Yatao Bian

Zongbo Han, Zhipeng Liang, Fan Yang et al.

Subpopulation shift widely exists in many real-world machine learning applications, referring to the training and test distributions containing the same subpopulation groups but varying in subpopulation frequencies. Importance reweighting is a normal way to handle the subpopulation shift issue by imposing constant or adaptive sampling weights on each sample in the training dataset. However, some recent studies have recognized that most of these approaches fail to improve the performance over empirical risk minimization especially when applied to over-parameterized neural networks. In this work, we propose a simple yet practical framework, called uncertainty-aware mixup (UMIX), to mitigate the overfitting issue in over-parameterized models by reweighting the ''mixed'' samples according to the sample uncertainty. The training-trajectories-based uncertainty estimation is equipped in the proposed UMIX for each sample to flexibly characterize the subpopulation distribution. We also provide insightful theoretical analysis to verify that UMIX achieves better generalization bounds over prior works. Further, we conduct extensive empirical studies across a wide range of tasks to validate the effectiveness of our method both qualitatively and quantitatively. Code is available at https://github.com/TencentAILabHealthcare/UMIX.

Huan Ma, Changqing Zhang, Yatao Bian et al. · tencent-ai

Large language models have demonstrated surprising ability to perform in-context learning, i.e., these models can be directly applied to solve numerous downstream tasks by conditioning on a prompt constructed by a few input-output examples. However, prior research has shown that in-context learning can suffer from high instability due to variations in training examples, example order, and prompt formats. Therefore, the construction of an appropriate prompt is essential for improving the performance of in-context learning. In this paper, we revisit this problem from the view of predictive bias. Specifically, we introduce a metric to evaluate the predictive bias of a fixed prompt against labels or a given attributes. Then we empirically show that prompts with higher bias always lead to unsatisfactory predictive quality. Based on this observation, we propose a novel search strategy based on the greedy search to identify the near-optimal prompt for improving the performance of in-context learning. We perform comprehensive experiments with state-of-the-art mainstream models such as GPT-3 on various downstream tasks. Our results indicate that our method can enhance the model's in-context learning performance in an effective and interpretable manner.

Lanqing Li, Liang Zeng, Ziqi Gao et al.

The last decade has witnessed a prosperous development of computational methods and dataset curation for AI-aided drug discovery (AIDD). However, real-world pharmaceutical datasets often exhibit highly imbalanced distribution, which is overlooked by the current literature but may severely compromise the fairness and generalization of machine learning applications. Motivated by this observation, we introduce ImDrug, a comprehensive benchmark with an open-source Python library which consists of 4 imbalance settings, 11 AI-ready datasets, 54 learning tasks and 16 baseline algorithms tailored for imbalanced learning. It provides an accessible and customizable testbed for problems and solutions spanning a broad spectrum of the drug discovery pipeline such as molecular modeling, drug-target interaction and retrosynthesis. We conduct extensive empirical studies with novel evaluation metrics, to demonstrate that the existing algorithms fall short of solving medicinal and pharmaceutical challenges in the data imbalance scenario. We believe that ImDrug opens up avenues for future research and development, on real-world challenges at the intersection of AIDD and deep imbalanced learning.

Qitian Wu, Wentao Zhao, Chenxiao Yang et al.

Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class of foundation encoders for graph-structured data, have shown promising performance on small graphs due to its global attention capable of capturing all-pair influence beyond neighboring nodes. Even so, existing approaches tend to inherit the spirit of Transformers in language and vision tasks, and embrace complicated models by stacking deep multi-head attentions. In this paper, we critically demonstrate that even using a one-layer attention can bring up surprisingly competitive performance across node property prediction benchmarks where node numbers range from thousand-level to billion-level. This encourages us to rethink the design philosophy for Transformers on large graphs, where the global attention is a computation overhead hindering the scalability. We frame the proposed scheme as Simplified Graph Transformers (SGFormer), which is empowered by a simple attention model that can efficiently propagate information among arbitrary nodes in one layer. SGFormer requires none of positional encodings, feature/graph pre-processing or augmented loss. Empirically, SGFormer successfully scales to the web-scale graph ogbn-papers100M and yields up to 141x inference acceleration over SOTA Transformers on medium-sized graphs. Beyond current results, we believe the proposed methodology alone enlightens a new technical path of independent interest for building Transformers on large graphs.

Yongqiang Chen, Kaiwen Zhou, Yatao Bian et al.

Recently, there has been a growing surge of interest in enabling machine learning systems to generalize well to Out-of-Distribution (OOD) data. Most efforts are devoted to advancing optimization objectives that regularize models to capture the underlying invariance; however, there often are compromises in the optimization process of these OOD objectives: i) Many OOD objectives have to be relaxed as penalty terms of Empirical Risk Minimization (ERM) for the ease of optimization, while the relaxed forms can weaken the robustness of the original objective; ii) The penalty terms also require careful tuning of the penalty weights due to the intrinsic conflicts between ERM and OOD objectives. Consequently, these compromises could easily lead to suboptimal performance of either the ERM or OOD objective. To address these issues, we introduce a multi-objective optimization (MOO) perspective to understand the OOD optimization process, and propose a new optimization scheme called PAreto Invariant Risk Minimization (PAIR). PAIR improves the robustness of OOD objectives by cooperatively optimizing with other OOD objectives, thereby bridging the gaps caused by the relaxations. Then PAIR approaches a Pareto optimal solution that trades off the ERM and OOD objectives properly. Extensive experiments on challenging benchmarks, WILDS, show that PAIR alleviates the compromises and yields top OOD performances.

Bingzhe Wu, Jintang Li, Junchi Yu et al.

Deep graph learning has achieved remarkable progresses in both business and scientific areas ranging from finance and e-commerce, to drug and advanced material discovery. Despite these progresses, how to ensure various deep graph learning algorithms behave in a socially responsible manner and meet regulatory compliance requirements becomes an emerging problem, especially in risk-sensitive domains. Trustworthy graph learning (TwGL) aims to solve the above problems from a technical viewpoint. In contrast to conventional graph learning research which mainly cares about model performance, TwGL considers various reliability and safety aspects of the graph learning framework including but not limited to robustness, explainability, and privacy. In this survey, we provide a comprehensive review of recent leading approaches in the TwGL field from three dimensions, namely, reliability, explainability, and privacy protection. We give a general categorization for existing work and review typical work for each category. To give further insights for TwGL research, we provide a unified view to inspect previous works and build the connection between them. We also point out some important open problems remaining to be solved in the future developments of TwGL.

Xiang Zhuang, Qiang Zhang, Keyan Ding et al.

