Molecule generation is to design new molecules with specific chemical properties and further to optimize the desired chemical properties. Following previous work, we encode molecules into continuous vectors in the latent space and then decode the vectors into molecules under the variational autoencoder (VAE) framework. We investigate the posterior collapse problem of current RNN-based VAEs for molecule sequence generation. For the first time, we find that underestimated reconstruction loss leads to posterior collapse, and provide both theoretical and experimental evidence. We propose an effective and efficient solution to fix the problem and avoid posterior collapse. Without bells and whistles, our method achieves SOTA reconstruction accuracy and competitive validity on the ZINC 250K dataset. When generating 10,000 unique valid SMILES from random prior sampling, it costs JT-VAE1450s while our method only needs 9s. Our implementation is at https://github.com/chaoyan1037/Re-balanced-VAE.

Recent advances in artificial intelligence (AI) and machine learning have created a general perception that AI could be used to solve complex problems, and in some situations over-hyped as a tool that can be so easily used. Unfortunately, the barrier to realization of mass adoption of AI on various business domains is too high because most domain experts have no background in AI. Developing AI applications involves multiple phases, namely data preparation, application modeling, and product deployment. The effort of AI research has been spent mostly on new AI models (in the model training stage) to improve the performance of benchmark tasks such as image recognition. Many other factors such as usability, efficiency and security of AI have not been well addressed, and therefore form a barrier to democratizing AI. Further, for many real world applications such as healthcare and autonomous driving, learning via huge amounts of possibility exploration is not feasible since humans are involved. In many complex applications such as healthcare, subject matter experts (e.g. Clinicians) are the ones who appreciate the importance of features that affect health, and their knowledge together with existing knowledge bases are critical to the end results. In this paper, we take a new perspective on developing AI solutions, and present a solution for making AI usable. We hope that this resolution will enable all subject matter experts (eg. Clinicians) to exploit AI like data scientists.

Big data analytics is gaining massive momentum in the last few years. Applying machine learning models to big data has become an implicit requirement or an expectation for most analysis tasks, especially on high-stakes applications.Typical applications include sentiment analysis against reviews for analyzing on-line products, image classification in food logging applications for monitoring user's daily intake and stock movement prediction. Extending traditional database systems to support the above analysis is intriguing but challenging. First, it is almost impossible to implement all machine learning models in the database engines. Second, expertise knowledge is required to optimize the training and inference procedures in terms of efficiency and effectiveness, which imposes heavy burden on the system users. In this paper, we develop and present a system, called Rafiki, to provide the training and inference service of machine learning models, and facilitate complex analytics on top of cloud platforms. Rafiki provides distributed hyper-parameter tuning for the training service, and online ensemble modeling for the inference service which trades off between latency and accuracy. Experimental results confirm the efficiency, effectiveness, scalability and usability of Rafiki.

Graph Convolutional Neural Networks (Graph CNNs) are generalizations of classical CNNs to handle graph data such as molecular data, point could and social networks. Current filters in graph CNNs are built for fixed and shared graph structure. However, for most real data, the graph structures varies in both size and connectivity. The paper proposes a generalized and flexible graph CNN taking data of arbitrary graph structure as input. In that way a task-driven adaptive graph is learned for each graph data while training. To efficiently learn the graph, a distance metric learning is proposed. Extensive experiments on nine graph-structured datasets have demonstrated the superior performance improvement on both convergence speed and predictive accuracy.

Graph Convolutional Neural Networks (Graph CNNs) are generalizations of classical CNNs to handle graph data such as molecular data, point could and social networks. Current filters in graph CNNs are built for fixed and shared graph structure. However, for most real data, the graph structures varies in both size and connectivity. The paper proposes a generalized and flexible graph CNN taking data of arbitrary graph structure as input. In that way a task-driven adaptive graph is learned for each graph data while training. To efficiently learn the graph, a distance metric learning is proposed. Extensive experiments on nine graph-structured datasets have demonstrated the superior performance improvement on both convergence speed and predictive accuracy.

