Applications and Techniques for Fast Machine Learning in Science

In this community review report, we discuss applications and techniques for fast machine learning (ML) in science -- the concept of integrating power ML methods into the real-time experimental data processing loop to accelerate scientific discovery. The material for the report builds on two workshops held by the Fast ML for Science community and covers three main areas: applications for fast ML across a number of scientific domains; techniques for training and implementing performant and resource-efficient ML algorithms; and computing architectures, platforms, and technologies for deploying these algorithms. We also present overlapping challenges across the multiple scientific domains where common solutions can be found. This community report is intended to give plenty of examples and inspiration for scientific discovery through integrated and accelerated ML solutions. This is followed by a high-level overview and organization of technical advances, including an abundance of pointers to source material, which can enable these breakthroughs.

Program-to-Circuit: Exploiting GNNs for Program Representation and Circuit Translation

Circuit design is complicated and requires extensive domain-specific expertise. One major obstacle stuck on the way to hardware agile development is the considerably time-consuming process of accurate circuit quality evaluation. To significantly expedite the circuit evaluation during the translation from behavioral languages to circuit designs, we formulate it as a Program-to-Circuit problem, aiming to exploit the representation power of graph neural networks (GNNs) by representing C/C++ programs as graphs. The goal of this work is four-fold. First, we build a standard benchmark containing 40k C/C++ programs, each of which is translated to a circuit design with actual hardware quality metrics, aiming to facilitate the development of effective GNNs targeting this high-demand circuit design area. Second, 14 state-of-the-art GNN models are analyzed on the Program-to-Circuit problem. We identify key design challenges of this problem, which should be carefully handled but not yet solved by existing GNNs. The goal is to provide domain-specific knowledge for designing GNNs with suitable inductive biases. Third, we discuss three sets of real-world benchmarks for GNN generalization evaluation, and analyze the performance gap between standard programs and the real-case ones. The goal is to enable transfer learning from limited training data to real-world large-scale circuit design problems. Fourth, the Program-to-Circuit problem is a representative within the Program-to-X framework, a set of program-based analysis problems with various downstream tasks. The in-depth understanding of strength and weaknesses in applying GNNs on Program-to-Circuit could largely benefit the entire family of Program-to-X. Pioneering in this direction, we expect more GNN endeavors to revolutionize this high-demand Program-to-Circuit problem and to enrich the expressiveness of GNNs on programs.

Generic Neural Architecture Search via Regression

Most existing neural architecture search (NAS) algorithms are dedicated to the downstream tasks, e.g., image classification in computer vision. However, extensive experiments have shown that, prominent neural architectures, such as ResNet in computer vision and LSTM in natural language processing, are generally good at extracting patterns from the input data and perform well on different downstream tasks. These observations inspire us to ask: Is it necessary to use the performance of specific downstream tasks to evaluate and search for good neural architectures? Can we perform NAS effectively and efficiently while being agnostic to the downstream task? In this work, we attempt to affirmatively answer the above two questions and improve the state-of-the-art NAS solution by proposing a novel and generic NAS framework, termed Generic NAS (GenNAS). GenNAS does not use task-specific labels but instead adopts \textit{regression} on a set of manually designed synthetic signal bases for architecture evaluation. Such a self-supervised regression task can effectively evaluate the intrinsic power of an architecture to capture and transform the input signal patterns, and allow more sufficient usage of training samples. We then propose an automatic task search to optimize the combination of synthetic signals using limited downstream-task-specific labels, further improving the performance of GenNAS. We also thoroughly evaluate GenNAS's generality and end-to-end NAS performance on all search spaces, which outperforms almost all existing works with significant speedup.

On Positional and Structural Node Features for Graph Neural Networks on Non-attributed Graphs

Graph neural networks (GNNs) have been widely used in various graph-related problems such as node classification and graph classification, where the superior performance is mainly established when natural node features are available. However, it is not well understood how GNNs work without natural node features, especially regarding the various ways to construct artificial ones. In this paper, we point out the two types of artificial node features,i.e., positional and structural node features, and provide insights on why each of them is more appropriate for certain tasks,i.e., positional node classification, structural node classification, and graph classification. Extensive experimental results on 10 benchmark datasets validate our insights, thus leading to a practical guideline on the choices between different artificial node features for GNNs on non-attributed graphs. The code is available at https://github.com/zjzijielu/gnn-exp/.

