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Modern biomedical datasets are increasingly high dimensional and exhibit complex correlation structures. Generalized Linear Mixed Models (GLMMs) have long been employed to account for such dependencies. However, proper specification of the fixed and random effects in GLMMs is increasingly difficult in high dimensions, and computational complexity grows with increasing dimension of the random effects. We present a novel reformulation of the GLMM using a factor model decomposition of the random effects, enabling scalable computation of GLMMs in high dimensions by reducing the latent space from a large number of random effects to a smaller set of latent factors. We also extend our prior work to estimate model parameters using a modified Monte Carlo Expectation Conditional Minimization algorithm, allowing us to perform variable selection on both the fixed and random effects simultaneously. We show through simulation that through this factor model decomposition, our method can fit high dimensional penalized GLMMs faster than comparable methods and more easily scale to larger dimensions not previously seen in existing approaches.

Federated learning (FL) has recently gained much attention due to its effectiveness in speeding up supervised learning tasks under communication and privacy constraints. However, whether similar speedups can be established for reinforcement learning remains much less understood theoretically. Towards this direction, we study a federated policy evaluation problem where agents communicate via a central aggregator to expedite the evaluation of a common policy. To capture typical communication constraints in FL, we consider finite capacity up-link channels that can drop packets based on a Bernoulli erasure model. Given this setting, we propose and analyze QFedTD - a quantized federated temporal difference learning algorithm with linear function approximation. Our main technical contribution is to provide a finite-sample analysis of QFedTD that (i) highlights the effect of quantization and erasures on the convergence rate; and (ii) establishes a linear speedup w.r.t. the number of agents under Markovian sampling. Notably, while different quantization mechanisms and packet drop models have been extensively studied in the federated learning, distributed optimization, and networked control systems literature, our work is the first to provide a non-asymptotic analysis of their effects in multi-agent and federated reinforcement learning.

Recent studies have experimentally shown that we can achieve in non-Euclidean metric space effective and efficient graph embedding, which aims to obtain the vertices' representations reflecting the graph's structure in the metric space. Specifically, graph embedding in hyperbolic space has experimentally succeeded in embedding graphs with hierarchical-tree structure, e.g., data in natural languages, social networks, and knowledge bases. However, recent theoretical analyses have shown a much higher upper bound on non-Euclidean graph embedding's generalization error than Euclidean one's, where a high generalization error indicates that the incompleteness and noise in the data can significantly damage learning performance. It implies that the existing bound cannot guarantee the success of graph embedding in non-Euclidean metric space in a practical training data size, which can prevent non-Euclidean graph embedding's application in real problems. This paper provides a novel upper bound of graph embedding's generalization error by evaluating the local Rademacher complexity of the model as a function set of the distances of representation couples. Our bound clarifies that the performance of graph embedding in non-Euclidean metric space, including hyperbolic space, is better than the existing upper bounds suggest. Specifically, our new upper bound is polynomial in the metric space's geometric radius $R$ and can be $O(\frac{1}{S})$ at the fastest, where $S$ is the training data size. Our bound is significantly tighter and faster than the existing one, which can be exponential to $R$ and $O(\frac{1}{\sqrt{S}})$ at the fastest. Specific calculations on example cases show that graph embedding in non-Euclidean metric space can outperform that in Euclidean space with much smaller training data than the existing bound has suggested.

Concept-based interpretability methods aim to explain deep neural network model predictions using a predefined set of semantic concepts. These methods evaluate a trained model on a new, "probe" dataset and correlate model predictions with the visual concepts labeled in that dataset. Despite their popularity, they suffer from limitations that are not well-understood and articulated by the literature. In this work, we analyze three commonly overlooked factors in concept-based explanations. First, the choice of the probe dataset has a profound impact on the generated explanations. Our analysis reveals that different probe datasets may lead to very different explanations, and suggests that the explanations are not generalizable outside the probe dataset. Second, we find that concepts in the probe dataset are often less salient and harder to learn than the classes they claim to explain, calling into question the correctness of the explanations. We argue that only visually salient concepts should be used in concept-based explanations. Finally, while existing methods use hundreds or even thousands of concepts, our human studies reveal a much stricter upper bound of 32 concepts or less, beyond which the explanations are much less practically useful. We make suggestions for future development and analysis of concept-based interpretability methods. Code for our analysis and user interface can be found at \url{//github.com/princetonvisualai/OverlookedFactors}