Molecular representation learning lays the foundation for drug discovery. However, existing methods suffer from poor out-of-distribution (OOD) generalization, particularly when data for training and testing originate from different environments. To address this issue, we propose a new framework for learning molecular representations that exhibit invariance and robustness against distribution shifts. Specifically, we propose a strategy called ``first-encoding-then-separation'' to identify invariant molecule features in the latent space, which deviates from conventional practices. Prior to the separation step, we introduce a residual vector quantization module that mitigates the over-fitting to training data distributions while preserving the expressivity of encoders. Furthermore, we design a task-agnostic self-supervised learning objective to encourage precise invariance identification, which enables our method widely applicable to a variety of tasks, such as regression and multi-label classification. Extensive experiments on 18 real-world molecular datasets demonstrate that our model achieves stronger generalization against state-of-the-art baselines in the presence of various distribution shifts. Our code is available at https://github.com/HICAI-ZJU/iMoLD.

Jie Liao, Jintang Li, Liang Chen et al.

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in representation learning for graphs recently. However, the effectiveness of GNNs, which capitalize on the key operation of message propagation, highly depends on the quality of the topology structure. Most of the graphs in real-world scenarios follow a long-tailed distribution on their node degrees, that is, a vast majority of the nodes in the graph are tail nodes with only a few connected edges. GNNs produce inferior node representations for tail nodes since they lack structural information. In the pursuit of promoting the expressiveness of GNNs for tail nodes, we explore how the deficiency of structural information deteriorates the performance of tail nodes and propose a general Structural Augmentation based taIL nOde Representation learning framework, dubbed as SAILOR, which can jointly learn to augment the graph structure and extract more informative representations for tail nodes. Extensive experiments on public benchmark datasets demonstrate that SAILOR can significantly improve the tail node representations and outperform the state-of-the-art baselines.

Jiying Zhang, Xi Xiao, Long-Kai Huang et al.

Recently, the pretrain-finetuning paradigm has attracted tons of attention in graph learning community due to its power of alleviating the lack of labels problem in many real-world applications. Current studies use existing techniques, such as weight constraint, representation constraint, which are derived from images or text data, to transfer the invariant knowledge from the pre-train stage to fine-tuning stage. However, these methods failed to preserve invariances from graph structure and Graph Neural Network (GNN) style models. In this paper, we present a novel optimal transport-based fine-tuning framework called GTOT-Tuning, namely, Graph Topology induced Optimal Transport fine-Tuning, for GNN style backbones. GTOT-Tuning is required to utilize the property of graph data to enhance the preservation of representation produced by fine-tuned networks. Toward this goal, we formulate graph local knowledge transfer as an Optimal Transport (OT) problem with a structural prior and construct the GTOT regularizer to constrain the fine-tuned model behaviors. By using the adjacency relationship amongst nodes, the GTOT regularizer achieves node-level optimal transport procedures and reduces redundant transport procedures, resulting in efficient knowledge transfer from the pre-trained models. We evaluate GTOT-Tuning on eight downstream tasks with various GNN backbones and demonstrate that it achieves state-of-the-art fine-tuning performance for GNNs.

Bingzhe Wu, Zhipeng Liang, Yuxuan Han et al.

Recently, federated learning has emerged as a promising approach for training a global model using data from multiple organizations without leaking their raw data. Nevertheless, directly applying federated learning to real-world tasks faces two challenges: (1) heterogeneity in the data among different organizations; and (2) data noises inside individual organizations. In this paper, we propose a general framework to solve the above two challenges simultaneously. Specifically, we propose using distributionally robust optimization to mitigate the negative effects caused by data heterogeneity paradigm to sample clients based on a learnable distribution at each iteration. Additionally, we observe that this optimization paradigm is easily affected by data noises inside local clients, which has a significant performance degradation in terms of global model prediction accuracy. To solve this problem, we propose to incorporate mixup techniques into the local training process of federated learning. We further provide comprehensive theoretical analysis including robustness analysis, convergence analysis, and generalization ability. Furthermore, we conduct empirical studies across different drug discovery tasks, such as ADMET property prediction and drug-target affinity prediction.

Ziqiao Zhang, Bangyi Zhao, Ailin Xie et al.

Activity cliffs (ACs), which are generally defined as pairs of structurally similar molecules that are active against the same bio-target but significantly different in the binding potency, are of great importance to drug discovery. Up to date, the AC prediction problem, i.e., to predict whether a pair of molecules exhibit the AC relationship, has not yet been fully explored. In this paper, we first introduce ACNet, a large-scale dataset for AC prediction. ACNet curates over 400K Matched Molecular Pairs (MMPs) against 190 targets, including over 20K MMP-cliffs and 380K non-AC MMPs, and provides five subsets for model development and evaluation. Then, we propose a baseline framework to benchmark the predictive performance of molecular representations encoded by deep neural networks for AC prediction, and 16 models are evaluated in experiments. Our experimental results show that deep learning models can achieve good performance when the models are trained on tasks with adequate amount of data, while the imbalanced, low-data and out-of-distribution features of the ACNet dataset still make it challenging for deep neural networks to cope with. In addition, the traditional ECFP method shows a natural advantage on MMP-cliff prediction, and outperforms other deep learning models on most of the data subsets. To the best of our knowledge, our work constructs the first large-scale dataset for AC prediction, which may stimulate the study of AC prediction models and prompt further breakthroughs in AI-aided drug discovery. The codes and dataset can be accessed by https://drugai.github.io/ACNet/.

Lu Zhang, Yang Wang, Jiaogen Zhou et al.

Few-shot object detection (FSOD) is to detect objects with a few examples. However, existing FSOD methods do not consider hierarchical fine-grained category structures of objects that exist widely in real life. For example, animals are taxonomically classified into orders, families, genera and species etc. In this paper, we propose and solve a new problem called hierarchical few-shot object detection (Hi-FSOD), which aims to detect objects with hierarchical categories in the FSOD paradigm. To this end, on the one hand, we build the first large-scale and high-quality Hi-FSOD benchmark dataset HiFSOD-Bird, which contains 176,350 wild-bird images falling to 1,432 categories. All the categories are organized into a 4-level taxonomy, consisting of 32 orders, 132 families, 572 genera and 1,432 species. On the other hand, we propose the first Hi-FSOD method HiCLPL, where a hierarchical contrastive learning approach is developed to constrain the feature space so that the feature distribution of objects is consistent with the hierarchical taxonomy and the model's generalization power is strengthened. Meanwhile, a probabilistic loss is designed to enable the child nodes to correct the classification errors of their parent nodes in the taxonomy. Extensive experiments on the benchmark dataset HiFSOD-Bird show that our method HiCLPL outperforms the existing FSOD methods.

