I2S Masters/ Doctoral Theses

The absence of a single, comprehensive database or repository cataloging all bioinformatics databases and software creates a significant barrier for researchers aiming to construct computational workflows. These workflows, which often integrate 10–15 specialized tools for tasks such as sequence alignment, variant calling, functional annotation, and data visualization, require researchers to explore diverse scientific literature to identify relevant resources. This process demands substantial expertise to evaluate the suitability of each tool for specific biological analyses, alongside considerable time to understand their applicability, compatibility, and implementation within a cohesive pipeline. The lack of a central, updated source leads to inefficiencies and the risk of using outdated tools, which can affect research quality and reproducibility. Consequently, there is a critical need for an automated, accurate tool to identify bioinformatics databases and software mentions directly from scientific texts, streamlining workflow development and enhancing research productivity. 

The bioNerDS system, a prior effort to address this challenge, uses a rule-based named entity recognition (NER) approach, achieving an F1 score of 63% on an evaluation set of 25 articles from BMC Bioinformatics and PLoS Computational Biology. By integrating the same set of features such as context patterns, word characteristics and dictionary matches into a machine learning model, we developed an approach using an XGBoost classifier. This model, carefully tuned to address the extreme class imbalance inherent in NER tasks through synthetic oversampling and refined via systematic hyperparameter optimization to balance precision and recall, excels at capturing complex linguistic patterns and non-linear relationships, ensuring robust generalization. It achieves an F1 score of 82% on the same evaluation set, significantly surpassing the baseline. By combining rule-based precision with machine learning adaptability, this approach enhances accuracy, reduces ambiguities, and provides a robust tool for large-scale bioinformatics resource identification, facilitating efficient workflow construction. Furthermore, this methodology holds potential for extension to other technological domains, enabling similar resource identification in fields like data science, artificial intelligence, or computational engineering.

This project presents an automated weather classification system utilizing transfer learning with pre-trained convolutional neural networks (CNNs) such as VGG19, InceptionV3, and ResNet50. Designed to classify weather conditions—sunny, cloudy, rainy, and sunrise—from images, the system addresses the challenge of limited labeled data by applying data augmentation techniques like zoom, shear, and flip, expanding the dataset images. By fine-tuning the final layers of pre-trained models, the solution achieves high accuracy while significantly reducing training time. VGG19 was selected as the baseline model for its simplicity, strong feature extraction capabilities, and widespread applicability in transfer learning scenarios. The system was trained using the Adam optimizer and evaluated on key performance metrics including accuracy, precision, recall, and F1 score. To enhance user accessibility, a Flask-based web interface was developed, allowing real-time image uploads and instant weather classification. The results demonstrate that transfer learning, combined with robust data preprocessing and fine-tuning, can produce a lightweight and accurate weather classification tool. This project contributes toward scalable, real-time weather recognition systems that can integrate into IoT applications, smart agriculture, and environmental monitoring.

Driver inattention and human error are the primary causes of traffic crashes. However, little is known about the relationship between driver aggressiveness and safety. Although several studies that group drivers into different classes based on their driving performance have been conducted, little has been done to explore how behavioral traits are linked to driver behavior. The study aims to link different driver profiles, assessed through psychological evaluations, with their likelihood of engaging in risky driving behaviors, as measured in a driving simulation experiment. By incorporating psychological factors into machine learning algorithms, our models were able to successfully relate self-reported decision-making and personality characteristics with actual driving actions. Our results hold promise toward refining existing models of driver behavior by understanding the psychological and behavioral characteristics that influence the risk of crashes.

Artificial Intelligence (AI) is being widely used in diverse domains such as industrial automation, traffic control, precision agriculture, and smart cities for major heavy lifting in terms of data analysis and decision making. However, the AI life- cycle is a major source of greenhouse gas (GHG) emission leading to devastating environmental impact. This is due to expensive neural architecture searches, training of countless number of models per day across the world, in-field AI processing of data in billions of edge devices, and advanced security measures across the AI life cycle. Modern applications often involve multitasking, which involves performing a variety of analyzes on the same dataset. These tasks are usually executed on resource-limited edge devices, necessitating AI models that exhibit efficiency across various measures such as power consumption, frame rate, and model size. To address these challenges, we introduce a novel neural network architecture model that incorporates a layer sharing principle to optimize the power usage. We propose a novel neural architecture, Layer Shared Neural Networks that merges multiple similar AI/NN tasks together (with shared layers) towards creating a single AI/NN model with reduced energy requirements and carbon footprint. The experimental findings reveal competitive accuracy and reduced power consumption. The layer shared model significantly reduces power consumption by 50% during training and 59.10% during inference causing as much as an 84.64% and 87.10% decrease in CO2 emissions respectively. 

