Boyuan Feng

Yuke Wang, Boyuan Feng, Zheng Wang et al. · deepmind

The increasing size of input graphs for graph neural networks (GNNs) highlights the demand for using multi-GPU platforms. However, existing multi-GPU GNN systems optimize the computation and communication individually based on the conventional practice of scaling dense DNNs. For irregularly sparse and fine-grained GNN workloads, such solutions miss the opportunity to jointly schedule/optimize the computation and communication operations for high-performance delivery. To this end, we propose MGG, a novel system design to accelerate full-graph GNNs on multi-GPU platforms. The core of MGG is its novel dynamic software pipeline to facilitate fine-grained computation-communication overlapping within a GPU kernel. Specifically, MGG introduces GNN-tailored pipeline construction and GPU-aware pipeline mapping to facilitate workload balancing and operation overlapping. MGG also incorporates an intelligent runtime design with analytical modeling and optimization heuristics to dynamically improve the execution performance. Extensive evaluation reveals that MGG outperforms state-of-the-art full-graph GNN systems across various settings: on average 4.41X, 4.81X, and 10.83X faster than DGL, MGG-UVM, and ROC, respectively.

Boyuan Feng, Tianqi Tang, Yuke Wang et al.

Transformer verification draws increasing attention in machine learning research and industry. It formally verifies the robustness of transformers against adversarial attacks such as exchanging words in a sentence with synonyms. However, the performance of transformer verification is still not satisfactory due to bound-centric computation which is significantly different from standard neural networks. In this paper, we propose Faith, an efficient framework for transformer verification on GPUs. We first propose a semantic-aware computation graph transformation to identify semantic information such as bound computation in transformer verification. We exploit such semantic information to enable efficient kernel fusion at the computation graph level. Second, we propose a verification-specialized kernel crafter to efficiently map transformer verification to modern GPUs. This crafter exploits a set of GPU hardware supports to accelerate verification specialized operations which are usually memory-intensive. Third, we propose an expert-guided autotuning to incorporate expert knowledge on GPU backends to facilitate large search space exploration. Extensive evaluations show that Faith achieves $2.1\times$ to $3.4\times$ ($2.6\times$ on average) speedup over state-of-the-art frameworks.

Juechu Dong, Boyuan Feng, Driss Guessous et al.

Over the past 7 years, attention has become one of the most important primitives in deep learning. The primary approach to optimize attention is FlashAttention, which fuses the operation together, drastically improving both the runtime and the memory consumption. However, the importance of FlashAttention combined with its monolithic nature poses a problem for researchers aiming to try new attention variants -- a "software lottery". This problem is exacerbated by the difficulty of writing efficient fused attention kernels, resisting traditional compiler-based approaches. We introduce FlexAttention, a novel compiler-driven programming model that allows implementing the majority of attention variants in a few lines of idiomatic PyTorch code. We demonstrate that many existing attention variants (e.g. Alibi, Document Masking, PagedAttention, etc.) can be implemented via FlexAttention, and that we achieve competitive performance compared to these handwritten kernels. Finally, we demonstrate how FlexAttention allows for easy composition of attention variants, solving the combinatorial explosion of attention variants.

Ruting Cheng, Boyuan Feng, Yijiang Zheng et al.

Accurately assessing the risk of cesarean section (CS) delivery is critical, especially in settings with limited medical resources, where access to healthcare is often restricted. Early and reliable risk prediction allows better-informed prenatal care decisions and can improve maternal and neonatal outcomes. However, most existing predictive models are tailored for in-hospital use during labor and rely on parameters that are often unavailable in resource-limited or home-based settings. In this study, we conduct a pilot investigation to examine the feasibility of using 3D body shape for CS risk assessment for future applications with more affordable general devices. We propose a novel multi-view-based Transformer network, MvBody, which predicts CS risk using only self-reported medical data and 3D optical body scans obtained between the 31st and 38th weeks of gestation. To enhance training efficiency and model generalizability in data-scarce environments, we incorporate a metric learning loss into the network. Compared to widely used machine learning models and the latest advanced 3D analysis methods, our method demonstrates superior performance, achieving an accuracy of 84.62% and an Area Under the Receiver Operating Characteristic Curve (AUC-ROC) of 0.724 on the independent test set. To improve transparency and trust in the model's predictions, we apply the Integrated Gradients algorithm to provide theoretically grounded explanations of the model's decision-making process. Our results indicate that pre-pregnancy weight, maternal age, obstetric history, previous CS history, and body shape, particularly around the head and shoulders, are key contributors to CS risk prediction.

Jiacen Xu, Zhe Zhou, Boyuan Feng et al.

