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Computational Methods For Single-Cell And Multi-Omic Data Integration And Regulatory Network Inference, Jianlan Ren

Dissertations

Single-cell and multi-omic technologies have transformed the dissection of cellular heterogeneity and regulatory dynamics in health and disease. However, the high dimensionality, technical variability, and biological complexity of these datasets present significant challenges for integration, annotation, and interpretation. In this dissertation, a suite of computational approaches is introduced to address key problems in single-cell and multi-omic data analysis through model-based innovations and applied statistical frameworks.

First, a constrained deep learning framework for single-cell data integration, label transfer, and clustering is proposed. By incorporating biologically motivated constraints into the training process, robust performance is achieved across simulated and benchmark datasets spanning …

Bifusenet: A Multimodal Network For Estimating Blood Alcohol Concentration Via Bidirectional Hierarchical Fusion, Abdullah Tariq, Arooba Maqsood, Martin Masek, Syed Zulqarnain Gilani

Research outputs 2022 to 2026

Drunk driving remains a significant public safety challenge, demanding innovative alternatives to conventional methods such as field sobriety tests and breathalysers. Estimating a driver's level of intoxication through facial cues is particularly challenging due to the subtle and person-specific nature of alcohol-induced behaviours. In this paper, we present BiFuseNet, a 3D spatio-temporal multi-modal network designed to classify alcohol impairment levels into three categories: sober, moderate, and severe. Unlike prior approaches that rely on either uni-modal RGB video or hand-crafted facial features, our method exploits complementary physiological cues from RGB and infrared (IR) facial videos. We introduce a Bi-directional Hierarchical Fusion …

Optimizing Hip And Knee Assistance For Walking And Sit-To-Stand Transitions: An Intrinsic Muscle Mechanics Based Predictive Approach, Neethan Ratnakumar

Dissertations

As the global population ages, the demand for wearable assistive technologies continues to rise, driven by their potential to enhance mobility and independence in older adults. Effectively designed controllers for lower-limb exoskeletons to assist sit-to-stand (STS) and walking are crucial for delivering efficient, safe, and comfortable assistance during daily activities. Traditionally, controller optimization involves biomechanical modeling and user-specific customization. Musculoskeletal simulations play a central role in this process by providing insights into human-exoskeleton interaction dynamics, thereby informing and refining control strategies.

This work presents a simulation-driven approach for developing exoskeleton controllers for walking and STS using two distinct methods: optimal …

Performance Analysis Of Computational Methods For Predicting Protein Function In Rare Diseases, Aichetou Mohamed Sidiya, Hanin Alzaher, Razan Almahdi, Tayeb Brahimi

Effat Undergraduate Research Journal

Protein function prediction is crucial for understanding the underlying mechanisms of rare diseases. With the increasing availability of computational methods including machine learning-based approaches, network-based methods, and sequence-based methods, predicting protein functions has become more accessible. However, it is not clear which of these methods performs better or how they compare to each other in terms of accuracy, efficiency, and scalability. In this study, we evaluate several computational methods for predicting protein functions in rare diseases using key performance indicators (KPIs). We analyze the strengths and weaknesses of each method and provide recommendations for researchers and clinicians interested in using …

Psilostachyin B As Potential Immune Checkpoint Inhibitor Targeting Ctla-4 And Pd-L1 In The Development Of Cancer Immunotherapy: A Computational Investigation, Moh Dliyauddin, Nabila Shafa Yumna Salsabila, Noviana Dwi Lestari, Sapti Puspitarini, Mansur Ibrahim, Sri Rahayu, Muhammad Sasmito Djati, Muhaimin Rifa’I

Karbala International Journal of Modern Science

Immunotherapy is a promising treatment approach by targeting immune checkpoints such as CTLA-4 and PD-L1 to overcome cancer progression. The utilization of Curcuma longa and Phyllanthus niruri as potential immune checkpoint inhibitors offers an alternative cancer therapy. Computational analyses including molecular docking and molecular dynamics with validation using Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA), Dynamic Cross-Correlation Matrix (DCCM), and Principal Component Analysis (PCA), were performed in this study. Results show that Psilostachyin B is the most promising inhibitor candidate against CTLA-4 and PD-L1, with binding affinity values of -6.9 and -6.8 kcal/mol, respectively. Molecular dynamics simulation results indicated that Psilostachyin B …

Neurophysiology And Endocrine Responses To Hunger And Satiety Mechanisms: The Brain-Gut Crosstalk, Nour Shakir Rezaieg, Muthanna M. Awad

