We introduce PyTorch Geometric, a library for deep learning on irregularly structured input data such as graphs, point clouds and manifolds, built upon PyTorch. In addition to general graph data structures and processing methods, it contains a variety of recently published methods from the domains of relational learning and 3D data processing. PyTorch Geometric achieves high data throughput by leveraging sparse GPU acceleration, by providing dedicated CUDA kernels and by introducing efficient mini-batch handling for input examples of different size. In this work, we present the library in detail and perform a comprehensive comparative study of the implemented methods in homogeneous evaluation scenarios.
Tiered latent representations and latent spaces for molecular graphs provide a simple but effective way to explicitly represent and utilize groups (e.g., functional groups), which consist of the atom (node) tier, the group tier and the molecule (graph) tier. They can be learned using the tiered graph autoencoder architecture. In this paper we discuss adapting tiered graph autoencoders for use with PyTorch Geometric, for both the deterministic tiered graph autoencoder model and the probabilistic tiered variational graph autoencoder model. We also discuss molecular structure information sources …
Heidelberg University（海德堡大学）；Max Planck Institute for Plant Breeding Research（马克斯·普朗克植物育种研究所）；Technical University of Munich（慕尼黑工业大学）
Classifying all cells in an organ is a relevant and difficult problem from plant developmental biology. We here abstract the problem into a new benchmark for node classification in a geo-referenced graph. Solving it requires learning the spatial layout of the organ including symmetries. To allow the convenient testing of new geometrical learning methods, the benchmark of Arabidopsis thaliana ovules is made available as a PyTorch data loader, along with a large number of precomputed features. Finally, we benchmark eight recent graph neural network architectures, finding that DeeperGCN currently…
Argonne National Laboratory（阿贡国家实验室）；University of Michigan（密歇根大学）
As Graph Neural Networks (GNNs) increase in popularity for scientific machine learning, their training and inference efficiency is becoming increasingly critical. Additionally, the deep learning field as a whole is trending towards wider and deeper networks, and ever increasing data sizes, to the point where hard hardware bottlenecks are often encountered. Emerging specialty hardware platforms provide an exciting solution to this problem. In this paper, we systematically profile and select low-level operations pertinent to GNNs for scientific computing implemented in the Pytorch Geometric soft…
AstraZeneca（阿斯利康）；University of Cambridge（剑桥大学）；University of Oxford（牛津大学）；École Polytechnique（巴黎综合理工学院）；Ernst-Abbe University for Applied Sciences（恩斯特·阿贝应用科学大学）；IT University of Copenhagen（哥本哈根信息技术大学）；Central European University（中欧大学）；ELKH SZTAKI（匈牙利科学院计算机科学与控制研究所）；Tryolabs；Pedal Me；The University of Edinburgh（爱丁堡大学）
We present PyTorch Geometric Temporal a deep learning framework combining state-of-the-art machine learning algorithms for neural spatiotemporal signal processing. The main goal of the library is to make temporal geometric deep learning available for researchers and machine learning practitioners in a unified easy-to-use framework. PyTorch Geometric Temporal was created with foundations on existing libraries in the PyTorch eco-system, streamlined neural network layer definitions, temporal snapshot generators for batching, and integrated benchmark datasets. These features are illustrated with a…
National Technical University of Athens（雅典国立技术大学）；Aristotle University of Thessaloniki（塞萨洛尼基亚里士多德大学）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）
Current state-of-the-art employs approximate multipliers to address the highly increased power demands of DNN accelerators. However, evaluating the accuracy of approximate DNNs is cumbersome due to the lack of adequate support for approximate arithmetic in DNN frameworks. We address this inefficiency by presenting AdaPT, a fast emulation framework that extends PyTorch to support approximate inference as well as approximation-aware retraining. AdaPT can be seamlessly deployed and is compatible with the most DNNs. We evaluate the framework on several DNN models and application fields including C…
PGT-I: Scaling Spatiotemporal GNNs with Memory-Efficient Distributed Training
University of Wisconsin-Madison（威斯康星大学麦迪逊分校）；Argonne National Laboratory（阿贡国家实验室）；Arizona State University（亚利桑那州立大学）；Sandia National Laboratories（桑塔纳国家实验室）
Representing and reasoning about 3D structures of macromolecules is emerging as a distinct challenge in machine learning. Here, we extend recent work on geometric vector perceptrons and apply equivariant graph neural networks to a wide range of tasks from structural biology. Our method outperforms all reference architectures on three out of eight tasks in the ATOM3D benchmark, is tied for first on two others, and is competitive with equivariant networks using higher-order representations and spherical harmonic convolutions. In addition, we demonstrate that transfer learning can further improve…
In spite of showing unreasonable effectiveness in modalities like Text and Image, Deep Learning has always lagged Gradient Boosting in tabular data - both in popularity and performance. But recently there have been newer models created specifically for tabular data, which is pushing the performance bar. But popularity is still a challenge because there is no easy, ready-to-use library like Sci-Kit Learn for deep learning. PyTorch Tabular is a new deep learning library which makes working with Deep Learning and tabular data easy and fast. It is a library built on top of PyTorch and PyTorch Ligh…
