Towards 3D Molecule-Text Interpretation in Language Models

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.

Large Language Model Can Interpret Latent Space of Sequential Recommender

Sequential recommendation is to predict the next item of interest for a user, based on her/his interaction history with previous items. In conventional sequential recommenders, a common approach is to model item sequences using discrete IDs, learning representations that encode sequential behaviors and reflect user preferences. Inspired by recent success in empowering large language models (LLMs) to understand and reason over diverse modality data (e.g., image, audio, 3D points), a compelling research question arises: ``Can LLMs understand and work with hidden representations from ID-based sequential recommenders?''.To answer this, we propose a simple framework, RecInterpreter, which examines the capacity of open-source LLMs to decipher the representation space of sequential recommenders. Specifically, with the multimodal pairs (\ie representations of interaction sequence and text narrations), RecInterpreter first uses a lightweight adapter to map the representations into the token embedding space of the LLM. Subsequently, it constructs a sequence-recovery prompt that encourages the LLM to generate textual descriptions for items within the interaction sequence. Taking a step further, we propose a sequence-residual prompt instead, which guides the LLM in identifying the residual item by contrasting the representations before and after integrating this residual into the existing sequence. Empirical results showcase that our RecInterpreter enhances the exemplar LLM, LLaMA, to understand hidden representations from ID-based sequential recommenders, especially when guided by our sequence-residual prompts. Furthermore, RecInterpreter enables LLaMA to instantiate the oracle items generated by generative recommenders like DreamRec, concreting the item a user would ideally like to interact with next. Codes are available at https://github.com/YangZhengyi98/RecInterpreter.

MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter

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.