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1. An Extensible Benchmark Suite for Learning to Simulate Physical Systems

   Otness, Karl; Gjoka, Arvi; Bruna, Joan; Panozzo, Daniele; Peherstorfer, Ben; Schneider, Teseo; Zorin, Denis (April 2021, International Conference on Learning Representations, physical simulation workshop)

   null (Ed.)

   Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations methods, motivated by the opportunity to reduce computational costs and/or learn new physical models leveraging access to large collections of data. However, the diversity of problem settings and applications has led to a plethora of approaches, each one evaluated on a different setup and with different evaluation metrics. We introduce a set of benchmark problems to take a step towards unified benchmarks and evaluation protocols. We propose four representative physical systems, as well as a collection of both widely used classical time integrators and representative data-driven methods (kernel-based, MLP, CNN, Nearest-Neighbors). Our framework allows to evaluate objectively and systematically the stability, accuracy, and computational efficiency of data-driven methods. Additionally, it is configurable to permit adjustments for accommodating other learning tasks and for establishing a foundation for future developments in machine learning for scientific computing. 

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2. An Extensible Benchmark Suite for Learning to Simulate Physical Systems

   Karl Otness; Arvi Gjoka; Teseo Schneider; Daniele Panozzo; Denis Zorin; Joan Bruna (December 2021, Advances in neural information processing systems)

   Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations methods, motivated by the opportunity to reduce computational costs and/or learn new physical models leveraging access to large collections of data. However, the diversity of problem settings and applications has led to a plethora of approaches, each one evaluated on a different setup and with different evaluation metrics. We introduce a set of benchmark problems to take a step towards unified benchmarks and evaluation protocols. We propose four representative physical systems, as well as a collection of both widely used classical time integrators and representative data-driven methods (kernel-based, MLP, CNN, nearest neighbors). Our framework allows evaluating objectively and systematically the stability, accuracy, and computational efficiency of data-driven methods. Additionally, it is configurable to permit adjustments for accommodating other learning tasks and for establishing a foundation for future developments in machine learning for scientific computing. 

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3. Machine Learning Methods in Drug Discovery

   https://doi.org/10.3390/molecules25225277  

   Patel, Lauv; Shukla, Tripti; Huang, Xiuzhen; Ussery, David W.; Wang, Shanzhi (November 2020, Molecules)

   null (Ed.)

   The advancements of information technology and related processing techniques have created a fertile base for progress in many scientific fields and industries. In the fields of drug discovery and development, machine learning techniques have been used for the development of novel drug candidates. The methods for designing drug targets and novel drug discovery now routinely combine machine learning and deep learning algorithms to enhance the efficiency, efficacy, and quality of developed outputs. The generation and incorporation of big data, through technologies such as high-throughput screening and high through-put computational analysis of databases used for both lead and target discovery, has increased the reliability of the machine learning and deep learning incorporated techniques. The use of these virtual screening and encompassing online information has also been highlighted in developing lead synthesis pathways. In this review, machine learning and deep learning algorithms utilized in drug discovery and associated techniques will be discussed. The applications that produce promising results and methods will be reviewed. 

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4. Privacy-Preserving Graph Machine Learning from Data to Computation: A Survey

   https://doi.org/10.1145/3606274.3606280  

   Fu, Dongqi; Bao, Wenxuan; Maciejewski, Ross; Tong, Hanghang; He, Jingrui (June 2023, ACM SIGKDD Explorations Newsletter)

   In graph machine learning, data collection, sharing, and analysis often involve multiple parties, each of which may require varying levels of data security and privacy. To this end, preserving privacy is of great importance in protecting sensitive information. In the era of big data, the relationships among data entities have become unprecedentedly complex, and more applications utilize advanced data structures (i.e., graphs) that can support network structures and relevant attribute information. To date, many graph-based AI models have been proposed (e.g., graph neural networks) for various domain tasks, like computer vision and natural language processing. In this paper, we focus on reviewing privacypreserving techniques of graph machine learning. We systematically review related works from the data to the computational aspects. We rst review methods for generating privacy-preserving graph data. Then we describe methods for transmitting privacy-preserved information (e.g., graph model parameters) to realize the optimization-based computation when data sharing among multiple parties is risky or impossible. In addition to discussing relevant theoretical methodology and software tools, we also discuss current challenges and highlight several possible future research opportunities for privacy-preserving graph machine learning. Finally, we envision a uni ed and comprehensive secure graph machine learning system. 

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5. Charged Particle Tracking via Edge-Classifying Interaction Networks

   https://doi.org/10.1007/s41781-021-00073-z  

   DeZoort, Gage; Thais, Savannah; Duarte, Javier; Razavimaleki, Vesal; Atkinson, Markus; Ojalvo, Isobel; Neubauer, Mark; Elmer, Peter (November 2021, Computing and Software for Big Science)

   Abstract Recent work has demonstrated that geometric deep learning methods such as graph neural networks (GNNs) are well suited to address a variety of reconstruction problems in high-energy particle physics. In particular, particle tracking data are naturally represented as a graph by identifying silicon tracker hits as nodes and particle trajectories as edges, given a set of hypothesized edges, edge-classifying GNNs identify those corresponding to real particle trajectories. In this work, we adapt the physics-motivated interaction network (IN) GNN toward the problem of particle tracking in pileup conditions similar to those expected at the high-luminosity Large Hadron Collider. Assuming idealized hit filtering at various particle momenta thresholds, we demonstrate the IN’s excellent edge-classification accuracy and tracking efficiency through a suite of measurements at each stage of GNN-based tracking: graph construction, edge classification, and track building. The proposed IN architecture is substantially smaller than previously studied GNN tracking architectures; this is particularly promising as a reduction in size is critical for enabling GNN-based tracking in constrained computing environments. Furthermore, the IN may be represented as either a set of explicit matrix operations or a message passing GNN. Efforts are underway to accelerate each representation via heterogeneous computing resources towards both high-level and low-latency triggering applications. 

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