Recent research efforts on 3D point cloud semantic segmentation (PCSS) have achieved outstanding performance by adopting neural networks. However, the robustness of these complex models have not been systematically analyzed. Given that PCSS has been applied in many safety-critical applications like autonomous driving, it is important to fill this knowledge gap, especially, how these models are affected under adversarial samples. As such, we present a comparative study of PCSS robustness. First, we formally define the attacker's objective under performance degradation and object hiding. Then, we develop new attack by whether to bound the norm. We evaluate different attack options on two datasets and three PCSS models. We found all the models are vulnerable and attacking point color is more effective. With this study, we call the attention of the research community to develop new approaches to harden PCSS models.

Yuke Wang, Boyuan Feng, Zheng Wang et al.

Recently, graph neural networks (GNNs), as the backbone of graph-based machine learning, demonstrate great success in various domains (e.g., e-commerce). However, the performance of GNNs is usually unsatisfactory due to the highly sparse and irregular graph-based operations. To this end, we propose TC-GNN, the first GNN acceleration framework based on GPU Tensor Core Units (TCUs). The core idea is to reconcile the "Sparse" GNN computation with the high-performance "Dense" TCUs. Specifically, we conduct an in-depth analysis of the sparse operations in mainstream GNN computing frameworks. We introduce a novel sparse graph translation technique to facilitate TCU processing of the sparse GNN workload. We implement an effective CUDA core and TCU collaboration design to fully utilize GPU resources. We integrate TC-GNN with the PyTorch framework for high programmability. Rigorous experiments show an average of 1.70X speedup over the state-of-the-art DGL framework across various models and datasets.

Anbang Wu, Gushu Li, Yuke Wang et al.

Variational quantum algorithms are expected to demonstrate the advantage of quantum computing on near-term noisy quantum computers. However, training such variational quantum algorithms suffers from gradient vanishing as the size of the algorithm increases. Previous work cannot handle the gradient vanishing induced by the inevitable noise effects on realistic quantum hardware. In this paper, we propose a novel training scheme to mitigate such noise-induced gradient vanishing. We first introduce a new cost function of which the gradients are significantly augmented by employing traceless observables in truncated subspace. We then prove that the same minimum can be reached by optimizing the original cost function with the gradients from the new cost function. Experiments show that our new training scheme is highly effective for major variational quantum algorithms of various tasks.

Yuke Wang, Boyuan Feng, Yufei Ding

As the key advancement of the convolutional neural networks (CNNs), depthwise separable convolutions (DSCs) are becoming one of the most popular techniques to reduce the computations and parameters size of CNNs meanwhile maintaining the model accuracy. It also brings profound impact to improve the applicability of the compute- and memory-intensive CNNs to a broad range of applications, such as mobile devices, which are generally short of computation power and memory. However, previous research in DSCs are largely focusing on compositing the limited existing DSC designs, thus, missing the opportunities to explore more potential designs that can achieve better accuracy and higher computation/parameter reduction. Besides, the off-the-shelf convolution implementations offer limited computing schemes, therefore, lacking support for DSCs with different convolution patterns. To this end, we introduce, DSXplore, the first optimized design for exploring DSCs on CNNs. Specifically, at the algorithm level, DSXplore incorporates a novel factorized kernel -- sliding-channel convolution (SCC), featured with input-channel overlapping to balance the accuracy performance and the reduction of computation and memory cost. SCC also offers enormous space for design exploration by introducing adjustable kernel parameters. Further, at the implementation level, we carry out an optimized GPU-implementation tailored for SCC by leveraging several key techniques, such as the input-centric backward design and the channel-cyclic optimization. Intensive experiments on different datasets across mainstream CNNs show the advantages of DSXplore in balancing accuracy and computation/parameter reduction over the standard convolution and the existing DSCs.

Boyuan Feng, Yuke Wang, Zheng Wang et al.

With the increasing popularity of graph-based learning, graph neural networks (GNNs) emerge as the essential tool for gaining insights from graphs. However, unlike the conventional CNNs that have been extensively explored and exhaustively tested, people are still worrying about the GNNs' robustness under the critical settings, such as financial services. The main reason is that existing GNNs usually serve as a black-box in predicting and do not provide the uncertainty on the predictions. On the other side, the recent advancement of Bayesian deep learning on CNNs has demonstrated its success of quantifying and explaining such uncertainties to fortify CNN models. Motivated by these observations, we propose UAG, the first systematic solution to defend adversarial attacks on GNNs through identifying and exploiting hierarchical uncertainties in GNNs. UAG develops a Bayesian Uncertainty Technique (BUT) to explicitly capture uncertainties in GNNs and further employs an Uncertainty-aware Attention Technique (UAT) to defend adversarial attacks on GNNs. Intensive experiments show that our proposed defense approach outperforms the state-of-the-art solutions by a significant margin.