Adversarial Graph Augmentation to Improve Graph Contrastive Learning

Self-supervised learning of graph neural networks (GNN) is in great need because of the widespread label scarcity issue in real-world graph/network data. Graph contrastive learning (GCL), by training GNNs to maximize the correspondence between the representations of the same graph in its different augmented forms, may yield robust and transferable GNNs even without using labels. However, GNNs trained by traditional GCL often risk capturing redundant graph features and thus may be brittle and provide sub-par performance in downstream tasks. Here, we propose a novel principle, termed adversarial-GCL (AD-GCL), which enables GNNs to avoid capturing redundant information during the training by optimizing adversarial graph augmentation strategies used in GCL. We pair AD-GCL with theoretical explanations and design a practical instantiation based on trainable edge-dropping graph augmentation. We experimentally validate AD-GCL by comparing with the state-of-the-art GCL methods and achieve performance gains of up-to $14\%$ in unsupervised, $6\%$ in transfer, and $3\%$ in semi-supervised learning settings overall with 18 different benchmark datasets for the tasks of molecule property regression and classification, and social network classification.

Principled Hyperedge Prediction with Structural Spectral Features and Neural Networks

Hypergraph offers a framework to depict the multilateral relationships in real-world complex data. Predicting higher-order relationships, i.e hyperedge, becomes a fundamental problem for the full understanding of complicated interactions. The development of graph neural network (GNN) has greatly advanced the analysis of ordinary graphs with pair-wise relations. However, these methods could not be easily extended to the case of hypergraph. In this paper, we generalize the challenges of GNN in representing higher-order data in principle, which are edge- and node-level ambiguities. To overcome the challenges, we present SNALS that utilizes bipartite graph neural network with structural features to collectively tackle the two ambiguity issues. SNALS captures the joint interactions of a hyperedge by its local environment, which is retrieved by collecting the spectrum information of their connections. As a result, SNALS achieves nearly 30% performance increase compared with most recent GNN-based models. In addition, we applied SNALS to predict genetic higher-order interactions on 3D genome organization data. SNALS showed consistently high prediction accuracy across different chromosomes, and generated novel findings on 4-way gene interaction, which is further validated by existing literature.

Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns

Graph neural networks (GNNs) have achieved tremendous success on multiple graph-based learning tasks by fusing network structure and node features. Modern GNN models are built upon iterative aggregation of neighbor's/proximity features by message passing. Its prediction performance has been shown to be strongly bounded by assortative mixing in the graph, a key property wherein nodes with similar attributes mix/connect with each other. We observe that real world networks exhibit heterogeneous or diverse mixing patterns and the conventional global measurement of assortativity, such as global assortativity coefficient, may not be a representative statistic in quantifying this mixing. We adopt a generalized concept, node-level assortativity, one that is based at the node level to better represent the diverse patterns and accurately quantify the learnability of GNNs. We find that the prediction performance of a wide range of GNN models is highly correlated with the node level assortativity. To break this limit, in this work, we focus on transforming the input graph into a computation graph which contains both proximity and structural information as distinct type of edges. The resulted multi-relational graph has an enhanced level of assortativity and, more importantly, preserves rich information from the original graph. We then propose to run GNNs on this computation graph and show that adaptively choosing between structure and proximity leads to improved performance under diverse mixing. Empirically, we show the benefits of adopting our transformation framework for semi-supervised node classification task on a variety of real world graph learning benchmarks.

Neural Higher-order Pattern (Motif) Prediction in Temporal Networks

Dynamic systems that consist of a set of interacting elements can be abstracted as temporal networks. Recently, higher-order patterns that involve multiple interacting nodes have been found crucial to indicate domain-specific laws of different temporal networks. This posts us the challenge of designing more sophisticated hypergraph models for these higher-order patterns and the associated new learning algorithms. Here, we propose the first model, named HIT, for higher-order pattern prediction in temporal hypergraphs. Particularly, we focus on predicting three types of common but important interaction patterns involving three interacting elements in temporal networks, which could be extended to even higher-order patterns. HIT extracts the structural representation of a node triplet of interest on the temporal hypergraph and uses it to tell what type of, when, and why the interaction expansion could happen in this triplet. HIT could achieve significant improvement(averaged 20% AUC gain to identify the interaction type, uniformly more accurate time estimation) compared to both heuristic and other neural-network-based baselines on 5 real-world large temporal hypergraphs. Moreover, HIT provides a certain degree of interpretability by identifying the most discriminatory structural features on the temporal hypergraphs for predicting different higher-order patterns.