MARS: Markov Molecular Sampling for Multi-objective Drug Discovery

Searching for novel molecules with desired chemical properties is crucial in drug discovery. Existing work focuses on developing neural models to generate either molecular sequences or chemical graphs. However, it remains a big challenge to find novel and diverse compounds satisfying several properties. In this paper, we propose MARS, a method for multi-objective drug molecule discovery. MARS is based on the idea of generating the chemical candidates by iteratively editing fragments of molecular graphs. To search for high-quality candidates, it employs Markov chain Monte Carlo sampling (MCMC) on molecules with an annealing scheme and an adaptive proposal. To further improve sample efficiency, MARS uses a graph neural network (GNN) to represent and select candidate edits, where the GNN is trained on-the-fly with samples from MCMC. Experiments show that MARS achieves state-of-the-art performance in various multi-objective settings where molecular bio-activity, drug-likeness, and synthesizability are considered. Remarkably, in the most challenging setting where all four objectives are simultaneously optimized, our approach outperforms previous methods significantly in comprehensive evaluations. The code is available at https://github.com/yutxie/mars.

Towards Generalized Implementation of Wasserstein Distance in GANs

Wasserstein GANs (WGANs), built upon the Kantorovich-Rubinstein (KR) duality of Wasserstein distance, is one of the most theoretically sound GAN models. However, in practice it does not always outperform other variants of GANs. This is mostly due to the imperfect implementation of the Lipschitz condition required by the KR duality. Extensive work has been done in the community with different implementations of the Lipschitz constraint, which, however, is still hard to satisfy the restriction perfectly in practice. In this paper, we argue that the strong Lipschitz constraint might be unnecessary for optimization. Instead, we take a step back and try to relax the Lipschitz constraint. Theoretically, we first demonstrate a more general dual form of the Wasserstein distance called the Sobolev duality, which relaxes the Lipschitz constraint but still maintains the favorable gradient property of the Wasserstein distance. Moreover, we show that the KR duality is actually a special case of the Sobolev duality. Based on the relaxed duality, we further propose a generalized WGAN training scheme named Sobolev Wasserstein GAN (SWGAN), and empirically demonstrate the improvement of SWGAN over existing methods with extensive experiments.

Improving Knowledge Tracing via Pre-training Question Embeddings

Knowledge tracing (KT) defines the task of predicting whether students can correctly answer questions based on their historical response. Although much research has been devoted to exploiting the question information, plentiful advanced information among questions and skills hasn't been well extracted, making it challenging for previous work to perform adequately. In this paper, we demonstrate that large gains on KT can be realized by pre-training embeddings for each question on abundant side information, followed by training deep KT models on the obtained embeddings. To be specific, the side information includes question difficulty and three kinds of relations contained in a bipartite graph between questions and skills. To pre-train the question embeddings, we propose to use product-based neural networks to recover the side information. As a result, adopting the pre-trained embeddings in existing deep KT models significantly outperforms state-of-the-art baselines on three common KT datasets.

Sobolev Wasserstein GAN

Wasserstein GANs (WGANs), built upon the Kantorovich-Rubinstein (KR) duality of Wasserstein distance, is one of the most theoretically sound GAN models. However, in practice it does not always outperform other variants of GANs. This is mostly due to the imperfect implementation of the Lipschitz condition required by the KR duality. Extensive work has been done in the community with different implementations of the Lipschitz constraint, which, however, is still hard to satisfy the restriction perfectly in practice. In this paper, we argue that the strong Lipschitz constraint might be unnecessary for optimization. Instead, we take a step back and try to relax the Lipschitz constraint. Theoretically, we first demonstrate a more general dual form of the Wasserstein distance called the Sobolev duality, which relaxes the Lipschitz constraint but still maintains the favorable gradient property of the Wasserstein distance. Moreover, we show that the KR duality is actually a special case of the Sobolev duality. Based on the relaxed duality, we further propose a generalized WGAN training scheme named Sobolev Wasserstein GAN (SWGAN), and empirically demonstrate the improvement of SWGAN over existing methods with extensive experiments.