Zijing Ou, Tingyang Xu, Qinliang Su et al.

Learning neural set functions becomes increasingly more important in many applications like product recommendation and compound selection in AI-aided drug discovery. The majority of existing works study methodologies of set function learning under the function value oracle, which, however, requires expensive supervision signals. This renders it impractical for applications with only weak supervisions under the Optimal Subset (OS) oracle, the study of which is surprisingly overlooked. In this work, we present a principled yet practical maximum likelihood learning framework, termed as EquiVSet, that simultaneously meets the following desiderata of learning set functions under the OS oracle: i) permutation invariance of the set mass function being modeled; ii) permission of varying ground set; iii) minimum prior; and iv) scalability. The main components of our framework involve: an energy-based treatment of the set mass function, DeepSet-style architectures to handle permutation invariance, mean-field variational inference, and its amortized variants. Thanks to the elegant combination of these advanced architectures, empirical studies on three real-world applications (including Amazon product recommendation, set anomaly detection, and compound selection for virtual screening) demonstrate that EquiVSet outperforms the baselines by a large margin.

Liang Chen, Yang Deng, Yatao Bian et al.

Large language models (LLMs) outperform information retrieval techniques for downstream knowledge-intensive tasks when being prompted to generate world knowledge. However, community concerns abound regarding the factuality and potential implications of using this uncensored knowledge. In light of this, we introduce CONNER, a COmpreheNsive kNowledge Evaluation fRamework, designed to systematically and automatically evaluate generated knowledge from six important perspectives -- Factuality, Relevance, Coherence, Informativeness, Helpfulness and Validity. We conduct an extensive empirical analysis of the generated knowledge from three different types of LLMs on two widely studied knowledge-intensive tasks, i.e., open-domain question answering and knowledge-grounded dialogue. Surprisingly, our study reveals that the factuality of generated knowledge, even if lower, does not significantly hinder downstream tasks. Instead, the relevance and coherence of the outputs are more important than small factual mistakes. Further, we show how to use CONNER to improve knowledge-intensive tasks by designing two strategies: Prompt Engineering and Knowledge Selection. Our evaluation code and LLM-generated knowledge with human annotations will be released to facilitate future research.

Yongqiang Chen, Wei Huang, Kaiwen Zhou et al.

A common explanation for the failure of out-of-distribution (OOD) generalization is that the model trained with empirical risk minimization (ERM) learns spurious features instead of invariant features. However, several recent studies challenged this explanation and found that deep networks may have already learned sufficiently good features for OOD generalization. Despite the contradictions at first glance, we theoretically show that ERM essentially learns both spurious and invariant features, while ERM tends to learn spurious features faster if the spurious correlation is stronger. Moreover, when fed the ERM learned features to the OOD objectives, the invariant feature learning quality significantly affects the final OOD performance, as OOD objectives rarely learn new features. Therefore, ERM feature learning can be a bottleneck to OOD generalization. To alleviate the reliance, we propose Feature Augmented Training (FeAT), to enforce the model to learn richer features ready for OOD generalization. FeAT iteratively augments the model to learn new features while retaining the already learned features. In each round, the retention and augmentation operations are performed on different subsets of the training data that capture distinct features. Extensive experiments show that FeAT effectively learns richer features thus boosting the performance of various OOD objectives.

Zongbo Han, Zhipeng Liang, Fan Yang et al.

Subpopulation shift exists widely in many real-world applications, which refers to the training and test distributions that contain the same subpopulation groups but with different subpopulation proportions. Ignoring subpopulation shifts may lead to significant performance degradation and fairness concerns. Importance reweighting is a classical and effective way to handle the subpopulation shift. However, recent studies have recognized that most of these approaches fail to improve the performance especially when applied to over-parameterized neural networks which are capable of fitting any training samples. In this work, we propose a simple yet practical framework, called reweighted mixup (RMIX), to mitigate the overfitting issue in over-parameterized models by conducting importance weighting on the ''mixed'' samples. Benefiting from leveraging reweighting in mixup, RMIX allows the model to explore the vicinal space of minority samples more, thereby obtaining more robust model against subpopulation shift. When the subpopulation memberships are unknown, the training-trajectories-based uncertainty estimation is equipped in the proposed RMIX to flexibly characterize the subpopulation distribution. We also provide insightful theoretical analysis to verify that RMIX achieves better generalization bounds over prior works. Further, we conduct extensive empirical studies across a wide range of tasks to validate the effectiveness of the proposed method.

Ziqiao Zhang, Yatao Bian, Ailin Xie et al.

Self-supervised pre-training is gaining increasingly more popularity in AI-aided drug discovery, leading to more and more pre-trained models with the promise that they can extract better feature representations for molecules. Yet, the quality of learned representations have not been fully explored. In this work, inspired by the two phenomena of Activity Cliffs (ACs) and Scaffold Hopping (SH) in traditional Quantitative Structure-Activity Relationship (QSAR) analysis, we propose a method named Representation-Property Relationship Analysis (RePRA) to evaluate the quality of the representations extracted by the pre-trained model and visualize the relationship between the representations and properties. The concepts of ACs and SH are generalized from the structure-activity context to the representation-property context, and the underlying principles of RePRA are analyzed theoretically. Two scores are designed to measure the generalized ACs and SH detected by RePRA, and therefore the quality of representations can be evaluated. In experiments, representations of molecules from 10 target tasks generated by 7 pre-trained models are analyzed. The results indicate that the state-of-the-art pre-trained models can overcome some shortcomings of canonical Extended-Connectivity FingerPrints (ECFP), while the correlation between the basis of the representation space and specific molecular substructures are not explicit. Thus, some representations could be even worse than the canonical fingerprints. Our method enables researchers to evaluate the quality of molecular representations generated by their proposed self-supervised pre-trained models. And our findings can guide the community to develop better pre-training techniques to regularize the occurrence of ACs and SH.

Zhiyin Yu, Yuchen Mou, Juncheng Yan et al. · pku

Reinforcement learning (RL) has emerged as a powerful post-training paradigm for enhancing the reasoning capabilities of large language models (LLMs). However, reinforcement learning for LLMs faces substantial data scarcity challenges, including the limited availability of high-quality external supervision and the constrained volume of model-generated experience. These limitations make data-efficient reinforcement learning a critical research direction. In this survey, we present the first systematic review of reinforcement learning for LLMs under data scarcity. We propose a bottom-up hierarchical framework built around three complementary perspectives: the data-centric perspective, the training-centric perspective, and the framework-centric perspective. We develop a taxonomy of existing methods, summarize representative approaches in each category, and analyze their strengths and limitations. Our taxonomy aims to provide a clear conceptual foundation for understanding the design space of data-efficient RL for LLMs and to guide researchers working in this emerging area. We hope this survey offers a comprehensive roadmap for future research and inspires new directions toward more efficient and scalable reinforcement learning post-training for LLMs.