An experimental comparison of two or more optimization algorithms requires the same computational resources to be assigned to each algorithm. When a maximum runtime is set as the stopping criterion, all algorithms need to be executed in the same machine if they are to use the same resources. Unfortunately, the implementation code of the algorithms is not always available, which means that running the algorithms to be compared in the same machine is not always possible. And even if they are available, some optimization algorithms might be costly to run, such as training large neural-networks in the cloud. In this paper, we consider the following problem: how do we compare the performance of a new optimization algorithm B with a known algorithm A in the literature if we only have the results (the objective values) and the runtime in each instance of algorithm A? Particularly, we present a methodology that enables a statistical analysis of the performance of algorithms executed in different machines. The proposed methodology has two parts. Firstly, we propose a model that, given the runtime of an algorithm in a machine, estimates the runtime of the same algorithm in another machine. This model can be adjusted so that the probability of estimating a runtime longer than what it should be is arbitrarily low. Secondly, we introduce an adaptation of the one-sided sign test that uses a modified \textit{p}-value and takes into account that probability. Such adaptation avoids increasing the probability of type I error associated with executing algorithms A and B in different machines.

Classic algorithms and machine learning systems like neural networks are both abundant in everyday life. While classic computer science algorithms are suitable for precise execution of exactly defined tasks such as finding the shortest path in a large graph, neural networks allow learning from data to predict the most likely answer in more complex tasks such as image classification, which cannot be reduced to an exact algorithm. To get the best of both worlds, this thesis explores combining both concepts leading to more robust, better performing, more interpretable, more computationally efficient, and more data efficient architectures. The thesis formalizes the idea of algorithmic supervision, which allows a neural network to learn from or in conjunction with an algorithm. When integrating an algorithm into a neural architecture, it is important that the algorithm is differentiable such that the architecture can be trained end-to-end and gradients can be propagated back through the algorithm in a meaningful way. To make algorithms differentiable, this thesis proposes a general method for continuously relaxing algorithms by perturbing variables and approximating the expectation value in closed form, i.e., without sampling. In addition, this thesis proposes differentiable algorithms, such as differentiable sorting networks, differentiable renderers, and differentiable logic gate networks. Finally, this thesis presents alternative training strategies for learning with algorithms.

Structural data well exists in Web applications, such as social networks in social media, citation networks in academic websites, and threads data in online forums. Due to the complex topology, it is difficult to process and make use of the rich information within such data. Graph Neural Networks (GNNs) have shown great advantages on learning representations for structural data. However, the non-transparency of the deep learning models makes it non-trivial to explain and interpret the predictions made by GNNs. Meanwhile, it is also a big challenge to evaluate the GNN explanations, since in many cases, the ground-truth explanations are unavailable. In this paper, we take insights of Counterfactual and Factual (CF^2) reasoning from causal inference theory, to solve both the learning and evaluation problems in explainable GNNs. For generating explanations, we propose a model-agnostic framework by formulating an optimization problem based on both of the two casual perspectives. This distinguishes CF^2 from previous explainable GNNs that only consider one of them. Another contribution of the work is the evaluation of GNN explanations. For quantitatively evaluating the generated explanations without the requirement of ground-truth, we design metrics based on Counterfactual and Factual reasoning to evaluate the necessity and sufficiency of the explanations. Experiments show that no matter ground-truth explanations are available or not, CF^2 generates better explanations than previous state-of-the-art methods on real-world datasets. Moreover, the statistic analysis justifies the correlation between the performance on ground-truth evaluation and our proposed metrics.

