Why Deep Models Often cannot Beat Non-deep Counterparts on Molecular Property Prediction?

Molecular property prediction (MPP) is a crucial task in the drug discovery pipeline, which has recently gained considerable attention thanks to advances in deep neural networks. However, recent research has revealed that deep models struggle to beat traditional non-deep ones on MPP. In this study, we benchmark 12 representative models (3 non-deep models and 9 deep models) on 14 molecule datasets. Through the most comprehensive study to date, we make the following key observations: \textbf{(\romannumeral 1)} Deep models are generally unable to outperform non-deep ones; \textbf{(\romannumeral 2)} The failure of deep models on MPP cannot be solely attributed to the small size of molecular datasets. What matters is the irregular molecule data pattern; \textbf{(\romannumeral 3)} In particular, tree models using molecular fingerprints as inputs tend to perform better than other competitors. Furthermore, we conduct extensive empirical investigations into the unique patterns of molecule data and inductive biases of various models underlying these phenomena.

Dink-Net: Neural Clustering on Large Graphs

Deep graph clustering, which aims to group the nodes of a graph into disjoint clusters with deep neural networks, has achieved promising progress in recent years. However, the existing methods fail to scale to the large graph with million nodes. To solve this problem, a scalable deep graph clustering method (Dink-Net) is proposed with the idea of dilation and shrink. Firstly, by discriminating nodes, whether being corrupted by augmentations, representations are learned in a self-supervised manner. Meanwhile, the cluster centres are initialized as learnable neural parameters. Subsequently, the clustering distribution is optimized by minimizing the proposed cluster dilation loss and cluster shrink loss in an adversarial manner. By these settings, we unify the two-step clustering, i.e., representation learning and clustering optimization, into an end-to-end framework, guiding the network to learn clustering-friendly features. Besides, Dink-Net scales well to large graphs since the designed loss functions adopt the mini-batch data to optimize the clustering distribution even without performance drops. Both experimental results and theoretical analyses demonstrate the superiority of our method. Compared to the runner-up, Dink-Net achieves 9.62% NMI improvement on the ogbn-papers100M dataset with 111 million nodes and 1.6 billion edges. The source code is released at https://github.com/yueliu1999/Dink-Net. Besides, a collection (papers, codes, and datasets) of deep graph clustering is shared at https://github.com/yueliu1999/Awesome-Deep-Graph-Clustering.

CVT-SLR: Contrastive Visual-Textual Transformation for Sign Language Recognition with Variational Alignment

Sign language recognition (SLR) is a weakly supervised task that annotates sign videos as textual glosses. Recent studies show that insufficient training caused by the lack of large-scale available sign datasets becomes the main bottleneck for SLR. Most SLR works thereby adopt pretrained visual modules and develop two mainstream solutions. The multi-stream architectures extend multi-cue visual features, yielding the current SOTA performances but requiring complex designs and might introduce potential noise. Alternatively, the advanced single-cue SLR frameworks using explicit cross-modal alignment between visual and textual modalities are simple and effective, potentially competitive with the multi-cue framework. In this work, we propose a novel contrastive visual-textual transformation for SLR, CVT-SLR, to fully explore the pretrained knowledge of both the visual and language modalities. Based on the single-cue cross-modal alignment framework, we propose a variational autoencoder (VAE) for pretrained contextual knowledge while introducing the complete pretrained language module. The VAE implicitly aligns visual and textual modalities while benefiting from pretrained contextual knowledge as the traditional contextual module. Meanwhile, a contrastive cross-modal alignment algorithm is designed to explicitly enhance the consistency constraints. Extensive experiments on public datasets (PHOENIX-2014 and PHOENIX-2014T) demonstrate that our proposed CVT-SLR consistently outperforms existing single-cue methods and even outperforms SOTA multi-cue methods.

HierarchyFL: Heterogeneous Federated Learning via Hierarchical Self-Distillation

Federated learning (FL) has been recognized as a privacy-preserving distributed machine learning paradigm that enables knowledge sharing among various heterogeneous artificial intelligence (AIoT) devices through centralized global model aggregation. FL suffers from model inaccuracy and slow convergence due to the model heterogeneity of the AIoT devices involved. Although various existing methods try to solve the bottleneck of the model heterogeneity problem, most of them improve the accuracy of heterogeneous models in a coarse-grained manner, which makes it still a great challenge to deploy large-scale AIoT devices. To alleviate the negative impact of this problem and take full advantage of the diversity of each heterogeneous model, we propose an efficient framework named HierarchyFL, which uses a small amount of public data for efficient and scalable knowledge across a variety of differently structured models. By using self-distillation and our proposed ensemble library, each hierarchical model can intelligently learn from each other on cloud servers. Experimental results on various well-known datasets show that HierarchyFL can not only maximize the knowledge sharing among various heterogeneous models in large-scale AIoT systems, but also greatly improve the model performance of each involved heterogeneous AIoT device.