Yongqiang Chen, Yatao Bian, Kaiwen Zhou et al.

Invariant graph representation learning aims to learn the invariance among data from different environments for out-of-distribution generalization on graphs. As the graph environment partitions are usually expensive to obtain, augmenting the environment information has become the de facto approach. However, the usefulness of the augmented environment information has never been verified. In this work, we find that it is fundamentally impossible to learn invariant graph representations via environment augmentation without additional assumptions. Therefore, we develop a set of minimal assumptions, including variation sufficiency and variation consistency, for feasible invariant graph learning. We then propose a new framework Graph invAriant Learning Assistant (GALA). GALA incorporates an assistant model that needs to be sensitive to graph environment changes or distribution shifts. The correctness of the proxy predictions by the assistant model hence can differentiate the variations in spurious subgraphs. We show that extracting the maximally invariant subgraph to the proxy predictions provably identifies the underlying invariant subgraph for successful OOD generalization under the established minimal assumptions. Extensive experiments on datasets including DrugOOD with various graph distribution shifts confirm the effectiveness of GALA.

Liang Chen, Yatao Bian, Yang Deng et al.

Text watermarking has emerged as a pivotal technique for identifying machine-generated text. However, existing methods often rely on arbitrary vocabulary partitioning during decoding to embed watermarks, which compromises the availability of suitable tokens and significantly degrades the quality of responses. This study assesses the impact of watermarking on different capabilities of large language models (LLMs) from a cognitive science lens. Our finding highlights a significant disparity; knowledge recall and logical reasoning are more adversely affected than language generation. These results suggest a more profound effect of watermarking on LLMs than previously understood. To address these challenges, we introduce Watermarking with Mutual Exclusion (WatME), a novel approach leveraging linguistic prior knowledge of inherent lexical redundancy in LLM vocabularies to seamlessly integrate watermarks. Specifically, WatME dynamically optimizes token usage during the decoding process by applying a mutually exclusive rule to the identified lexical redundancies. This strategy effectively prevents the unavailability of appropriate tokens and preserves the expressive power of LLMs. We provide both theoretical analysis and empirical evidence showing that WatME effectively preserves the diverse capabilities of LLMs while ensuring watermark detectability.

Yiqiang Yi, Xu Wan, Yatao Bian et al.

Predicting the docking between proteins and ligands is a crucial and challenging task for drug discovery. However, traditional docking methods mainly rely on scoring functions, and deep learning-based docking approaches usually neglect the 3D spatial information of proteins and ligands, as well as the graph-level features of ligands, which limits their performance. To address these limitations, we propose an equivariant transformer neural network for protein-ligand docking pose prediction. Our approach involves the fusion of ligand graph-level features by feature processing, followed by the learning of ligand and protein representations using our proposed TAMformer module. Additionally, we employ an iterative optimization approach based on the predicted distance matrix to generate refined ligand poses. The experimental results on real datasets show that our model can achieve state-of-the-art performance.

Shuhan Guo, Yatao Bian, Ruibing Wang et al.

The remarkable success of Large Language Models (LLMs) across diverse tasks has driven the research community to extend their capabilities to molecular applications. However, most molecular LLMs employ adapter-based architectures that do not treat molecule and text modalities equally and lack a supervision signal for the molecule modality. To address these issues, we introduce UniMoT, a Unified Molecule-Text LLM adopting a tokenizer-based architecture that expands the vocabulary of LLM with molecule tokens. Specifically, we introduce a Vector Quantization-driven tokenizer that incorporates a Q-Former to bridge the modality gap between molecule and text. This tokenizer transforms molecules into sequences of molecule tokens with causal dependency, encapsulating high-level molecular and textual information. Equipped with this tokenizer, UniMoT can unify molecule and text modalities under a shared token representation and an autoregressive training paradigm, enabling it to interpret molecules as a foreign language and generate them as text. Following a four-stage training scheme, UniMoT emerges as a multi-modal generalist capable of performing both molecule-to-text and text-to-molecule tasks. Extensive experiments demonstrate that UniMoT achieves state-of-the-art performance across a wide range of molecule comprehension and generation tasks.

Xi Leng, Xiaoying Tang, Yatao Bian

Machine learning algorithms minimizing the average training loss usually suffer from poor generalization performance due to the greedy exploitation of correlations among the training data, which are not stable under distributional shifts. It inspires various works for domain generalization (DG), where a series of methods, such as Causal Matching and FISH, work by pairwise domain operations. They would need $O(n^2)$ pairwise domain operations with $n$ domains, where each one is often highly expensive. Moreover, while a common objective in the DG literature is to learn invariant representations against domain-induced spurious correlations, we highlight the importance of mitigating spurious correlations caused by objects. Based on the observation that diversity helps mitigate spurious correlations, we propose a Diversity boosted twO-level saMplIng framework (DOMI) utilizing Determinantal Point Processes (DPPs) to efficiently sample the most informative ones among large number of domains. We show that DOMI helps train robust models against spurious correlations from both domain-side and object-side, substantially enhancing the performance of the backbone DG algorithms on rotated MNIST, rotated Fashion MNIST, and iwildcam datasets.

Qingyang Zhang, Haitao Wu, Changqing Zhang et al.

Existing methods to enhance the reasoning capability of large language models predominantly rely on supervised fine-tuning (SFT) followed by reinforcement learning (RL) on reasoning-specific data. These approaches critically depend on external supervisions--such as labeled reasoning traces, verified golden answers, or pre-trained reward models. In this work, we propose Entropy Minimized Policy Optimization (\ours), which makes an early attempt at fully unsupervised LLM reasoning incentivization. By continuously minimizing the predictive entropy of LLMs on unlabeled questions in a latent semantic space, \ours achieves competitive performance compared to supervised counterparts on both mathematical and free-form natural reasoning tasks. Specifically, without any supervised signals, \ours boosts the accuracy of Qwen2.5-Math-7B Base from 30.7\% to 48.1\% on mathematical benchmarks and improves the accuracy of Qwen2.5-7B Base from 32.1\% to 50.1\% on MMLU-Pro. Primary experiments and analysis are also provided to interpret the effectiveness of \ours. Code is available at https://github.com/QingyangZhang/EMPO.

