Xiaohui Fan

Yin Fang, Ningyu Zhang, Zhuo Chen et al.

The generation of molecules with desired properties has become increasingly popular, revolutionizing the way scientists design molecular structures and providing valuable support for chemical and drug design. However, despite the potential of language models in molecule generation, they face challenges such as generating syntactically or chemically flawed molecules, having narrow domain focus, and struggling to create diverse and feasible molecules due to limited annotated data or external molecular databases. To tackle these challenges, we introduce MolGen, a pre-trained molecular language model tailored specifically for molecule generation. Through the reconstruction of over 100 million molecular SELFIES, MolGen internalizes structural and grammatical insights. This is further enhanced by domain-agnostic molecular prefix tuning, fostering robust knowledge transfer across diverse domains. Importantly, our chemical feedback paradigm steers the model away from molecular hallucinations, ensuring alignment between the model's estimated probabilities and real-world chemical preferences. Extensive experiments on well-known benchmarks underscore MolGen's optimization capabilities in properties such as penalized logP, QED, and molecular docking. Additional analyses confirm its proficiency in accurately capturing molecule distributions, discerning intricate structural patterns, and efficiently exploring the chemical space. Code is available at https://github.com/zjunlp/MolGen.

Yin Fang, Xiaozhuan Liang, Ningyu Zhang et al.

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a comprehensive instruction dataset designed for the biomolecular domain. Mol-Instructions encompasses three key components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions. Each component aims to improve the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on LLMs, we demonstrate the effectiveness of Mol-Instructions in enhancing large models' performance in the intricate realm of biomolecular studies, thus fostering progress in the biomolecular research community. Mol-Instructions is publicly available for ongoing research and will undergo regular updates to enhance its applicability.

Yongjin Cui, Xiaohui Fan, Huajun Chen

Transformer has significantly propelled the development of artificial intelligence, and certainly the development of agents as well. We categorize attention structures of Transformer into two types based on the source of the input information: homogenous and heterogenous attention structures. Heterogenous attention structures, with co-attention as a typical example, process information from different sources. Heterogenous attention structure is the foundation for Transformer models to achieve more complex functions and integrate more modal information. Whether for research purposes or policy requirements, the interpretation of Transformer models with heterogenous attention structures is an important task. The fusion of information from different sources brings new challenges. Our work mainly includes two parts: method and experimentation. In terms of method, we propose an interpretation method for Transformer models with heterogenous attention structures. In terms of experimentation, based on our experimental analysis paradigm, we interpret the operating mechanisms of representative models, conduct semantic interpretation and logical interpretation.

Yongjin Cui, Xiaohui Fan

We observe that existing model interpretation methods generally ignore the baseline, and such neglect often results in imprecise or even incorrect interpretation. In this paper, we reformulate the task of model interpretation and the interpretation principles for model interpretation results to demonstrate the importance of the baseline. We further unify gradient-based methods, Integrated Gradients (IG) methods, and Taylor expansion, clarifying the connections among them and explicitly identifying the baseline for each method. On this basis, we analyze the flaws and errors in related model interpretation methods (IG, LayerCAM, ODAM, Difference Map). We advocate evaluating the quality of model interpretation results precisely through the attribution error between the attribution result and the attribution target, rather than adopting flawed evaluation methods, such as those based on marginal-effect or the assumption of perfect model performance. We revise IG and develope a model interpretation method with a clear and reasonable baseline, achieving better results. Our method supports model interpretation based on features from any layer. Interpretation based on features from different layers are all reasonable, and the differences among these results reflect varying degrees of feature extraction at different feature extraction stages.

Yongjin Cui, Xiaohui Fan

Grad-ECLIP is published at ICML 2024 and represents a new Transformer interpretation technical route (intermediate features-based). First, this paper demonstrates that the intermediate features-based technical route is not a novel one. Based on the existing attention-based route, we have developed Attention-ECLIP, which is completely equivalent to Grad-ECLIP but with simpler computation. Both through formal derivation and experimental validation, we prove that the intermediate feature-based route represented by Grad-ECLIP is actually an equivalent variant of the attention-based route. Next, this paper demonstrates that the Grad-ECLIP method is flawed. The model interpretation results obtained by Grad-ECLIP are not those of the original model, and the interpretation results are misaligned with the model's performance. We analyze the causes of Grad-ECLIP's flaws and propose, or rather, explicitly emphasize two fundamental principles that model interpretation should adhere to in order to avoid similar errors.

Jun Xie, Yingjian Zhu, Feng Chen et al.

In this paper, we present our solution for the semi-supervised learning track (MER-SEMI) in MER2025. We propose a comprehensive framework, grounded in the principle that "more is better," to construct a robust Mixture of Experts (MoE) emotion recognition system. Our approach integrates a diverse range of input modalities as independent experts, including novel signals such as knowledge from large Vision-Language Models (VLMs) and temporal Action Unit (AU) information. To effectively utilize unlabeled data, we introduce a consensus-based pseudo-labeling strategy, generating high-quality labels from the agreement between a baseline model and Gemini, which are then used in a two-stage training paradigm. Finally, we employ a multi-expert voting ensemble combined with a rule-based re-ranking process to correct prediction bias and better align the outputs with human preferences. Evaluated on the MER2025-SEMI challenge dataset, our method achieves an F1-score of 0.8772 on the test set, ranking 2nd in the track. Our code is available at https://github.com/zhuyjan/MER2025-MRAC25.

