Knowledge-enhanced Relation Graph and Task Sampling for Few-shot Molecular Property Prediction

Recently, few-shot molecular property prediction (FSMPP) has garnered increasing attention. Despite impressive breakthroughs achieved by existing methods, they often overlook the inherent many-to-many relationships between molecules and properties, which limits their performance. For instance, similar substructures of molecules can inspire the exploration of new compounds. Additionally, the relationships between properties can be quantified, with high-related properties providing more information in exploring the target property than those low-related. To this end, this paper proposes a novel meta-learning FSMPP framework (KRGTS), which comprises the Knowledge-enhanced Relation Graph module and the Task Sampling module. The knowledge-enhanced relation graph module constructs the molecule-property multi-relation graph (MPMRG) to capture the many-to-many relationships between molecules and properties. The task sampling module includes a meta-training task sampler and an auxiliary task sampler, responsible for scheduling the meta-training process and sampling high-related auxiliary tasks, respectively, thereby achieving efficient meta-knowledge learning and reducing noise introduction. Empirically, extensive experiments on five datasets demonstrate the superiority of KRGTS over a variety of state-of-the-art methods. The code is available in https://github.com/Vencent-Won/KRGTS-public.

A Federated Parameter Aggregation Method for Node Classification Tasks with Different Graph Network Structures

Over the past few years, federated learning has become widely used in various classical machine learning fields because of its collaborative ability to train data from multiple sources without compromising privacy. However, in the area of graph neural networks, the nodes and network structures of graphs held by clients are different in many practical applications, and the aggregation method that directly shares model gradients cannot be directly applied to this scenario. Therefore, this work proposes a federated aggregation method FLGNN applied to various graph federation scenarios and investigates the aggregation effect of parameter sharing at each layer of the graph neural network model. The effectiveness of the federated aggregation method FLGNN is verified by experiments on real datasets. Additionally, for the privacy security of FLGNN, this paper designs membership inference attack experiments and differential privacy defense experiments. The results show that FLGNN performs good robustness, and the success rate of privacy theft is further reduced by adding differential privacy defense methods.

Exploring the Impact of Dataset Bias on Dataset Distillation

Dataset Distillation (DD) is a promising technique to synthesize a smaller dataset that preserves essential information from the original dataset. This synthetic dataset can serve as a substitute for the original large-scale one, and help alleviate the training workload. However, current DD methods typically operate under the assumption that the dataset is unbiased, overlooking potential bias issues within the dataset itself. To fill in this blank, we systematically investigate the influence of dataset bias on DD. To the best of our knowledge, this is the first exploration in the DD domain. Given that there are no suitable biased datasets for DD, we first construct two biased datasets, CMNIST-DD and CCIFAR10-DD, to establish a foundation for subsequent analysis. Then we utilize existing DD methods to generate synthetic datasets on CMNIST-DD and CCIFAR10-DD, and evaluate their performance following the standard process. Experiments demonstrate that biases present in the original dataset significantly impact the performance of the synthetic dataset in most cases, which highlights the necessity of identifying and mitigating biases in the original datasets during DD. Finally, we reformulate DD within the context of a biased dataset. Our code along with biased datasets are available at https://github.com/yaolu-zjut/Biased-DD.

Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry

Molecular property prediction refers to the task of labeling molecules with some biochemical properties, playing a pivotal role in the drug discovery and design process. Recently, with the advancement of machine learning, deep learning-based molecular property prediction has emerged as a solution to the resource-intensive nature of traditional methods, garnering significant attention. Among them, molecular representation learning is the key factor for molecular property prediction performance. And there are lots of sequence-based, graph-based, and geometry-based methods that have been proposed. However, the majority of existing studies focus solely on one modality for learning molecular representations, failing to comprehensively capture molecular characteristics and information. In this paper, a novel multi-modal representation learning model, which integrates the sequence, graph, and geometry characteristics, is proposed for molecular property prediction, called SGGRL. Specifically, we design a fusion layer to fusion the representation of different modalities. Furthermore, to ensure consistency across modalities, SGGRL is trained to maximize the similarity of representations for the same molecule while minimizing similarity for different molecules. To verify the effectiveness of SGGRL, seven molecular datasets, and several baselines are used for evaluation and comparison. The experimental results demonstrate that SGGRL consistently outperforms the baselines in most cases. This further underscores the capability of SGGRL to comprehensively capture molecular information. Overall, the proposed SGGRL model showcases its potential to revolutionize molecular property prediction by leveraging multi-modal representation learning to extract diverse and comprehensive molecular insights. Our code is released at https://github.com/Vencent-Won/SGGRL.

Augmenting Radio Signals with Wavelet Transform for Deep Learning-Based Modulation Recognition

The use of deep learning for radio modulation recognition has become prevalent in recent years. This approach automatically extracts high-dimensional features from large datasets, facilitating the accurate classification of modulation schemes. However, in real-world scenarios, it may not be feasible to gather sufficient training data in advance. Data augmentation is a method used to increase the diversity and quantity of training dataset and to reduce data sparsity and imbalance. In this paper, we propose data augmentation methods that involve replacing detail coefficients decomposed by discrete wavelet transform for reconstructing to generate new samples and expand the training set. Different generation methods are used to generate replacement sequences. Simulation results indicate that our proposed methods significantly outperform the other augmentation methods.

