WikiGraphs: A Wikipedia Text - Knowledge Graph Paired Dataset

We present a new dataset of Wikipedia articles each paired with a knowledge graph, to facilitate the research in conditional text generation, graph generation and graph representation learning. Existing graph-text paired datasets typically contain small graphs and short text (1 or few sentences), thus limiting the capabilities of the models that can be learned on the data. Our new dataset WikiGraphs is collected by pairing each Wikipedia article from the established WikiText-103 benchmark (Merity et al., 2016) with a subgraph from the Freebase knowledge graph (Bollacker et al., 2008). This makes it easy to benchmark against other state-of-the-art text generative models that are capable of generating long paragraphs of coherent text. Both the graphs and the text data are of significantly larger scale compared to prior graph-text paired datasets. We present baseline graph neural network and transformer model results on our dataset for 3 tasks: graph -> text generation, graph -> text retrieval and text -> graph retrieval. We show that better conditioning on the graph provides gains in generation and retrieval quality but there is still large room for improvement.

Computer-Aided Design as Language

Computer-Aided Design (CAD) applications are used in manufacturing to model everything from coffee mugs to sports cars. These programs are complex and require years of training and experience to master. A component of all CAD models particularly difficult to make are the highly structured 2D sketches that lie at the heart of every 3D construction. In this work, we propose a machine learning model capable of automatically generating such sketches. Through this, we pave the way for developing intelligent tools that would help engineers create better designs with less effort. Our method is a combination of a general-purpose language modeling technique alongside an off-the-shelf data serialization protocol. We show that our approach has enough flexibility to accommodate the complexity of the domain and performs well for both unconditional synthesis and image-to-sketch translation.

Solving Mixed Integer Programs Using Neural Networks

Mixed Integer Programming (MIP) solvers rely on an array of sophisticated heuristics developed with decades of research to solve large-scale MIP instances encountered in practice. Machine learning offers to automatically construct better heuristics from data by exploiting shared structure among instances in the data. This paper applies learning to the two key sub-tasks of a MIP solver, generating a high-quality joint variable assignment, and bounding the gap in objective value between that assignment and an optimal one. Our approach constructs two corresponding neural network-based components, Neural Diving and Neural Branching, to use in a base MIP solver such as SCIP. Neural Diving learns a deep neural network to generate multiple partial assignments for its integer variables, and the resulting smaller MIPs for un-assigned variables are solved with SCIP to construct high quality joint assignments. Neural Branching learns a deep neural network to make variable selection decisions in branch-and-bound to bound the objective value gap with a small tree. This is done by imitating a new variant of Full Strong Branching we propose that scales to large instances using GPUs. We evaluate our approach on six diverse real-world datasets, including two Google production datasets and MIPLIB, by training separate neural networks on each. Most instances in all the datasets combined have $10^3-10^6$ variables and constraints after presolve, which is significantly larger than previous learning approaches. Comparing solvers with respect to primal-dual gap averaged over a held-out set of instances, the learning-augmented SCIP is 2x to 10x better on all datasets except one on which it is $10^5$x better, at large time limits. To the best of our knowledge, ours is the first learning approach to demonstrate such large improvements over SCIP on both large-scale real-world application datasets and MIPLIB.

Strong Generalization and Efficiency in Neural Programs

We study the problem of learning efficient algorithms that strongly generalize in the framework of neural program induction. By carefully designing the input / output interfaces of the neural model and through imitation, we are able to learn models that produce correct results for arbitrary input sizes, achieving strong generalization. Moreover, by using reinforcement learning, we optimize for program efficiency metrics, and discover new algorithms that surpass the teacher used in imitation. With this, our approach can learn to outperform custom-written solutions for a variety of problems, as we tested it on sorting, searching in ordered lists and the NP-complete 0/1 knapsack problem, which sets a notable milestone in the field of Neural Program Induction. As highlights, our learned model can perform sorting perfectly on any input data size we tested on, with $O(n log n)$ complexity, whilst outperforming hand-coded algorithms, including quick sort, in number of operations even for list sizes far beyond those seen during training.

Scalable Deep Generative Modeling for Sparse Graphs

Learning graph generative models is a challenging task for deep learning and has wide applicability to a range of domains like chemistry, biology and social science. However current deep neural methods suffer from limited scalability: for a graph with $n$ nodes and $m$ edges, existing deep neural methods require $\Omega(n^2)$ complexity by building up the adjacency matrix. On the other hand, many real world graphs are actually sparse in the sense that $m\ll n^2$. Based on this, we develop a novel autoregressive model, named BiGG, that utilizes this sparsity to avoid generating the full adjacency matrix, and importantly reduces the graph generation time complexity to $O((n + m)\log n)$. Furthermore, during training this autoregressive model can be parallelized with $O(\log n)$ synchronization stages, which makes it much more efficient than other autoregressive models that require $\Omega(n)$. Experiments on several benchmarks show that the proposed approach not only scales to orders of magnitude larger graphs than previously possible with deep autoregressive graph generative models, but also yields better graph generation quality.

