Yaorui Shi

Zhiyuan Liu, Yaorui Shi, An Zhang et al.

Masked graph modeling excels in the self-supervised representation learning of molecular graphs. Scrutinizing previous studies, we can reveal a common scheme consisting of three key components: (1) graph tokenizer, which breaks a molecular graph into smaller fragments (i.e., subgraphs) and converts them into tokens; (2) graph masking, which corrupts the graph with masks; (3) graph autoencoder, which first applies an encoder on the masked graph to generate the representations, and then employs a decoder on the representations to recover the tokens of the original graph. However, the previous MGM studies focus extensively on graph masking and encoder, while there is limited understanding of tokenizer and decoder. To bridge the gap, we first summarize popular molecule tokenizers at the granularity of node, edge, motif, and Graph Neural Networks (GNNs), and then examine their roles as the MGM's reconstruction targets. Further, we explore the potential of adopting an expressive decoder in MGM. Our results show that a subgraph-level tokenizer and a sufficiently expressive decoder with remask decoding have a large impact on the encoder's representation learning. Finally, we propose a novel MGM method SimSGT, featuring a Simple GNN-based Tokenizer (SGT) and an effective decoding strategy. We empirically validate that our method outperforms the existing molecule self-supervised learning methods. Our codes and checkpoints are available at https://github.com/syr-cn/SimSGT.

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.

Zhiyuan Liu, Yaorui Shi, An Zhang et al.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

Zhiyuan Liu, Yanchen Luo, Han Huang et al.

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

Yaorui Shi, Yuxin Chen, Siyuan Wang et al.

Large language models face challenges in long-context question answering, where key evidence of a query may be dispersed across millions of tokens. Existing works equip large language models with a memory corpus that is dynamically updated during a single-pass document scan, also known as the "memorize while reading" methods. While this approach scales efficiently, it suffers from irreversible forward-only processing, information loss through overwriting, and sparse reinforcement learning signals. To tackle these challenges, we present ReMemR1, a memory-augmented agent with callback-enhanced memory that allows selective retrieval from the entire memory history and allows non-linear reasoning and revisiting of early evidence. To further strengthen training, we propose Reinforcement Learning with Multi-Level Rewards (RLMLR), which combines final-answer rewards with dense, step-level signals that guide effective memory use. Together, these contributions mitigate information degradation, improve supervision, and support multi-hop memory utilizing. Experiments on long-document QA show significant gains over existing memory-based approaches, which validates ReMemR1 as an effective solution for long-context reasoning agents.