Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.
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The need for large amounts of training data in modern machine learning is one of the biggest challenges of the field. Compared to the brain, current artificial algorithms are much less capable of learning invariance transformations and employing them to extrapolate knowledge from small sample sets. It has recently been proposed that the brain might encode perceptual invariances as approximate graph symmetries in the network of synaptic connections. Such symmetries may arise naturally through a biologically plausible process of unsupervised Hebbian learning. In the present paper, we illustrate this proposal on numerical examples, showing that invariance transformations can indeed be recovered from the structure of recurrent synaptic connections which form within a layer of feature detector neurons via a simple Hebbian learning rule. In order to numerically recover the invariance transformations from the resulting recurrent network, we develop a general algorithmic framework for finding approximate graph automorphisms. We discuss how this framework can be used to find approximate automorphisms in weighted graphs in general.
Multivariate functional data that are cross-sectionally compositional data are attracting increasing interest in the statistical modeling literature, a major example being trajectories over time of compositions derived from cause-specific mortality rates. In this work, we develop a novel functional concurrent regression model in which independent variables are functional compositions. This allows us to investigate the relationship over time between life expectancy at birth and compositions derived from cause-specific mortality rates of four distinct age classes, namely 0--4, 5--39, 40--64 and 65+. A penalized approach is developed to estimate the regression coefficients and select the relevant variables. Then an efficient computational strategy based on an augmented Lagrangian algorithm is derived to solve the resulting optimization problem. The good performances of the model in predicting the response function and estimating the unknown functional coefficients are shown in a simulation study. The results on real data confirm the important role of neoplasms and cardiovascular diseases in determining life expectancy emerged in other studies and reveal several other contributions not yet observed.
Contemporary graph learning algorithms are not well-defined for large molecules since they do not consider the hierarchical interactions among the atoms, which are essential to determine the molecular properties of macromolecules. In this work, we propose Multiresolution Graph Transformers (MGT), the first graph transformer architecture that can learn to represent large molecules at multiple scales. MGT can learn to produce representations for the atoms and group them into meaningful functional groups or repeating units. We also introduce Wavelet Positional Encoding (WavePE), a new positional encoding method that can guarantee localization in both spectral and spatial domains. Our proposed model achieves competitive results on two macromolecule datasets consisting of polymers and peptides, and one drug-like molecule dataset. Importantly, our model outperforms other state-of-the-art methods and achieves chemical accuracy in estimating molecular properties (e.g., GAP, HOMO and LUMO) calculated by Density Functional Theory (DFT) in the polymers dataset. Furthermore, the visualizations, including clustering results on macromolecules and low-dimensional spaces of their representations, demonstrate the capability of our methodology in learning to represent long-range and hierarchical structures. Our PyTorch implementation is publicly available at //github.com/HySonLab/Multires-Graph-Transformer
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.
Learning disentanglement aims at finding a low dimensional representation which consists of multiple explanatory and generative factors of the observational data. The framework of variational autoencoder (VAE) is commonly used to disentangle independent factors from observations. However, in real scenarios, factors with semantics are not necessarily independent. Instead, there might be an underlying causal structure which renders these factors dependent. We thus propose a new VAE based framework named CausalVAE, which includes a Causal Layer to transform independent exogenous factors into causal endogenous ones that correspond to causally related concepts in data. We further analyze the model identifiabitily, showing that the proposed model learned from observations recovers the true one up to a certain degree. Experiments are conducted on various datasets, including synthetic and real word benchmark CelebA. Results show that the causal representations learned by CausalVAE are semantically interpretable, and their causal relationship as a Directed Acyclic Graph (DAG) is identified with good accuracy. Furthermore, we demonstrate that the proposed CausalVAE model is able to generate counterfactual data through "do-operation" to the causal factors.
Graph Neural Networks (GNNs) are widely used for analyzing graph-structured data. Most GNN methods are highly sensitive to the quality of graph structures and usually require a perfect graph structure for learning informative embeddings. However, the pervasiveness of noise in graphs necessitates learning robust representations for real-world problems. To improve the robustness of GNN models, many studies have been proposed around the central concept of Graph Structure Learning (GSL), which aims to jointly learn an optimized graph structure and corresponding representations. Towards this end, in the presented survey, we broadly review recent progress of GSL methods for learning robust representations. Specifically, we first formulate a general paradigm of GSL, and then review state-of-the-art methods classified by how they model graph structures, followed by applications that incorporate the idea of GSL in other graph tasks. Finally, we point out some issues in current studies and discuss future directions.
This paper focuses on the expected difference in borrower's repayment when there is a change in the lender's credit decisions. Classical estimators overlook the confounding effects and hence the estimation error can be magnificent. As such, we propose another approach to construct the estimators such that the error can be greatly reduced. The proposed estimators are shown to be unbiased, consistent, and robust through a combination of theoretical analysis and numerical testing. Moreover, we compare the power of estimating the causal quantities between the classical estimators and the proposed estimators. The comparison is tested across a wide range of models, including linear regression models, tree-based models, and neural network-based models, under different simulated datasets that exhibit different levels of causality, different degrees of nonlinearity, and different distributional properties. Most importantly, we apply our approaches to a large observational dataset provided by a global technology firm that operates in both the e-commerce and the lending business. We find that the relative reduction of estimation error is strikingly substantial if the causal effects are accounted for correctly.
There has been appreciable progress in unsupervised network representation learning (UNRL) approaches over graphs recently with flexible random-walk approaches, new optimization objectives and deep architectures. However, there is no common ground for systematic comparison of embeddings to understand their behavior for different graphs and tasks. In this paper we theoretically group different approaches under a unifying framework and empirically investigate the effectiveness of different network representation methods. In particular, we argue that most of the UNRL approaches either explicitly or implicit model and exploit context information of a node. Consequently, we propose a framework that casts a variety of approaches -- random walk based, matrix factorization and deep learning based -- into a unified context-based optimization function. We systematically group the methods based on their similarities and differences. We study the differences among these methods in detail which we later use to explain their performance differences (on downstream tasks). We conduct a large-scale empirical study considering 9 popular and recent UNRL techniques and 11 real-world datasets with varying structural properties and two common tasks -- node classification and link prediction. We find that there is no single method that is a clear winner and that the choice of a suitable method is dictated by certain properties of the embedding methods, task and structural properties of the underlying graph. In addition we also report the common pitfalls in evaluation of UNRL methods and come up with suggestions for experimental design and interpretation of results.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Traditional methods for link prediction can be categorized into three main types: graph structure feature-based, latent feature-based, and explicit feature-based. Graph structure feature methods leverage some handcrafted node proximity scores, e.g., common neighbors, to estimate the likelihood of links. Latent feature methods rely on factorizing networks' matrix representations to learn an embedding for each node. Explicit feature methods train a machine learning model on two nodes' explicit attributes. Each of the three types of methods has its unique merits. In this paper, we propose SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction), a new framework for link prediction which combines the power of all the three types into a single graph neural network (GNN). GNN is a new type of neural network which directly accepts graphs as input and outputs their labels. In SEAL, the input to the GNN is a local subgraph around each target link. We prove theoretically that our local subgraphs also reserve a great deal of high-order graph structure features related to link existence. Another key feature is that our GNN can naturally incorporate latent features and explicit features. It is achieved by concatenating node embeddings (latent features) and node attributes (explicit features) in the node information matrix for each subgraph, thus combining the three types of features to enhance GNN learning. Through extensive experiments, SEAL shows unprecedentedly strong performance against a wide range of baseline methods, including various link prediction heuristics and network embedding methods.
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