在半监督的学习领域中，作为GNN的变体模型，图形卷积网络（GCN）通过将卷积引入GNN来实现非欧盟数据的有希望的结果。但是，GCN及其变体模型无法安全地使用风险未标记数据的信息，这将降低半监督学习的性能。因此，我们提出了一个安全的GCN框架（SAFE-GCN），以提高学习绩效。在Safe-GCN中，我们设计了一个迭代过程来标记未标记的数据。在每次迭代中，学会了GCN及其监督版本（S-GCN），以高信任地找到未标记的数据。然后将高信心的未标记数据及其伪标签添加到标签集中。最后，两者都添加了未标记的数据和标记的数据来训练S-GCN，该S-GCN可以安全地探索风险未标记的数据，并可以安全使用大量未标记的数据。在三个众所周知的引用网络数据集上评估了安全性GCN的性能，并且获得的结果证明了该框架对几种基于图的半监督学习方法的有效性。

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of sequence-structure data. With the development of Artificial Intelligence (AI) techniques, Protein Representation Learning (PRL) has recently emerged as a promising research topic for extracting informative knowledge from massive protein sequences or structures. To pave the way for AI researchers with little bioinformatics background, we present a timely and comprehensive review of PRL formulations and existing PRL methods from the perspective of model architectures, pretext tasks, and downstream applications. We first briefly introduce the motivations for protein representation learning and formulate it in a general and unified framework. Next, we divide existing PRL methods into three main categories: sequence-based, structure-based, and sequence-structure co-modeling. Finally, we discuss some technical challenges and potential directions for improving protein representation learning. The latest advances in PRL methods are summarized in a GitHub repository https://github.com/LirongWu/awesome-protein-representation-learning.

Datasets serve as crucial training resources and model performance trackers. However, existing datasets have exposed a plethora of problems, inducing biased models and unreliable evaluation results. In this paper, we propose a model-agnostic dataset evaluation framework for automatic dataset quality evaluation. We seek the statistical properties of the datasets and address three fundamental dimensions: reliability, difficulty, and validity, following a classical testing theory. Taking the Named Entity Recognition (NER) datasets as a case study, we introduce $9$ statistical metrics for a statistical dataset evaluation framework. Experimental results and human evaluation validate that our evaluation framework effectively assesses various aspects of the dataset quality. Furthermore, we study how the dataset scores on our statistical metrics affect the model performance, and appeal for dataset quality evaluation or targeted dataset improvement before training or testing models.

Semantic Change Detection (SCD) refers to the task of simultaneously extracting the changed areas and the semantic categories (before and after the changes) in Remote Sensing Images (RSIs). This is more meaningful than Binary Change Detection (BCD) since it enables detailed change analysis in the observed areas. Previous works established triple-branch Convolutional Neural Network (CNN) architectures as the paradigm for SCD. However, it remains challenging to exploit semantic information with a limited amount of change samples. In this work, we investigate to jointly consider the spatio-temporal dependencies to improve the accuracy of SCD. First, we propose a SCanFormer (Semantic Change Transformer) to explicitly model the 'from-to' semantic transitions between the bi-temporal RSIs. Then, we introduce a semantic learning scheme to leverage the spatio-temporal constraints, which are coherent to the SCD task, to guide the learning of semantic changes. The resulting network (ScanNet) significantly outperforms the baseline method in terms of both detection of critical semantic changes and semantic consistency in the obtained bi-temporal results. It achieves the SOTA accuracy on two benchmark datasets for the SCD.

Solving partial differential equations is difficult. Recently proposed neural resolution-invariant models, despite their effectiveness and efficiency, usually require equispaced spatial points of data. However, sampling in spatial domain is sometimes inevitably non-equispaced in real-world systems, limiting their applicability. In this paper, we propose a Non-equispaced Fourier PDE Solver (\textsc{NFS}) with adaptive interpolation on resampled equispaced points and a variant of Fourier Neural Operators as its components. Experimental results on complex PDEs demonstrate its advantages in accuracy and efficiency. Compared with the spatially-equispaced benchmark methods, it achieves superior performance with $42.85\%$ improvements on MAE, and is able to handle non-equispaced data with a tiny loss of accuracy. Besides, to our best knowledge, \textsc{NFS} is the first ML-based method with mesh invariant inference ability to successfully model turbulent flows in non-equispaced scenarios, with a minor deviation of the error on unseen spatial points.

