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At least 1,513 records · Page 84

wa-hls4ml and lui-gnn: A benchmark and GNN-based surrogate model for hls4ml resource and latency estimation

As machine learning (ML) increasingly serves as a tool for addressing real-time challenges in scientific applications, the development of advanced tooling has significantly reduced the time required to iterate on various designs. These advancements have solved major obstacles, but also exposed new challenges. For example, processes that were not previously considered bottlenecks, such as model synthesis, are now becoming limiting factors in the rapid iteration of designs. To reduce these emerging constraints, multiple efforts are being launched toward designing an ML-based surrogate model that estimates resource usage of synthesized accelerator architectures. This model would reduce the design iteration time, especially when designing within a set of given hardware constraints. This approach shows considerable potential, but as it stands, the effort is early and would benefit from coordination and standardization to assist future work as it emerges. We introduce wa-hls4ml, a benchmark for ML accelerator resource and latency estimation, and its corresponding initial dataset of more than 100,000 fully connected neural networks, all synthesized using hls4ml and targeting Xilinx FPGAs. In addition to the resource utilization and latency data provided, the dataset includes generated artifacts and log files for many of the synthesized neural networks, in order to support future research in ML-based code generation. The benchmark evaluates the performance of resource and latency predictors against several common ML model architectures, primarily originating from scientific domains, as exemplar models, as well as the average performance across a subset of the dataset. We measure the performance of a given predictor model through multiple metrics, including $R^2$ score and SMAPE on regression tasks, as well as inference time to further characterize the estimator under test. Additionally, we introduce the latency/utilization inference graph neural network (lui-gnn), a surrogate model that uses a graph neural network to represent input architectures in the form of a directed graph. This graph representation allows for a diverse set of model architectures to all be effectively handled by a surrogate model. We present the architecture and performance of the model, as evaluated by the new proposed benchmark, including SMAPE, $R^2$ score, and inference times, and find that lui-gnn generally predicts latency and utilization for the 75\% quantile within several percent of the synthesized resources on the synthetic test dataset, indicating that this approach of estimating resource and latency via a surrogate models has promise and warrants further research.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Kinematic flow from the flow of cuts

The wavefunction coefficients of conformally coupled scalars in power-law FRW cosmologies satisfy differential equations governed by a set of simple combinatorial rules known as the kinematic flow. In this paper we derive the kinematic flow, expressed using a set of differential forms referred to as the cut basis, from a geometric perspective, relying solely on the cosmological hyperplane arrangement and without invoking bulk physics. Each element of the cut basis corresponds to the positive geometry associated to an independent cut of the physical FRW-form and can be labeled by decorating (minors of) the truncated Feynman graph with an acyclic orientation. We provide a straightforward prescription to associate a logarithmic differential form to each element of the cut basis by considering its corresponding decorated graph. Moreover, we show that the residues of the physical FRW-form are canonical forms of certain graphical zonotopes labeled by the same set of decorated graphs. These zonotopes control the cut combinatorics -- flow of cuts -- of the physical FRW-form and the cut basis (by construction). Using the theory of relative twisted cohomology and intersection theory, we derive a closed form formula for the differential equations of the cut basis. We also introduce combinatorial rules that compute the kinematic differential of any basis element without explicit calculation. The combinatorics of our differential equations is a natural consequence of the flow of cuts and is equivalent (up to rescaling) to the kinematic flow for the recently studied time integral basis. In particular, our differential equations decouple into exponentially many sectors, one for each way of cutting a subset of edges of the graph.

General Relativity and Quantum Cosmology↗

Integrating multiple data sources for malware classification

Disclosed herein are representative embodiments of tools and techniques for classifying programs. According to one exemplary technique, at least one graph representation of at least one dynamic data source of at least one program is generated. Also, at least one graph representation of at least one static data source of the at least one program is generated. Additionally, at least using the at least one graph representation of the at least one dynamic data source and the at least one graph representation of the at least one static data source, the at least one program is classified.

97 MATHEMATICS AND COMPUTING↗

Path Finder

PathFinder is a graph search program, traversing a directed cyclic graph to find pathways between labeled nodes. Searches for paths through ordered sequences of labels are termed signatures. Determining the presence of signatures within one or more graphs is the primary function of Path Finder. Path Finder can work in either batch mode or interactively with an analyst. Results are limited to Path Finder whether or not a given signature is present in the graph(s).