Yongqiang Chen, Binghui Xie, Kaiwen Zhou et al.

In-context learning (ICL) refers to the ability of a model to condition on a few in-context demonstrations (input-output examples of the underlying task) to generate the answer for a new query input, without updating parameters. Despite the impressive ICL ability of LLMs, it has also been found that ICL in LLMs is sensitive to input demonstrations and limited to short context lengths. To understand the limitations and principles for successful ICL, we conduct an investigation with ICL linear regression of transformers. We characterize several Out-of-Distribution (OOD) cases for ICL inspired by realistic LLM ICL failures and compare transformers with DeepSet, a simple yet powerful architecture for ICL. Surprisingly, DeepSet outperforms transformers across a variety of distribution shifts, implying that preserving permutation invariance symmetry to input demonstrations is crucial for OOD ICL. The phenomenon specifies a fundamental requirement by ICL, which we termed as ICL invariance. Nevertheless, the positional encodings in LLMs will break ICL invariance. To this end, we further evaluate transformers with identical positional encodings and find preserving ICL invariance in transformers achieves state-of-the-art performance across various ICL distribution shifts

Haoyu Wang, Bingzhe Wu, Yatao Bian et al.

Large Language Models (LLMs) are implicit troublemakers. While they provide valuable insights and assist in problem-solving, they can also potentially serve as a resource for malicious activities. Implementing safety alignment could mitigate the risk of LLMs generating harmful responses. We argue that: even when an LLM appears to successfully block harmful queries, there may still be hidden vulnerabilities that could act as ticking time bombs. To identify these underlying weaknesses, we propose to use a cost value model as both a detector and an attacker. Trained on external or self-generated harmful datasets, the cost value model could successfully influence the original safe LLM to output toxic content in decoding process. For instance, LLaMA-2-chat 7B outputs 39.18% concrete toxic content, along with only 22.16% refusals without any harmful suffixes. These potential weaknesses can then be exploited via prompt optimization such as soft prompts on images. We name this decoding strategy: Jailbreak Value Decoding (JVD), emphasizing that seemingly secure LLMs may not be as safe as we initially believe. They could be used to gather harmful data or launch covert attacks.

Yuchang Zhu, Huizhe Zhang, Bingzhe Wu et al.

Large language models (LLMs) are widely adopted to generate synthetic datasets for various natural language processing (NLP) tasks, such as text classification and summarization. However, accurately measuring the diversity of these synthetic datasets-an aspect crucial for robust model performance-remains a significant challenge. In this paper, we introduce DCScore, a novel method for measuring synthetic dataset diversity from a classification perspective. Specifically, DCScore formulates diversity evaluation as a sample classification task, leveraging mutual relationships among samples. We further provide theoretical verification of the diversity-related axioms satisfied by DCScore, highlighting its role as a principled diversity evaluation method. Experimental results on synthetic datasets reveal that DCScore enjoys a stronger correlation with multiple diversity pseudo-truths of evaluated datasets, underscoring its effectiveness. Moreover, both empirical and theoretical evidence demonstrate that DCScore substantially reduces computational costs compared to existing methods. Code is available at: https://github.com/bluewhalelab/dcscore.

Guikun Xu, Xiaohan Yi, Peilin Zhao et al.

Generating low-energy conformer ensembles and identifying ground-state conformations from molecular graphs remain computationally demanding with physics-based pipelines. Current learning-based approaches often suffer from a fragmented paradigm: generative models capture diversity but lack reliable energy calibration, whereas deterministic predictors target a single structure and fail to represent ensemble variability. Here we present EnFlow, a unified framework that couples flow matching (FM) with an explicitly learned energy model through an energy-guided sampling scheme defined along a non-Gaussian FM path. By incorporating energy-gradient guidance during sampling, our method steers trajectories toward lower-energy regions, substantially improving conformational fidelity, particularly in the few-step regime. The learned energy function further enables efficient energy-based ranking of generated ensembles for accurate ground-state identification. Extensive experiments on GEOM-QM9 and GEOM-Drugs demonstrate that EnFlow simultaneously improves generation metrics with 1--2 ODE-steps and reduces ground-state prediction errors compared with state-of-the-art methods.

Chang Wu, Zhiyuan Liu, Wen Shu et al.

Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL).However, extending the success of re-mask decoding from 2D to 3D MGM is non-trivial, primarily due to two conflicting challenges: avoiding 2D structure leakage to the decoder, while still providing sufficient 2D context for reconstructing re-masked atoms. To address these challenges, we propose 3D-GSRD: a 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding. The core innovation of 3D-GSRD lies in its Selective Re-mask Decoding(SRD), which re-masks only 3D-relevant information from encoder representations while preserving the 2D graph structures. This SRD is synergistically integrated with a 3D Relational-Transformer(3D-ReTrans) encoder alongside a structure-independent decoder. We analyze that SRD, combined with the structure-independent decoder, enhances the encoder's role in MRL. Extensive experiments show that 3D-GSRD achieves strong downstream performance, setting a new state-of-the-art on 7 out of 8 targets in the widely used MD17 molecular property prediction benchmark. The code is released at https://github.com/WuChang0124/3D-GSRD.

Yuchang Zhu, Jintang Li, Yatao Bian et al.

Recent studies have highlighted fairness issues in Graph Neural Networks (GNNs), where they produce discriminatory predictions against specific protected groups categorized by sensitive attributes such as race and age. While various efforts to enhance GNN fairness have made significant progress, these approaches are often tailored to specific sensitive attributes. Consequently, they necessitate retraining the model from scratch to accommodate changes in the sensitive attribute requirement, resulting in high computational costs. To gain deeper insights into this issue, we approach the graph fairness problem from a causal modeling perspective, where we identify the confounding effect induced by the sensitive attribute as the underlying reason. Motivated by this observation, we formulate the fairness problem in graphs from an invariant learning perspective, which aims to learn invariant representations across environments. Accordingly, we propose a graph fairness framework based on invariant learning, namely FairINV, which enables the training of fair GNNs to accommodate various sensitive attributes within a single training session. Specifically, FairINV incorporates sensitive attribute partition and trains fair GNNs by eliminating spurious correlations between the label and various sensitive attributes. Experimental results on several real-world datasets demonstrate that FairINV significantly outperforms state-of-the-art fairness approaches, underscoring its effectiveness. Our code is available via: https://github.com/ZzoomD/FairINV/.

Qingyang Zhang, Qiuxuan Feng, Joey Tianyi Zhou et al.

