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Madhulatha Mandarapu

Publications and source records attributed to Madhulatha Mandarapu.

20 records · Page 2Linked to original sources

Graph-Grounded Optimization: Rao-Family Metaheuristics, Classical OR, and SLM-Driven Formulation over Knowledge Graphs

We propose graph-grounded optimization: a paradigm in which the decision variables, constraints, and objective coefficients of a real-world optimization problem are sourced from a property knowledge graph (KG) via Cypher queries, rather than supplied as free-form natural-language text or static tabular input. We motivate the paradigm by surveying recent LLM/SLM-driven optimization systems -- OptiMUS, Chain-of-Experts, LLMOPT, OPRO, FunSearch, Eureka -- none of which consume property graphs as the primary input modality. We instantiate the paradigm in the open-source samyama-graph database and evaluate seven real-world public-domain KG-backed problems spanning drug repurposing (245K-node biomedical KG), clinical-trial site selection (7.78M-node trial registry), Indian supply-chain rerouting (5.34M-node OSM road graph), healthcare equity allocation (WHO/GAVI/IHME KG), economic-environmental grid dispatch, antimicrobial-resistance stewardship (NCBI AMRFinderPlus, 10.4K resistance genes), and wildfire evacuation routing (OSM Paradise, CA). We compare a portfolio of Rao-family metaheuristics (BMWR, Jaya, SAMP-Jaya, EHR-Jaya, Rao-1) against Google OR-tools (CP-SAT and GLOP) reference solvers. We find that (i) no single Rao variant dominates: BMWR wins on discrete-with-tradeoff and high-dim-with-hard-constraint problems while Rao-1 wins on continuous low-/mid-dim problems, empirically supporting a portfolio approach; (ii) OR-tools dominates on small linear/MILP-friendly sub-problems but cannot encode the non-linear objectives that emerge in several of the real-world settings; (iii) graph-grounded formulations surface data-quality issues (missing properties, degenerate aggregates) that purely text-formulated optimizations would silently mask

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Open Biomedical Knowledge Graphs at Scale: Construction, Federation, and AI Agent Access with Samyama Graph Database

Biomedical knowledge is fragmented across siloed databases -- Reactome for pathways, STRING for protein interactions, ClinicalTrials.gov for study registries, DrugBank for drug vocabularies, DGIdb for drug-gene interactions, SIDER for side effects. We present three open-source biomedical knowledge graphs -- Pathways KG (118,686 nodes, 834,785 edges from 5 sources), Clinical Trials KG (7,774,446 nodes, 26,973,997 edges from 5 sources), and Drug Interactions KG (32,726 nodes, 191,970 edges from 3 sources) -- built on Samyama, a high-performance graph database written in Rust. Our contributions are threefold. First, we describe a reproducible ETL pattern for constructing large-scale KGs from heterogeneous public data sources, with cross-source deduplication, batch loading (Python Cypher and Rust native loaders), and portable snapshot export. Second, we demonstrate cross-KG federation: loading all three snapshots into a single graph tenant enables property-based joins across datasets. Third, we introduce schema-driven MCP server generation for LLM agent access, evaluated on a new BiomedQA benchmark (40 pharmacology questions): domain-specific MCP tools achieve 98% accuracy vs. 85% for schema-aware text-to-Cypher and 75% for standalone GPT-4o, with zero schema errors. All data sources are open-license. The combined federated graph (7.9M nodes, 28M edges) loads in approximately 3 minutes on commodity cloud hardware, with single-KG queries completing in 80-100ms and cross-KG federation joins in 1-4s

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