Cambridge Centre for AI in Medicine is a heavy hitter at NeurIPS 2020

Many important problems in science and engineering, such as drug design, involve optimizing an expensive black-box objective function over a complex, high-dimensional, and structured input space. Although machine learning techniques have shown promise in solving such problems, existing approaches substantially lack sample efficiency. We introduce an improved method for efficient black-box optimization, which performs the optimization in the low-dimensional, continuous latent manifold learned by a deep generative model. In contrast to previous approaches, we actively steer the generative model to maintain a latent manifold that is highly useful for efficiently optimizing the objective. We achieve this by periodically retraining the generative model on the data points queried along the optimization trajectory, as well as weighting those data points according to their objective function value. This weighted retraining can be easily implemented on top of existing methods, and is empirically shown to significantly improve their efficiency and performance on synthetic and real-world optimization problems.

Variational Autoencoders (VAEs) have seen widespread use in learned image compression. They are used to learn expressive latent representations on which downstream compression methods can operate with high efficiency. Recently proposed ‘bits-back’ methods can indirectly encode the latent representation of images with codelength close to the relative entropy between the latent posterior and the prior. However, due to the underlying algorithm, these methods can only be used for lossless compression, and they only achieve their nominal efficiency when compressing multiple images simultaneously; they are inefficient for compressing single images. As an alternative, we propose a novel method, Relative Entropy Coding (REC), that can directly encode the latent representation with codelength close to the relative entropy for single images, supported by our empirical results obtained on the Cifar10, ImageNet32 and Kodak datasets. Moreover, unlike previous bits-back methods, REC is immediately applicable to lossy compression, where it is competitive with the state-of-the-art on the Kodak dataset.

Existing methods for estimating uncertainty in deep learning tend to require multiple forward passes, making them unsuitable for applications where computational resources are limited. To solve this, we perform probabilistic reasoning over the depth of neural networks. Different depths correspond to subnetworks which share weights and whose predictions are combined via marginalisation, yielding model uncertainty. By exploiting the sequential structure of feed-forward networks, we are able to both evaluate our training objective and make predictions with a single forward pass. We validate our approach on real-world regression and image classification tasks. Our approach provides uncertainty calibration, robustness to dataset shift, and accuracies competitive with more computationally expensive baselines.

When suggesting new molecules with particular properties to a chemist, it is not only important what to make but crucially how to make it. These instructions form a synthesis directed acyclic graph (DAG), describing how a large vocabulary of simple building blocks can be recursively combined through chemical reactions to create more complicated molecules of interest. In contrast, many current deep generative models for molecules ignore synthesizability. We therefore propose a deep generative model that better represents the real world process, by directly outputting molecule synthesis DAGs. We argue that this provides sensible inductive biases, ensuring that our model searches over the same chemical space that a chemist would, as well as interoperability. We show that our approach is able to model chemical space well, producing a wide range of diverse molecules, and allow for unconstrained optimization of an inherently constrained problem: maximize certain chemical properties such that discovered molecules are synthesizable.

Deep generative models often perform poorly in real-world applications due to the heterogeneity of natural data sets. Heterogeneity arises from data containing different types of features (categorical, ordinal, continuous, etc.) and features of the same type having different marginal distributions. We propose an extension of variational autoencoders (VAEs) called VAEM to handle such heterogeneous data. VAEM is a deep generative model that is trained in a two stage manner, such that the first stage provides a more uniform representation of the data to the second stage, thereby sidestepping the problems caused by heterogeneous data. We provide extensions of VAEM to handle partially observed data, and demonstrate its performance in data generation, missing data prediction and sequential feature selection tasks. Our results show that VAEM broadens the range of real-world applications where deep generative models can be successfully deployed.

Neural Ordinary Differential Equations (NODEs) are a new class of models that transform data continuously through infinite-depth architectures. The continuous nature of NODEs has made them particularly suitable for learning the dynamics of complex physical systems. While previous work has mostly been focused on first order ODEs, the dynamics of many systems, especially in classical physics, are governed by second order laws. In this work, we consider Second Order Neural ODEs (SONODEs). We show how the adjoint sensitivity method can be extended to SONODEs and prove that the optimisation of a first order coupled ODE is equivalent and computationally more efficient. Furthermore, we extend the theoretical understanding of the broader class of Augmented NODEs (ANODEs) by showing they can also learn higher order dynamics with a minimal number of augmented dimensions, but at the cost of interpretability. This indicates that the advantages of ANODEs go beyond the extra space offered by the augmented dimensions, as originally thought. Finally, we compare SONODEs and ANODEs on synthetic and real dynamical systems and demonstrate that the inductive biases of the former generally result in faster training and better performance.

Graph neural networks (GNNs) extends the functionality of traditional neural networks to graph-structured data. Similar to CNNs, an optimized design of graph convolution and pooling is key to success. Borrowing ideas from physics, we propose a path integral based graph neural networks (PAN) for classification and regression tasks on graphs. Specifically, we consider a convolution operation that involves every path linking the message sender and receiver with learnable weights depending on the path length, which corresponds to the maximal entropy random walk. It generalizes the graph Laplacian to a new transition matrix we call \emph{maximal entropy transition} (MET) matrix derived from a path integral formalism. Importantly, the diagonal entries of the MET matrix are directly related to the subgraph centrality, thus lead to a natural and adaptive pooling mechanism. PAN provides a versatile framework that can be tailored for different graph data with varying sizes and structures. We can view most existing GNN architectures as special cases of PAN. Experimental results show that PAN achieves state-of-the-art performance on various graph classification/regression tasks, including a new benchmark dataset from statistical mechanics we propose to boost applications of GNN in physical sciences.

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features—which occur regularly in real-world input domains and within the hidden layers of GNNs—and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator).

Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

We examine the problem of controlling divergences for latent space regularisation in variational autoencoders. Specifically, when aiming to reconstruct example x∈Rm via latent space z∈Rn (n≤m), while balancing this against the need for generalisable latent representations. We present a regularisation mechanism based on the skew-geometric Jensen-Shannon divergence (JSGα). We find a variation in JSGα, motivated by limiting cases, which leads to an intuitive interpolation between forward and reverse KL in the space of both distributions and divergences. We motivate its potential benefits for VAEs through low-dimensional examples, before presenting quantitative and qualitative results. Our experiments demonstrate that skewing our variant of JSGα, in the context of JSGα-VAEs, leads to better reconstruction and generation when compared to several baseline VAEs. Our approach is entirely unsupervised and utilises only one hyperparameter which can be easily interpreted in latent space.