Karbala International Journal of Modern Science

Background: Obesity is a main public health problem which substantially increases the risk of many diseases. The complex neural circuitry controls energy homeostasis and food consumption by the incorporation of hormonal and neural signals. Circulating hormones, in specific the gut hormones, have been found to be very important in appetite regulation. These hormones transfer energy situation signs to the brain throughout three principle paths: the circulation system, activation of the vagus nerve, and direct modification of main brain regions such as the hypothalamus and brainstem. The control of food eating is not exclusively dependent on the homeostatic processes, rather it …

Biocomputing Approach To Modeling And Modulating Calcium Signaling, Sehee Sun

School of Computing: Dissertations, Theses, and Student Research

Biocomputing is an emerging field that seeks to perform computational tasks using biological substrates and processes. Unlike conventional computing systems based on silicon hardware, biocomputing leverages the parallelism, energy efficiency, and complex dynamics of living systems. Among various cellular mechanisms, calcium (Ca2+) signaling stands out as a central regulator of diverse biological functions, offering a promising basis for programmable logic and control in living cells.

This thesis introduces a novel framework for modeling and modulating Ca2+ dynamics using biologically inspired Boolean logic circuits. Specifically, we propose the Ca2+ Boolean Logic (CaBL) model, in which Ca2+ fluxes and interactions are abstracted …

Computational Design Of Potent Sirna For Braf Oncogene Silencing For Enhancing Cancer Therapy, Muhammad Hermawan Widyananda, Ricadonna Raissa

Karbala International Journal of Modern Science

The discovery of oncogenic BRAF mutations has prompted the development of inhibitors, yet resistance remains widespread. A more effective strategy involves targeting BRAF mRNA with siRNA to overcome resistance to BRAF inhibitors. This study aims to design potent siRNA for BRAF oncogene silencing using a computational approach. The full coding sequence of BRAF was retrieved from the NCBI database and potential siRNAs were predicted using the Ui-Tei, Reynolds, and Amarzguioui rules. Identified siRNAs were further analyzed using various prediction systems and parameters, including their interaction with the hAgo2 protein. The results identified that seven siRNAs (siRNA 23, siRNA 24, siRNA …

Seg-Swin: A Dual-Attention Transformer Model For Advanced Amd Classification And Lesion Detection Using Color Fundus Imaging, Niveen Nasr El-Den, Mohamed Elsharkawy, Ibrahim Saleh, Ali H. Mahmoud, Mohammed Ghazal, Ashraf Khalil, Ashraf Sewelam, Hani Mahdi, Ayman El-Baz

All Works

Age-related macular degeneration (AMD) is a prevalent retinal disorder in the elderly, often leading to significant vision impairment. The diagnosis of AMD is confirmed through various medical imaging modalities, with color fundus photography (CFP) being a primary tool. The detection and staging of AMD-severity depend on several factors, including the number and size of drusen, the presence of pigmentary changes, geographic atrophy, and neovascularization, all of which are identifiable through CFP. In this study, we introduce an innovative dual-vision transformer-based network designed to automatically detect AMD and classify its severity into either dry AMD or wet AMD using CFP. Early …

Heartdj - Music Recommendation And Generation Through Biofeedback From Heart Rate Variability, Egemen Şahin

Dartmouth College Master’s Theses

This study investigates the integration of real-time physiological data with AI-generated music to enhance emotional well-being, stress regulation, and focus, using Heart Rate Variability (HRV) as a biomarker of autonomic function. Conducted in two phases—Stable Audio Open (SAO) and Suno (SUNO)—the research evaluates biofeedback-driven music interventions across varying daily music-listening habits.

In the SAO phase, short AI-generated instrumental tracks were compared with Spotify recommendations and guided meditation. Modest HRV improvements were observed in biofeedback conditions, but participants noted emotional limitations, citing short track lengths and abrupt transitions.

The SUNO phase addressed these limitations with longer, more complex AI-generated compositions combined …

Automated Methods For Estimating Blood Alcohol Concentration Level From Facial Cues, Ensiyeh Keshtkaran

Theses: Doctorates and Masters

This thesis investigates different approaches for detecting alcohol intoxication in drivers by analysing facial video data. Tackling this issue necessitates the creation of a novel dataset to overcome the limitations of existing datasets. The dataset constructed in this study is the first to include RGB video recordings of individual faces at varying levels of alcohol intoxication during simulated driving, featuring 60 participants with BAC levels ranging from 0 to 0.165 g/100ml. The constructed dataset not only supports this thesis, but also offers the broader scientific community a valuable resource for further study and development.

