Search

Graph neural networks (GNNs) enable the analysis of graphs using deep learning, with promising results in capturing structured information in graphs. This paper focuses on creating a small graph to represent the original graph, so that GNNs trained on the size-reduced graph can make accurate predictions. We view the original graph as a distribution of receptive fields and aim to synthesize a small graph whose receptive fields share a similar distribution. Thus, we propose Graph Condesation via Receptive Field Distribution Matching (GCDM), which is accomplished by optimizing the synthetic graph through the use of a distribution matching loss quantified by maximum mean discrepancy (MMD). Additionally, we demonstrate that the synthetic graph generated by GCDM is highly generalizable to a variety of models in evaluation phase and that the condensing speed is significantly improved using this framework.

Probabilistic Graphical Models (PGMs) are generative models of complex systems. They rely on conditional independence assumptions between variables to learn sparse representations which can be visualized in a form of a graph. Such models are used for domain exploration and structure discovery in poorly understood domains. This work introduces a novel technique to perform sparse graph recovery by optimizing deep unrolled networks. Assuming that the input data $X\in\mathbb{R}^{M\times D}$ comes from an underlying multivariate Gaussian distribution, we apply a deep model on $X$ that outputs the precision matrix $\hat{\Theta}$, which can also be interpreted as the adjacency matrix. Our model, uGLAD, builds upon and extends the state-of-the-art model GLAD to the unsupervised setting. The key benefits of our model are (1) uGLAD automatically optimizes sparsity-related regularization parameters leading to better performance than existing algorithms. (2) We introduce multi-task learning based `consensus' strategy for robust handling of missing data in an unsupervised setting. We evaluate model results on synthetic Gaussian data, non-Gaussian data generated from Gene Regulatory Networks, and present a case study in anaerobic digestion.

Dynamic graphs with ordered sequences of events between nodes are prevalent in real-world industrial applications such as e-commerce and social platforms. However, representation learning for dynamic graphs has posed great computational challenges due to the time and structure dependency and irregular nature of the data, preventing such models from being deployed to real-world applications. To tackle this challenge, we propose an efficient algorithm, Efficient Dynamic Graph lEarning (EDGE), which selectively expresses certain temporal dependency via training loss to improve the parallelism in computations. We show that EDGE can scale to dynamic graphs with millions of nodes and hundreds of millions of temporal events and achieve new state-of-the-art (SOTA) performance.

We consider the problem of discovering $K$ related Gaussian directed acyclic graphs (DAGs), where the involved graph structures share a consistent causal order and sparse unions of supports. Under the multi-task learning setting, we propose a $l_1/l_2$-regularized maximum likelihood estimator (MLE) for learning $K$ linear structural equation models. We theoretically show that the joint estimator, by leveraging data across related tasks, can achieve a better sample complexity for recovering the causal order (or topological order) than separate estimations. Moreover, the joint estimator is able to recover non-identifiable DAGs, by estimating them together with some identifiable DAGs. Lastly, our analysis also shows the consistency of union support recovery of the structures. To allow practical implementation, we design a continuous optimization problem whose optimizer is the same as the joint estimator and can be approximated efficiently by an iterative algorithm. We validate the theoretical analysis and the effectiveness of the joint estimator in experiments., Comment: 35th Conference on Neural Information Processing Systems (NeurIPS 2021)

Recently, there has been a surge of interest in combining deep learning models with reasoning in order to handle more sophisticated learning tasks. In many cases, a reasoning task can be solved by an iterative algorithm. This algorithm is often unrolled, and used as a specialized layer in the deep architecture, which can be trained end-to-end with other neural components. Although such hybrid deep architectures have led to many empirical successes, the theoretical foundation of such architectures, especially the interplay between algorithm layers and other neural layers, remains largely unexplored. In this paper, we take an initial step towards an understanding of such hybrid deep architectures by showing that properties of the algorithm layers, such as convergence, stability, and sensitivity, are intimately related to the approximation and generalization abilities of the end-to-end model. Furthermore, our analysis matches closely our experimental observations under various conditions, suggesting that our theory can provide useful guidelines for designing deep architectures with reasoning layers., Comment: 34th Conference on Neural Information Processing Systems (NeurIPS 2020)