The accurate prediction of small molecule binding affinity and toxicity remains a central challenge in drug discovery, with significant implications for reducing development costs, improving candidate prioritization, and enhancing safety profiles. Traditional computational approaches, such as molecular docking and quantitative structure-activity relationship (QSAR) models, often rely on handcrafted features and require extensive domain knowledge, which can limit scalability and generalization to novel chemical scaffolds. Recent advances in language models (LMs), particularly those adapted to chemical representations such as SMILES (Simplified Molecular Input Line Entry System), have opened new ways for learning data-driven molecular representations that capture complex structural and functional properties. However, achieving both high binding affinity and low toxicity through a resource-efficient computational pipeline is inherently difficult due to the multi-objective nature of the task. This study presents a novel dual-paradigm approach to critical challenges in drug discovery: predicting small molecules with high binding affinity and low cardiotoxicity profiles. For binding affinity prediction, we implement a specialized graph neural network (GNN) architecture that operates directly on molecular structures represented as graphs, where atoms serve as nodes and bonds as edges. This topology-aware approach enables the model to capture complex spatial arrangements and electronic interactions critical for protein-ligand binding. For toxicity prediction, we leverage chemical language models (CLMs) fine-tuned with Low-Rank Adaptation (LoRA), allowing efficient adaptation of large pre-trained models to specialized toxicological endpoints while maintaining the generalized chemical knowledge embedded in the base model. Our hybrid methodology demonstrates significant improvements over existing computational approaches, with the GNN component achieving an average area under the ROC curve (AUROC) of 0.92 on three protein targets and the LoRA-adapted CLM reaching (AUROC) of 0.90 with 60% reduction in parameter usage in predicting cardiotoxicity. This work establishes a powerful computational framework that accelerates drug discovery by enabling both higher binding affinity and low toxicity compounds with optimized efficacy and safety profiles. 

Compiler optimizations are critical for performance and have been extensively studied, especially for C/C++ language compilers. Our overall goal in this thesis is to investigate and compare the properties and behavior of optimization passes across multiple contemporary, state-of-the-art (SOTA)  C/C++ compilers to understand if they adopt similar optimization implementation and orchestration strategies. Given the maturity of pre-existing knowledge in the field, it seems conceivable that different compiler teams will adopt consistent optimization passes, pipeline and application techniques. However, our preliminary results indicate that such expectation may be misguided. If so, then we will attempt to understand the differences, and study and quantify their impact on the performance of generated code.

In our first work, we study and compare the behavior of profile-guided optimizations (PGO) in two popular SOTA C/C++ compilers, GCC and Clang. This study reveals many interesting, and several counter-intuitive, properties about PGOs in C/C++ compilers. The behavior and benefits of PGOs also vary significantly across our selected compilers. We present our observations, along with plans to further explore these inconsistencies in this report. Likewise, we have also measured noticeable differences in the performance delivered by optimizations across our compilers. We propose to explore and understand these differences in this work. We present further details regarding our proposed directions and planned experiments in this report. We hope that this work will show and suggest opportunities for compilers to learn from each other and motivate researchers to find mechanisms to combine the benefits of multiple compilers to deliver higher overall program performance.

Stimming refers to repetitive actions or behaviors used to regulate sensory input or express feelings. Children with developmental disorders like autism (ASD) frequently perform stimming. This includes arm flapping, head banging, finger flicking, spinning, etc. This is exhibited by 80-90% of children with Autism, which is seen in 1 among 36 children in the US. Head banging is one of these self-stimulatory habits that can be harmful. If these behaviors are automatically identified and notified using live video monitoring, parents and other caregivers can better watch over and assist children with ASD.

Classifying these actions is important to recognize harmful stimming, so this study focuses on developing a deep learning-based approach for stimming action recognition. We implemented and evaluated four models leveraging three deep learning architectures based on Convolutional Neural Networks (CNNs), Autoencoders, and Vision Transformers. For the first time in this area, we use skeletal joints extracted from video sequences. Previous works relied solely on raw RGB videos, vulnerable to lighting and environmental changes. This research explores Deep Learning based skeletal action recognition and data processing techniques for a small unstructured dataset that consists of 89 home recorded videos collected from publicly available sources like YouTube. Our robust data cleaning and pre-processing techniques helped the integration of skeletal data in stimming action recognition, which performed better than state-of-the-art with a classification accuracy of up to 87%.

