Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe-drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe-drug associations. In this paper, we proposed a novel method, Graph2MDA, to predict microbe-drug associations by using variational graph autoencoder (VGAE). We constructed multi-modal attributed graphs based on multiple features of microbes and drugs, such as molecular structures, microbe genetic sequences, and function annotations. Taking as input the multi-modal attribute graphs, VGAE was trained to learn the informative and interpretable latent representations of each node and the whole graph, and then a deep neural network classifier was used to predict microbe-drug associations. The hyperparameter analysis and model ablation studies showed the sensitivity and robustness of our model. We evaluated our method on three independent datasets and the experimental results showed that our proposed method outperformed six existing state-of-the-art methods. We also explored the meaningness of the learned latent representations of drugs and found that the drugs show obvious clustering patterns that are significantly consistent with drug ATC classification. Moreover, we conducted case studies on two microbes and two drugs and found 75%-95% predicted associations have been reported in PubMed literature. Our extensive performance evaluations validated the effectiveness of our proposed method.

Dynamic Control for Random Access in Deadline-Constrained Broadcasting

This paper considers random access in deadline-constrained broadcasting with frame-synchronized traffic. To enhance the maximum achievable timely delivery ratio (TDR), we define a dynamic control scheme that allows each active node to determine the transmission probability with certainty based on the current delivery urgency and the knowledge of current contention intensity. For an idealized environment where the contention intensity is completely known, we develop an analytical framework based on the theory of Markov Decision Process (MDP), which leads to an optimal scheme by applying backward induction. For a realistic environment where the contention intensity is incompletely known, we develop a framework using Partially Observable Markov Decision Process (POMDP), which can in theory be solved. We show that for both environments, there exists an optimal scheme that is optimal over all types of policies. To overcome the infeasibility in obtaining an optimal or near-optimal scheme from the POMDP framework, we investigate the behaviors of the optimal scheme for two extreme cases in the MDP framework, and leverage intuition gained from these behaviors to propose a heuristic scheme for the realistic environment with TDR close to the maximum achievable TDR in the idealized environment. In addition, we propose an approximation on the knowledge of contention intensity to further simplify this heuristic scheme. Numerical results with respect to a wide range of configurations are provided to validate our study.

Exploiting Spiking Dynamics with Spatial-temporal Feature Normalization in Graph Learning

Biological spiking neurons with intrinsic dynamics underlie the powerful representation and learning capabilities of the brain for processing multimodal information in complex environments. Despite recent tremendous progress in spiking neural networks (SNNs) for handling Euclidean-space tasks, it still remains challenging to exploit SNNs in processing non-Euclidean-space data represented by graph data, mainly due to the lack of effective modeling framework and useful training techniques. Here we present a general spike-based modeling framework that enables the direct training of SNNs for graph learning. Through spatial-temporal unfolding for spiking data flows of node features, we incorporate graph convolution filters into spiking dynamics and formalize a synergistic learning paradigm. Considering the unique features of spike representation and spiking dynamics, we propose a spatial-temporal feature normalization (STFN) technique suitable for SNN to accelerate convergence. We instantiate our methods into two spiking graph models, including graph convolution SNNs and graph attention SNNs, and validate their performance on three node-classification benchmarks, including Cora, Citeseer, and Pubmed. Our model can achieve comparable performance with the state-of-the-art graph neural network (GNN) models with much lower computation costs, demonstrating great benefits for the execution on neuromorphic hardware and prompting neuromorphic applications in graphical scenarios.

Towards Efficient Full 8-bit Integer DNN Online Training on Resource-limited Devices without Batch Normalization

Huge computational costs brought by convolution and batch normalization (BN) have caused great challenges for the online training and corresponding applications of deep neural networks (DNNs), especially in resource-limited devices. Existing works only focus on the convolution or BN acceleration and no solution can alleviate both problems with satisfactory performance. Online training has gradually become a trend in resource-limited devices like mobile phones while there is still no complete technical scheme with acceptable model performance, processing speed, and computational cost. In this research, an efficient online-training quantization framework termed EOQ is proposed by combining Fixup initialization and a novel quantization scheme for DNN model compression and acceleration. Based on the proposed framework, we have successfully realized full 8-bit integer network training and removed BN in large-scale DNNs. Especially, weight updates are quantized to 8-bit integers for the first time. Theoretical analyses of EOQ utilizing Fixup initialization for removing BN have been further given using a novel Block Dynamical Isometry theory with weaker assumptions. Benefiting from rational quantization strategies and the absence of BN, the full 8-bit networks based on EOQ can achieve state-of-the-art accuracy and immense advantages in computational cost and processing speed. What is more, the design of deep learning chips can be profoundly simplified for the absence of unfriendly square root operations in BN. Beyond this, EOQ has been evidenced to be more advantageous in small-batch online training with fewer batch samples. In summary, the EOQ framework is specially designed for reducing the high cost of convolution and BN in network training, demonstrating a broad application prospect of online training in resource-limited devices.