There is a recent surge of interest in designing deep architectures based on the update steps in traditional algorithms, or learning neural networks to improve and replace traditional algorithms. While traditional algorithms have certain stopping criteria for outputting results at different iterations, many algorithm-inspired deep models are restricted to a ``fixed-depth'' for all inputs. Similar to algorithms, the optimal depth of a deep architecture may be different for different input instances, either to avoid ``over-thinking'', or because we want to compute less for operations converged already. In this paper, we tackle this varying depth problem using a steerable architecture, where a feed-forward deep model and a variational stopping policy are learned together to sequentially determine the optimal number of layers for each input instance. Training such architecture is very challenging. We provide a variational Bayes perspective and design a novel and effective training procedure which decomposes the task into an oracle model learning stage and an imitation stage. Experimentally, we show that the learned deep model along with the stopping policy improves the performances on a diverse set of tasks, including learning sparse recovery, few-shot meta learning, and computer vision tasks., Comment: Proceedings of the 37th International Conference on Machine Learning

In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly predict the RNA base-pairing matrix, and use an unrolled algorithm for constrained programming as the template for deep architectures to enforce constraints. With comprehensive experiments on benchmark datasets, we demonstrate the superior performance of E2Efold: it predicts significantly better structures compared to previous SOTA (especially for pseudoknotted structures), while being as efficient as the fastest algorithms in terms of inference time., Comment: International Conference on Learning Representations 2020

Markov Logic Networks (MLNs), which elegantly combine logic rules and probabilistic graphical models, can be used to address many knowledge graph problems. However, inference in MLN is computationally intensive, making the industrial-scale application of MLN very difficult. In recent years, graph neural networks (GNNs) have emerged as efficient and effective tools for large-scale graph problems. Nevertheless, GNNs do not explicitly incorporate prior logic rules into the models, and may require many labeled examples for a target task. In this paper, we explore the combination of MLNs and GNNs, and use graph neural networks for variational inference in MLN. We propose a GNN variant, named ExpressGNN, which strikes a nice balance between the representation power and the simplicity of the model. Our extensive experiments on several benchmark datasets demonstrate that ExpressGNN leads to effective and efficient probabilistic logic reasoning.

To better understand and improve the behavior of neural networks, a recent line of works bridged the connection between ordinary differential equations (ODEs) and deep neural networks (DNNs). The connections are made in two folds: (1) View DNN as ODE discretization; (2) View the training of DNN as solving an optimal control problem. The former connection motivates people either to design neural architectures based on ODE discretization schemes or to replace DNN by a continuous model characterized by ODEs. Several works demonstrated distinct advantages of using a continuous model instead of traditional DNN in some specific applications. The latter connection is inspiring. Based on Pontryagin's maximum principle, which is popular in the optimal control literature, some developed new optimization methods for training neural networks and some developed algorithms to train the infinite-deep continuous model with low memory-cost. This paper is organized as follows: In Section 2, the relation between neural architecture and ODE discretization is introduced. Some architectures are not motivated by ODE, but they are later found to be associated with some specific discretization schemes. Some architectures are designed based on ODE discretization and expected to achieve some special properties. Section 3 formulates the optimization problem where a traditional neural network is replaced by a continuous model (ODE). The formulated optimization problem is an optimal control problem. Therefore, two different types of controls will also be discussed in this section. In Section 4, we will discuss how we can utilize the optimization methods that are popular in optimal control literature to help the training of machine learning problems. Finally, two applications of using a continuous model will be shown in Section 5 and 6 to demonstrate some of its advantages over traditional neural networks., Comment: arXiv admin note: substantial text overlap with arXiv:1902.00640

