Zhiyuan Liu

Zhiyuan Liu, Sihang Li, Yanchen Luo et al.

Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception - a critical ability of human professionals in comprehending molecules' topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (e.g., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder's representation space and an LM's text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM's efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM's ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines. Our codes and checkpoints can be found at https://github.com/acharkq/MolCA.

Yaorui Shi, An Zhang, Enzhi Zhang et al.

Predicting chemical reactions, a fundamental challenge in chemistry, involves forecasting the resulting products from a given reaction process. Conventional techniques, notably those employing Graph Neural Networks (GNNs), are often limited by insufficient training data and their inability to utilize textual information, undermining their applicability in real-world applications. In this work, we propose ReLM, a novel framework that leverages the chemical knowledge encoded in language models (LMs) to assist GNNs, thereby enhancing the accuracy of real-world chemical reaction predictions. To further enhance the model's robustness and interpretability, we incorporate the confidence score strategy, enabling the LMs to self-assess the reliability of their predictions. Our experimental results demonstrate that ReLM improves the performance of state-of-the-art GNN-based methods across various chemical reaction datasets, especially in out-of-distribution settings. Codes are available at https://github.com/syr-cn/ReLM.

Zheni Zeng, Bangchen Yin, Shipeng Wang et al.

Natural language is expected to be a key medium for various human-machine interactions in the era of large language models. When it comes to the biochemistry field, a series of tasks around molecules (e.g., property prediction, molecule mining, etc.) are of great significance while having a high technical threshold. Bridging the molecule expressions in natural language and chemical language can not only hugely improve the interpretability and reduce the operation difficulty of these tasks, but also fuse the chemical knowledge scattered in complementary materials for a deeper comprehension of molecules. Based on these benefits, we propose the conversational molecular design, a novel task adopting natural language for describing and editing target molecules. To better accomplish this task, we design ChatMol, a knowledgeable and versatile generative pre-trained model, enhanced by injecting experimental property information, molecular spatial knowledge, and the associations between natural and chemical languages into it. Several typical solutions including large language models (e.g., ChatGPT) are evaluated, proving the challenge of conversational molecular design and the effectiveness of our knowledge enhancement method. Case observations and analysis are conducted to provide directions for further exploration of natural-language interaction in molecular discovery.

Yudong Wang, Zixuan Fu, Hengyu Zhao et al.

The development of artificial intelligence can be viewed as an evolution of data-driven learning paradigms, with successive shifts in data organization and utilization continuously driving advances in model capability. Current LLM research is dominated by a paradigm that relies heavily on unidirectional scaling of data size, increasingly encountering bottlenecks in data availability, acquisition cost, and training efficiency. In this work, we argue that the development of AGI is entering a new phase of data-model co-evolution, in which models actively guide data management while high-quality data, in turn, amplifies model capabilities. To implement this vision, we propose a tiered data management framework, designed to support the full LLM training lifecycle across heterogeneous learning objectives and cost constraints. Specifically, we introduce an L0-L4 tiered data management framework, ranging from raw uncurated resources to organized and verifiable knowledge. Importantly, LLMs are fully used in data management processes, such as quality scoring and content editing, to refine data across tiers. Each tier is characterized by distinct data properties, management strategies, and training roles, enabling data to be strategically allocated across LLM training stages, including pre-training, mid-training, and alignment. The framework balances data quality, acquisition cost, and marginal training benefit, providing a systematic approach to scalable and sustainable data management. We validate the effectiveness of the proposed framework through empirical studies, in which tiered datasets are constructed from raw corpora and used across multiple training phases. Experimental results demonstrate that tier-aware data utilization significantly improves training efficiency and model performance. To facilitate further research, we release our tiered datasets and processing tools to the community.

Sihang Li, Zhiyuan Liu, Yanchen Luo et al.

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties. We release our codes and datasets at https://github.com/lsh0520/3D-MoLM.