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For a system with N residues, frame-wise pairwise interaction data is naturally quadratic, and each residue is often represented by local one-hop information rather than network-level communication structure. This thesis presents SAWNERGY, a Python software framework that converts MD-derived non-bonded interactions into compact residue embeddings through a fully reproducible pipeline: residue interaction network (RIN) construction, random and self-avoiding walk sampling, skip-gram training, and archive-based persistence.</p><p>The framework integrates established physical and graph-learning components into a coherent scientific software system. Atomic electrostatic and van der Waals interactions are extracted with cpptraj, projected to residue resolution, split into attractive and repulsive channels, quantile-pruned, symmetrized, and row-normalized into transition matrices. Walk corpora are sampled over time-indexed transition stacks, with support for random walks (RW), self-avoiding walks (SAW), and an optional time-aware stepping mode. Embeddings are learned per frame with either SGNS or full-softmax skip-gram objectives using interchangeable PureML and PyTorch backends.</p><p>An important contribution is SAWNERGY's archive-contract design. Each pipeline stage reads and writes compressed Zarr v3 archives with explicit metadata for dataset discovery, parameter provenance, and deterministic seed tracking. This yields strong decoupling between modules and practical reproducibility across runs and environments. The thesis details the mathematical formulation, software architecture, implementation decisions, testing strategy, and usage patterns of the released system. The result is a balanced scientific software approach that preserves physical interpretability while enabling scalable representation learning for MD analysis.</p>"},{"label":"Digital Identifier","value":"b2026-mishchyriak"},{"label":"Digital Object Identifier (DOI)","value":"https://doi.org/10.14418/fbzn3s9i"},{"label":"Digital Origin","value":["born digital"]},{"label":"Discipline","value":["Computer Science"]},{"label":"Date","value":"April 15, 2026"},{"label":"EDTF Date","value":"D:00 M:00 Y:2026"},{"label":"File Format","value":["application/pdf"]},{"label":"Genre","value":["theses"]},{"label":"Group","value":["Theses & Dissertations"]},{"label":"Held By","value":"Wesleyan University Library, Wesleyan University, Middletown, CT, USA"},{"label":"Language","value":["English"]},{"label":"Repository","value":["University Archives"]},{"label":"Rights","value":["In Copyright"]},{"label":"Thesis Advisor(s)","value":["Thayer, 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