Learning to Play in a Day: Faster Deep Reinforcement Learning by Optimality Tightening

We propose a novel training algorithm for reinforcement learning which combines the strength of deep Q-learning with a constrained optimization approach to tighten optimality and encourage faster reward propagation. Our novel technique makes deep reinforcement learning more practical by drastically reducing the training time. We evaluate the performance of our approach on the 49 games of the challenging Arcade Learning Environment, and report significant improvements in both training time and accuracy.

DPPred: An Effective Prediction Framework with Concise Discriminative Patterns

In the literature, two series of models have been proposed to address prediction problems including classification and regression. Simple models, such as generalized linear models, have ordinary performance but strong interpretability on a set of simple features. The other series, including tree-based models, organize numerical, categorical and high dimensional features into a comprehensive structure with rich interpretable information in the data. In this paper, we propose a novel Discriminative Pattern-based Prediction framework (DPPred) to accomplish the prediction tasks by taking their advantages of both effectiveness and interpretability. Specifically, DPPred adopts the concise discriminative patterns that are on the prefix paths from the root to leaf nodes in the tree-based models. DPPred selects a limited number of the useful discriminative patterns by searching for the most effective pattern combination to fit generalized linear models. Extensive experiments show that in many scenarios, DPPred provides competitive accuracy with the state-of-the-art as well as the valuable interpretability for developers and experts. In particular, taking a clinical application dataset as a case study, our DPPred outperforms the baselines by using only 40 concise discriminative patterns out of a potentially exponentially large set of patterns.

Meta-Path Guided Embedding for Similarity Search in Large-Scale Heterogeneous Information Networks

Most real-world data can be modeled as heterogeneous information networks (HINs) consisting of vertices of multiple types and their relationships. Search for similar vertices of the same type in large HINs, such as bibliographic networks and business-review networks, is a fundamental problem with broad applications. Although similarity search in HINs has been studied previously, most existing approaches neither explore rich semantic information embedded in the network structures nor take user's preference as a guidance. In this paper, we re-examine similarity search in HINs and propose a novel embedding-based framework. It models vertices as low-dimensional vectors to explore network structure-embedded similarity. To accommodate user preferences at defining similarity semantics, our proposed framework, ESim, accepts user-defined meta-paths as guidance to learn vertex vectors in a user-preferred embedding space. Moreover, an efficient and parallel sampling-based optimization algorithm has been developed to learn embeddings in large-scale HINs. Extensive experiments on real-world large-scale HINs demonstrate a significant improvement on the effectiveness of ESim over several state-of-the-art algorithms as well as its scalability.

Protein secondary structure prediction using deep convolutional neural fields

Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

Exact Hybrid Covariance Thresholding for Joint Graphical Lasso

This paper considers the problem of estimating multiple related Gaussian graphical models from a $p$-dimensional dataset consisting of different classes. Our work is based upon the formulation of this problem as group graphical lasso. This paper proposes a novel hybrid covariance thresholding algorithm that can effectively identify zero entries in the precision matrices and split a large joint graphical lasso problem into small subproblems. Our hybrid covariance thresholding method is superior to existing uniform thresholding methods in that our method can split the precision matrix of each individual class using different partition schemes and thus split group graphical lasso into much smaller subproblems, each of which can be solved very fast. In addition, this paper establishes necessary and sufficient conditions for our hybrid covariance thresholding algorithm. The superior performance of our thresholding method is thoroughly analyzed and illustrated by a few experiments on simulated data and real gene expression data.

Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks

Complex biological systems have been successfully modeled by biochemical and genetic interaction networks, typically gathered from high-throughput (HTP) data. These networks can be used to infer functional relationships between genes or proteins. Using the intuition that the topological role of a gene in a network relates to its biological function, local or diffusion based "guilt-by-association" and graph-theoretic methods have had success in inferring gene functions. Here we seek to improve function prediction by integrating diffusion-based methods with a novel dimensionality reduction technique to overcome the incomplete and noisy nature of network data. In this paper, we introduce diffusion component analysis (DCA), a framework that plugs in a diffusion model and learns a low-dimensional vector representation of each node to encode the topological properties of a network. As a proof of concept, we demonstrate DCA's substantial improvement over state-of-the-art diffusion-based approaches in predicting protein function from molecular interaction networks. Moreover, our DCA framework can integrate multiple networks from heterogeneous sources, consisting of genomic information, biochemical experiments and other resources, to even further improve function prediction. Yet another layer of performance gain is achieved by integrating the DCA framework with support vector machines that take our node vector representations as features. Overall, our DCA framework provides a novel representation of nodes in a network that can be used as a plug-in architecture to other machine learning algorithms to decipher topological properties of and obtain novel insights into interactomes.

Tightening Fractional Covering Upper Bounds on the Partition Function for High-Order Region Graphs

In this paper we present a new approach for tightening upper bounds on the partition function. Our upper bounds are based on fractional covering bounds on the entropy function, and result in a concave program to compute these bounds and a convex program to tighten them. To solve these programs effectively for general region graphs we utilize the entropy barrier method, thus decomposing the original programs by their dual programs and solve them with dual block optimization scheme. The entropy barrier method provides an elegant framework to generalize the message-passing scheme to high-order region graph, as well as to solve the block dual steps in closed-form. This is a key for computational relevancy for large problems with thousands of regions.