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3D Infomax improves GNNs for Molecular Property Prediction

arXiv.org Artificial Intelligence

Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Including 3D molecular structure as input to learned models improves their performance for many molecular tasks. However, this information is infeasible to compute at the scale required by several real-world applications. We propose pre-training a model to reason about the geometry of molecules given only their 2D molecular graphs. Using methods from self-supervised learning, we maximize the mutual information between 3D summary vectors and the representations of a Graph Neural Network (GNN) such that they contain latent 3D information. During fine-tuning on molecules with unknown geometry, the GNN still produces implicit 3D information and can use it to improve downstream tasks. We show that 3D pre-training provides significant improvements for a wide range of properties, such as a 22% average MAE reduction on eight quantum mechanical properties. Moreover, the learned representations can be effectively transferred between datasets in different molecular spaces. The understanding of molecular and quantum chemistry is a rapidly growing area for deep learning with models having direct real-world impacts in quantum chemistry (Dral, 2020), protein structure prediction (Jumper et al., 2021), materials science (Schmidt et al., 2019), and drug discovery (Stokes et al., 2020). In particular, for the task of molecular property prediction, GNNs have had great success (Yang et al., 2019). GNNs operate on the molecular graph by updating each atom's representation based on the atoms connected to it via covalent bonds. However, these models reason poorly about other important interatomic forces that depend on the atoms' relative positions in space. Previous works showed that using the atoms' 3D coordinates in space improves the accuracy of molecular property prediction (Schütt et al., 2017; Klicpera et al., 2020b; Liu et al., 2021; Klicpera et al., 2021). However, using classical molecular dynamics simulations to explicitly compute a molecule's geometry before predicting its properties is computationally intractable for many real-world applications. Even recent Machine Learning (ML) methods for conformation generation (Xu et al., 2021b; Shi et al., 2021; Ganea et al., 2021) are still too slow for large-scale applications. A GNN is pre-trained by maximizing the mutual information (MI) between its embedding of a 2D molecular graph and a representation capturing the 3D information that is produced by a separate network.


Graphs as Tools to Improve Deep Learning Methods

arXiv.org Artificial Intelligence

In recent years, deep neural networks (DNNs) have known an important rise in popularity. However, although they are state-of-the-art in many machine learning challenges, they still suffer from several limitations. For example, DNNs require a lot of training data, which might not be available in some practical applications. In addition, when small perturbations are added to the inputs, DNNs are prone to misclassification errors. DNNs are also viewed as black-boxes and as such their decisions are often criticized for their lack of interpretability. In this chapter, we review recent works that aim at using graphs as tools to improve deep learning methods. These graphs are defined considering a specific layer in a deep learning architecture. Their vertices represent distinct samples, and their edges depend on the similarity of the corresponding intermediate representations. These graphs can then be leveraged using various methodologies, many of which built on top of graph signal processing. This chapter is composed of four main parts: tools for visualizing intermediate layers in a DNN, denoising data representations, optimizing graph objective functions and regularizing the learning process.


RelaySum for Decentralized Deep Learning on Heterogeneous Data

arXiv.org Machine Learning

In decentralized machine learning, workers compute model updates on their local data. Because the workers only communicate with few neighbors without central coordination, these updates propagate progressively over the network. This paradigm enables distributed training on networks without all-to-all connectivity, helping to protect data privacy as well as to reduce the communication cost of distributed training in data centers. A key challenge, primarily in decentralized deep learning, remains the handling of differences between the workers' local data distributions. To tackle this challenge, we introduce the RelaySum mechanism for information propagation in decentralized learning. RelaySum uses spanning trees to distribute information exactly uniformly across all workers with finite delays depending on the distance between nodes. In contrast, the typical gossip averaging mechanism only distributes data uniformly asymptotically while using the same communication volume per step as RelaySum. We prove that RelaySGD, based on this mechanism, is independent of data heterogeneity and scales to many workers, enabling highly accurate decentralized deep learning on heterogeneous data. Our code is available at http://github.com/epfml/relaysgd.


A Regularized Wasserstein Framework for Graph Kernels

arXiv.org Machine Learning

We propose a learning framework for graph kernels, which is theoretically grounded on regularizing optimal transport. This framework provides a novel optimal transport distance metric, namely Regularized Wasserstein (RW) discrepancy, which can preserve both features and structure of graphs via Wasserstein distances on features and their local variations, local barycenters and global connectivity. Two strongly convex regularization terms are introduced to improve the learning ability. One is to relax an optimal alignment between graphs to be a cluster-to-cluster mapping between their locally connected vertices, thereby preserving the local clustering structure of graphs. The other is to take into account node degree distributions in order to better preserve the global structure of graphs. We also design an efficient algorithm to enable a fast approximation for solving the optimization problem. Theoretically, our framework is robust and can guarantee the convergence and numerical stability in optimization. We have empirically validated our method using 12 datasets against 16 state-of-the-art baselines. The experimental results show that our method consistently outperforms all state-of-the-art methods on all benchmark databases for both graphs with discrete attributes and graphs with continuous attributes.