Rigdon, J. Brian↗

Graph500 in OpenSHMEM

This document describes the effort to implement the Graph 500 benchmark using OpenSHMEM based on the MPI-2 one-side version. The Graph 500 benchmark performs a breadth-first search in parallel on a large randomly generated undirected graph and can be implemented using basic MPI-1 and MPI-2 one-sided communication. Graph 500 requires atomic bit-wise operations on unsigned long integers but neither atomic bit-wise operations nor OpenSHMEM for unsigned long are available in OpenSHEM. Such needed bit-wise atomic operations and support for unsigned long are implemented using atomic condition swap (CSWAP) on signed long integers. Preliminary results on comparing the OpenSHMEM and MPI-2 one-sided implementations on a Silicon Graphics Incorporated (SGI) cluster and the Cray XK7 are presented.

openshmem graph500↗

Path scanning for the detection of anomalous subgraphs and use of DNS requests and host agents for anomaly/change detection and network situational awareness

A system, apparatus, computer-readable medium, and computer-implemented method are provided for detecting anomalous behavior in a network. Historical parameters of the network are determined in order to determine normal activity levels. A plurality of paths in the network are enumerated as part of a graph representing the network, where each computing system in the network may be a node in the graph and the sequence of connections between two computing systems may be a directed edge in the graph. A statistical model is applied to the plurality of paths in the graph on a sliding window basis to detect anomalous behavior. Data collected by a Unified Host Collection Agent ("UHCA") may also be used to detect anomalous behavior.

97 MATHEMATICS AND COMPUTING↗

Considerations on the Use of Custom Accelerators for Big Data Analytics

Accelerators, including Graphic Processing Units (GPUs) for gen- eral purpose computation, many-core designs with wide vector units (e.g., Intel Phi), have become a common component of many high performance clusters. The appearance of more stable and reliable tools tools that can automatically convert code written in high-level specifications with annotations (such as C or C++) to hardware de- scription languages (High-Level Synthesis - HLS), is also setting the stage for a broader use of reconfigurable devices (e.g., Field Pro- grammable Gate Arrays - FPGAs) in high performance system for the implementation of custom accelerators, helped by the fact that new processors include advanced cache-coherent interconnects for these components. In this chapter, we briefly survey the status of the use of accelerators in high performance systems targeted at big data analytics applications. We argue that, although the progress in the use of accelerators for this class of applications has been sig- nificant, differently from scientific simulations there still are gaps to close. This is particularly true for the ”irregular” behaviors exhibited by no-SQL, graph databases. We focus our attention on the limits of HLS tools for data analytics and graph methods, and discuss a new architectural template that better fits the requirement of this class of applications. We validate the new architectural templates by mod- ifying the Graph Engine for Multithreaded System (GEMS) frame- work to support accelerators generated with such a methodology, and testing with queries coming from the Lehigh University Benchmark (LUBM). The architectural template enables better supporting the task and memory level parallelism present in graph methods by sup- porting a new control model and a enhanced memory interface. We show that out solution allows generating parallel accelerators, pro- viding speed ups with respect to conventional HLS flows. We finally draw conclusions and present a perspective on the use of reconfig- urable devices and Design Automation tools for data analytics.

Data Analytics↗

Exploiting Literature-Based Discovery to Study Effects of Bullying

Bullying represents an aggressive behavioral problem. It can create severe mental illness in children, adolescents, and adults. Researchers are interested in studying bullying to understand its long-term negative consequences and design better-targeted intervention programs. Broadly researchers in psychology and education have conducted studies on bullying without using advanced analytical features offered by the computer science domain. However, researchers could benefit from power of advanced analytics for an in-depth understanding of bullying. In this paper, we present graph-based advanced analytics by employing a literature-based discovery (LBD) approach to study the direct and indirect consequences of bullying from published literature. In addition, we describe a graph-based study on the evolution of research on bullying consequences in the last two decades. Our graph-based study reveals a summary view of associations of bullying with other diseases and disorders from published literature. Further, we employ literature reference information to quantify the strength of the graph-derived relationships. We demonstrate that LBD is a valuable approach to perform advanced analytics on bullying that helps us to understand the severity of its consequences.