Out-of-distribution (OOD) detection is essential for model trustworthiness which aims to sensitively identify semantic OOD samples and robustly generalize for covariate-shifted OOD samples. However, we discover that the superior OOD detection performance of state-of-the-art methods is achieved by secretly sacrificing the OOD generalization ability. Specifically, the classification accuracy of these models could deteriorate dramatically when they encounter even minor noise. This phenomenon contradicts the goal of model trustworthiness and severely restricts their applicability in real-world scenarios. What is the hidden reason behind such a limitation? In this work, we theoretically demystify the ``\textit{sensitive-robust}'' dilemma that lies in many existing OOD detection methods. Consequently, a theory-inspired algorithm is induced to overcome such a dilemma. By decoupling the uncertainty learning objective from a Bayesian perspective, the conflict between OOD detection and OOD generalization is naturally harmonized and a dual-optimal performance could be expected. Empirical studies show that our method achieves superior performance on standard benchmarks. To our best knowledge, this work is the first principled OOD detection method that achieves state-of-the-art OOD detection performance without compromising OOD generalization ability. Our code is available at \href{https://github.com/QingyangZhang/DUL}{https://github.com/QingyangZhang/DUL}.

Yuanfeng Ji, Lu Zhang, Jiaxiang Wu et al.

AI-aided drug discovery (AIDD) is gaining increasing popularity due to its promise of making the search for new pharmaceuticals quicker, cheaper and more efficient. In spite of its extensive use in many fields, such as ADMET prediction, virtual screening, protein folding and generative chemistry, little has been explored in terms of the out-of-distribution (OOD) learning problem with \emph{noise}, which is inevitable in real world AIDD applications. In this work, we present DrugOOD, a systematic OOD dataset curator and benchmark for AI-aided drug discovery, which comes with an open-source Python package that fully automates the data curation and OOD benchmarking processes. We focus on one of the most crucial problems in AIDD: drug target binding affinity prediction, which involves both macromolecule (protein target) and small-molecule (drug compound). In contrast to only providing fixed datasets, DrugOOD offers automated dataset curator with user-friendly customization scripts, rich domain annotations aligned with biochemistry knowledge, realistic noise annotations and rigorous benchmarking of state-of-the-art OOD algorithms. Since the molecular data is often modeled as irregular graphs using graph neural network (GNN) backbones, DrugOOD also serves as a valuable testbed for \emph{graph OOD learning} problems. Extensive empirical studies have shown a significant performance gap between in-distribution and out-of-distribution experiments, which highlights the need to develop better schemes that can allow for OOD generalization under noise for AIDD.

Bingliang Li, Zhenhong Sun, Jiaming Bian et al.

Storyboarding is a core skill in visual storytelling for film, animation, and games. However, automating this process requires a system to achieve two properties that current approaches rarely satisfy simultaneously: inter-shot consistency and explicit editability. While 2D diffusion-based generators produce vivid imagery, they often suffer from identity drift along with limited geometric control; conversely, traditional 3D animation workflows are consistent and editable but require expert-heavy, labor-intensive authoring. We present StoryBlender, a grounded 3D storyboard generation framework governed by a Story-centric Reflection Scheme. At its core, we propose the StoryBlender system, which is built on a three-stage pipeline: (1) Semantic-Spatial Grounding, to construct a continuity memory graph to decouple global assets from shot-specific variables for long-horizon consistency; (2) Canonical Asset Materialization, to instantiate entities in a unified coordinate space to maintain visual identity; and (3) Spatial-Temporal Dynamics, to achieve layout design and cinematic evolution through visual metrics. By orchestrating multiple agents in a hierarchical manner within a verification loop, StoryBlender iteratively self-corrects spatial hallucinations via engine-verified feedback. The resulting native 3D scenes support direct, precise editing of cameras and visual assets while preserving unwavering multi-shot continuity. Experiments demonstrate that StoryBlender significantly improves consistency and editability over both diffusion-based and 3D-grounded baselines. Code, data, and demonstration video will be available on https://engineeringai-lab.github.io/StoryBlender/

Jiatong Li, Yuxuan Ren, Weida Wang et al.

Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents with predefined tools, enabling chemists to express arbitrarily complex, customized workflows. Unlike general coding tasks, molecular coding imposes a distinctive challenge that LLMs should jointly equip programming, molecular understanding, and domain-specific reasoning capabilities. However, existing benchmarks remain disconnected. General code generation benchmarks such as HumanEval and SWE-bench require no chemistry knowledge, while chemistry-focused benchmarks such as S^2-Bench and ChemCoTBench evaluate knowledge recall or property prediction rather than executable code generation. To bridge this gap, we introduce MolViBench, the first benchmark tailored for Molecular Vibe Coding. MolViBench comprises 358 curated tasks across five cognitive levels, ranging from single-API recall to end-to-end virtual screening pipeline design, spanning 12 real-world drug discovery workflows. To rigorously assess generated code, we also propose a multi-layered evaluation framework that combines type-aware output comparison and AST-based API-semantic fallback analysis, which jointly measures executability and chemical correctness. We systematically evaluate 9 frontier coding LLMs and compare three real-world Molecular Vibe Coding paradigms, providing a practical and fine-grained testbed for diagnosing LLMs' coding capabilities in AI-accelerated molecular discovery.

Haoyu Wang, Guozheng Ma, Ziqiao Meng et al.

Self-alignment is an effective way to reduce the cost of human annotation while ensuring promising model capability. However, most current methods complete the data collection and training steps in a single round, which may overlook the continuously improving ability of self-aligned models. This gives rise to a key query: What if we do multi-time bootstrapping self-alignment? Does this strategy enhance model performance or lead to rapid degradation? In this paper, our pioneering exploration delves into the impact of bootstrapping self-alignment on large language models. Our findings reveal that bootstrapping self-alignment markedly surpasses the single-round approach, by guaranteeing data diversity from in-context learning. To further exploit the capabilities of bootstrapping, we investigate and adjust the training order of data, which yields improved performance of the model. Drawing on these findings, we propose Step-On-Feet Tuning (SOFT) which leverages model's continuously enhanced few-shot ability to boost zero or one-shot performance. Based on easy-to-hard training recipe, we propose SOFT+ which further boost self-alignment's performance. Our experiments demonstrate the efficiency of SOFT (SOFT+) across various classification and generation tasks, highlighting the potential of bootstrapping self-alignment on continually enhancing model alignment performance.

Wangbin Sun, Jintang Li, Liang Chen et al.

