MolE-RAG: Molecular Structure-Enhanced Retrieval-Augmented Generation for Chemistry

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. To bridge this semantic and chemical knowledge gap, we propose MolE-RAG, a training-free, molecule-centric retrieval-augmented generation framework for LLM-based molecular property prediction. MolE-RAG augments each prediction with three complementary sources of inference-time context: retrieved chemistry literature, molecule-specific information including compound synonyms, identifiers, functional group annotations, and physicochemical descriptors, and structurally similar molecules retrieved from the training set. We evaluate MolE-RAG across nine molecular property prediction tasks using proprietary, chemistry-specialized, and open-source LLMs. Across general-purpose LLMs, MolE-RAG improves ROC-AUC by up to 28 percentage points on classification tasks and reduces regression RMSE by up to 67% relative to a SMILES-only baseline. We further find that the utility of each context source varies across models and tasks, with different models benefiting most from textual retrieval, molecular context, or structural retrieval. These results suggest that molecule-centric retrieval can improve LLM-based molecular property prediction without model fine-tuning while providing a flexible framework for integrating heterogeneous chemical knowledge at inference time.

Generating Long Semantic IDs in Parallel for Recommendation

Semantic ID-based recommendation models tokenize each item into a small number of discrete tokens that preserve specific semantics, leading to better performance, scalability, and memory efficiency. While recent models adopt a generative approach, they often suffer from inefficient inference due to the reliance on resource-intensive beam search and multiple forward passes through the neural sequence model. As a result, the length of semantic IDs is typically restricted (e.g. to just 4 tokens), limiting their expressiveness. To address these challenges, we propose RPG, a lightweight framework for semantic ID-based recommendation. The key idea is to produce unordered, long semantic IDs, allowing the model to predict all tokens in parallel. We train the model to predict each token independently using a multi-token prediction loss, directly integrating semantics into the learning objective. During inference, we construct a graph connecting similar semantic IDs and guide decoding to avoid generating invalid IDs. Experiments show that scaling up semantic ID length to 64 enables RPG to outperform generative baselines by an average of 12.6% on the NDCG@10, while also improving inference efficiency. Code is available at: https://github.com/facebookresearch/RPG_KDD2025.

Harnessing PubMed User Query Logs for Post Hoc Explanations of Recommended Similar Articles

Searching for a related article based on a reference article is an integral part of scientific research. PubMed, like many academic search engines, has a "similar articles" feature that recommends articles relevant to the current article viewed by a user. Explaining recommended items can be of great utility to users, particularly in the literature search process. With more than a million biomedical papers being published each year, explaining the recommended similar articles would facilitate researchers and clinicians in searching for related articles. Nonetheless, the majority of current literature recommendation systems lack explanations for their suggestions. We employ a post hoc approach to explaining recommendations by identifying relevant tokens in the titles of similar articles. Our major contribution is building PubCLogs by repurposing 5.6 million pairs of coclicked articles from PubMed's user query logs. Using our PubCLogs dataset, we train the Highlight Similar Article Title (HSAT), a transformer-based model designed to select the most relevant parts of the title of a similar article, based on the title and abstract of a seed article. HSAT demonstrates strong performance in our empirical evaluations, achieving an F1 score of 91.72 percent on the PubCLogs test set, considerably outperforming several baselines including BM25 (70.62), MPNet (67.11), MedCPT (62.22), GPT-3.5 (46.00), and GPT-4 (64.89). Additional evaluations on a separate, manually annotated test set further verifies HSAT's performance. Moreover, participants of our user study indicate a preference for HSAT, due to its superior balance between conciseness and comprehensiveness. Our study suggests that repurposing user query logs of academic search engines can be a promising way to train state-of-the-art models for explaining literature recommendation.