Graphene is one of the most researched two dimensional (2D) material due to its unique combination of mechanical, thermal and electrical properties. Special 2D structure of graphene enables it to exhibit a wide range of peculiar material properties like high Young's modulus, high specific strength etc. which are critical for myriad of applications including light weight structural materials, multi-functional coating and flexible electronics. It is quite challenging and costly to experimentally investigate graphene/graphene based nanocomposites, computational simulations such as molecular dynamics (MD) simulations are widely adopted for understanding the microscopic origins of their unique properties. However, disparate results were reported from computational studies, especially MD simulations using various empirical inter-atomic potentials. In this work, an artificial neural network based interatomic potential has been developed for graphene to represent the potential energy surface based on first principle calculations. The developed machine learning potential (MLP) facilitates high fidelity MD simulations to approach the accuracy of ab initio methods but with a fraction of computational cost, which allows larger simulation size/length, and thereby enables accelerated discovery/design of graphene-based novel materials. Lattice parameter, coefficient of thermal expansion (CTE), Young's modulus and yield strength are estimated using machine learning accelerated MD simulations (MLMD), which are compared to experimental/first principle calculations from previous literatures. It is demonstrated that MLMD can capture the dominating mechanism governing CTE of graphene, including effects from lattice parameter and out of plane rippling.
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Identification of nonlinear dynamical systems has been popularized by sparse identification of the nonlinear dynamics (SINDy) via the sequentially thresholded least squares (STLS) algorithm. Many extensions SINDy have emerged in the literature to deal with experimental data which are finite in length and noisy. Recently, the computationally intensive method of ensembling bootstrapped SINDy models (E-SINDy) was proposed for model identification, handling finite, highly noisy data. While the extensions of SINDy are numerous, their sparsity-promoting estimators occasionally provide sparse approximations of the dynamics as opposed to exact recovery. Furthermore, these estimators suffer under multicollinearity, e.g. the irrepresentable condition for the Lasso. In this paper, we demonstrate that the Trimmed Lasso for robust identification of models (TRIM) can provide exact recovery under more severe noise, finite data, and multicollinearity as opposed to E-SINDy. Additionally, the computational cost of TRIM is asymptotically equal to STLS since the sparsity parameter of the TRIM can be solved efficiently by convex solvers. We compare these methodologies on challenging nonlinear systems, specifically the Lorenz 63 system, the Bouc Wen oscillator from the nonlinear dynamics benchmark of No\"el and Schoukens, 2016, and a time delay system describing tool cutting dynamics. This study emphasizes the comparisons between STLS, reweighted $\ell_1$ minimization, and Trimmed Lasso in identification with respect to problems faced by practitioners: the problem of finite and noisy data, the performance of the sparse regression of when the library grows in dimension (multicollinearity), and automatic methods for choice of regularization parameters.
An established normative approach for understanding the algorithmic basis of neural computation is to derive online algorithms from principled computational objectives and evaluate their compatibility with anatomical and physiological observations. Similarity matching objectives have served as successful starting points for deriving online algorithms that map onto neural networks (NNs) with point neurons and Hebbian/anti-Hebbian plasticity. These NN models account for many anatomical and physiological observations; however, the objectives have limited computational power and the derived NNs do not explain multi-compartmental neuronal structures and non-Hebbian forms of plasticity that are prevalent throughout the brain. In this article, we unify and generalize recent extensions of the similarity matching approach to address more complex objectives, including a large class of unsupervised and self-supervised learning tasks that can be formulated as symmetric generalized eigenvalue problems or nonnegative matrix factorization problems. Interestingly, the online algorithms derived from these objectives naturally map onto NNs with multi-compartmental neurons and local, non-Hebbian learning rules. Therefore, this unified extension of the similarity matching approach provides a normative framework that facilitates understanding multi-compartmental neuronal structures and non-Hebbian plasticity found throughout the brain.