RK-core: An Established Methodology for Exploring the Hierarchical Structure within Datasets

Recently, the field of machine learning has undergone a transition from model-centric to data-centric. The advancements in diverse learning tasks have been propelled by the accumulation of more extensive datasets, subsequently facilitating the training of larger models on these datasets. However, these datasets remain relatively under-explored. To this end, we introduce a pioneering approach known as RK-core, to empower gaining a deeper understanding of the intricate hierarchical structure within datasets. Across several benchmark datasets, we find that samples with low coreness values appear less representative of their respective categories, and conversely, those with high coreness values exhibit greater representativeness. Correspondingly, samples with high coreness values make a more substantial contribution to the performance in comparison to those with low coreness values. Building upon this, we further employ RK-core to analyze the hierarchical structure of samples with different coreset selection methods. Remarkably, we find that a high-quality coreset should exhibit hierarchical diversity instead of solely opting for representative samples. The code is available at https://github.com/yaolu-zjut/Kcore.

Can pre-trained models assist in dataset distillation?

Dataset Distillation (DD) is a prominent technique that encapsulates knowledge from a large-scale original dataset into a small synthetic dataset for efficient training. Meanwhile, Pre-trained Models (PTMs) function as knowledge repositories, containing extensive information from the original dataset. This naturally raises a question: Can PTMs effectively transfer knowledge to synthetic datasets, guiding DD accurately? To this end, we conduct preliminary experiments, confirming the contribution of PTMs to DD. Afterwards, we systematically study different options in PTMs, including initialization parameters, model architecture, training epoch and domain knowledge, revealing that: 1) Increasing model diversity enhances the performance of synthetic datasets; 2) Sub-optimal models can also assist in DD and outperform well-trained ones in certain cases; 3) Domain-specific PTMs are not mandatory for DD, but a reasonable domain match is crucial. Finally, by selecting optimal options, we significantly improve the cross-architecture generalization over baseline DD methods. We hope our work will facilitate researchers to develop better DD techniques. Our code is available at https://github.com/yaolu-zjut/DDInterpreter.

PathMLP: Smooth Path Towards High-order Homophily

Real-world graphs exhibit increasing heterophily, where nodes no longer tend to be connected to nodes with the same label, challenging the homophily assumption of classical graph neural networks (GNNs) and impeding their performance. Intriguingly, we observe that certain high-order information on heterophilous data exhibits high homophily, which motivates us to involve high-order information in node representation learning. However, common practices in GNNs to acquire high-order information mainly through increasing model depth and altering message-passing mechanisms, which, albeit effective to a certain extent, suffer from three shortcomings: 1) over-smoothing due to excessive model depth and propagation times; 2) high-order information is not fully utilized; 3) low computational efficiency. In this regard, we design a similarity-based path sampling strategy to capture smooth paths containing high-order homophily. Then we propose a lightweight model based on multi-layer perceptrons (MLP), named PathMLP, which can encode messages carried by paths via simple transformation and concatenation operations, and effectively learn node representations in heterophilous graphs through adaptive path aggregation. Extensive experiments demonstrate that our method outperforms baselines on 16 out of 20 datasets, underlining its effectiveness and superiority in alleviating the heterophily problem. In addition, our method is immune to over-smoothing and has high computational efficiency.

Subgraph Networks Based Contrastive Learning

Graph contrastive learning (GCL), as a self-supervised learning method, can solve the problem of annotated data scarcity. It mines explicit features in unannotated graphs to generate favorable graph representations for downstream tasks. Most existing GCL methods focus on the design of graph augmentation strategies and mutual information estimation operations. Graph augmentation produces augmented views by graph perturbations. These views preserve a locally similar structure and exploit explicit features. However, these methods have not considered the interaction existing in subgraphs. To explore the impact of substructure interactions on graph representations, we propose a novel framework called subgraph network-based contrastive learning (SGNCL). SGNCL applies a subgraph network generation strategy to produce augmented views. This strategy converts the original graph into an Edge-to-Node mapping network with both topological and attribute features. The single-shot augmented view is a first-order subgraph network that mines the interaction between nodes, node-edge, and edges. In addition, we also investigate the impact of the second-order subgraph augmentation on mining graph structure interactions, and further, propose a contrastive objective that fuses the first-order and second-order subgraph information. We compare SGNCL with classical and state-of-the-art graph contrastive learning methods on multiple benchmark datasets of different domains. Extensive experiments show that SGNCL achieves competitive or better performance (top three) on all datasets in unsupervised learning settings. Furthermore, SGNCL achieves the best average gain of 6.9\% in transfer learning compared to the best method. Finally, experiments also demonstrate that mining substructure interactions have positive implications for graph contrastive learning.

Clarify Confused Nodes Through Separated Learning

Graph neural networks (GNNs) have achieved remarkable advances in graph-oriented tasks. However, real-world graphs invariably contain a certain proportion of heterophilous nodes, challenging the homophily assumption of classical GNNs and hindering their performance. Most existing studies continue to design generic models with shared weights between heterophilous and homophilous nodes. Despite the incorporation of high-order message or multi-channel architectures, these efforts often fall short. A minority of studies attempt to train different node groups separately, but suffering from inappropriate separation metric and low efficiency. In this paper, we first propose a new metric, termed Neighborhood Confusion (NC), to facilitate a more reliable separation of nodes. We observe that node groups with different levels of NC values exhibit certain differences in intra-group accuracy and visualized embeddings. These pave a way for Neighborhood Confusion-guided Graph Convolutional Network (NCGCN), in which nodes are grouped by their NC values and accept intra-group weight sharing and message passing. Extensive experiments on both homophilous and heterophilous benchmarks demonstrate that NCGCN can effectively separate nodes and offers significant performance improvement compared to latest methods.