Can a Robot Invent? The Fight Around AI and Patents Explained

#artificialintelligence

Patent offices and courts around the world are being asked to tackle a similar question: can an artificial intelligence system qualify as an inventor for a patent? A test case making its way through several countries--from Saudi Arabia to Australia to Brazil--has spurred debate about advancements in artificial intelligence technology and questions about whether patent laws need to be revised to recognize machines as inventors. A judge in the U.S. District Court for the Eastern District of Virginia recently ruled that, under current U.S. law, AI can't be listed as an inventor on a patent. The ruling was in line with what U.S., British, and EU patent officials have concluded. The push to recognize AI as an inventor comes from Ryan Abbott, a University of Surrey law professor, and Stephen Thaler, a computer scientist from Missouri.


Machine Learning Project Predict Will it Rain Tomorrow in Australia - Projects Based Learning

#artificialintelligence

In this project we will be working with a data set, indicating whether it rain the next day in Australia, Yes or No? This column is Yes if the rain for that day was 1mm or more. We will try to create a model that will predict using the available data. Welcome to this project on predict whether it will rain tomorrow in Australia in Apache Spark Machine Learning using Databricks platform community edition server which allows you to execute your spark code, free of cost on their server just by registering through email id. In this project, we explore Apache Spark and Machine Learning on the Databricks platform.


US-EU agreement on artificial intelligence seen as a swipe at China – but little else for now

#artificialintelligence

The US and EU are talking up the significance of their new pact on artificial intelligence, but a closer inspection indicates the two sides still have precious little common when it comes to regulating the technology – except a desire to take the moral high ground against China. The long-awaited agreement was reached when the Trade and Technology Council met for the first time on 29 September in Pittsburgh, with Brussels and Washington vowing to make sure AI systems are "innovative and trustworthy" and "respect universal human rights and shared democratic values". The EU and US will "seek to develop a mutual understanding on the principles underlining trustworthy and responsible AI," the agreement says. But exactly what this means in practice remains to be fleshed out. While both sides said they have noted each other's domestic regulatory proposals on AI, there is no mention of coordinating their approaches.


DABUS Will Need to Wait--U.S. District Court Affirms USPTO's Denial of AI System as Inventor

#artificialintelligence

Earlier this month, a federal district court issued the first judicial decision in the country addressing whether an AI system can be an "inventor" under U.S. patent law. The decision was rendered by the U.S. District Court for the Eastern District of Virginia in Thaler v. Hirshfeld on appeal from the U.S. Patent and Trademark Office's (USPTO) decision that refused to allow Thaler's two patent applications to proceed because he listed DABUS (an AI machine) as the inventor. Thaler filed the applications in 2018--one for an invention used to contain food and the other for a flashing beacon for attracting attention in emergencies. In statements filed in support of the applications, Thaler listed DABUS as the inventor, claiming that he had acquired the right to the grant of the patents by "ownership of the creativity machine." In affirming the USPTO's denial of the applications, the court held that based on the plain statutory language of the U.S. Patent Act and Federal Circuit authority, an AI machine cannot be an inventor because an inventor must be an "individual," which under common interpretation and court precedent means a natural person. The court stated that Thaler's argument was based on policy considerations and the purpose of the patent clause of the U.S. Constitution, and that the decision to expand the scope of inventorship is squarely within the authority of Congress.


Transformer-based Map Matching Model with Limited Ground-Truth Data using Transfer-Learning Approach

arXiv.org Artificial Intelligence

In many spatial trajectory-based applications, it is necessary to map raw trajectory data points onto road networks in digital maps, which is commonly referred to as a map-matching process. While most previous map-matching methods have focused on using rule-based algorithms to deal with the map-matching problems, in this paper, we consider the map-matching task from the data-driven perspective, proposing a deep learning-based map-matching model. We build a Transformer-based map-matching model with a transfer learning approach. We generate trajectory data to pre-train the Transformer model and then fine-tune the model with a limited number of ground-truth data to minimize the model development cost and reduce the real-to-virtual gap. Three metrics (Average Hamming Distance, F-score, and BLEU) at two levels (point and segment level) are used to evaluate the model performance. The results indicate that the proposed model outperforms existing models. Furthermore, we use the attention weights of the Transformer to plot the map-matching process and find how the model matches the road segments correctly.


ABCP: Automatic Block-wise and Channel-wise Network Pruning via Joint Search

arXiv.org Artificial Intelligence

Currently, an increasing number of model pruning methods are proposed to resolve the contradictions between the computer powers required by the deep learning models and the resource-constrained devices. However, most of the traditional rule-based network pruning methods can not reach a sufficient compression ratio with low accuracy loss and are time-consuming as well as laborious. In this paper, we propose Automatic Block-wise and Channel-wise Network Pruning (ABCP) to jointly search the block-wise and channel-wise pruning action with deep reinforcement learning. A joint sample algorithm is proposed to simultaneously generate the pruning choice of each residual block and the channel pruning ratio of each convolutional layer from the discrete and continuous search space respectively. The best pruning action taking both the accuracy and the complexity of the model into account is obtained finally. Compared with the traditional rule-based pruning method, this pipeline saves human labor and achieves a higher compression ratio with lower accuracy loss. Tested on the mobile robot detection dataset, the pruned YOLOv3 model saves 99.5% FLOPs, reduces 99.5% parameters, and achieves 37.3 times speed up with only 2.8% mAP loss. The results of the transfer task on the sim2real detection dataset also show that our pruned model has much better robustness performance.