For many biological applications, exploration of the massive parametric space of a mechanism-based model can impose a prohibitive computational demand. To overcome this limitation, we present a framework to improve computational efficiency by orders of magnitude. The key concept is to train a neural network using a limited number of simulations generated by a mechanistic model. This number is small enough such that the simulations can be completed in a short time frame but large enough to enable reliable training. The trained neural network can then be used to explore a much larger parametric space. We demonstrate this notion by training neural networks to predict pattern formation and stochastic gene expression. We further demonstrate that using an ensemble of neural networks enables the self-contained evaluation of the quality of each prediction. Our work can be a platform for fast parametric space screening of biological models with user defined objectives.

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Unsupervised neural machine translation (UNMT) has recently achieved remarkable results [19] with only large monolingual corpora in each language. However, the uncertainty of associating target with source sentences makes UNMT theoretically an ill-posed problem. This work investigates the possibility of utilizing images for disambiguation to improve the performance of UNMT. Our assumption is intuitively based on the invariant property of image, i.e., the description of the same visual content by different languages should be approximately similar. We propose an unsupervised multi-modal machine translation (UMNMT) framework based on the language translation cycle consistency loss conditional on the image, targeting to learn the bidirectional multi-modal translation simultaneously. Through an alternate training between multi-modal and uni-modal, our inference model can translate with or without the image. On the widely used Multi30K dataset, the experimental results of our approach are significantly better than those of the text-only UNMT on the 2016 test dataset. * indicates equal contribution. Work performed while Yuanhang Su was an internship at Alibaba.

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The performances of machine translation (MT) systems are usually evaluated by the metric BLEU when the golden references are provided. However, in the case of model inference or production deployment, golden references are usually expensively available, such as human annotation with bilingual expertise. In order to address the issue of translation quality estimation (QE) without reference, we propose a general framework for automatic evaluation of the translation output for the QE task in the Conference on Statistical Machine Translation (WMT). We first build a conditional target language model with a novel bidirectional transformer, named neural bilingual expert model, which is pre-trained on large parallel corpora for feature extraction. For QE inference, the bilingual expert model can simultaneously produce the joint latent representation between the source and the translation, and real-valued measurements of possible erroneous tokens based on the prior knowledge learned from parallel data. Subsequently, the features will further be fed into a simple Bi-LSTM predictive model for quality estimation.

Mechanism-based mathematical models are the foundation for diverse applications. It is often critical to explore the massive parametric space for each model. However, for many applications, such as agent-based models, partial differential equations, and stochastic differential equations, this practice can impose a prohibitive computational demand. To overcome this limitation, we present a fundamentally new framework to improve computational efficiency by orders of magnitude. The key concept is to train an artificial neural network using a limited number of simulations generated by a mechanistic model. This number is small enough such that the simulations can be completed in a short time frame but large enough to enable reliable training of the neural network. The trained neural network can then be used to explore the system dynamics of a much larger parametric space. We demonstrate this notion by training neural networks to predict self-organized pattern formation and stochastic gene expression. With this framework, we can predict not only the 1-D distribution in space (for partial differential equation models) and probability density function (for stochastic differential equation models) of variables of interest with high accuracy, but also novel system dynamics not present in the training sets. We further demonstrate that using an ensemble of neural networks enables the self-contained evaluation of the quality of each prediction. Our work can potentially be a platform for faster parametric space screening of biological models with user defined objectives.

Distant supervised relation extraction has been successfully applied to large corpus with thousands of relations. However, the inevitable wrong labeling problem by distant supervision will hurt the performance of relation extraction. In this paper, we propose a method with neural noise converter to alleviate the impact of noisy data, and a conditional optimal selector to make proper prediction. Our noise converter learns the structured transition matrix on logit level and captures the property of distant supervised relation extraction dataset. The conditional optimal selector on the other hand helps to make proper prediction decision of an entity pair even if the group of sentences is overwhelmed by no-relation sentences. We conduct experiments on a widely used dataset and the results show significant improvement over competitive baseline methods.

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