Building on this, this thesis presents …

Advancing Emotional Health Assessments: A Hybrid Deep Learning Approach Using Physiological Signals For Robust Emotion Recognition, Amna Waheed Awan, Imran Taj, Shehzad Khalid, Syed Muhammad Usman, Ali Shariq Imran, Muhammad Usman Akram

All Works

Emotional health significantly impacts physical and psychological well-being, with emotional imbalances and cognitive disorders leading to various health issues. Timely diagnosis of mental illnesses is crucial for preventing severe disorders and enhancing medical care quality. Physiological signals, such as Electrocardiograms (ECG) and Electroencephalograms (EEG), which reflect cardiac and neuronal activities, are reliable for emotion recognition as they are less susceptible to manipulation than physical signals. Galvanic Skin Response (GSR) is also closely linked to emotional states. Researchers have developed various methods for classifying signals to detect emotions. However, these signals are susceptible to noise and are inherently non-stationary, meaning they …

Advancing Sentiment Analysis Through Emotionally-Agnostic Text Mining In Large Language Models (Llms), Jay Ratican, James Hutson

Faculty Scholarship

The conventional methodology for sentiment analysis within large language models (LLMs) has predominantly drawn upon human emotional frameworks, incorporating physiological cues that are inherently absent in text-only communication. This research proposes a paradigm shift towards an emotionallyagnostic approach to sentiment analysis in LLMs, which concentrates on purely textual expressions of sentiment, circumventing the confounding effects of human physiological responses. The aim is to refine sentiment analysis algorithms to discern and generate emotionally congruent responses strictly from text-based cues. This study presents a comprehensive framework for an emotionally-agnostic sentiment analysis model that systematically excludes physiological indicators whilst maintaining the analytical depth …

Ur2m: Uncertainty And Resource-Aware Event Detection On Microcontrollers, Hong Jia, Young D. Kwon, Dong Ma, Nhat Pham, Lorena Qendro, Tam Vu, Cecilia Mascolo

Research Collection School Of Computing and Information Systems

Traditional machine learning techniques are prone to generating inaccurate predictions when confronted with shifts in the distribution of data between the training and testing phases. This vulnerability can lead to severe consequences, especially in applications such as mobile healthcare. Uncertainty estimation has the potential to mitigate this issue by assessing the reliability of a model's output. However, existing uncertainty estimation techniques often require substantial computational resources and memory, making them impractical for implementation on microcontrollers (MCUs). This limitation hinders the feasibility of many important on-device wearable event detection (WED) applications, such as heart attack detection. In this paper, we present …

Reinforcement Learning For Team Based Air Combat Maneuvering Decisions With Directed Energy Weaponry, Joshua D. Combs

Theses and Dissertations

Leveraging the Advanced Framework for Simulation, Integration, and Modeling (AFSIM) we investigate the use of reinforcement learning (RL) techniques for imbuing AUCAV agents with high-quality behaviors for the within-visual-range air combat maneuvering problem (ACMP). We formulate the 2v2 WVR ACMP as a Markov decision process wherein friendly AUCAVs are equipped with DEW capabilities and operate with 6 degrees of freedom. We utilize the Double Deep Q-Network RL algorithm, which centrally trains two friendly AUCAVs and employ a phased learning approach, initially exposing the AUCAVs to a dense reward environment for early training, followed by a sparse reward environment to encourage …

Cyclistai: A Smartphone Solution For Cyclist Stress Assessment Using Deep Learning, Aairish Singh

Computer Science and Engineering Theses - Archive

Cycling presents a compelling solution for promoting personal health and environmental well-being, particularly for short-distance travel. Despite its numerous advantages, cycling uptake in the United States remains disproportionately low, primarily due to safety concerns. Traditional frameworks for assessing cyclist stress are hindered by their impracticality and inability to provide real-time evaluations. Self-report surveys and physiological measurements offer alternative approaches but suffer from limitations such as retrospective reporting biases and accessibility challenges, respectively. This thesis introduces CyclistAI, a novel smartphone-based cyclist stress assessment model that leverages context sensing. By combining Convolutional Neural Network (CNN) and Long Short-Term Memory (LSTM) techniques, CyclistAI …

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 …

A Novel Computing Scheme Based On Pattern Matching For Identification Of Nephron Loss And Chronic Kidney Disease Stage, Rehan Ahmad, Basant Mohanty

Turkish Journal of Electrical Engineering and Computer Sciences

Nephrons are the basic filtering units of the kidneys. Progression of chronic kidney disease (CKD) destroys nephrons permanently. Although there are many computing schemes suggested in recent years to identify CKD stages, no computing method has been suggested for identifying the nephron loss within kidney regions during CKD progression. In this paper, a novel pattern matching-based computation scheme is proposed to detect nephron loss in the kidney regions during CKD progression. We consider image registration (IR) with different transforms and a structural similarity index algorithm (SSIM) to match patterns of ultrasound images of kidney regions to identify the nephron loss. …