Model-based Policy Optimization with Unsupervised Model Adaptation

Model-based reinforcement learning methods learn a dynamics model with real data sampled from the environment and leverage it to generate simulated data to derive an agent. However, due to the potential distribution mismatch between simulated data and real data, this could lead to degraded performance. Despite much effort being devoted to reducing this distribution mismatch, existing methods fail to solve it explicitly. In this paper, we investigate how to bridge the gap between real and simulated data due to inaccurate model estimation for better policy optimization. To begin with, we first derive a lower bound of the expected return, which naturally inspires a bound maximization algorithm by aligning the simulated and real data distributions. To this end, we propose a novel model-based reinforcement learning framework AMPO, which introduces unsupervised model adaptation to minimize the integral probability metric (IPM) between feature distributions from real and simulated data. Instantiating our framework with Wasserstein-1 distance gives a practical model-based approach. Empirically, our approach achieves state-of-the-art performance in terms of sample efficiency on a range of continuous control benchmark tasks.

Efficient Projection-Free Algorithms for Saddle Point Problems

The Frank-Wolfe algorithm is a classic method for constrained optimization problems. It has recently been popular in many machine learning applications because its projection-free property leads to more efficient iterations. In this paper, we study projection-free algorithms for convex-strongly-concave saddle point problems with complicated constraints. Our method combines Conditional Gradient Sliding with Mirror-Prox and shows that it only requires $\tilde{O}(1/\sqrt{\epsilon})$ gradient evaluations and $\tilde{O}(1/\epsilon^2)$ linear optimizations in the batch setting. We also extend our method to the stochastic setting and propose first stochastic projection-free algorithms for saddle point problems. Experimental results demonstrate the effectiveness of our algorithms and verify our theoretical guarantees.

GeneraLight: Improving Environment Generalization of Traffic Signal Control via Meta Reinforcement Learning

The heavy traffic congestion problem has always been a concern for modern cities. To alleviate traffic congestion, researchers use reinforcement learning (RL) to develop better traffic signal control (TSC) algorithms in recent years. However, most RL models are trained and tested in the same traffic flow environment, which results in a serious overfitting problem. Since the traffic flow environment in the real world keeps varying, these models can hardly be applied due to the lack of generalization ability. Besides, the limited number of accessible traffic flow data brings extra difficulty in testing the generalization ability of the models. In this paper, we design a novel traffic flow generator based on Wasserstein generative adversarial network to generate sufficient diverse and quality traffic flows and use them to build proper training and testing environments. Then we propose a meta-RL TSC framework GeneraLight to improve the generalization ability of TSC models. GeneraLight boosts the generalization performance by combining the idea of flow clustering and model-agnostic meta-learning. We conduct extensive experiments on multiple real-world datasets to show the superior performance of GeneraLight on generalizing to different traffic flows.

GIKT: A Graph-based Interaction Model for Knowledge Tracing

With the rapid development in online education, knowledge tracing (KT) has become a fundamental problem which traces students' knowledge status and predicts their performance on new questions. Questions are often numerous in online education systems, and are always associated with much fewer skills. However, the previous literature fails to involve question information together with high-order question-skill correlations, which is mostly limited by data sparsity and multi-skill problems. From the model perspective, previous models can hardly capture the long-term dependency of student exercise history, and cannot model the interactions between student-questions, and student-skills in a consistent way. In this paper, we propose a Graph-based Interaction model for Knowledge Tracing (GIKT) to tackle the above probems. More specifically, GIKT utilizes graph convolutional network (GCN) to substantially incorporate question-skill correlations via embedding propagation. Besides, considering that relevant questions are usually scattered throughout the exercise history, and that question and skill are just different instantiations of knowledge, GIKT generalizes the degree of students' master of the question to the interactions between the student's current state, the student's history related exercises, the target question, and related skills. Experiments on three datasets demonstrate that GIKT achieves the new state-of-the-art performance, with at least 1% absolute AUC improvement.

Glancing Transformer for Non-Autoregressive Neural Machine Translation

Non-autoregressive neural machine translation achieves remarkable inference acceleration compared to autoregressive models. However, current non-autoregressive models still fall behind their autoregressive counterparts in prediction accuracy. We attribute the accuracy gaps to two disadvantages of non-autoregressive models: a) learning simultaneous generation under the overly strong conditional independence assumption; b) lacking explicit target language modeling. In this paper, we propose Glancing Transformer (GLAT) to address the above disadvantages, which reduces the difficulty of learning simultaneous generation and introduces explicit target language modeling in the non-autoregressive setting at the same time. Experiments on several benchmarks demonstrate that our approach significantly improves the accuracy of non-autoregressive models without sacrificing any inference efficiency. In particular, GLAT achieves 30.91 BLEU on WMT 2014 German-English, which narrows the gap between autoregressive models and non-autoregressive models to less than 0.5 BLEU score.