Reinforcement Learning Random Access for Delay-Constrained Heterogeneous Wireless Networks: A Two-User Case

In this paper, we investigate the random access problem for a delay-constrained heterogeneous wireless network. As a first attempt to study this new problem, we consider a network with two users who deliver delay-constrained traffic to an access point (AP) via a common unreliable collision wireless channel. We assume that one user (called user 1) adopts ALOHA and we optimize the random access scheme of the other user (called user 2). The most intriguing part of this problem is that user 2 does not know the information of user 1 but needs to maximize the system timely throughput. Such a paradigm of collaboratively sharing spectrum is envisioned by DARPA to better dynamically match the supply and demand in the future [1], [2]. We first propose a Markov Decision Process (MDP) formulation to derive a modelbased upper bound, which can quantify the performance gap of any designed schemes. We then utilize reinforcement learning (RL) to design an R-learning-based [3]-[5] random access scheme, called TSRA. We finally carry out extensive simulations to show that TSRA achieves close-to-upper-bound performance and better performance than the existing baseline DLMA [6], which is our counterpart scheme for delay-unconstrained heterogeneous wireless network. All source code is publicly available in https://github.com/DanzhouWu/TSRA.

Sampling methods for efficient training of graph convolutional networks: A survey

Graph Convolutional Networks (GCNs) have received significant attention from various research fields due to the excellent performance in learning graph representations. Although GCN performs well compared with other methods, it still faces challenges. Training a GCN model for large-scale graphs in a conventional way requires high computation and storage costs. Therefore, motivated by an urgent need in terms of efficiency and scalability in training GCN, sampling methods have been proposed and achieved a significant effect. In this paper, we categorize sampling methods based on the sampling mechanisms and provide a comprehensive survey of sampling methods for efficient training of GCN. To highlight the characteristics and differences of sampling methods, we present a detailed comparison within each category and further give an overall comparative analysis for the sampling methods in all categories. Finally, we discuss some challenges and future research directions of the sampling methods.

Technical Report for A Joint User Scheduling and Trajectory Planning Data Collection Strategy for the UAV-assisted WSN

Unmanned aerial vehicles (UAVs) are usually dispatched as mobile sinks to assist data collection in large-scale wireless sensor networks (WSNs). However, when considering the limitations of UAVs mobility and communication capabilities in a large-scale WSN, some sensor nodes may run out of storage space as they fail to offload their data to the UAV for an extended period of time. To minimize the data loss caused by the above issue, a joint user scheduling and trajectory planning data collection strategy is proposed in this letter, which is formulated as a non-convex optimization problem. The problem is further divided into two sub-problems and solved sequentially. Simulation results show that the proposed strategy is more effective in minimizing data loss rate than other strategies.

Training and Inference for Integer-Based Semantic Segmentation Network

Semantic segmentation has been a major topic in research and industry in recent years. However, due to the computation complexity of pixel-wise prediction and backpropagation algorithm, semantic segmentation has been demanding in computation resources, resulting in slow training and inference speed and large storage space to store models. Existing schemes that speed up segmentation network change the network structure and come with noticeable accuracy degradation. However, neural network quantization can be used to reduce computation load while maintaining comparable accuracy and original network structure. Semantic segmentation networks are different from traditional deep convolutional neural networks (DCNNs) in many ways, and this topic has not been thoroughly explored in existing works. In this paper, we propose a new quantization framework for training and inference of segmentation networks, where parameters and operations are constrained to 8-bit integer-based values for the first time. Full quantization of the data flow and the removal of square and root operations in batch normalization give our framework the ability to perform inference on fixed-point devices. Our proposed framework is evaluated on mainstream semantic segmentation networks like FCN-VGG16 and DeepLabv3-ResNet50, achieving comparable accuracy against floating-point framework on ADE20K dataset and PASCAL VOC 2012 dataset.

Going Deeper With Directly-Trained Larger Spiking Neural Networks

Spiking neural networks (SNNs) are promising in a bio-plausible coding for spatio-temporal information and event-driven signal processing, which is very suited for energy-efficient implementation in neuromorphic hardware. However, the unique working mode of SNNs makes them more difficult to train than traditional networks. Currently, there are two main routes to explore the training of deep SNNs with high performance. The first is to convert a pre-trained ANN model to its SNN version, which usually requires a long coding window for convergence and cannot exploit the spatio-temporal features during training for solving temporal tasks. The other is to directly train SNNs in the spatio-temporal domain. But due to the binary spike activity of the firing function and the problem of gradient vanishing or explosion, current methods are restricted to shallow architectures and thereby difficult in harnessing large-scale datasets (e.g. ImageNet). To this end, we propose a threshold-dependent batch normalization (tdBN) method based on the emerging spatio-temporal backpropagation, termed STBP-tdBN, enabling direct training of a very deep SNN and the efficient implementation of its inference on neuromorphic hardware. With the proposed method and elaborated shortcut connection, we significantly extend directly-trained SNNs from a shallow structure ( < 10 layer) to a very deep structure (50 layers). Furthermore, we theoretically analyze the effectiveness of our method based on Block Dynamical Isometry theory. Finally, we report superior accuracy results including 93.15 % on CIFAR-10, 67.8 % on DVS-CIFAR10, and 67.05% on ImageNet with very few timesteps. To our best knowledge, its the first time to explore the directly-trained deep SNNs with high performance on ImageNet.

Characterizing and Understanding GCNs on GPU

Graph convolutional neural networks (GCNs) have achieved state-of-the-art performance on graph-structured data analysis. Like traditional neural networks, training and inference of GCNs are accelerated with GPUs. Therefore, characterizing and understanding the execution pattern of GCNs on GPU is important for both software and hardware optimization. Unfortunately, to the best of our knowledge, there is no detailed characterization effort of GCN workloads on GPU. In this paper, we characterize GCN workloads at inference stage and explore GCN models on NVIDIA V100 GPU. Given the characterization and exploration, we propose several useful guidelines for both software optimization and hardware optimization for the efficient execution of GCNs on GPU.