Chuan Shi

Nian Liu, Xiao Wang, Deyu Bo et al.

Graph Contrastive Learning (GCL), learning the node representations by augmenting graphs, has attracted considerable attentions. Despite the proliferation of various graph augmentation strategies, some fundamental questions still remain unclear: what information is essentially encoded into the learned representations by GCL? Are there some general graph augmentation rules behind different augmentations? If so, what are they and what insights can they bring? In this paper, we answer these questions by establishing the connection between GCL and graph spectrum. By an experimental investigation in spectral domain, we firstly find the General grAph augMEntation (GAME) rule for GCL, i.e., the difference of the high-frequency parts between two augmented graphs should be larger than that of low-frequency parts. This rule reveals the fundamental principle to revisit the current graph augmentations and design new effective graph augmentations. Then we theoretically prove that GCL is able to learn the invariance information by contrastive invariance theorem, together with our GAME rule, for the first time, we uncover that the learned representations by GCL essentially encode the low-frequency information, which explains why GCL works. Guided by this rule, we propose a spectral graph contrastive learning module (SpCo), which is a general and GCL-friendly plug-in. We combine it with different existing GCL models, and extensive experiments well demonstrate that it can further improve the performances of a wide variety of different GCL methods.

Yining Wang, Xumeng Gong, Shaochuan Li et al.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

Shan Shen, Shenglu Hua, Jiajun Zou et al.

Graph representation learning on Analog-Mixed Signal (AMS) circuits is crucial for various downstream tasks, e.g., parasitic estimation. However, the scarcity of design data, the unbalanced distribution of labels, and the inherent diversity of circuit implementations pose significant challenges to learning robust and transferable circuit representations. To address these limitations, we propose CircuitGCL, a novel graph contrastive learning framework that integrates representation scattering and label rebalancing to enhance transferability across heterogeneous circuit graphs. CircuitGCL employs a self-supervised strategy to learn topology-invariant node embeddings through hyperspherical representation scattering, eliminating dependency on large-scale data. Simultaneously, balanced mean squared error (BMSE) and balanced softmax cross-entropy (BSCE) losses are introduced to mitigate label distribution disparities between circuits, enabling robust and transferable parasitic estimation. Evaluated on parasitic capacitance estimation (edge-level task) and ground capacitance classification (node-level task) across TSMC 28nm AMS designs, CircuitGCL outperforms all state-of-the-art (SOTA) methods, with the $R^2$ improvement of $33.64\% \sim 44.20\%$ for edge regression and F1-score gain of $0.9\times \sim 2.1\times$ for node classification. Our code is available at https://github.com/ShenShan123/CircuitGCL.

Ting Bai, Yue Yu, Le Huang et al.

The sparse Mixture-of-Experts (MoE) architecture of large language models (LLMs) confronts an inherent issue of load imbalance arising from the simplistic linear router strategy, which ultimately causes the instability and inefficient learning of LLMs. To address this challenge, we introduce a novel MoE graph-based framework $\textbf{GMoE}$, aimed at enhancing the collaboration among multiple experts. In GMoE, a graph router function is designed to capture the collaboration signals among experts. This enables all experts to dynamically allocate information derived from input data by sharing information with their neighboring experts. Moreover, we put forward two coordination strategies in GMoE: the $\textit{Poisson distribution-based distinction strategy}$ and the $\textit{Normal distribution-based balance strategy}$, to further release the capacity of each expert and increase the model stability in the fine-tuning of LLMs. Specifically, we leverage a parameter-efficient fine-tuning technique, i.e., Low-Rank Adaptation (LoRA), to implement the graph MoE architecture. Extensive experiments on four real-world benchmark datasets demonstrate the effectiveness of GMoE, showing the benefits of facilitating collaborations of multiple experts in LLM fine-tuning. The code of experimental implementation is available at https://github.com/BAI-LAB/GMoE

Le Huang, Hengzhi Lan, Zijun Sun et al.

As LLMs exhibit a high degree of human-like capability, increasing attention has been paid to role-playing research areas in which responses generated by LLMs are expected to mimic human replies. This has promoted the exploration of role-playing agents in various applications, such as chatbots that can engage in natural conversations with users and virtual assistants that can provide personalized support and guidance. The crucial factor in the role-playing task is the effective utilization of character memory, which stores characters' profiles, experiences, and historical dialogues. Retrieval Augmented Generation (RAG) technology is used to access the related memory to enhance the response generation of role-playing agents. Most existing studies retrieve related information based on the semantic similarity of memory to maintain characters' personalized traits, and few attempts have been made to incorporate the emotional factor in the retrieval argument generation (RAG) of LLMs. Inspired by the Mood-Dependent Memory theory, which indicates that people recall an event better if they somehow reinstate during recall the original emotion they experienced during learning, we propose a novel emotion-aware memory retrieval framework, termed Emotional RAG, which recalls the related memory with consideration of emotional state in role-playing agents. Specifically, we design two kinds of retrieval strategies, i.e., combination strategy and sequential strategy, to incorporate both memory semantic and emotional states during the retrieval process. Extensive experiments on three representative role-playing datasets demonstrate that our Emotional RAG framework outperforms the method without considering the emotional factor in maintaining the personalities of role-playing agents. This provides evidence to further reinforce the Mood-Dependent Memory theory in psychology.

Chuan Shi, Jian Liu, Fuzhen Zhuang et al.

Recently, there is a surge of social recommendation, which leverages social relations among users to improve recommendation performance. However, in many applications, social relations are absent or very sparse. Meanwhile, the attribute information of users or items may be rich. It is a big challenge to exploit these attribute information for the improvement of recommendation performance. In this paper, we organize objects and relations in recommendation system as a heterogeneous information network, and introduce meta path based similarity measure to evaluate the similarity of users or items. Furthermore, a matrix factorization based dual regularization framework SimMF is proposed to flexibly integrate different types of information through adopting the similarity of users and items as regularization on latent factors of users and items. Extensive experiments not only validate the effectiveness of SimMF but also reveal some interesting findings. We find that attribute information of users and items can significantly improve recommendation accuracy, and their contribution seems more important than that of social relations. The experiments also reveal that different regularization models have obviously different impact on users and items.

Yitong Li, Chuan Shi, Philip S. Yu et al.

Recently, there is a surge of interests on heterogeneous information network analysis. As a newly emerging network model, heterogeneous information networks have many unique features (e.g., complex structure and rich semantics) and a number of interesting data mining tasks have been exploited in this kind of networks, such as similarity measure, clustering, and classification. Although evaluating the importance of objects has been well studied in homogeneous networks, it is not yet exploited in heterogeneous networks. In this paper, we study the ranking problem in heterogeneous networks and propose the HRank framework to evaluate the importance of multiple types of objects and meta paths. Since the importance of objects depends upon the meta paths in heterogeneous networks, HRank develops a path based random walk process. Moreover, a constrained meta path is proposed to subtly capture the rich semantics in heterogeneous networks. Furthermore, HRank can simultaneously determine the importance of objects and meta paths through applying the tensor analysis. Extensive experiments on three real datasets show that HRank can effectively evaluate the importance of objects and paths together. Moreover, the constrained meta path shows its potential on mining subtle semantics by obtaining more accurate ranking results.