Educational Data Mining (EDM) field, which leverages statistical, machine learning, and data mining technologies to explore large-scale educational data and develop methods to better understand student learning.
In this dissertation, we investigate two essential topics in EDM: Student Knowledge Tracing (KT) and Behavior Modeling (BM). KT aims to quantify and model student knowledge gained from learning activities, while BM focuses on tasks such as modeling student …
Computational Study Of The Effect Of Geometry On Molecular Interactions, Sarika Kumar
Computational Study Of The Effect Of Geometry On Molecular Interactions, Sarika Kumar
Computer Science ETDs
The specificity and predictability of DNA make it an excellent programmable material and have allowed bio-programmers to build sophisticated molecular circuits. These molecular devices should be precise, correct, and function as intended. In order to implement these circuits, the challenge is to build a robust, reliable, and scalable logic circuit with ideally minimum unwanted signal release. Performing experiments are expensive and time-consuming, so modeling and analyzing these bio-molecular systems become crucial in designing molecular circuits. This dissertation aimed to develop algorithms and build computational tools for automated analysis of molecular circuits that incorporate the molecular geometry of nanostructures. Molecular circuits …