Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

AsySQN: Faster Vertical Federated Learning Algorithms with Better Computation Resource Utilization

Vertical federated learning (VFL) is an effective paradigm of training the emerging cross-organizational (e.g., different corporations, companies and organizations) collaborative learning with privacy preserving. Stochastic gradient descent (SGD) methods are the popular choices for training VFL models because of the low per-iteration computation. However, existing SGD-based VFL algorithms are communication-expensive due to a large number of communication rounds. Meanwhile, most existing VFL algorithms use synchronous computation which seriously hamper the computation resource utilization in real-world applications. To address the challenges of communication and computation resource utilization, we propose an asynchronous stochastic quasi-Newton (AsySQN) framework for VFL, under which three algorithms, i.e. AsySQN-SGD, -SVRG and -SAGA, are proposed. The proposed AsySQN-type algorithms making descent steps scaled by approximate (without calculating the inverse Hessian matrix explicitly) Hessian information convergence much faster than SGD-based methods in practice and thus can dramatically reduce the number of communication rounds. Moreover, the adopted asynchronous computation can make better use of the computation resource. We theoretically prove the convergence rates of our proposed algorithms for strongly convex problems. Extensive numerical experiments on real-word datasets demonstrate the lower communication costs and better computation resource utilization of our algorithms compared with state-of-the-art VFL algorithms.

Group Contrastive Self-Supervised Learning on Graphs

We study self-supervised learning on graphs using contrastive methods. A general scheme of prior methods is to optimize two-view representations of input graphs. In many studies, a single graph-level representation is computed as one of the contrastive objectives, capturing limited characteristics of graphs. We argue that contrasting graphs in multiple subspaces enables graph encoders to capture more abundant characteristics. To this end, we propose a group contrastive learning framework in this work. Our framework embeds the given graph into multiple subspaces, of which each representation is prompted to encode specific characteristics of graphs. To learn diverse and informative representations, we develop principled objectives that enable us to capture the relations among both intra-space and inter-space representations in groups. Under the proposed framework, we further develop an attention-based representor function to compute representations that capture different substructures of a given graph. Built upon our framework, we extend two current methods into GroupCL and GroupIG, equipped with the proposed objective. Comprehensive experimental results show our framework achieves a promising boost in performance on a variety of datasets. In addition, our qualitative results show that features generated from our representor successfully capture various specific characteristics of graphs.

Domain-Smoothing Network for Zero-Shot Sketch-Based Image Retrieval

Zero-Shot Sketch-Based Image Retrieval (ZS-SBIR) is a novel cross-modal retrieval task, where abstract sketches are used as queries to retrieve natural images under zero-shot scenario. Most existing methods regard ZS-SBIR as a traditional classification problem and employ a cross-entropy or triplet-based loss to achieve retrieval, which neglect the problems of the domain gap between sketches and natural images and the large intra-class diversity in sketches. Toward this end, we propose a novel Domain-Smoothing Network (DSN) for ZS-SBIR. Specifically, a cross-modal contrastive method is proposed to learn generalized representations to smooth the domain gap by mining relations with additional augmented samples. Furthermore, a category-specific memory bank with sketch features is explored to reduce intra-class diversity in the sketch domain. Extensive experiments demonstrate that our approach notably outperforms the state-of-the-art methods in both Sketchy and TU-Berlin datasets. Our source code is publicly available at https://github.com/haowang1992/DSN.

Doubly Contrastive Deep Clustering

Deep clustering successfully provides more effective features than conventional ones and thus becomes an important technique in current unsupervised learning. However, most deep clustering methods ignore the vital positive and negative pairs introduced by data augmentation and further the significance of contrastive learning, which leads to suboptimal performance. In this paper, we present a novel Doubly Contrastive Deep Clustering (DCDC) framework, which constructs contrastive loss over both sample and class views to obtain more discriminative features and competitive results. Specifically, for the sample view, we set the class distribution of the original sample and its augmented version as positive sample pairs and set one of the other augmented samples as negative sample pairs. After that, we can adopt the sample-wise contrastive loss to pull positive sample pairs together and push negative sample pairs apart. Similarly, for the class view, we build the positive and negative pairs from the sample distribution of the class. In this way, two contrastive losses successfully constrain the clustering results of mini-batch samples in both sample and class level. Extensive experimental results on six benchmark datasets demonstrate the superiority of our proposed model against state-of-the-art methods. Particularly in the challenging dataset Tiny-ImageNet, our method leads 5.6\% against the latest comparison method. Our code will be available at \url{https://github.com/ZhiyuanDang/DCDC}.

Universal-Prototype Augmentation for Few-Shot Object Detection

Few-shot object detection (FSOD) aims to strengthen the performance of novel object detection with few labeled samples. To alleviate the constraint of few samples, enhancing the generalization ability of learned features for novel objects plays a key role. Thus, the feature learning process of FSOD should focus more on intrinsical object characteristics, which are invariant under different visual changes and therefore are helpful for feature generalization. Unlike previous attempts of the meta-learning paradigm, in this paper, we explore how to smooth object features with intrinsical characteristics that are universal across different object categories. We propose a new prototype, namely universal prototype, that is learned from all object categories. Besides the advantage of characterizing invariant characteristics, the universal prototypes alleviate the impact of unbalanced object categories. After augmenting object features with the universal prototypes, we impose a consistency loss to maximize the agreement between the augmented features and the original one, which is beneficial for learning invariant object characteristics. Thus, we develop a new framework of few-shot object detection with universal prototypes (${FSOD}^{up}$) that owns the merit of feature generalization towards novel objects. Experimental results on PASCAL VOC and MS COCO demonstrate the effectiveness of ${FSOD}^{up}$. Particularly, for the 1-shot case of VOC Split2, ${FSOD}^{up}$ outperforms the baseline by 6.8\% in terms of mAP. Moreover, we further verify ${FSOD}^{up}$ on a long-tail detection dataset, i.e., LVIS. And employing ${FSOD}^{up}$ outperforms the state-of-the-art method.

