While dense biomedical embeddings achieve strong performance, their opaque dimensions limit transparency in biomedical NLP. Recent question-based interpretable embeddings represent text through binary answers to natural-language questions, but existing approaches rely primarily on corpus-driven signals, often capturing topical or stylistic differences rather than fine-grained biomedical distinctions. We propose QIME, an ontology-grounded framework for interpretable biomedical text embeddings in which each dimension corresponds to an explicit biomedical-domain yes/no question. QIME leverages a biomedical ontology to guide contrastive question generation from semantic clusters, producing atomic, domain-grounded questions. It constructs embeddings via similarity-based semantic activation with MMR-based diversity-aware dimension selection, yielding sparse representations efficiently. Experiments on biomedical clustering, STS and retrieval benchmarks show that QIME consistently outperforms prior interpretable embedding methods and substantially narrows the gap to strong black-box biomedical encoders. It also imposes substantially lower cognitive burden than existing methods, providing concise and domain-specific interpretations. The code is available at https://github.com/L1nzh/QIME.

Taxonomy induction aims to organize concept sets into coherent hierarchical structures. Recent LLM-based methods can induce taxonomies directly from flat term lists, avoiding the need for corpora, but degrade sharply as concept sets scale up. We argue that this degradation stems not only from context length limitations, but also from structural failures in hierarchical reasoning. To address this, we adopt a divide-and-merge paradigm that partitions concepts into smaller subsets, induces local taxonomies, and merges them into a global hierarchy. However, we identify two structural failure modes inherent to this paradigm: Structural Fragmentation, where partitioning weakens local hierarchical signals, and Parent Displacement, where locally plausible relations are misplaced in the global hierarchy. To address both, we propose SPARROW, a scalable taxonomy induction framework that combines structure-preserving spectral partitioning to retain hierarchical connectivity within each block, and constraint-guided incremental fusion that treats block-level relations as structural constraints rather than ground truth for global placement. Experiments on large-scale benchmarks show that SPARROW consistently achieves the strongest global structural quality, as measured by Ancestor F1, across backbones. The code is available at https://github.com/rebeccazyr/SPARROW.

In this work, we investigate an important task named instruction-following text embedding, which generates dynamic text embeddings that adapt to user instructions, highlighting specific attributes of text. Despite recent advancements, existing approaches suffer from significant computational overhead, as they require re-encoding the entire corpus for each new instruction. To address this challenge, we propose GSTransform, a novel instruction-following text embedding framework based on Guided Space Transformation. Our key observation is that instruction-relevant information is inherently encoded in generic embeddings but remains underutilized. Instead of repeatedly encoding the corpus for each instruction, GSTransform is a lightweight transformation mechanism that adapts pre-computed embeddings in real time to align with user instructions, guided by a small amount of text data with instruction-focused label annotation. We conduct extensive experiments on three instruction-awareness downstream tasks across nine real-world datasets, demonstrating that GSTransform improves instruction-following text embedding quality over state-of-the-art methods while achieving dramatic speedups of 6~300× in real-time processing on large-scale datasets. The source code is available at https://github.com/YingchaojieFeng/GSTransform.