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Cheriton School of Computer Science

Master's Thesis Presentation • Computer Graphics • VR GAViewer: Immersive Visualisation and Direct Manipulation of the Conformal Model in Virtual Reality | Cheriton School of Computer Science | University of Waterloo Seminar • Algorithms and Complexity • Lower Bounds for Private Optimization Via Reconstruction Attacks | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Data Systems • Efficient Oblivious Query Processing for Property Graph Databases | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Artificial Intelligence | Machine Learning • Inferred Author Gender as a Variable Affecting LLM Behaviour | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Bioinformatics • From Candidates to Evidence: Diagnostics for Trustworthy Biological Discovery | Cheriton School of Computer Science | University of Waterloo PhD Defence • Algorithms and Complexity • Graph Property Testing and the Container Method | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Software Engineering • An Empirical Study of Transitive Vulnerability Exposure in PyPI | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Human–Computer Interaction • The Design and Development of a Virtual Patient System for Medical Education | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Algorithms and Complexity • On the Black-Box Impossibility of Hardness in TFNP from One-Way Functions | Cheriton School of Computer Science | University of Waterloo Seminar • Algorithms and Complexity • Geometric Distances for Curves and Graphs: From Matching to Simplification | Cheriton School of Computer Science | University of Waterloo PhD Defence • Computer Algebra | Symbolic Computation • On the Effective Algebraic Geometry of Determinantal Varieties | Cheriton School of Computer Science | University of Waterloo Seminar • Algorithms and Complexity • Computing with Full Memory in 2026 | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Algorithms and Complexity • Bipartite Density: From Mixing Time to Local Algorithms for Dense Subgraphs | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Cryptography, Security, and Privacy (CrySP) • Upgrading Security Properties for Updatable Public-Key Encryption through Modular Transformations | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Programming Languages • The Defensive Tax: Price of Defenses That Never Defend | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Algorithms and Complexity • Algorithms for Analytic Combinatorics: Positivity Bounds and D-finite Operators | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Cryptography, Security, and Privacy (CrySP) • IPFSCover: Examining Website Fingerprinting Threats in the InterPlanetary File System | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Programming Languages • Reified Generic Types for Scala 3 on the JVM | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Artificial Intelligence | Machine Learning • Abstract Reasoning with Vector Symbolic Algebras | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Artificial Intelligence | Machine Learning • Learning at Test Time: Adapting Models with Synthetic Data and Environment Interaction | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Formal Methods • Counterexample Guided Abstraction and Refinement in Dash Models | Cheriton School of Computer Science | University of Waterloo Master’s Thesis Presentation • Systems and Networking • Runtime Configuration of GPU Workloads for Energy-efficient Execution | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Artificial Intelligence | Machine Learning • Beyond Semantic Similarity: Direct Corpus Interaction for Agentic Search | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Artificial Intelligence | Machine Learning • OpenResearcher: Reproducible Training for Long-Horizon Deep Research Agents | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Software Engineering • SLA-Awareness for AI-assisted coding | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Software Engineering • Context-Aware CodeLLM Eviction for AI-assisted Coding | Cheriton School of Computer Science | University of Waterloo PhD Seminar • Bioinformatics • Recurrent Energy-Based Modeling of Side-Chain Allostery | Cheriton School of Computer Science | University of Waterloo Seminar • Bioinformatics | Artificial Intelligence • Advancing Drug Discovery with FAIR Data and Explainable AI in Biomedical Research | Cheriton School of Computer Science | University of Waterloo PhD Defence • Artificial Intelligence | Machine Learning | Bioinformatics • Generative Synthetic Data for Pre-Clinical Drug Discovery | Cheriton School of Computer Science | University of Waterloo PhD Defence • Human–Computer Interaction • Tangible World-in-Miniature Interaction in Virtual Reality | Cheriton School of Computer Science | University of Waterloo
PhD Seminar • Software Engineering • Decoupling CLI Agent...
Mayuri Punithan · 2026-08-07 · via Cheriton School of Computer Science

Please note: This PhD seminar will take place online.

Kishanthan Thangarajah, PhD candidate
David R. Cheriton School of Computer Science

Supervisor: Professor Meiyappan Nagappan

CLI-based software-engineering agents have matured rapidly, yet the open ecosystem has converged on a single training environment: trajectory datasets used to fine-tune open models are collected almost exclusively under OpenHands. Models fine-tuned on this data score well under OpenHands but degrade substantially when deployed under any non-training scaffold. Untrained base models do not show this divergence, indicating the gap is fine-tuning-induced and tied to the conventions of the training scaffold. We argue the load-bearing scaffold-specific behavior is planning structure, in two senses this paper distinguishes: explicit planning, a pre-execution plan produced as a first-class artifact, and implicit planning, the structural conventions that shape execution throughout the agent loop.

Under this hypothesis, closing the gap requires moving planning from a fixed scaffold artifact to a learned model capability. We introduce Decoupling CLI Agent Scaffolding (DCAS), a backend substitution interception layer that routes API traffic between any CLI scaffold and any backend model without modifying the scaffold, enabling cross-scaffold evaluation and planning-aware trajectory collection. Using DCAS, a controlled plan-source intervention confirms planning quality is a high-leverage component, with gains exceeding the cross-scaffold drops we observe. A model fine-tuned on a small set of DCAS-collected planning-aware trajectories under a single scaffold gains consistently across non-training scaffolds, and the two senses of planning are empirically separable in training data.


Attend this PhD seminar virtually on Zoom.