Hasan, S M Shamimul↗

Path scanning for the detection of anomalous subgraphs and use of DNS requests and host agents for anomaly/change detection and network situational awareness

A system, apparatus, computer-readable medium, and computer-implemented method are provided for detecting anomalous behavior in a network. Historical parameters of the network are determined in order to determine normal activity levels. A plurality of paths in the network are enumerated as part of a graph representing the network, where each computing system in the network may be a node in the graph and the sequence of connections between two computing systems may be a directed edge in the graph. A statistical model is applied to the plurality of paths in the graph on a sliding window basis to detect anomalous behavior. Data collected by a Unified Host Collection Agent (“UHCA”) may also be used to detect anomalous behavior.

Neil, Joshua Charles↗

A Scalable Parallel Hypergraph Generator (HyGen)

Graphs are extensively used to model real-world complex systems. An edge in a graph can model pairwise relationships. However, multiway relationships (connections between three or more vertices) are common in many complex systems such as cellular process, image segmentation, and circuit design. A graph edge cannot model multiway relationships. A hypergraph, which can connect more than two vertices, is thus a better option to model multiway relationships. A large-scale hypergraph analysis has the potential to find useful insights from a complex system and assist in knowledge discovery. Currently a limited number of hypergraphs exists that are representative of real-world datasets. Moreover, real-world hypergraph datasets are small in size and inadequate to incorporate future needs. A graph generator that can produce large-scale synthetic hypergraphs can solve the above mentioned problems. In this paper, we present a scalable parallel hypergraph generator (HyGen) based on the Message Passing Interface (MPI) standard. To generate hypergraphs, HyGen takes the following parameter values as inputs: i) number of vertices, ii) number of hyperedges, iii) number of clusters, iv) vertex distribution, v) hyperedge distribution, vi) local cluster cardinality, and vii) global cluster cardinality. We have demonstrated that HyGen can generate hypergraphs of various sizes in a scalable fashion. HyGen takes approximately four minutes to generate a hypergraph with 4.8 million vertices, 1.6 million hyperedges, and 800 clusters using 1,024 processes on a leadership class computing platform. Our strong and weak scaling experiments on supercomputers demonstrate that HyGen can quickly create large-scale hypergraphs in a parallel manner, thus providing a useful capability for hypergraph analysis.

Hasan, S M Shamimul↗

Accelerating the Inference of the Exa.TrkX Pipeline

Recently, graph neural networks (GNNs) have been successfully used for a variety of particle reconstruction problems in high energy physics, including particle tracking. The Exa.TrkX pipeline based on GNNs demonstrated promising performance in reconstructing particle tracks in dense environments. It includes five discrete steps: data encoding, graph building, edge filtering, GNN, and track labeling. All steps were written in Python and run on both GPUs and CPUs. In this work, we accelerate the Python implementation of the pipeline through customized and commercial GPU-enabled software libraries, and develop a C++ implementation for inferencing the pipeline. The implementation features an improved, CUDA-enabled fixed-radius nearest neighbor search for graph building and a weakly connected component graph algorithm for track labeling. GNNs and other trained deep learning models are converted to ONNX and inferenced via the ONNX Runtime C++ API. The complete C++ implementation of the pipeline allows integration with existing tracking software. We report the memory usage and average event latency tracking performance of our implementation applied to the TrackML benchmark dataset.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Fuzzy cyber detection pattern matching

Mechanisms for identifying a pattern of computing resource activity of interest, in activity data characterizing activities of computer system elements, are provided. A temporal graph of the activity data is generated and a filter is applied to the temporal graph to generate one or more first vector representations, each characterizing nodes and edges within a moving window defined by the filter. The filter is applied to a pattern graph representing a pattern of entities and events indicative of the pattern of interest, to generate a second vector representation. The second vector representation is compared to the one or more first vector representations to identify one or more nearby vectors, and one or more corresponding subgraph instances are output to an intelligence console computing system as inexact matches of the temporal graph.

