TeroSeek: An AI-Powered Knowledge Base and Retrieval Generation Platform for Terpenoid Research

Terpenoids are a crucial class of natural products that have been studied for over 150 years, but their interdisciplinary nature (spanning chemistry, pharmacology, and biology) complicates knowledge integration. To address this, the authors developed TeroSeek, a curated knowledge base (KB) built from two decades of terpenoid literature, coupled with an AI-powered question-answering chatbot and web service. Leveraging a retrieval-augmented generation (RAG) framework, TeroSeek provides structured, high-quality information and outperforms general-purpose large language models (LLMs) in terpenoid-related queries. It serves as a domain-specific expert tool for multidisciplinary research and is publicly available at http://teroseek.qmclab.com.

Bidirectional Mamba for Single-Cell Data: Efficient Context Learning with Biological Fidelity

Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges. Transformer-based models have made significant advances in this domain but are often limited by their quadratic complexity and suboptimal handling of long-range dependencies. In this work, we introduce GeneMamba, a scalable and efficient foundation model for single-cell transcriptomics built on state space modeling. Leveraging the Bi-Mamba architecture, GeneMamba captures bidirectional gene context with linear-time complexity, offering substantial computational gains over transformer baselines. The model is pretrained on nearly 30 million cells and incorporates biologically informed objectives, including pathway-aware contrastive loss and rank-based gene encoding. We evaluate GeneMamba across diverse tasks, including multi-batch integration, cell type annotation, and gene-gene correlation, demonstrating strong performance, interpretability, and robustness. These results position GeneMamba as a practical and powerful alternative to transformer-based methods, advancing the development of biologically grounded, scalable tools for large-scale single-cell data analysis.