A sparse negative binomial mixture model for clustering RNA-seq count data

Clustering with variable selection is a challenging but critical task for modern small-n-large-p data. Existing methods based on Gaussian mixture models or sparse K-means provide solutions to continuous data. With the prevalence of RNA-seq technology and lack of count data modeling for clustering, the current practice is to normalize count expression data into continuous measures and apply existing models with Gaussian assumption. In this paper, we develop a negative binomial mixture model with gene regularization to cluster samples (small $n$) with high-dimensional gene features (large $p$). EM algorithm and Bayesian information criterion are used for inference and determining tuning parameters. The method is compared with sparse Gaussian mixture model and sparse K-means using extensive simulations and two real transcriptomic applications in breast cancer and rat brain studies. The result shows superior performance of the proposed count data model in clustering accuracy, feature selection and biological interpretation by pathway enrichment analysis.

Prioritized Unit Propagation with Periodic Resetting is (Almost) All You Need for Random SAT Solving

We propose prioritized unit propagation with periodic resetting, which is a simple but surprisingly effective algorithm for solving random SAT instances that are meant to be hard. In particular, an evaluation on the Random Track of the 2017 and 2018 SAT competitions shows that a basic prototype of this simple idea already ranks at second place in both years. We share this observation in the hope that it helps the SAT community better understand the hardness of random instances used in competitions and inspire other interesting ideas on SAT solving.

Learning Transferable Graph Exploration

This paper considers the problem of efficient exploration of unseen environments, a key challenge in AI. We propose a `learning to explore' framework where we learn a policy from a distribution of environments. At test time, presented with an unseen environment from the same distribution, the policy aims to generalize the exploration strategy to visit the maximum number of unique states in a limited number of steps. We particularly focus on environments with graph-structured state-spaces that are encountered in many important real-world applications like software testing and map building. We formulate this task as a reinforcement learning problem where the `exploration' agent is rewarded for transitioning to previously unseen environment states and employ a graph-structured memory to encode the agent's past trajectory. Experimental results demonstrate that our approach is extremely effective for exploration of spatial maps; and when applied on the challenging problems of coverage-guided software-testing of domain-specific programs and real-world mobile applications, it outperforms methods that have been hand-engineered by human experts.

Efficient Graph Generation with Graph Recurrent Attention Networks

We propose a new family of efficient and expressive deep generative models of graphs, called Graph Recurrent Attention Networks (GRANs). Our model generates graphs one block of nodes and associated edges at a time. The block size and sampling stride allow us to trade off sample quality for efficiency. Compared to previous RNN-based graph generative models, our framework better captures the auto-regressive conditioning between the already-generated and to-be-generated parts of the graph using Graph Neural Networks (GNNs) with attention. This not only reduces the dependency on node ordering but also bypasses the long-term bottleneck caused by the sequential nature of RNNs. Moreover, we parameterize the output distribution per block using a mixture of Bernoulli, which captures the correlations among generated edges within the block. Finally, we propose to handle node orderings in generation by marginalizing over a family of canonical orderings. On standard benchmarks, we achieve state-of-the-art time efficiency and sample quality compared to previous models. Additionally, we show our model is capable of generating large graphs of up to 5K nodes with good quality. To the best of our knowledge, GRAN is the first deep graph generative model that can scale to this size. Our code is released at: https://github.com/lrjconan/GRAN.

Graph Convolutional Transformer: Learning the Graphical Structure of Electronic Health Records

Effective modeling of electronic health records (EHR) is rapidly becoming an important topic in both academia and industry. A recent study showed that utilizing the graphical structure underlying EHR data (e.g. relationship between diagnoses and treatments) improves the performance of prediction tasks such as heart failure diagnosis prediction. However, EHR data do not always contain complete structure information. Moreover, when it comes to claims data, structure information is completely unavailable to begin with. Under such circumstances, can we still do better than just treating EHR data as a flat-structured bag-of-features? In this paper, we study the possibility of utilizing the implicit structure of EHR by using the Transformer for prediction tasks on EHR data. Specifically, we argue that the Transformer is a suitable model to learn the hidden EHR structure, and propose the Graph Convolutional Transformer, which uses data statistics to guide the structure learning process. Our model empirically demonstrated superior prediction performance to previous approaches on both synthetic data and publicly available EHR data on encounter-based prediction tasks such as graph reconstruction and readmission prediction, indicating that it can serve as an effective general-purpose representation learning algorithm for EHR data.