Transformer-based pre-trained models have become the de-facto solution for NLP tasks. Fine-tuning such pre-trained models for downstream tasks often requires tremendous amount of data that is both private and labeled. However, in reality: 1) such private data cannot be collected and is distributed across mobile devices, and 2) well-curated labeled data is scarce. To tackle those issues, we first define a data generator for federated few-shot learning tasks, which encompasses the quantity and distribution of scarce labeled data in a realistic setting. Then we propose AUG-FedPrompt, a prompt-based federated learning algorithm that carefully annotates abundant unlabeled data for data augmentation. AUG-FedPrompt can perform on par with full-set fine-tuning with very few initial labeled data.

Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one by one. However, in real-world molecular systems, the interactions among atoms in an entire molecule are global, leading to the energy function pair-coupled among atoms. With such energy-based consideration, the modeling of probability should be based on joint distributions, rather than sequentially conditional ones. Thus, the unnatural sequentially auto-regressive modeling of molecule generation is likely to violate the physical rules, thus resulting in poor properties of the generated molecules. In this work, a generative diffusion model for molecular 3D structures based on target proteins as contextual constraints is established, at a full-atom level in a non-autoregressive way. Given a designated 3D protein binding site, our model learns the generative process that denoises both element types and 3D coordinates of an entire molecule, with an equivariant network. Experimentally, the proposed method shows competitive performance compared with prevailing works in terms of high affinity with proteins and appropriate molecule sizes as well as other drug properties such as drug-likeness of the generated molecules.

Current natural language processing (NLP) models such as BERT and RoBERTa have achieved high overall performance, but they often make systematic errors due to bias or certain difficult features to learn. Thus research on slice detection models (SDM) which automatically identifies underperforming groups of datapoints has gradually caught more attention, which aims at both understanding model behaviors and providing insights for future model training and designing. However, there is little systematic research on SDM and quantitative evaluation of its assessment for NLP models. Our paper fills this gap by proposing "Discover, Explanation, Improvement" framework that discovers coherent and underperforming groups of datapoints and unites datapoints of each slice under human-understandable concepts; it also provides comprehensive evaluation tasks and the corresponding quantitative metrics, which enable convenient comparison for future works. Results show that our framework can accurately select error-prone datapoints with informative semantic features that summarize error patterns, based on which it directly boosts model performance by an average of 2.85 points based on trained models without tuning any parameters across multiple datasets.

Since the recent success of Vision Transformers (ViTs), explorations toward transformer-style architectures have triggered the resurgence of modern ConvNets. In this work, we explore the representation ability of DNNs through the lens of interaction complexities. We empirically show that interaction complexity is an overlooked but essential indicator for visual recognition. Accordingly, a new family of efficient ConvNets, named MogaNet, is presented to pursue informative context mining in pure ConvNet-based models, with preferable complexity-performance trade-offs. In MogaNet, interactions across multiple complexities are facilitated and contextualized by leveraging two specially designed aggregation blocks in both spatial and channel interaction spaces. Extensive studies are conducted on ImageNet classification, COCO object detection, and ADE20K semantic segmentation tasks. The results demonstrate that our MogaNet establishes new state-of-the-art over other popular methods in mainstream scenarios and all model scales. Typically, the lightweight MogaNet-T achieves 80.0\% top-1 accuracy with only 1.44G FLOPs using a refined training setup on ImageNet-1K, surpassing ParC-Net-S by 1.4\% accuracy but saving 59\% (2.04G) FLOPs.

Recent years have witnessed great success in handling graph-related tasks with Graph Neural Networks (GNNs). Despite their great academic success, Multi-Layer Perceptrons (MLPs) remain the primary workhorse for practical industrial applications. One reason for this academic-industrial gap is the neighborhood-fetching latency incurred by data dependency in GNNs, which make it hard to deploy for latency-sensitive applications that require fast inference. Conversely, without involving any feature aggregation, MLPs have no data dependency and infer much faster than GNNs, but their performance is less competitive. Motivated by these complementary strengths and weaknesses, we propose a Graph Self-Distillation on Neighborhood (GSDN) framework to reduce the gap between GNNs and MLPs. Specifically, the GSDN framework is based purely on MLPs, where structural information is only implicitly used as prior to guide knowledge self-distillation between the neighborhood and the target, substituting the explicit neighborhood information propagation as in GNNs. As a result, GSDN enjoys the benefits of graph topology-awareness in training but has no data dependency in inference. Extensive experiments have shown that the performance of vanilla MLPs can be greatly improved with self-distillation, e.g., GSDN improves over stand-alone MLPs by 15.54\% on average and outperforms the state-of-the-art GNNs on six datasets. Regarding inference speed, GSDN infers 75X-89X faster than existing GNNs and 16X-25X faster than other inference acceleration methods.