Graph contrastive learning (GCL) has emerged as a representative paradigm in graph self-supervised learning, where negative samples are commonly regarded as the key to preventing model collapse and producing distinguishable representations. Recent studies have shown that GCL without negative samples can achieve state-of-the-art performance as well as scalability improvement, with bootstrapped graph latent (BGRL) as a prominent step forward. However, BGRL relies on a complex architecture to maintain the ability to scatter representations, and the underlying mechanisms enabling the success remain largely unexplored. In this paper, we introduce an instance-level decorrelation perspective to tackle the aforementioned issue and leverage it as a springboard to reveal the potential unnecessary model complexity within BGRL. Based on our findings, we present SGCL, a simple yet effective GCL framework that utilizes the outputs from two consecutive iterations as positive pairs, eliminating the negative samples. SGCL only requires a single graph augmentation and a single graph encoder without additional parameters. Extensive experiments conducted on various graph benchmarks demonstrate that SGCL can achieve competitive performance with fewer parameters, lower time and space costs, and significant convergence speedup.

Zhikang Chen, Sen Cui, Deheng Ye et al.

Large Language Models (LLMs) have demonstrated strong reasoning capabilities through \emph{Chain-of-Thought} (CoT) prompting, which enables step-by-step intermediate reasoning. However, explicit CoT methods rely on discrete token-level reasoning processes that are prone to error propagation and limited by vocabulary expressiveness, often resulting in rigid and inconsistent reasoning trajectories. Recent research has explored implicit or continuous reasoning in latent spaces, allowing models to perform internal reasoning before generating explicit output. Although such approaches alleviate some limitations of discrete CoT, they generally lack explicit mechanisms to enforce consistency among reasoning steps, leading to divergent reasoning paths and unstable outcomes. To address this issue, we propose EBM-CoT, an Energy-Based Chain-of-Thought Calibration framework that refines latent thought representations through an energy-based model (EBM). Our method dynamically adjusts latent reasoning trajectories toward lower-energy, high-consistency regions in the embedding space, improving both reasoning accuracy and consistency without modifying the base language model. Extensive experiments across mathematical, commonsense, and symbolic reasoning benchmarks demonstrate that the proposed framework significantly enhances the consistency and efficiency of multi-step reasoning in LLMs.

Qingyang Zhang, Yatao Bian, Xinke Kong et al.

Machine learning models must continuously self-adjust themselves for novel data distribution in the open world. As the predominant principle, entropy minimization (EM) has been proven to be a simple yet effective cornerstone in existing test-time adaption (TTA) methods. While unfortunately its fatal limitation (i.e., overconfidence) tends to result in model collapse. For this issue, we propose to Conservatively Minimize the Entropy (COME), which is a simple drop-in replacement of traditional EM to elegantly address the limitation. In essence, COME explicitly models the uncertainty by characterizing a Dirichlet prior distribution over model predictions during TTA. By doing so, COME naturally regularizes the model to favor conservative confidence on unreliable samples. Theoretically, we provide a preliminary analysis to reveal the ability of COME in enhancing the optimization stability by introducing a data-adaptive lower bound on the entropy. Empirically, our method achieves state-of-the-art performance on commonly used benchmarks, showing significant improvements in terms of classification accuracy and uncertainty estimation under various settings including standard, life-long and open-world TTA, i.e., up to $34.5\%$ improvement on accuracy and $15.1\%$ on false positive rate.

Youzhi Qu, Chen Wei, Penghui Du et al.

During the evolution of large models, performance evaluation is necessarily performed to assess their capabilities and ensure safety before practical application. However, current model evaluations mainly rely on specific tasks and datasets, lacking a united framework for assessing the multidimensional intelligence of large models. In this perspective, we advocate for a comprehensive framework of cognitive science-inspired artificial general intelligence (AGI) tests, aimed at fulfilling the testing needs of large models with enhanced capabilities. The cognitive science-inspired AGI tests encompass the full spectrum of intelligence facets, including crystallized intelligence, fluid intelligence, social intelligence, and embodied intelligence. To assess the multidimensional intelligence of large models, the AGI tests consist of a battery of well-designed cognitive tests adopted from human intelligence tests, and then naturally encapsulates into an immersive virtual community. We propose increasing the complexity of AGI testing tasks commensurate with advancements in large models and emphasizing the necessity for the interpretation of test results to avoid false negatives and false positives. We believe that cognitive science-inspired AGI tests will effectively guide the targeted improvement of large models in specific dimensions of intelligence and accelerate the integration of large models into human society.

Haiquan Qiu, Yatao Bian, Quanming Yao

Message passing mechanism contributes to the success of GNNs in various applications, but also brings the oversquashing problem. Recent works combat oversquashing by improving the graph spectrums with rewiring techniques, disrupting the structural bias in graphs, and having limited improvement on oversquashing in terms of oversquashing measure. Motivated by unitary RNN, we propose Graph Unitary Message Passing (GUMP) to alleviate oversquashing in GNNs by applying unitary adjacency matrix for message passing. To design GUMP, a transformation is first proposed to make general graphs have unitary adjacency matrix and keep its structural bias. Then, unitary adjacency matrix is obtained with a unitary projection algorithm, which is implemented by utilizing the intrinsic structure of unitary adjacency matrix and allows GUMP to be permutation-equivariant. Experimental results show the effectiveness of GUMP in improving the performance on various graph learning tasks.

Yifan Niu, Ziqi Gao, Tingyang Xu et al.

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

Binghui Xie, Yatao Bian, Kaiwen zhou et al.

Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function values and subsets within their respective supersets. However, these approaches tend to overlook the valuable information contained within the superset when utilizing neural networks to model set functions. In this work, we address this oversight by adopting a probabilistic perspective. Our theoretical findings demonstrate that when the target value is conditioned on both the input set and subset, it is essential to incorporate an \textit{invariant sufficient statistic} of the superset into the subset of interest for effective learning. This ensures that the output value remains invariant to permutations of the subset and its corresponding superset, enabling identification of the specific superset from which the subset originated. Motivated by these insights, we propose a simple yet effective information aggregation module designed to merge the representations of subsets and supersets from a permutation invariance perspective. Comprehensive empirical evaluations across diverse tasks and datasets validate the enhanced efficacy of our approach over conventional methods, underscoring the practicality and potency of our proposed strategies in real-world contexts.

Xiaohan Yi, Guikun Xu, Xi Xiao et al.

We present CrystalDiT, a diffusion transformer for crystal structure generation that achieves state-of-the-art performance by challenging the trend of architectural complexity. Instead of intricate, multi-stream designs, CrystalDiT employs a unified transformer that imposes a powerful inductive bias: treating lattice and atomic properties as a single, interdependent system. Combined with a periodic table-based atomic representation and a balanced training strategy, our approach achieves 9.62% SUN (Stable, Unique, Novel) rate on MP-20, substantially outperforming recent methods including FlowMM (4.38%) and MatterGen (3.42%). Notably, CrystalDiT generates 63.28% unique and novel structures while maintaining comparable stability rates, demonstrating that architectural simplicity can be more effective than complexity for materials discovery. Our results suggest that in data-limited scientific domains, carefully designed simple architectures outperform sophisticated alternatives that are prone to overfitting.

