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Generating new molecules with specified chemical and biological properties via generative models has emerged as a promising direction for drug discovery. However, existing methods require extensive training/fine-tuning with a large dataset, often unavailable in real-world generation tasks. In this work, we propose a new retrieval-based framework for controllable molecule generation. We use a small set of exemplar molecules, i.e., those that (partially) satisfy the design criteria, to steer the pre-trained generative model towards synthesizing molecules that satisfy the given design criteria. We design a retrieval mechanism that retrieves and fuses the exemplar molecules with the input molecule, which is trained by a new self-supervised objective that predicts the nearest neighbor of the input molecule. We also propose an iterative refinement process to dynamically update the generated molecules and retrieval database for better generalization. Our approach is agnostic to the choice of generative models and requires no task-specific fine-tuning. On various tasks ranging from simple design criteria to a challenging real-world scenario for designing lead compounds that bind to the SARS-CoV-2 main protease, we demonstrate our approach extrapolates well beyond the retrieval database, and achieves better performance and wider applicability than previous methods. 

Computing or approximating the convex hull of a dataset plays a role in a wide range of applications, including economics, statistics, and physics, to name just a few. However, convex hull computation and approximation is exponentially complex, in terms of both memory and computation, as the ambient space dimension increases. In this paper, we propose DeepHull, a new convex hull approximation algorithm based on convex deep networks (DNs) with continuous piecewise-affine nonlinearities and nonnegative weights. The idea is that binary classification between true data samples and adversarially generated samples with such a DN naturally induces a polytope decision boundary that approximates the true data convex hull. A range of exploratory experiments demonstrates that DeepHull efficiently produces a meaningful convex hull approximation, even in a high-dimensional ambient space. 

The study of deep neural networks (DNNs) in the infinite-width limit, via the so-called neural tangent kernel (NTK) approach, has provided new insights into the dynamics of learning, generalization, and the impact of initialization. One key DNN architecture remains to be kernelized, namely, the recurrent neural network (RNN). In this paper we introduce and study the Recurrent Neural Tangent Kernel (RNTK), which provides new insights into the behavior of overparametrized RNNs. A key property of the RNTK should greatly benefit practitioners is its ability to compare inputs of different length. To this end, we characterize how the RNTK weights different time steps to form its output under different initialization parameters and nonlinearity choices. A synthetic and 56 real-world data experiments demonstrate that the RNTK offers significant performance gains over other kernels, including standard NTKs, across a wide array of data sets.