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Graduate Program Computer Science and Engineering Start Over

1. A Bioinformatics Pipeline for Integrating Long-read Transcriptomics and Genomic Predictions to Annotate Immunoglobulin (ig) Loci

open_access
Open Access
Author:
Pulhani, Rachit
Title:
A Bioinformatics Pipeline for Integrating Long-read Transcriptomics and Genomic Predictions to Annotate Immunoglobulin (ig) Loci
Graduate Program:
Computer Science and Engineering
Keywords:
Immunoglobulin gene annotation
adaptive immunity
V(D)J recombination
long-read transcriptomics
genomic–transcriptomic integration
novel gene discovery
immune repertoire diversity
Committee Members:
Yana Safonova, Thesis Advisor/Co-Advisor
David Koslicki, Committee Member
Mahmut Kandemir, Program Head/Chair

2. A Deterministic Natural-Language-to-TRAPI Framework for Biomedical Knowledge Graph Query Automation

open_access
Open Access
Author:
Matta, Venkata Sesh
Title:
A Deterministic Natural-Language-to-TRAPI Framework for Biomedical Knowledge Graph Query Automation
Graduate Program:
Computer Science and Engineering
Keywords:
TRAPI
Biomedical Knowledge Graphs
Natural Language Interface
Biolink Model
CURIE Normalization
Biomedical Translator
Query Automation
Entity Grounding
Knowledge Graph Reasoning
Natural Language Processing
Route-Based Query Graph Construction
Query Graph Generation
Machine Learning
Committee Members:
David Koslicki, Thesis Advisor/Co-Advisor
Mingfu Shao, Committee Member
Mahmut Kandemir, Program Head/Chair

3. A Systematic Approach to Formal Verification and Vulnerability Analysis of Access Control Mechanisms in 5G Core Network

open_access
Open Access
Author:
Akon, Mujtahid Al
Title:
A Systematic Approach to Formal Verification and Vulnerability Analysis of Access Control Mechanisms in 5G Core Network
Graduate Program:
Computer Science and Engineering
Keywords:
5G Core Network
Access Control
Formal Analysis
Vulnerabilities
Cellular Network Security
Committee Members:
Syed Rafiul Hussain, Thesis Advisor/Co-Advisor
G. Gary Tan, Committee Member
Mahmut Kandemir, Program Head/Chair

4. Adaptive Multimodal Learning Under Resource and Modality Constraints

open_access
Open Access
Author:
Zhao, Shu
Title:
Adaptive Multimodal Learning Under Resource and Modality Constraints
Graduate Program:
Computer Science and Engineering
Keywords:
Multimodal
Missing Modality
Large Language Models
Vision Language Models
Parameter-Efficient Fine-Tuning
Retrieval-Augmented Generation
Committee Members:
Vijaykrishnan Narayanan, Chair & Dissertation Advisor
Rui Zhang, Major Field Member
Chaopeng Shen, Outside Unit Member
Wenpeng Yin, Outside Field Member
Nilesh Ahuja, Special Member
Mahmut Kandemir, Program Head/Chair

6. Bandits with Noisy Surrogates: Applications in LLM Routing and Variance Reduction

restricted_to_institution
Restricted (Penn State Only)
Author:
Singh, Ronak
Title:
Bandits with Noisy Surrogates: Applications in LLM Routing and Variance Reduction
Graduate Program:
Computer Science and Engineering
Keywords:
Bandit Learning
Multi-Armed Bandits
LLM Routing
Online Learning
Contextual Bandits
Linear Bandits
Variance-Aware Bandits
Model Routing
Surrogate Rewards
Committee Members:
Mehrdad Mahdavi, Thesis Advisor/Co-Advisor
Hadi Hosseini, Committee Member
Antonio Blanca, Professor in Charge/Director of Graduate Studies

7. Bridging the Gap Between Safe Memory Management and Non-Blocking Data Structures

open_access
Open Access
Author:
Arovi, Md Amit
Title:
Bridging the Gap Between Safe Memory Management and Non-Blocking Data Structures
Graduate Program:
Computer Science and Engineering
Keywords:
safe memory reclamation
non-blocking data structures
lock-free algorithms
concurrent data structures
memory reuse
recyclability
optimistic traversals
hazard pointers
hazard eras
interval-based reclamation
Hyaline
epoch-based reclamation
RRR-SMR
SCOT
R-SCOT
safe memory reclamation
non-blocking data structures
lock-free algorithms
wait-free traversals
concurrent data structures
memory reuse
recyclability
optimistic traversals
hazard pointers
hazard eras
interval-based reclamation
Hyaline
epoch-based reclamation
RRR-SMR
SCOT
R-SCOT
Committee Members:
Hong Hu, Outside Unit & Field Member
Ruslan Nikolaev, Chair & Dissertation Advisor
Timothy Zhu, Major Field Member
Bhuvan Urgaonkar, Major Field Member
Mahmut Kandemir, Program Head/Chair

8. Computational Approaches for Full-Length Circular RNA Assembly from RNA Sequencing Data

open_access
Open Access
Author:
Zahin, Tasfia
Title:
Computational Approaches for Full-Length Circular RNA Assembly from RNA Sequencing Data
Graduate Program:
Computer Science and Engineering
Keywords:
RNA-seq
circular RNA
assembly
Committee Members:
Shaun Mahony, Outside Unit & Field Member
Anton Bankevich, Major Field Member
Mingfu Shao, Chair & Dissertation Advisor
Yana Safonova, Major Field Member
Mahmut Kandemir, Program Head/Chair