Toward A Simulation Model Complexity Measure, J. Scott Thompson, Douglas D. Hodson, Michael R. Grimaila, Nicholas Hanlon, Richard Dill

Faculty Publications

Is it possible to develop a meaningful measure for the complexity of a simulation model? Algorithmic information theory provides concepts that have been applied in other areas of research for the practical measurement of object complexity. This article offers an overview of the complexity from a variety of perspectives and provides a body of knowledge with respect to the complexity of simulation models. The key terms model detail, resolution, and scope are defined. An important concept from algorithmic information theory, Kolmogorov complexity, and an application of this concept, normalized compression distance, are used to indicate the possibility of measuring changes …

Wearables For In-Situ Monitoring Of Cognitive States: Challenges And Opportunities, Meeralakshmi Radhakrishnan, Thivya Kandappu, Manoj Gulati, Archan Misra

Research Collection School Of Computing and Information Systems

We propose using wrist and ear-based sensing, via multiple novel and complementary modalities, to unobtrusively infer activity-aware, complex cognitive and affective states (such as confusion, boredom, and recall failure) of individuals. While state-of-the-art wearable devices are predominantly used (a) independently, with limited coordination among multiple devices, and (b) to capture macro-level physical activity and physiological state, we seek to expand the ambit of unobtrusive wearable sensing to capture the cognitive states while performing commonplace physical activities. Such states typically manifest via fine-grained, almost unobservable, microscopic head, face, and eye movements. We identify some of these fine-grained physical markers that serve …

Wearables For In-Situ Monitoring Of Cognitive States: Challenges And Opportunities, Meera Radhakrishnan, Thivya Kandappu, Manoj Gulati, Archan Misra

Research Collection School Of Computing and Information Systems

We propose using wrist and ear-based sensing, via multiple novel and complementary modalities, to unobtrusively infer activity-aware, complex cognitive and affective states (such as confusion, boredom, and recall failure) of individuals. While state-of-the-art wearable devices are predominantly used (a) independently, with limited coordination among multiple devices, and (b) to capture macro-level physical activity and physiological state, we seek to expand the ambit of unobtrusive wearable sensing to capture the cognitive states while performing commonplace physical activities. Such states typically manifest via fine-grained, almost unobservable, microscopic head, face, and eye movements. We identify some of these fine-grained physical markers that serve …

Systems Thinking Activities Used In K-12 For Up To Two Decades, Diana Fisher, Systems Thinking Association

Complex Systems Faculty Publications and Presentations

Infusing systems thinking activities in pre-college education (grades K-12) means updating precollege education so it includes a study of many systemic behavior patterns that are ubiquitous in the real world. Systems thinking tools include those using both paper and pencil and the computer and enhance learning in the classroom making it more student-centered, more active, and allowing students to analyze problems that have been heretofore beyond the scope of K-12 classrooms. Students in primary school have used behavior over time graphs to demonstrate dynamics described in story books, like the Lorax, and created stock-flow diagrams to describe what was needed …

Towards A Machine Learning-Based Digital Twin For Non-Invasive Human Bio-Signal Fusion, Izaldein Al-Zyoud, Fedwa Laamarti, Xiaocong Ma, Diana Tobón, Abdulmotaleb Elsaddik

Computer Vision Faculty Publications

Human bio-signal fusion is considered a critical technological solution that needs to be advanced to enable modern and secure digital health and well-being applications in the metaverse. To support such efforts, we propose a new data-driven digital twin (DT) system to fuse three human physiological bio-signals: heart rate (HR), breathing rate (BR), and blood oxygen saturation level (SpO2). To accomplish this goal, we design a computer vision technology based on the non-invasive photoplethysmography (PPG) technique to extract raw time-series bio-signal data from facial video frames. Then, we implement machine learning (ML) technology to model and measure the bio-signals. We accurately …

Mems Ultrasonic Transducers For Safe, Low-Power And Portable Eye-Blinking Monitoring, Sheng Sun, Jianyuan Wang, Menglun Zhang, Yuan Ning, Dong Ma, Yi Yuan, Pengfei Niu, Zhicong Rong, Zhuochen Wang, Wei Pang