Yongqiang Chen, Quanming Yao, Juzheng Zhang et al.

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

Yongqiang Chen, Yatao Bian, Bo Han et al.

Interpretable graph neural networks (XGNNs ) are widely adopted in various scientific applications involving graph-structured data. Existing XGNNs predominantly adopt the attention-based mechanism to learn edge or node importance for extracting and making predictions with the interpretable subgraph. However, the representational properties and limitations of these methods remain inadequately explored. In this work, we present a theoretical framework that formulates interpretable subgraph learning with the multilinear extension of the subgraph distribution, coined as subgraph multilinear extension (SubMT). Extracting the desired interpretable subgraph requires an accurate approximation of SubMT, yet we find that the existing XGNNs can have a huge gap in fitting SubMT. Consequently, the SubMT approximation failure will lead to the degenerated interpretability of the extracted subgraphs. To mitigate the issue, we design a new XGNN architecture called Graph Multilinear neT (GMT), which is provably more powerful in approximating SubMT. We empirically validate our theoretical findings on a number of graph classification benchmarks. The results demonstrate that GMT outperforms the state-of-the-art up to 10% in terms of both interpretability and generalizability across 12 regular and geometric graph benchmarks.

Yuanfeng Ji, Yatao Bian, Guoji Fu et al.

The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While neural docking techniques have exhibited promising outcomes in binary protein docking, the application of advanced neural architectures to multimeric protein docking remains uncertain. This study introduces SyNDock, an automated framework that swiftly assembles precise multimeric complexes within seconds, showcasing performance that can potentially surpass or be on par with recent advanced approaches. SyNDock possesses several appealing advantages not present in previous approaches. Firstly, SyNDock formulates multimeric protein docking as a problem of learning global transformations to holistically depict the placement of chain units of a complex, enabling a learning-centric solution. Secondly, SyNDock proposes a trainable two-step SE(3) algorithm, involving initial pairwise transformation and confidence estimation, followed by global transformation synchronization. This enables effective learning for assembling the complex in a globally consistent manner. Lastly, extensive experiments conducted on our proposed benchmark dataset demonstrate that SyNDock outperforms existing docking software in crucial performance metrics, including accuracy and runtime. For instance, it achieves a 4.5% improvement in performance and a remarkable millionfold acceleration in speed.

Jiying Zhang, Fuyang Li, Xi Xiao et al.

As a powerful tool for modeling complex relationships, hypergraphs are gaining popularity from the graph learning community. However, commonly used frameworks in deep hypergraph learning focus on hypergraphs with edge-independent vertex weights (EIVWs), without considering hypergraphs with edge-dependent vertex weights (EDVWs) that have more modeling power. To compensate for this, we present General Hypergraph Spectral Convolution (GHSC), a general learning framework that not only handles EDVW and EIVW hypergraphs, but more importantly, enables theoretically explicitly utilizing the existing powerful Graph Convolutional Neural Networks (GCNNs) such that largely ease the design of Hypergraph Neural Networks. In this framework, the graph Laplacian of the given undirected GCNNs is replaced with a unified hypergraph Laplacian that incorporates vertex weight information from a random walk perspective by equating our defined generalized hypergraphs with simple undirected graphs. Extensive experiments from various domains including social network analysis, visual objective classification, and protein learning demonstrate the state-of-the-art performance of the proposed framework.

Erxue Min, Runfa Chen, Yatao Bian et al.

Recently, Transformer model, which has achieved great success in many artificial intelligence fields, has demonstrated its great potential in modeling graph-structured data. Till now, a great variety of Transformers has been proposed to adapt to the graph-structured data. However, a comprehensive literature review and systematical evaluation of these Transformer variants for graphs are still unavailable. It's imperative to sort out the existing Transformer models for graphs and systematically investigate their effectiveness on various graph tasks. In this survey, we provide a comprehensive review of various Graph Transformer models from the architectural design perspective. We first disassemble the existing models and conclude three typical ways to incorporate the graph information into the vanilla Transformer: 1) GNNs as Auxiliary Modules, 2) Improved Positional Embedding from Graphs, and 3) Improved Attention Matrix from Graphs. Furthermore, we implement the representative components in three groups and conduct a comprehensive comparison on various kinds of famous graph data benchmarks to investigate the real performance gain of each component. Our experiments confirm the benefits of current graph-specific modules on Transformer and reveal their advantages on different kinds of graph tasks.

Jintang Li, Bingzhe Wu, Chengbin Hou et al.

Deep graph learning (DGL) has achieved remarkable progress in both business and scientific areas ranging from finance and e-commerce to drug and advanced material discovery. Despite the progress, applying DGL to real-world applications faces a series of reliability threats including inherent noise, distribution shift, and adversarial attacks. This survey aims to provide a comprehensive review of recent advances for improving the reliability of DGL algorithms against the above threats. In contrast to prior related surveys which mainly focus on adversarial attacks and defense, our survey covers more reliability-related aspects of DGL, i.e., inherent noise and distribution shift. Additionally, we discuss the relationships among above aspects and highlight some important issues to be explored in future research.

Yongqiang Chen, Yonggang Zhang, Yatao Bian et al.

Despite recent success in using the invariance principle for out-of-distribution (OOD) generalization on Euclidean data (e.g., images), studies on graph data are still limited. Different from images, the complex nature of graphs poses unique challenges to adopting the invariance principle. In particular, distribution shifts on graphs can appear in a variety of forms such as attributes and structures, making it difficult to identify the invariance. Moreover, domain or environment partitions, which are often required by OOD methods on Euclidean data, could be highly expensive to obtain for graphs. To bridge this gap, we propose a new framework, called Causality Inspired Invariant Graph LeArning (CIGA), to capture the invariance of graphs for guaranteed OOD generalization under various distribution shifts. Specifically, we characterize potential distribution shifts on graphs with causal models, concluding that OOD generalization on graphs is achievable when models focus only on subgraphs containing the most information about the causes of labels. Accordingly, we propose an information-theoretic objective to extract the desired subgraphs that maximally preserve the invariant intra-class information. Learning with these subgraphs is immune to distribution shifts. Extensive experiments on 16 synthetic or real-world datasets, including a challenging setting -- DrugOOD, from AI-aided drug discovery, validate the superior OOD performance of CIGA.