In addition to using traditional deep learning models like CNNs for action recognition, this study is among the first to apply data-hungry models like Vision Transformers (ViTs) and Autoencoders for stimming action recognition on the dataset. The results prove that using skeletal data reduces the processing time and significantly improves action recognition, promising a real-time approach for video monitoring applications. This research advances the development of automated systems that can assist caregivers in more efficiently tracking stimming activities.
 

Just as the internet-of-things leverages machine learning over a vast amount of data produced by an innumerable number of sensors, the Internet of Catalysis program uses similar strategies with catalysis research. One application of the Internet of Catalysis strategy is treating research papers as datapoints, rich with text, figures, and tables. Prior research within the program focused on machine learning models applied strictly over text.This project is the first step of the program in creating a machine learning model from the images of catalysis research papers. Specifically, this project creates a dataset of faradaic efficiency graphs using transfer learning from pretrained models. The project utilizes FasterRCNN_ResNet50_FPN, LayoutLMv3SequenceClassification, and computer vision techniques to recognize figures, extract all graphs, then classify the faradaic efficiency graphs.

Downstream of this project, researchers will create a graph reading model to integrate with large language models. This could potentially lead to a multimodal model capable of fully learning from images, tables, and texts of catalysis research papers. Such a model could then guide experimentation on reaction conditions, catalysts, and production.

Significant advances in information and networking technologies have transformed Cyber-Physical Systems (CPS) into networked cyber-physical systems (NCPS). A noteworthy example of such systems is smart grid networks, which include distributed energy resources (DERs), renewable generation, and the widespread adoption of Electric Vehicles (EVs). Such complex NCPS require intelligent and autonomous control solutions. For example, the increasing number of EVs introduces significant sources of demand and user behavior uncertainty that can jeopardize grid stability during peak hours. Traditional model-based demand-supply controls fail to accurately model and capture the complex nature of smart grid systems in the presence of different uncertainties and as the system size grows. To address these challenges, data-driven approaches have emerged as an effective solution for informed decision-making, predictive modeling, and adaptive control to enhance the resiliency of NCPS in uncertain environments.

As a powerful data-driven approach, Multi-Agent Reinforcement Learning (MARL) enables agents to learn and adapt in dynamic and uncertain environments. However, MARL techniques introduce complexities related to communication, coordination, and synchronization among agents. In this PhD research, we investigate autonomous control for smart grid decision networks using MARL. First, we examine the issue of imperfect state information, which frequently arises due to the inherent uncertainties and limitations in observing the system state.

Second, we focus on the cooperative behavior of agents in distributed MARL frameworks, particularly under the central training with decentralized execution (CTDE) paradigm. We provide theoretical results and variance analysis for stochastic and deterministic cooperative MARL algorithms, including Multi-Agent Deep Deterministic Policy Gradient (MADDPG), Multi-Agent Proximal Policy Optimization (MAPPO), and Dueling MAPPO. These analyses highlight how coordinated learning can improve system-wide decision-making in uncertain and dynamic environments like EV networks.

Third, we address the scalability challenge in large-scale NCPS by introducing a hierarchical MARL framework based on a cluster-based architecture. This framework organizes agents into coordinated subgroups, improving scalability while preserving local coordination. We conduct a detailed variance analysis of this approach to demonstrate its effectiveness in reducing communication overhead and learning complexity. This analysis establishes a theoretical foundation for scalable and efficient control in large-scale smart grid applications.

This project presents the development of a custom Convolutional Neural Network (CNN) designed to classify object states—such as sliced, diced, or peeled—in robotic cooking environments. Recognizing fine-grained object states is critical for context-aware manipulation yet remains a challenging task due to the visual similarity between states and the limited availability of cooking-specific datasets. To address these challenges, we built a lightweight, non-pretrained CNN trained on a curated dataset of 11 object states. Starting with a baseline architecture, we progressively enhanced the model using data augmentation, optimized dropout, batch normalization, Inception modules, and residual connections. These improvements led to a performance increase from ~45% to ~52% test accuracy. The final model demonstrates improved generalization and training stability, showcasing the effectiveness of combining classical and advanced deep learning techniques. This work contributes toward real-time state recognition for autonomous robotic cooking systems, with implications for assistive technologies in domestic and elder care settings.