We introduce the IBM Analog Hardware Acceleration Kit, a new and first of a kind open source toolkit to simulate analog crossbar arrays in a convenient fashion from within PyTorch (freely available at https://github.com/IBM/aihwkit). The toolkit is under active development and is centered around the concept of an "analog tile" which captures the computations performed on a crossbar array. Analog tiles are building blocks that can be used to extend existing network modules with analog components and compose arbitrary artificial neural networks (ANNs) using the flexibility of the PyTorch framewo…
Tsinghua University（清华大学）；Beijing Academy of Artificial Intelligence (BAAI)（北京人工智能研究院）
Mixture-of-Expert (MoE) presents a strong potential in enlarging the size of language model to trillions of parameters. However, training trillion-scale MoE requires algorithm and system co-design for a well-tuned high performance distributed training system. Unfortunately, the only existing platform that meets the requirements strongly depends on Google's hardware (TPU) and software (Mesh Tensorflow) stack, and is not open and available to the public, especially GPU and PyTorch communities. In this paper, we present FastMoE, a distributed MoE training system based on PyTorch with common accel…
We introduce an ODE solver for the PyTorch ecosystem that can solve multiple ODEs in parallel independently from each other while achieving significant performance gains. Our implementation tracks each ODE's progress separately and is carefully optimized for GPUs and compatibility with PyTorch's JIT compiler. Its design lets researchers easily augment any aspect of the solver and collect and analyze internal solver statistics. In our experiments, our implementation is up to 4.3 times faster per step than other ODE solvers and it is robust against within-batch interactions that lead other solve…
FasterAI is a PyTorch-based library, aiming to facilitate the utilization of deep neural networks compression techniques such as sparsification, pruning, knowledge distillation, or regularization. The library is built with the purpose of enabling quick implementation and experimentation. More particularly, compression techniques are leveraging Callback systems of libraries such as fastai and Pytorch Lightning to bring a user-friendly and high-level API. The main asset of FasterAI is its lightweight, yet powerful, simplicity of use. Indeed, because it was developed in a very granular way, users…
This work presents TorchRadon -- an open source CUDA library which contains a set of differentiable routines for solving computed tomography (CT) reconstruction problems. The library is designed to help researchers working on CT problems to combine deep learning and model-based approaches. The package is developed as a PyTorch extension and can be seamlessly integrated into existing deep learning training code. Compared to the existing Astra Toolbox, TorchRadon is up to 125 faster. The operators implemented by TorchRadon allow the computation of gradients using PyTorch backward(), and can ther…
Federated Learning (FL) has emerged as a promising technique for edge devices to collaboratively learn a shared machine learning model while keeping training data locally on the device, thereby removing the need to store and access the full data in the cloud. However, FL is difficult to implement, test and deploy in practice considering heterogeneity in common edge device settings, making it fundamentally hard for researchers to efficiently prototype and test their optimization algorithms. In this work, our aim is to alleviate this problem by introducing FL_PyTorch : a suite of open-source sof…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Princeton University（普林斯顿大学）
Machine Learning graphs (or models) can be challenging or impossible to train when either devices have limited memory, or models are large. To split the model across devices, learning-based approaches are still popular. While these result in model placements that train fast on data (i.e., low step times), learning-based model-parallelism is time-consuming, taking many hours or days to create a placement plan of operators on devices. We present the Baechi system, the first to adopt an algorithmic approach to the placement problem for running machine learning training graphs on small clusters of…
Rescaling a vector $\vecδ \in \mathbb{R}^n$ to a desired length is a common operation in many areas such as data science and machine learning. When the rescaled perturbation $η\vecδ$ is added to a starting point $\vec{x} \in D$ (where $D$ is the data domain, e.g. $D = [0, 1]^n$), the resulting vector $\vec{v} = \vec{x} + η\vecδ$ will in general not be in $D$. To enforce that the perturbed vector $v$ is in $D$, the values of $\vec{v}$ can be clipped to $D$. This subsequent element-wise clipping to the data domain does however reduce the effective perturbation size and thus interferes with the r…
MLPGradientFlow is a software package to solve numerically the gradient flow differential equation $\dot θ= -\nabla \mathcal L(θ; \mathcal D)$, where $θ$ are the parameters of a multi-layer perceptron, $\mathcal D$ is some data set, and $\nabla \mathcal L$ is the gradient of a loss function. We show numerically that adaptive first- or higher-order integration methods based on Runge-Kutta schemes have better accuracy and convergence speed than gradient descent with the Adam optimizer. However, we find Newton's method and approximations like BFGS preferable to find fixed points (local and global…