Effectively combining logic reasoning and probabilistic inference has been a long-standing goal of machine learning: the former has the ability to generalize with small training data, while the latter provides a principled framework for dealing with noisy data. However, existing methods for combining the best of both worlds are typically computationally intensive. In this paper, we focus on Markov Logic Networks and explore the use of graph neural networks (GNNs) for representing probabilistic logic inference. It is revealed from our analysis that the representation power of GNN alone is not enough for such a task. We instead propose a more expressive variant, called ExpressGNN, which can perform effective probabilistic logic inference while being able to scale to a large number of entities. We demonstrate by several benchmark datasets that ExpressGNN has the potential to advance probabilistic logic reasoning to the next stage.

Recovering sparse conditional independence graphs from data is a fundamental problem in machine learning with wide applications. A popular formulation of the problem is an $\ell_1$ regularized maximum likelihood estimation. Many convex optimization algorithms have been designed to solve this formulation to recover the graph structure. Recently, there is a surge of interest to learn algorithms directly based on data, and in this case, learn to map empirical covariance to the sparse precision matrix. However, it is a challenging task in this case, since the symmetric positive definiteness (SPD) and sparsity of the matrix are not easy to enforce in learned algorithms, and a direct mapping from data to precision matrix may contain many parameters. We propose a deep learning architecture, GLAD, which uses an Alternating Minimization (AM) algorithm as our model inductive bias, and learns the model parameters via supervised learning. We show that GLAD learns a very compact and effective model for recovering sparse graphs from data.

The thesis is about an application of the shape optimization to the morphological evolution of Golgi stack. Golgi stack consists of multiple layers of cisternae. It is an organelle in the biological cells. Inspired by the Helfrich Model \cite{Helfrich}, which is a model for vesicles typically applied to biological cells, a new model specially designed for Golgi stack is developed and then implemented using FEM in this thesis. In the Golgi model, each cisternae of the Golgi stack is viewed as a closed vesicle without topological changes, and our model is adaptable to both single-vesicle case and multiple-vesicle case. The main idea of the math model is to minimize the elastic energy(bending energy) of the vesicles, with some constraints designed regarding the biological properties of Golgi stack. With these constraints attached to the math model, we could extend this model to an obstacle-type problem. Hence, in the thesis, not only the simulations of Golgi stack are shown, but some interesting examples without biological meanings are also demonstrated. Also, as multiple cisternaes are considered as a whole, this is also a model handling multiple objects. A set of numerical examples is shown to compare with the observed shape of Golgi stack, so we can lay down some possible explanations to the morphological performance of trans-Golgi cisternae., Comment: M.Phil. thesis paper (Chinese University of Hong Kong, department of mathematics )

We present a particle flow realization of Bayes' rule, where an ODE-based neural operator is used to transport particles from a prior to its posterior after a new observation. We prove that such an ODE operator exists. Its neural parameterization can be trained in a meta-learning framework, allowing this operator to reason about the effect of an individual observation on the posterior, and thus generalize across different priors, observations and to sequential Bayesian inference. We demonstrated the generalization ability of our particle flow Bayes operator in several canonical and high dimensional examples.

There are great interests as well as many challenges in applying reinforcement learning (RL) to recommendation systems. In this setting, an online user is the environment; neither the reward function nor the environment dynamics are clearly defined, making the application of RL challenging. In this paper, we propose a novel model-based reinforcement learning framework for recommendation systems, where we develop a generative adversarial network to imitate user behavior dynamics and learn her reward function. Using this user model as the simulation environment, we develop a novel Cascading DQN algorithm to obtain a combinatorial recommendation policy which can handle a large number of candidate items efficiently. In our experiments with real data, we show this generative adversarial user model can better explain user behavior than alternatives, and the RL policy based on this model can lead to a better long-term reward for the user and higher click rate for the system.