The study investigates how document segmentation and chunk representation affect retrieval-augmented generation (RAG) for chemistry texts. Using the ChemQuests corpus, the authors benchmark 41 embedding models and evaluate them across five chunking strategies, seven chunk sizes, and various overlap settings. They find that embedding choice has the largest impact, with models like E5, BGE, and Nomic performing best, and recommend medium-to-large chunks with fixed-token, recursive-token, or hierarchical-section chunking and low overlap for effective chemistry-aware RAG.
arXiv:2601. 19827v4 Announce Type: replace-cross Abstract: Retrieval-Augmented Generation (RAG) extends large language models (LLMs) beyond parametric knowledge, yet it is unclear when iterative retrieval-reasoning loops meaningfully outperform static RAG, particularly in scientific domains with multi-hop reasoning, sparse domain knowledge, and heterogeneous evidence.
arXiv:2608. 03860v1 Announce Type: cross Abstract: We introduce SciRet, a compute-aware empirical study of retrieval-augmented generation for scientific question answering over CORD-19.
arXiv:2505. 05232v3 Announce Type: replace Abstract: The rapid expansion of chemistry literature poses significant challenges for researchers seeking to efficiently access domain-specific knowledge.
arXiv:2607. 23507v1 Announce Type: cross Abstract: Choosing the right text embedding model is one of the most consequential -- and most frequently under-examined -- decisions in building a retrieval or search system, yet the model that tops a leaderboard is rarely the best choice for a given deployment.
arXiv:2608. 03855v1 Announce Type: new Abstract: Transformer models have revolutionized natural language processing (NLP), and text-based molecular representations like SMILES have successfully extended these architectures to chemistry.
arXiv:2607. 23006v1 Announce Type: cross Abstract: Scientific question answering requires a retrieval system to solve two distinct problems: identifying which papers are relevant and locating the supporting evidence within those papers.
The paper presents a controlled comparison of six retrieval-augmented generation (RAG) strategies for scientific question answering on a large arXiv corpus. All pipelines use the same LLM generator and evaluation protocol, differing only in retrieval design—ranging from classic dense retrieval to late‑interaction methods like ColBERTv2. The authors also release a synthetic question dataset and code to enable reproducible, large‑scale evaluation of RAG trade‑offs.
arXiv:2606. 03057v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used for molecular tasks, but it remains unclear which molecular representation to use.
arXiv:2606. 05693v1 Announce Type: new Abstract: Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained.
The paper introduces ORDER, a task‑conditioned retrieval‑augmented generation framework that dynamically adapts both indexing and retrieval strategies to each incoming query. It first clusters questions to learn cluster‑specific chunking, metadata filtering, and reranking settings, then routes queries to the appropriate pre‑built index via nearest‑centroid assignment. Additionally, a supervised query router predicts relevant collections and a Uniform Multi‑source Sampler distributes the retrieval budget evenly across selected sources, yielding superior performance on heterogeneous historical archives compared to existing RAG systems.
MolEmb is a lightweight framework that adapts multimodal large language models (MLLMs) to serve as general molecular embedding models. By aligning molecular profiles with textual descriptions in a shared embedding space using a bidirectional contrastive objective, MolEmb produces embeddings conditioned on both a molecular profile and a natural‑language semantic context. The model performs competitively on molecular property prediction and enables cross‑modal molecule‑text retrieval, while the newly introduced MolCAR benchmark demonstrates that context‑aware molecular embedding is largely a data property of the supervision.
arXiv:2608. 03148v1 Announce Type: cross Abstract: RAG improves the factual grounding of LLM by incorporating external knowledge, but deploying RAG on mobile and edge devices remains challenging because retrieved context increases computation and memory.