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TaxoMFM: A Taxonomy-Aware Foundation Model for the Human Gut Microbiome

Haochen Xue, Anastasia Godneva, Yulong Li, Qi Cao, Zhaodong Wu, Kaiyu Liang, Jionglong Su, Eran Segal 等 9 位作者

Existing gut microbiome foundation models typically use flat taxon representations, limiting their ability to exploit known taxonomic hierarchies. We introduce TaxoMFM, a microbiome foundation model that integrates taxonomic structure into self-supervised learning. TaxoMFM jointly learns abundance patterns across taxonomic ranks and relative proportions within groups through taxonomy-aware encoding and hierarchical compositional reconstruction. We further construct TaxoGut-HPP, comprising 100,806 gut microbiome profiles from 231 source cohorts and covering 40 classification and 8 regression tasks. TaxoMFM achieves competitive performance across disease, gut health, host trait, and liver ultrasound phenotype prediction. In cross-cohort zero-shot transfer, where target cohorts are excluded from both pretraining and downstream adaptation, TaxoMFM achieves AUROCs of 0.838, 0.736, and 0.722 for colorectal cancer, type 2 diabetes, and inflammatory bowel disease, respectively. Further analyses show that TaxoMFM recovers community changes across taxonomic scales, while preserving community information and producing consistent representations under database updates and species-vocabulary shifts. Our code is available at https://anonymous.4open.science/r/TaxoMFM-F16D/.

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Long Context Modeling with Ranked Memory-Augmented Retrieval

Ghadir Alselwi, Hao Xue The Hong Kong University of Science and Technology, Shoaib Jameel University of Southampton, Basem Suleiman University of New South Wales, Flora D. Salim, Imran Razzak Mohamed bin Zayed University of Artificial Intelligence

Effective long-term memory management is crucial for language models handling extended contexts. We introduce the Enhanced Ranked Memory Augmented Retrieval ERMAR framework, which dynamically ranks memory entries based on relevance. Unlike prior models, ERMAR employs a novel relevance scoring mechanism and a pointwise re-ranking model for key-value embeddings, inspired by learning-to-rank techniques in information retrieval. By integrating historical usage patterns and adaptive retrieval, ERMAR achieves state-of-the-art results on standard benchmarks, demonstrating superior scalability and performance in long-context tasks.

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Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表