Research Collection School Of Computing and Information Systems

Eye blinking is closely related to human physiology and psychology. It is an effective method of communication among people and can be used in human–machine interactions. Existing blink monitoring methods include video-oculography, electro-oculograms and infrared oculography. However, these methods suffer from uncomfortable use, safety risks, limited reliability in strong light or dark environments, and infringed informational security. In this paper, we propose an ultrasound-based portable approach for eye-blinking activity monitoring. Low-power pulse-echo ultrasound featuring biosafety is transmitted and received by microelectromechanical system (MEMS) ultrasonic transducers seamlessly integrated on glasses. The size, weight and power consumption of the transducers are 2.5 …

The Applications Of The Internet Of Things In The Medical Field, Cody Repass

Theses and Dissertations

The Internet of Things (IoT) paradigm promises to make “things” include a more generic set of entities such as smart devices, sensors, human beings, and any other IoT objects to be accessible at anytime and anywhere. IoT varies widely in its applications, and one of its most beneficial uses is in the medical field. However, the large attack surface and vulnerabilities of IoT systems needs to be secured and protected. Security is a requirement for IoT systems in the medical field where the Health Insurance Portability and Accountability Act (HIPAA) applies.

This work investigates various applications of IoT in healthcare …

Two Person Interaction Recognition Based On A Dual-Coded Modified Metacognitive (Dcmmc) Extreme Learning Machine, Saman Nikzad, Afshin Ebrahimi

Turkish Journal of Electrical Engineering and Computer Sciences

Human action recognition has been an active research area for over three decades. However, state-of-the-art proposed algorithms are still far from developing error-free and fully-generalized systems to perform accurate interaction recognition. This work proposes a new method for two-person interaction recognition from videos, based on well-known cognitive theories. The main idea is to perform classification based on a theory of cognition known as dual coding theory. The theory states that human brain processes and represents two types of information to learn/classify data named analogue and symbolic codes, i.e. (verbal as analogue and visual as symbolic). To implement such a theory …

On The Security Of Bluetooth Low Energy In Two Consumer Wearable Heart Rate Monitors/Sensing Devices, Yesem Kurt Peker, Gabriel Bello, Alfredo J. Perez

Computer Science Faculty Publications

Since its inception in 2013, Bluetooth Low Energy (BLE) has become the standard for short-distance wireless communication in many consumer devices, as well as special-purpose devices. In this study, we analyze the security features available in Bluetooth LE standards and evaluate the features implemented in two BLE wearable devices (a Fitbit heart rate wristband and a Polar heart rate chest wearable) and a BLE keyboard to explore which security features in the BLE standards are implemented in the devices. In this study, we used the ComProbe Bluetooth Protocol Analyzer, along with the ComProbe software to capture the BLE traffic of …

Pranayama Breathing Detection With Deep Learning, Bikash Shrestha

Theses

Yoga, a complementary health approach, according to a 2017 National Health Interview Survey by the Center for Disease Control and Prevention (CDC), is a choice of around 14.3% adults in the US. Kapalbhati pranayama, a yoga practice of alternating fast exhales and longer passive inhales, is understood to improve our health. Incorrect and irregular practices, however, can cause injuries and adverse effects. To avoid these undesired effects, it is essential to maintain a pace fit for the practitioner. In the absence of any tools to observe a pace of practice, this work develops a deep learning method that listens to …

Exploiting Group Structures To Infer Social Interactions From Videos, Maksim Bolonkin

Dartmouth College Ph.D Dissertations

In this thesis, we consider the task of inferring the social interactions between humans by analyzing multi-modal data. Specifically, we attempt to solve some of the problems in interaction analysis, such as long-term deception detection, political deception detection, and impression prediction. In this work, we emphasize the importance of using knowledge about the group structure of the analyzed interactions. Previous works on the matter mostly neglected this aspect and analyzed a single subject at a time. Using the new Resistance dataset, collected by our collaborators, we approach the problem of long-term deception detection by designing a class of histogram-based features …

Ar-Based Simulation Interaction And Human Factor Assessment For Human Robot Cooperation Assembly Planning, Wang Qiang, Xiumin Fan, Qichang He, Wenmin Zhu

Journal of System Simulation

Abstract: To improve assembly efficiency, it has become a trend for traditional manual assembly workstations to be carried out human-robot collaboration transformation. To realize the safe and fast evaluation of the improvement scheme, a general human-robot collaboration simulation method and human factor evaluation method based on Augmented Reality are proposed. Four levels of human-robot collaboration assembly simulation are established. An interactive scheme between real human and virtual robot for visual detection, perception and feedback is established. A fuzzy comprehensive evaluation model of human physiological and psychological indicators for workstation design is constructed. The prototype system is developed. Taking the assembly …