Shu, Xiaokui↗

Verification, Validation, and Calibration Through a Causal Lens

While typical validation and verification approaches focus on identifying the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on identifying causal relationships between data elements. Statistical and machine-learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between data sets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify, and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles, it is known as a directed acyclic graph. A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts can identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗

VALIDATION, VERIFICATION, AND CALIBRATION THROUGH A CAUSAL LENS

This paper presents an alternative method based on causal inference to perform validation, verification, and calibration of simulation models. While classical validation and verification approaches focus on the identification of the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on the identification of causal relationships between data elements. Statistical and machine learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between datasets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, then the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles it is known as a directed acyclic graph (DAG). A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and from experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts have a means to identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗

Spectral Threshold for Extremal Cyclic Edge-Connectivity

In this report, the cyclic edge-connectivity of a graph G is the least k such that there exists a set of k edges whose removal disconnects G into components where every component contains a cycle. We show that for graphs of minimum degree at least 3 and girth g at least 4, the cyclic edge-connectivity is bounded above by (Δ-2)g where Δ is the maximum degree. We then prove that if the second eigenvalue of the adjacency matrix of a d-regular graph of girth g ≥ 4 is sufficiently small, then the cyclic edge-connectivity is (d-2)g, providing a spectral condition for when this upper bound on cyclic edge-connectivity is tight.

97 MATHEMATICS AND COMPUTING↗

Geometric and algebraic structures associated with the channel quantization problem

We consider the use of surfaces as topological spaces in order to provide an answer to the quantization problem of a discrete memoryless channel (DMC). The aim is to identify the geometric and algebraic properties of the surface associated with the embedding of such a DMC. The procedure is based on the following steps: knowing the complete bipartite graph associated with a given DMC: (1) to determine the minimum and the maximum genus of the corresponding surfaces in which the given graph is embedded; (2) knowing the genus, to specify the roots as the elements of a Farey sequence of a planar algebraic curve; (3) to determine the solutions of a second-order Fuchsian differential equation as the generators of the corresponding Fuchsian group. We consider the cases of the hypergeometric and Heun equations, with three and four regular singular points, respectively. By means of this procedure, the fundamental region associated with the Fuchsian group is identified and this is the region where the planar algebraic curve is uniformized. A generalization of the quantization problem related to an m-ary input n-ary output symmetric channel viewed as a complete bipartite graph K{sub m,n}, by use of the embedding of this channel in compact surfaces is straightforward.

97 MATHEMATICS AND COMPUTING↗

Intermolecular Network Theory:A General Approach for Understanding the Structural and Dynamic Properties of Liquids and Solutions

Graph theory applications within the physical sciences have a long history. However, it has never moved to the forefront of analytical techniques employed by the computational chemistry community. Though much of the earliest work leveraged percolation theory as a backdrop for understanding critical phenomena and phase transitions within statistical mechanical simulations, modern data science has much to contribute. Here in this paper, we focus on the realm of intermolecular networks, where vertices represent molecules or particles, and an edge represents an intermolecular or interparticle interaction. These interactions are widely understood to dictate many of the physical properties of soft matter, and for liquids in particular, understanding this network is essential. Consider the sheer volume of ~70 years of literature associated with the hydrogen bond network of water, a topic that remains an active area of research even today. The aim of this work is twofold: first, to put into context prior algorithms and analyses that employed “connectedness theory” or lattice-based models to understand the intermolecular networks of chemical systems; and second to discuss a more general strategy for analyzing the multiscale structural and dynamic properties of chemical systems—intermolecular network theory. This approach encompasses foundational methods such as percolation theory, but also utilizes contemporary graph theoretical analyses that have evolved alongside the development of the World Wide Web, cloud computing, and big data. It is the realm of intermolecular network theory to determine the relationships between the essential physics of a system and the topological properties of the network and to derive new techniques in graph theory that can be related to the underlying physico-chemical or reactive properties of a system. Examples are used throughout this chapter that demonstrate applications to a wide variety of complex chemical systems, including ion association within electrolytes, mass transport and the properties of liquid–liquid phase boundaries, and multicomponent solutions.

Complex networks↗

Inherent limits on optimization and discovery in physical systems

Topological mapping of a large physical system on a graph, and its decomposition using universal measures are proposed. We find inherent limits to the potential for optimization of a given system and its approximate representations by motifs, and the ability to reconstruct the full system given approximate representations. The approximate representation of the system most suited for optimization may be different from that which most accurately describes the full system. - Highlights: • Graph-based approach to analyze full and partial representations of physical systems. • Direct link between a change in the physical system and complexity of the graph. • Inherent limits to the potential for optimization of a general system. • Inherent limits to the reconstruction of full system from partial representations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