Analyzing Learned Molecular Representations for Property Prediction

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows

Neural‑Brane: Neural Bayesian Personalized Ranking for Attributed Network Embedding

Network embedding methodologies, which learn a distributed vector representation for each vertex in a network, have attracted considerable interest in recent years. Existing works have demonstrated that vertex representation learned through an embedding method provides superior performance in many real-world applications, such as node classification, link prediction, and community detection. However, most of the existing methods for network embedding only utilize topological information of a vertex, ignoring a rich set of nodal attributes (such as user profiles of an online social network, or textual contents of a citation network), which is abundant in all real-life networks. A joint network embedding that takes into account both attributional and relational information entails a complete network information and could further enrich the learned vector representations. In this work, we present Neural-Brane, a novel Neural Bayesian Personalized Ranking based Attributed Network Embedding. For a given network, Neural-Brane extracts latent feature representation of its vertices using a designed neural network model that unifies network topological information and nodal attributes. Besides, it utilizes Bayesian personalized ranking objective, which exploits the proximity ordering between a similar node pair and a dissimilar node pair. We evaluate the quality of vertex embedding produced by Neural-Brane by solving the node classification and clustering tasks on four real-world datasets. Experimental results demonstrate the superiority of our proposed method over the state-of-the-art existing methods

Data-efficient Neuroevolution with Kernel-Based Surrogate Models

Surrogate-assistance approaches have long been used in computationally expensive domains to improve the data-efficiency of optimization algorithms. Neuroevolution, however, has so far resisted the application of these techniques because it requires the surrogate model to make fitness predictions based on variable topologies, instead of a vector of parameters. Our main insight is that we can sidestep this problem by using kernel-based surrogate models, which require only the definition of a distance measure between individuals. Our second insight is that the well-established Neuroevolution of Augmenting Topologies (NEAT) algorithm provides a computationally efficient distance measure between dissimilar networks in the form of "compatibility distance", initially designed to maintain topological diversity. Combining these two ideas, we introduce a surrogate-assisted neuroevolution algorithm that combines NEAT and a surrogate model built using a compatibility distance kernel. We demonstrate the data-efficiency of this new algorithm on the low dimensional cart-pole swing-up problem, as well as the higher dimensional half-cheetah running task. In both tasks the surrogate-assisted variant achieves the same or better results with several times fewer function evaluations as the original NEAT.Comment: In GECCO 201

Causal Confusion in Imitation Learning

Behavioral cloning reduces policy learning to supervised learning by training a discriminative model to predict expert actions given observations. Such discriminative models are non-causal: the training procedure is unaware of the causal structure of the interaction between the expert and the environment. We point out that ignoring causality is particularly damaging because of the distributional shift in imitation learning. In particular, it leads to a counter-intuitive "causal misidentification" phenomenon: access to more information can yield worse performance. We investigate how this problem arises, and propose a solution to combat it through targeted interventions---either environment interaction or expert queries---to determine the correct causal model. We show that causal misidentification occurs in several benchmark control domains as well as realistic driving settings, and validate our solution against DAgger and other baselines and ablations.Comment: Published at NeurIPS 2019 9 pages, plus references and appendice