Local robustness ensures that a model classifies all inputs within an $\ell_2$-ball consistently, which precludes various forms of adversarial inputs. In this paper, we present a fast procedure for checking local robustness in feed-forward neural networks with piecewise-linear activation functions. Such networks partition the input space into a set of convex polyhedral regions in which the network's behavior is linear; hence, a systematic search for decision boundaries within the regions around a given input is sufficient for assessing robustness. Crucially, we show how the regions around a po…
Deep reinforcement learning has been one of the fastest growing fields of machine learning over the past years and numerous libraries have been open sourced to support research. However, most codebases have a steep learning curve or limited flexibility that do not satisfy a need for fast prototyping in fundamental research. This paper introduces Tonic, a Python library allowing researchers to quickly implement new ideas and measure their importance by providing: 1) general-purpose configurable modules 2) several baseline agents: A2C, TRPO, PPO, MPO, DDPG, D4PG, TD3 and SAC built with these mod…
University of California, Irvine（加州大学欧文分校）；State University of New York at Albany（纽约州立大学奥尔巴尼分校）
In this paper, we study the dynamics of gradient descent in learning neural networks for classification problems. Unlike in existing works, we consider the linearly non-separable case where the training data of different classes lie in orthogonal subspaces. We show that when the network has sufficient (but not exceedingly large) number of neurons, (1) the corresponding minimization problem has a desirable landscape where all critical points are global minima with perfect classification; (2) gradient descent is guaranteed to converge to the global minima. Moreover, we discovered a geometric con…
AstraZeneca（阿斯利康）；Harvard Medical School（哈佛医学院）；Vanderbilt University（范德堡大学）
In this paper, we introduce ChemicalX, a PyTorch-based deep learning library designed for providing a range of state of the art models to solve the drug pair scoring task. The primary objective of the library is to make deep drug pair scoring models accessible to machine learning researchers and practitioners in a streamlined framework.The design of ChemicalX reuses existing high level model training utilities, geometric deep learning, and deep chemistry layers from the PyTorch ecosystem. Our system provides neural network layers, custom pair scoring architectures, data loaders, and batch iter…
We design and implement a Python library to help the non-expert using all these powerful tools in a way that is efficient, extensible, and simple to incorporate into the workflow of the data scientist, practitioner, and applied researcher. The algorithms implemented in this library have been designed with usability and GPU efficiency in mind, and they can be added to any PyTorch model with just one extra line of code. We showcase the effectiveness of these tools on an application of optimisation on manifolds in the setting of time series analysis. In this setting, orthogonal and unitary optimi…
Meta Platforms（元平台公司）；Carnegie Mellon University（卡内基梅隆大学）
Deep learning recommendation models (DLRMs) are used across many business-critical services at Facebook and are the single largest AI application in terms of infrastructure demand in its data-centers. In this paper we discuss the SW/HW co-designed solution for high-performance distributed training of large-scale DLRMs. We introduce a high-performance scalable software stack based on PyTorch and pair it with the new evolution of Zion platform, namely ZionEX. We demonstrate the capability to train very large DLRMs with up to 12 Trillion parameters and show that we can attain 40X speedup in terms…
fastai is a deep learning library which provides practitioners with high-level components that can quickly and easily provide state-of-the-art results in standard deep learning domains, and provides researchers with low-level components that can be mixed and matched to build new approaches. It aims to do both things without substantial compromises in ease of use, flexibility, or performance. This is possible thanks to a carefully layered architecture, which expresses common underlying patterns of many deep learning and data processing techniques in terms of decoupled abstractions. These abstra…
IBM Research（IBM研究院）；Hasso Plattner Institute（哈索·普拉特纳研究所）；Williams College（威廉姆斯学院）；Seoul National University（首尔国立大学）
Dimensionality reduction algorithms are standard tools in a researcher's toolbox. Dimensionality reduction algorithms are frequently used to augment downstream tasks such as machine learning, data science, and also are exploratory methods for understanding complex phenomena. For instance, dimensionality reduction is commonly used in Biology as well as Neuroscience to understand data collected from biological subjects. However, dimensionality reduction techniques are limited by the von-Neumann architectures that they execute on. Specifically, data intensive algorithms such as dimensionality red…
Federated learning (FL) enables resource-constrained edge nodes to collaboratively learn a global model under the orchestration of a central server while keeping privacy-sensitive data locally. The non-independent-and-identically-distributed (non-IID) data samples across participating nodes slow model training and impose additional communication rounds for FL to converge. In this paper, we propose Federated Adaptive Weighting (FedAdp) algorithm that aims to accelerate model convergence under the presence of nodes with non-IID dataset. We observe the implicit connection between the node contrib…