Yongjin Cui, Xiaohui Fan, Huajun Chen

Although researchers' attention is more focused on the performance of Transformer models, the interpretation of Transformer can never be ignored. Gradient is widely utilized in Transformer interpretation. From the perspective of attention and gradient, we conduct an in-depth study of Transformer interpretation and propose a method to achieve it by guiding the gradient direction, or more precisely, the attention direction. The method enables more comprehensive interpretation of feature regions, offers detail interpretation, and helps to better understand Transformer mechanism. Leveraging the difference in how Vision Transformer (ViT) and humans perceive images, we alter the class of an image in a way that is almost imperceptible to the human eye. This class rewriting phenomenon may potentially pose security risks in certain scenarios.

Yin Fang, Qiang Zhang, Haihong Yang et al.

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

Yin Fang, Kangwei Liu, Ningyu Zhang et al.

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry and biology. However, the field of single-cell biology, which forms the foundational building blocks of living organisms, still faces several challenges. High knowledge barriers and limited scalability in current methods restrict the full exploitation of LLMs in mastering single-cell data, impeding direct accessibility and rapid iteration. To this end, we introduce ChatCell, which signifies a paradigm shift by facilitating single-cell analysis with natural language. Leveraging vocabulary adaptation and unified sequence generation, ChatCell has acquired profound expertise in single-cell biology and the capability to accommodate a diverse range of analysis tasks. Extensive experiments further demonstrate ChatCell's robust performance and potential to deepen single-cell insights, paving the way for more accessible and intuitive exploration in this pivotal field. Our project homepage is available at https://zjunlp.github.io/project/ChatCell.

Yin Fang, Xinle Deng, Kangwei Liu et al.

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular biology", capturing intricate gene expression patterns at the single-cell level. However, interacting with this "language" through conventional tools is often inefficient and unintuitive, posing challenges for researchers. To address these limitations, we present InstructCell, a multi-modal AI copilot that leverages natural language as a medium for more direct and flexible single-cell analysis. We construct a comprehensive multi-modal instruction dataset that pairs text-based instructions with scRNA-seq profiles from diverse tissues and species. Building on this, we develop a multi-modal cell language architecture capable of simultaneously interpreting and processing both modalities. InstructCell empowers researchers to accomplish critical tasks-such as cell type annotation, conditional pseudo-cell generation, and drug sensitivity prediction-using straightforward natural language commands. Extensive evaluations demonstrate that InstructCell consistently meets or exceeds the performance of existing single-cell foundation models, while adapting to diverse experimental conditions. More importantly, InstructCell provides an accessible and intuitive tool for exploring complex single-cell data, lowering technical barriers and enabling deeper biological insights.

Feng Chen, Kanokphan Lertniphonphan, Qiancheng Yan et al.

This report introduces our team's (PCIE_EgoPose) solutions for the EgoExo4D Pose and Proficiency Estimation Challenges at CVPR2025. Focused on the intricate task of estimating 21 3D hand joints from RGB egocentric videos, which are complicated by subtle movements and frequent occlusions, we developed the Hand Pose Vision Transformer (HP-ViT+). This architecture synergizes a Vision Transformer and a CNN backbone, using weighted fusion to refine the hand pose predictions. For the EgoExo4D Body Pose Challenge, we adopted a multimodal spatio-temporal feature integration strategy to address the complexities of body pose estimation across dynamic contexts. Our methods achieved remarkable performance: 8.31 PA-MPJPE in the Hand Pose Challenge and 11.25 MPJPE in the Body Pose Challenge, securing championship titles in both competitions. We extended our pose estimation solutions to the Proficiency Estimation task, applying core technologies such as transformer-based architectures. This extension enabled us to achieve a top-1 accuracy of 0.53, a SOTA result, in the Demonstrator Proficiency Estimation competition.

Qiang Zhang, Keyang Ding, Tianwen Lyv et al.

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional linguistic boundaries, encompassing specialized linguistic systems developed within various scientific disciplines. This growing interest has led to the advent of scientific LLMs, a novel subclass specifically engineered for facilitating scientific discovery. As a burgeoning area in the community of AI for Science, scientific LLMs warrant comprehensive exploration. However, a systematic and up-to-date survey introducing them is currently lacking. In this paper, we endeavor to methodically delineate the concept of "scientific language", whilst providing a thorough review of the latest advancements in scientific LLMs. Given the expansive realm of scientific disciplines, our analysis adopts a focused lens, concentrating on the biological and chemical domains. This includes an in-depth examination of LLMs for textual knowledge, small molecules, macromolecular proteins, genomic sequences, and their combinations, analyzing them in terms of model architectures, capabilities, datasets, and evaluation. Finally, we critically examine the prevailing challenges and point out promising research directions along with the advances of LLMs. By offering a comprehensive overview of technical developments in this field, this survey aspires to be an invaluable resource for researchers navigating the intricate landscape of scientific LLMs.

Yin Fang, Zhuo Chen, Xiaohui Fan et al.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Yin Fang, Haihong Yang, Xiang Zhuang et al.

Leveraging domain knowledge including fingerprints and functional groups in molecular representation learning is crucial for chemical property prediction and drug discovery. When modeling the relation between graph structure and molecular properties implicitly, existing works can hardly capture structural or property changes and complex structure, with much smaller atom vocabulary and highly frequent atoms. In this paper, we propose the Contrastive Knowledge-aware GNN (CKGNN) for self-supervised molecular representation learning to fuse domain knowledge into molecular graph representation. We explicitly encode domain knowledge via knowledge-aware molecular encoder under the contrastive learning framework, ensuring that the generated molecular embeddings equipped with chemical domain knowledge to distinguish molecules with similar chemical formula but dissimilar functions. Extensive experiments on 8 public datasets demonstrate the effectiveness of our model with a 6\% absolute improvement on average against strong competitors. Ablation study and further investigation also verify the best of both worlds: incorporation of chemical domain knowledge into self-supervised learning.