Protein Language Models and Structure Prediction: Connection and Progression

The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the protein sequence databases, which inherit the advantages of attention networks and capture useful information in learning representations for proteins. The past two years have witnessed remarkable success in tertiary protein structure prediction (PSP), including evolution-based and single-sequence-based PSP. It seems that instead of using energy-based models and sampling procedures, protein language model (pLM)-based pipelines have emerged as mainstream paradigms in PSP. Despite the fruitful progress, the PSP community needs a systematic and up-to-date survey to help bridge the gap between LMs in the natural language processing (NLP) and PSP domains and introduce their methodologies, advancements and practical applications. To this end, in this paper, we first introduce the similarities between protein and human languages that allow LMs extended to pLMs, and applied to protein databases. Then, we systematically review recent advances in LMs and pLMs from the perspectives of network architectures, pre-training strategies, applications, and commonly-used protein databases. Next, different types of methods for PSP are discussed, particularly how the pLM-based architectures function in the process of protein folding. Finally, we identify challenges faced by the PSP community and foresee promising research directions along with the advances of pLMs. This survey aims to be a hands-on guide for researchers to understand PSP methods, develop pLMs and tackle challenging problems in this field for practical purposes.

A Survey of Deep Graph Clustering: Taxonomy, Challenge, and Application

Graph clustering, which aims to divide the nodes in the graph into several distinct clusters, is a fundamental and challenging task. In recent years, deep graph clustering methods have been increasingly proposed and achieved promising performance. However, the corresponding survey paper is scarce and it is imminent to make a summary in this field. From this motivation, this paper makes the first comprehensive survey of deep graph clustering. Firstly, the detailed definition of deep graph clustering and the important baseline methods are introduced. Besides, the taxonomy of deep graph clustering methods is proposed based on four different criteria including graph type, network architecture, learning paradigm, and clustering method. In addition, through the careful analysis of the existing works, the challenges and opportunities from five perspectives are summarized. At last, the applications of deep graph clustering in four domains are presented. It is worth mentioning that a collection of state-of-the-art deep graph clustering methods including papers, codes, and datasets is available on GitHub. We hope this work will serve as a quick guide and help researchers to overcome challenges in this vibrant field.

GitFL: Adaptive Asynchronous Federated Learning using Version Control

As a promising distributed machine learning paradigm that enables collaborative training without compromising data privacy, Federated Learning (FL) has been increasingly used in AIoT (Artificial Intelligence of Things) design. However, due to the lack of efficient management of straggling devices, existing FL methods greatly suffer from the problems of low inference accuracy and long training time. Things become even worse when taking various uncertain factors (e.g., network delays, performance variances caused by process variation) existing in AIoT scenarios into account. To address this issue, this paper proposes a novel asynchronous FL framework named GitFL, whose implementation is inspired by the famous version control system Git. Unlike traditional FL, the cloud server of GitFL maintains a master model (i.e., the global model) together with a set of branch models indicating the trained local models committed by selected devices, where the master model is updated based on both all the pushed branch models and their version information, and only the branch models after the pull operation are dispatched to devices. By using our proposed Reinforcement Learning (RL)-based device selection mechanism, a pulled branch model with an older version will be more likely to be dispatched to a faster and less frequently selected device for the next round of local training. In this way, GitFL enables both effective control of model staleness and adaptive load balance of versioned models among straggling devices, thus avoiding the performance deterioration. Comprehensive experimental results on well-known models and datasets show that, compared with state-of-the-art asynchronous FL methods, GitFL can achieve up to 2.64X training acceleration and 7.88% inference accuracy improvements in various uncertain scenarios.

Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings

Although contextualized embeddings generated from large-scale pre-trained models perform well in many tasks, traditional static embeddings (e.g., Skip-gram, Word2Vec) still play an important role in low-resource and lightweight settings due to their low computational cost, ease of deployment, and stability. In this paper, we aim to improve word embeddings by 1) incorporating more contextual information from existing pre-trained models into the Skip-gram framework, which we call Context-to-Vec; 2) proposing a post-processing retrofitting method for static embeddings independent of training by employing priori synonym knowledge and weighted vector distribution. Through extrinsic and intrinsic tasks, our methods are well proven to outperform the baselines by a large margin.