Daily Papers

Text-guided molecular generation with LLMs often yields invalid SMILES. We argue that invalid drafts should be addressed through a shift from validity-oriented repair to identity-preserving molecular recovery: the objective is not only to restore chemical validity, but also to preserve target-relevant structural cues and recover the molecular identity implied by the description. This perspective reveals the limitations of existing correction strategies. Post-hoc repair can recover validity while distorting key structures, LLM-only correction can introduce unintended global drift, and generic agentic correction remains constrained by greedy single-candidate trajectories even when equipped with executable RDKit edit tools. To address these limitations, we propose AMREC, which couples molecule-aware mismatch tracking with expanded candidate exploration and trajectory-level selection. On invalid ChEBI-20 drafts from three backbone models, AMREC achieves the strongest overall recovery profile across structural, exact-match, and string-level metrics.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

Despite recent progress, Graphic User Interface (GUI) agents powered by Large Language Models (LLMs) struggle with complex mobile tasks due to limited app-specific knowledge. While UI Transition Graphs (UTGs) offer structured navigation representations, they are underutilized due to poor extraction and inefficient integration. We introduce KG-RAG, a Knowledge Graph-driven Retrieval-Augmented Generation framework that transforms fragmented UTGs into structured vector databases for efficient real-time retrieval. By leveraging an intent-guided LLM search method, KG-RAG generates actionable navigation paths, enhancing agent decision-making. Experiments across diverse mobile apps show that KG-RAG outperforms existing methods, achieving a 75.8% success rate (8.9% improvement over AutoDroid), 84.6% decision accuracy (8.1% improvement), and reducing average task steps from 4.5 to 4.1. Additionally, we present KG-Android-Bench and KG-Harmony-Bench, two benchmarks tailored to the Chinese mobile ecosystem for future research. Finally, KG-RAG transfers to web/desktop (+40% SR on Weibo-web; +20% on QQ Music-desktop), and a UTG cost ablation shows accuracy saturates at ~4h per complex app, enabling practical deployment trade-offs.

Understanding the chemical structure from a graphical representation of a molecule is a challenging image caption task that would greatly benefit molecule-centric scientific discovery. Variations in molecular images and caption subtasks pose a significant challenge in both image representation learning and task modeling. Yet, existing methods only focus on a specific caption task that translates a molecular image into its graph structure, i.e., OCSR. In this paper, we propose the Optical Chemical Structure Understanding (OCSU) task, which extends OCSR to molecular image caption from motif level to molecule level and abstract level. We present two approaches for that, including an OCSR-based method and an end-to-end OCSR-free method. The proposed Double-Check achieves SOTA OCSR performance on real-world patent and journal article scenarios via attentive feature enhancement for local ambiguous atoms. Cascading with SMILES-based molecule understanding methods, it can leverage the power of existing task-specific models for OCSU. While Mol-VL is an end-to-end optimized VLM-based model. An OCSU dataset, Vis-CheBI20, is built based on the widely used CheBI20 dataset for training and evaluation. Extensive experimental results on Vis-CheBI20 demonstrate the effectiveness of the proposed approaches. Improving OCSR capability can lead to a better OCSU performance for OCSR-based approach, and the SOTA performance of Mol-VL demonstrates the great potential of end-to-end approach.