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Register a new userC5T5: Controllable Generation of Organic Molecules with Transformers
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Added by
Daniel Rothchild
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Methods for designing organic materials with desired properties have high potential impact across fields such as medicine, renewable energy, petrochemical engineering, and agriculture. However, using generative modeling to design substances with desired properties is difficult because candidate compounds must satisfy multiple constraints, including synthetic accessibility and other metrics that are intuitive to domain experts but challenging to quantify. We propose C5T5, a novel self-supervised pretraining method that enables transformers to make zero-shot select-and-replace edits, altering organic substances towards desired property values. C5T5 operates on IUPAC names -- a standardized molecular representation that intuitively encodes rich structural information for organic chemists but that has been largely ignored by the ML community. Our technique requires no edited molecule pairs to train and only a rough estimate of molecular properties, and it has the potential to model long-range dependencies and symmetric molecular structures more easily than graph-based methods. C5T5 also provides a powerful interface to domain experts: it grants users fine-grained control over the generative process by selecting and replacing IUPAC name fragments, which enables experts to leverage their intuitions about structure-activity relationships. We demonstrate C5T5s effectiveness on four physical properties relevant for drug discovery, showing that it learns successful and chemically intuitive strategies for altering molecules towards desired property values.
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Recent generative adversarial networks (GANs) are able to generate impressive photo-realistic images. However, controllable generation with GANs remains a challenging research problem. Achieving controllable generation requires semantically interpretable and disentangled factors of variation. It is challenging to achieve this goal using simple fixed distributions such as Gaussian distribution. Instead, we propose an unsupervised framework to learn a distribution of latent codes that control the generator through self-training. Self-training provides an iterative feedback in the GAN training, from the discriminator to the generator, and progressively improves the proposal of the latent codes as training proceeds. The latent codes are sampled from a latent variable model that is learned in the feature space of the discriminator. We consider a normalized independent component analysis model and learn its parameters through tensor factorization of the higher-order moments. Our framework exhibits better disentanglement compared to other variants such as the variational autoencoder, and is able to discover semantically meaningful latent codes without any supervision. We demonstrate empirically on both cars and faces datasets that each group of elements in the learned code controls a mode of variation with a semantic meaning, e.g. pose or background change. We also demonstrate with quantitative metrics that our method generates better results compared to other approaches.
In applications such as molecule design or drug discovery, it is desirable to have an algorithm which recommends new candidate molecules based on the results of past tests. These molecules first need to be synthesized and then tested for objective properties. We describe ChemBO, a Bayesian optimization framework for generating and optimizing organic molecules for desired molecular properties. While most existing data-driven methods for this problem do not account for sample efficiency or fail to enforce realistic constraints on synthesizability, our approach explores the synthesis graph in a sample-efficient way and produces synthesizable candidates. We implement ChemBO as a Gaussian process model and explore existing molecular kernels for it. Moreover, we propose a novel optimal-transport based distance and kernel that accounts for graphical information explicitly. In our experiments, we demonstrate the efficacy of the proposed approach on several molecular optimization problems.
In E-commerce, a key challenge in text generation is to find a good trade-off between word diversity and accuracy (relevance) in order to make generated text appear more natural and human-like. In order to improve the relevance of generated results, conditional text generators were developed that use input keywords or attributes to produce the corresponding text. Prior work, however, do not finely control the diversity of automatically generated sentences. For example, it does not control the order of keywords to put more relevant ones first. Moreover, it does not explicitly control the balance between diversity and accuracy. To remedy these problems, we propose a fine-grained controllable generative model, called~textit{Apex}, that uses an algorithm borrowed from automatic control (namely, a variant of the textit{proportional, integral, and derivative (PID) controller}) to precisely manipulate the diversity/accuracy trade-off of generated text. The algorithm is injected into a Conditional Variational Autoencoder (CVAE), allowing textit{Apex} to control both (i) the order of keywords in the generated sentences (conditioned on the input keywords and their order), and (ii) the trade-off between diversity and accuracy. Evaluation results on real-world datasets show that the proposed method outperforms existing generative models in terms of diversity and relevance. Apex is currently deployed to generate production descriptions and item recommendation reasons in Taobao owned by Alibaba, the largest E-commerce platform in China. The A/B production test results show that our method improves click-through rate (CTR) by 13.17% compared to the existing method for production descriptions. For item recommendation reason, it is able to increase CTR by 6.89% and 1.42% compared to user reviews and top-K item recommendation without reviews, respectively.
Automatic surgical instruction generation is a prerequisite towards intra-operative context-aware surgical assistance. However, generating instructions from surgical scenes is challenging, as it requires jointly understanding the surgical activity of current view and modelling relationships between visual information and textual description. Inspired by the neural machine translation and imaging captioning tasks in open domain, we introduce a transformer-backboned encoder-decoder network with self-critical reinforcement learning to generate instructions from surgical images. We evaluate the effectiveness of our method on DAISI dataset, which includes 290 procedures from various medical disciplines. Our approach outperforms the existing baseline over all caption evaluation metrics. The results demonstrate the benefits of the encoder-decoder structure backboned by transformer in handling multimodal context.
A set is an unordered collection of unique elements--and yet many machine learning models that generate sets impose an implicit or explicit ordering. Since model performance can depend on the choice of order, any particular ordering can lead to sub-optimal results. An alternative solution is to use a permutation-equivariant set generator, which does not specify an order-ing. An example of such a generator is the DeepSet Prediction Network (DSPN). We introduce the Transformer Set Prediction Network (TSPN), a flexible permutation-equivariant model for set prediction based on the transformer, that builds upon and outperforms DSPN in the quality of predicted set elements and in the accuracy of their predicted sizes. We test our model on MNIST-as-point-clouds (SET-MNIST) for point-cloud generation and on CLEVR for object detection.
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