# OntoAligner-Ensemble: Voting-Based Fusion across Heterogeneous Ontology Alignment Techniques

arXiv: https://arxiv.org/abs/2608.31137 · HTML: https://mlsanity.com/paper/2608.31137/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 35 references that are in the map.
- First posted on arXiv 31 Aug 2026.

## Builds on (most cited first, 8 of 8)

- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [OWL2Vec*: Embedding of OWL Ontologies](https://mlsanity.com/paper/2009.14654/) (2020)
- [BERTMap: A BERT-based Ontology Alignment System](https://mlsanity.com/paper/2112.02682/) (2021)
- [OLaLa: Ontology Matching with Large Language Models](https://mlsanity.com/paper/2311.03837/) (2023)
- [Agent-OM: Leveraging LLM Agents for Ontology Matching](https://mlsanity.com/paper/2312.00326/) (2023)
- [LLMs4OM: Matching Ontologies with Large Language Models](https://mlsanity.com/paper/2404.10317/) (2024)
- [OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignment](https://mlsanity.com/paper/2503.21902/) (2025)
- [OntoAligner Meets Knowledge Graph Embedding Aligners](https://mlsanity.com/paper/2509.26417/) (2025)

## Abstract (arXiv)

Ontology alignment (OA) has evolved through several methodological paradigms, ranging from lexical and structural aligners to knowledge graph embedding (KGE) models and, more recently, Large Language Model (LLM)-based approaches. Although modern OA frameworks provide unified ecosystems for deploying these heterogeneous aligners, mechanisms for systematically reconciling their complementary and sometimes conflicting predictions remain relatively underexplored. We present OntoAligner-Ensemble, a modular and aligner-agnostic framework that combines candidate correspondences through a configurable two-stage process comprising voting-based fusion strategies followed by post-fusion selection policies. The framework supports any aligner implemented within OntoAligner that produces candidate correspondences, enabling diverse alignment paradigms to be integrated through a unified decision process. To demonstrate its effectiveness, we instantiate the framework using representative lightweight string-aligner, KGE-based, and Retrieval-Augmented Generation aligners powered by both open-weight and API-based LLMs. We evaluate individual aligners and ensemble configurations across eight benchmark tasks from five OAEI tracks spanning biomedical to beyond-equivalence. The results show that ensemble fusion consistently improves the balance between precision and recall and frequently outperforms standalone aligners across diverse domains. Furthermore, our analysis reveals that ensemble composition directly affects the precision-recall trade-off: heterogeneous cross-paradigm ensembles generally improve precision, whereas homogeneous LLM ensembles more often achieve higher overall F1-scores. These findings demonstrate that systematic ensemble learning offers a robust and reproducible strategy for OA while providing practical guidance for selecting ensemble compositions under different alignment scenarios.