This paper considers the actor-critic contextual bandit for the mobile health (mHealth) intervention. The state-of-the-art decision-making methods in mHealth generally assume that the noise in the dynamic system follows the Gaussian distribution. Those methods use the least-square-based algorithm to estimate the expected reward, which is prone to the existence of outliers. To deal with the issue of outliers, we propose a novel robust actor-critic contextual bandit method for the mHealth intervention. In the critic updating, the capped-$\ell_{2}$ norm is used to measure the approximation error, which prevents outliers from dominating our objective. A set of weights could be achieved from the critic updating. Considering them gives a weighted objective for the actor updating. It provides the badly noised sample in the critic updating with zero weights for the actor updating. As a result, the robustness of both actor-critic updating is enhanced. There is a key parameter in the capped-$\ell_{2}$ norm. We provide a reliable method to properly set it by making use of one of the most fundamental definitions of outliers in statistics. Extensive experiment results demonstrate that our method can achieve almost identical results compared with the state-of-the-art methods on the dataset without outliers and dramatically outperform them on the datasets noised by outliers.

Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual networks. This deep neural network allows us to model very complex sequence-contact relationship as well as long-range inter-contact correlation. Our method greatly outperforms existing contact prediction methods and leads to much more accurate contact-assisted protein folding. Tested on three datasets of 579 proteins, the average top L long-range prediction accuracy obtained our method, the representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints can yield correct folds (i.e., TMscore>0.6) for 203 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 proteins, respectively. Further, our contact-assisted models have much better quality than template-based models. Using our predicted contacts as restraints, we can (ab initio) fold 208 of the 398 membrane proteins with TMscore>0.5. By contrast, when the training proteins of our method are used as templates, homology modeling can only do so for 10 of them. One interesting finding is that even if we do not train our prediction models with any membrane proteins, our method works very well on membrane protein prediction. Finally, in recent blind CAMEO benchmark our method successfully folded 5 test proteins with a novel fold.

Deep Convolutional Neural Networks (DCNN) has shown excellent performance in a variety of machine learning tasks. This manuscript presents Deep Convolutional Neural Fields (DeepCNF), a combination of DCNN with Conditional Random Field (CRF), for sequence labeling with highly imbalanced label distribution. The widely-used training methods, such as maximum-likelihood and maximum labelwise accuracy, do not work well on highly imbalanced data. To handle this, we present a new training algorithm called maximum-AUC for DeepCNF. That is, we train DeepCNF by directly maximizing the empirical Area Under the ROC Curve (AUC), which is an unbiased measurement for imbalanced data. To fulfill this, we formulate AUC in a pairwise ranking framework, approximate it by a polynomial function and then apply a gradient-based procedure to optimize it. We then test our AUC-maximized DeepCNF on three very different protein sequence labeling tasks: solvent accessibility prediction, 8-state secondary structure prediction, and disorder prediction. Our experimental results confirm that maximum-AUC greatly outperforms the other two training methods on 8-state secondary structure prediction and disorder prediction since their label distributions are highly imbalanced and also have similar performance as the other two training methods on the solvent accessibility prediction problem which has three equally-distributed labels. Furthermore, our experimental results also show that our AUC-trained DeepCNF models greatly outperform existing popular predictors of these three tasks.

Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence remains very challenging. Both evolutionary coupling (EC) analysis and supervised machine learning methods are developed to predict contacts, making use of different types of information, respectively. This paper presents a group graphical lasso (GGL) method for contact prediction that integrates joint multi-family EC analysis and supervised learning. Different from existing single-family EC analysis that uses residue co-evolution information in only the target protein family, our joint EC analysis uses residue co-evolution in both the target family and its related families, which may have divergent sequences but similar folds. To implement joint EC analysis, we model a set of related protein families using Gaussian graphical models (GGM) and then co-estimate their precision matrices by maximum-likelihood, subject to the constraint that the precision matrices shall share similar residue co-evolution patterns. To further improve the accuracy of the estimated precision matrices, we employ a supervised learning method to predict contact probability from a variety of evolutionary and non-evolutionary information and then incorporate the predicted probability as prior into our GGL framework. Experiments show that our method can predict contacts much more accurately than existing methods, and that our method performs better on both conserved and family-specific contacts.

Probabilistic topic models have been widely used for sentiment analysis. However, most of existing topic methods only model the sentiment text, but do not consider the user, who expresses the sentiment, and the item, which the sentiment is expressed on. Since different users may use different sentiment expressions for different items, we argue that it is better to incorporate the user and item information into the topic model for sentiment analysis. In this paper, we propose a new Supervised User-Item based Topic model, called SUIT model, for sentiment analysis. It can simultaneously utilize the textual topic and latent user-item factors. Our proposed method uses the tensor outer product of text topic proportion vector, user latent factor and item latent factor to model the sentiment label generalization. Extensive experiments are conducted on two datasets: review dataset and microblog dataset. The results demonstrate the advantages of our model. It shows significant improvement compared with supervised topic models and collaborative filtering methods.