Secure Bilevel Asynchronous Vertical Federated Learning with Backward Updating

Vertical federated learning (VFL) attracts increasing attention due to the emerging demands of multi-party collaborative modeling and concerns of privacy leakage. In the real VFL applications, usually only one or partial parties hold labels, which makes it challenging for all parties to collaboratively learn the model without privacy leakage. Meanwhile, most existing VFL algorithms are trapped in the synchronous computations, which leads to inefficiency in their real-world applications. To address these challenging problems, we propose a novel {\bf VF}L framework integrated with new {\bf b}ackward updating mechanism and {\bf b}ilevel asynchronous parallel architecture (VF{${\textbf{B}}^2$}), under which three new algorithms, including VF{${\textbf{B}}^2$}-SGD, -SVRG, and -SAGA, are proposed. We derive the theoretical results of the convergence rates of these three algorithms under both strongly convex and nonconvex conditions. We also prove the security of VF{${\textbf{B}}^2$} under semi-honest threat models. Extensive experiments on benchmark datasets demonstrate that our algorithms are efficient, scalable and lossless.

Incremental Embedding Learning via Zero-Shot Translation

Modern deep learning methods have achieved great success in machine learning and computer vision fields by learning a set of pre-defined datasets. Howerver, these methods perform unsatisfactorily when applied into real-world situations. The reason of this phenomenon is that learning new tasks leads the trained model quickly forget the knowledge of old tasks, which is referred to as catastrophic forgetting. Current state-of-the-art incremental learning methods tackle catastrophic forgetting problem in traditional classification networks and ignore the problem existing in embedding networks, which are the basic networks for image retrieval, face recognition, zero-shot learning, etc. Different from traditional incremental classification networks, the semantic gap between the embedding spaces of two adjacent tasks is the main challenge for embedding networks under incremental learning setting. Thus, we propose a novel class-incremental method for embedding network, named as zero-shot translation class-incremental method (ZSTCI), which leverages zero-shot translation to estimate and compensate the semantic gap without any exemplars. Then, we try to learn a unified representation for two adjacent tasks in sequential learning process, which captures the relationships of previous classes and current classes precisely. In addition, ZSTCI can easily be combined with existing regularization-based incremental learning methods to further improve performance of embedding networks. We conduct extensive experiments on CUB-200-2011 and CIFAR100, and the experiment results prove the effectiveness of our method. The code of our method has been released.

Towards Improved and Interpretable Deep Metric Learning via Attentive Grouping

Grouping has been commonly used in deep metric learning for computing diverse features. However, current methods are prone to overfitting and lack interpretability. In this work, we propose an improved and interpretable grouping method to be integrated flexibly with any metric learning framework. Our method is based on the attention mechanism with a learnable query for each group. The query is fully trainable and can capture group-specific information when combined with the diversity loss. An appealing property of our method is that it naturally lends itself interpretability. The attention scores between the learnable query and each spatial position can be interpreted as the importance of that position. We formally show that our proposed grouping method is invariant to spatial permutations of features. When used as a module in convolutional neural networks, our method leads to translational invariance. We conduct comprehensive experiments to evaluate our method. Our quantitative results indicate that the proposed method outperforms prior methods consistently and significantly across different datasets, evaluation metrics, base models, and loss functions. For the first time to the best of our knowledge, our interpretation results clearly demonstrate that the proposed method enables the learning of distinct and diverse features across groups.

Fewer is More: A Deep Graph Metric Learning Perspective Using Fewer Proxies

Deep metric learning plays a key role in various machine learning tasks. Most of the previous works have been confined to sampling from a mini-batch, which cannot precisely characterize the global geometry of the embedding space. Although researchers have developed proxy- and classification-based methods to tackle the sampling issue, those methods inevitably incur a redundant computational cost. In this paper, we propose a novel Proxy-based deep Graph Metric Learning (ProxyGML) approach from the perspective of graph classification, which uses fewer proxies yet achieves better comprehensive performance. Specifically, multiple global proxies are leveraged to collectively approximate the original data points for each class. To efficiently capture local neighbor relationships, a small number of such proxies are adaptively selected to construct similarity subgraphs between these proxies and each data point. Further, we design a novel reverse label propagation algorithm, by which the neighbor relationships are adjusted according to ground-truth labels, so that a discriminative metric space can be learned during the process of subgraph classification. Extensive experiments carried out on widely-used CUB-200-2011, Cars196, and Stanford Online Products datasets demonstrate the superiority of the proposed ProxyGML over the state-of-the-art methods in terms of both effectiveness and efficiency. The source code is publicly available at https://github.com/YuehuaZhu/ProxyGML.