Mesh-based simulations play a key role when modeling complex physical systems that, in many disciplines across science and engineering, require the solution of parametrized time-dependent nonlinear partial differential equations (PDEs). In this context, full order models (FOMs), such as those relying on the finite element method, can reach high levels of accuracy, however often yielding intensive simulations to run. For this reason, surrogate models are developed to replace computationally expensive solvers with more efficient ones, which can strike favorable trade-offs between accuracy and efficiency. This work explores the potential usage of graph neural networks (GNNs) for the simulation of time-dependent PDEs in the presence of geometrical variability. In particular, we propose a systematic strategy to build surrogate models based on a data-driven time-stepping scheme where a GNN architecture is used to efficiently evolve the system. With respect to the majority of surrogate models, the proposed approach stands out for its ability of tackling problems with parameter dependent spatial domains, while simultaneously generalizing to different geometries and mesh resolutions. We assess the effectiveness of the proposed approach through a series of numerical experiments, involving both two- and three-dimensional problems, showing that GNNs can provide a valid alternative to traditional surrogate models in terms of computational efficiency and generalization to new scenarios. We also assess, from a numerical standpoint, the importance of using GNNs, rather than classical dense deep neural networks, for the proposed framework.
We present Surjective Sequential Neural Likelihood (SSNL) estimation, a novel method for simulation-based inference in models where the evaluation of the likelihood function is not tractable and only a simulator that can generate synthetic data is available. SSNL fits a dimensionality-reducing surjective normalizing flow model and uses it as a surrogate likelihood function which allows for conventional Bayesian inference using either Markov chain Monte Carlo methods or variational inference. By embedding the data in a low-dimensional space, SSNL solves several issues previous likelihood-based methods had when applied to high-dimensional data sets that, for instance, contain non-informative data dimensions or lie along a lower-dimensional manifold. We evaluate SSNL on a wide variety of experiments and show that it generally outperforms contemporary methods used in simulation-based inference, for instance, on a challenging real-world example from astrophysics which models the magnetic field strength of the sun using a solar dynamo model.
We propose a novel stochastic algorithm that randomly samples entire rows and columns of the matrix as a way to approximate an arbitrary matrix function. This contrasts with the "classical" Monte Carlo method which only works with one entry at a time, resulting in a significant better convergence rate than the "classical" approach. To assess the applicability of our method, we compute the subgraph centrality and total communicability of several large networks. In all benchmarks analyzed so far, the performance of our method was significantly superior to the competition, being able to scale up to 64 CPU cores with a remarkable efficiency.
Nonlinear extensions to the active subspaces method have brought remarkable results for dimension reduction in the parameter space and response surface design. We further develop a kernel-based nonlinear method. In particular we introduce it in a broader mathematical framework that contemplates also the reduction in parameter space of multivariate objective functions. The implementation is thoroughly discussed and tested on more challenging benchmarks than the ones already present in the literature, for which dimension reduction with active subspaces produces already good results. Finally, we show a whole pipeline for the design of response surfaces with the new methodology in the context of a parametric CFD application solved with the Discontinuous Galerkin method.
Graph Neural Networks (GNNs) are becoming increasingly popular due to their superior performance in critical graph-related tasks. While quantization is widely used to accelerate GNN computation, quantized training faces unprecedented challenges. Current quantized GNN training systems often have longer training times than their full-precision counterparts for two reasons: (i) addressing the accuracy challenge leads to excessive overhead, and (ii) the optimization potential exposed by quantization is not adequately leveraged. This paper introduces Tango which re-thinks quantization challenges and opportunities for graph neural network training on GPUs with three contributions: Firstly, we introduce efficient rules to maintain accuracy during quantized GNN training. Secondly, we design and implement quantization-aware primitives and inter-primitive optimizations that can speed up GNN training. Finally, we integrate Tango with the popular Deep Graph Library (DGL) system and demonstrate its superior performance over state-of-the-art approaches on various GNN models and datasets.
Most state-of-the-art machine learning techniques revolve around the optimisation of loss functions. Defining appropriate loss functions is therefore critical to successfully solving problems in this field. We present a survey of the most commonly used loss functions for a wide range of different applications, divided into classification, regression, ranking, sample generation and energy based modelling. Overall, we introduce 33 different loss functions and we organise them into an intuitive taxonomy. Each loss function is given a theoretical backing and we describe where it is best used. This survey aims to provide a reference of the most essential loss functions for both beginner and advanced machine learning practitioners.
We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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