Boyuan Feng, Yuke Wang, Xu Li et al.

Graph neural networks (GNNs) have achieved high performance in analyzing graph-structured data and have been widely deployed in safety-critical areas, such as finance and autonomous driving. However, only a few works have explored GNNs' robustness to adversarial attacks, and their designs are usually limited by the scale of input datasets (i.e., focusing on small graphs with only thousands of nodes). In this work, we propose, SAG, the first scalable adversarial attack method with Alternating Direction Method of Multipliers (ADMM). We first decouple the large-scale graph into several smaller graph partitions and cast the original problem into several subproblems. Then, we propose to solve these subproblems using projected gradient descent on both the graph topology and the node features that lead to considerably lower memory consumption compared to the conventional attack methods. Rigorous experiments further demonstrate that SAG can significantly reduce the computation and memory overhead compared with the state-of-the-art approach, making SAG applicable towards graphs with large size of nodes and edges.

Yuke Wang, Boyuan Feng, Xueqiao Peng et al.

With the increasing popularity of deep learning, Convolutional Neural Networks (CNNs) have been widely applied in various domains, such as image classification and object detection, and achieve stunning success in terms of their high accuracy over the traditional statistical methods. To exploit the potential of CNN models, a huge amount of research and industry efforts have been devoted to optimizing CNNs. Among these endeavors, CNN architecture design has attracted tremendous attention because of its great potential of improving model accuracy or reducing model complexity. However, existing work either introduces repeated training overhead in the search process or lacks an interpretable metric to guide the design. To clear these hurdles, we propose 3D-Receptive Field (3DRF), an explainable and easy-to-compute metric, to estimate the quality of a CNN architecture and guide the search process of designs. To validate the effectiveness of 3DRF, we build a static optimizer to improve the CNN architectures at both the stage level and the kernel level. Our optimizer not only provides a clear and reproducible procedure but also mitigates unnecessary training efforts in the architecture search process. Extensive experiments and studies show that the models generated by our optimizer can achieve up to 5.47% accuracy improvement and up to 65.38% parameters deduction, compared with state-of-the-art CNN structures like MobileNet and ResNet.

Boyuan Feng, Yuke Wang, Xu Li et al.

With the increasing popularity of graph-based learning, Graph Neural Networks (GNNs) win lots of attention from the research and industry field because of their high accuracy. However, existing GNNs suffer from high memory footprints (e.g., node embedding features). This high memory footprint hurdles the potential applications towards memory-constrained devices, such as the widely-deployed IoT devices. To this end, we propose a specialized GNN quantization scheme, SGQuant, to systematically reduce the GNN memory consumption. Specifically, we first propose a GNN-tailored quantization algorithm design and a GNN quantization fine-tuning scheme to reduce memory consumption while maintaining accuracy. Then, we investigate the multi-granularity quantization strategy that operates at different levels (components, graph topology, and layers) of GNN computation. Moreover, we offer an automatic bit-selecting (ABS) to pinpoint the most appropriate quantization bits for the above multi-granularity quantizations. Intensive experiments show that SGQuant can effectively reduce the memory footprint from 4.25x to 31.9x compared with the original full-precision GNNs while limiting the accuracy drop to 0.4% on average.

Lingwei Xie, Song He, Shu Yang et al.

With the rapid development of high-throughput technologies, parallel acquisition of large-scale drug-informatics data provides huge opportunities to improve pharmaceutical research and development. One significant application is the purpose prediction of small molecule compounds, aiming to specify therapeutic properties of extensive purpose-unknown compounds and to repurpose novel therapeutic properties of FDA-approved drugs. Such problem is very challenging since compound attributes contain heterogeneous data with various feature patterns such as drug fingerprint, drug physicochemical property, drug perturbation gene expression. Moreover, there is complex nonlinear dependency among heterogeneous data. In this paper, we propose a novel domain-adversarial multi-task framework for integrating shared knowledge from multiple domains. The framework utilizes the adversarial strategy to effectively learn target representations and models their nonlinear dependency. Experiments on two real-world datasets illustrate that the performance of our approach obtains an obvious improvement over competitive baselines. The novel therapeutic properties of purpose-unknown compounds we predicted are mostly reported or brought to the clinics. Furthermore, our framework can integrate various attributes beyond the three domains examined here and can be applied in the industry for screening the purpose of huge amounts of as yet unidentified compounds. Source codes of this paper are available on Github.