Since real-world objects and their interactions are often multi-modal and multi-typed, heterogeneous networks have been widely used as a more powerful, realistic, and generic superclass of traditional homogeneous networks (graphs). Meanwhile, representation learning (\aka~embedding) has recently been intensively studied and shown effective for various network mining and analytical tasks. In this work, we aim to provide a unified framework to deeply summarize and evaluate existing research on heterogeneous network embedding (HNE), which includes but goes beyond a normal survey. Since there has already been a broad body of HNE algorithms, as the first contribution of this work, we provide a generic paradigm for the systematic categorization and analysis over the merits of various existing HNE algorithms. Moreover, existing HNE algorithms, though mostly claimed generic, are often evaluated on different datasets. Understandable due to the application favor of HNE, such indirect comparisons largely hinder the proper attribution of improved task performance towards effective data preprocessing and novel technical design, especially considering the various ways possible to construct a heterogeneous network from real-world application data. Therefore, as the second contribution, we create four benchmark datasets with various properties regarding scale, structure, attribute/label availability, and \etc.~from different sources, towards handy and fair evaluations of HNE algorithms. As the third contribution, we carefully refactor and amend the implementations and create friendly interfaces for 13 popular HNE algorithms, and provide all-around comparisons among them over multiple tasks and experimental settings.

Graph convolution networks (GCN) are increasingly popular in many applications, yet remain notoriously hard to train over large graph datasets. They need to compute node representations recursively from their neighbors. Current GCN training algorithms suffer from either high computational costs that grow exponentially with the number of layers, or high memory usage for loading the entire graph and node embeddings. In this paper, we propose a novel efficient layer-wise training framework for GCN (L-GCN), that disentangles feature aggregation and feature transformation during training, hence greatly reducing time and memory complexities. We present theoretical analysis for L-GCN under the graph isomorphism framework, that L-GCN leads to as powerful GCNs as the more costly conventional training algorithm does, under mild conditions. We further propose L^2-GCN, which learns a controller for each layer that can automatically adjust the training epochs per layer in L-GCN. Experiments show that L-GCN is faster than state-of-the-arts by at least an order of magnitude, with a consistent of memory usage not dependent on dataset size, while maintaining comparable prediction performance. With the learned controller, L^2-GCN can further cut the training time in half. Our codes are available at //github.com/Shen-Lab/L2-GCN.

Graph convolutional network (GCN) has been successfully applied to many graph-based applications; however, training a large-scale GCN remains challenging. Current SGD-based algorithms suffer from either a high computational cost that exponentially grows with number of GCN layers, or a large space requirement for keeping the entire graph and the embedding of each node in memory. In this paper, we propose Cluster-GCN, a novel GCN algorithm that is suitable for SGD-based training by exploiting the graph clustering structure. Cluster-GCN works as the following: at each step, it samples a block of nodes that associate with a dense subgraph identified by a graph clustering algorithm, and restricts the neighborhood search within this subgraph. This simple but effective strategy leads to significantly improved memory and computational efficiency while being able to achieve comparable test accuracy with previous algorithms. To test the scalability of our algorithm, we create a new Amazon2M data with 2 million nodes and 61 million edges which is more than 5 times larger than the previous largest publicly available dataset (Reddit). For training a 3-layer GCN on this data, Cluster-GCN is faster than the previous state-of-the-art VR-GCN (1523 seconds vs 1961 seconds) and using much less memory (2.2GB vs 11.2GB). Furthermore, for training 4 layer GCN on this data, our algorithm can finish in around 36 minutes while all the existing GCN training algorithms fail to train due to the out-of-memory issue. Furthermore, Cluster-GCN allows us to train much deeper GCN without much time and memory overhead, which leads to improved prediction accuracy---using a 5-layer Cluster-GCN, we achieve state-of-the-art test F1 score 99.36 on the PPI dataset, while the previous best result was 98.71 by [16]. Our codes are publicly available at //github.com/google-research/google-research/tree/master/cluster_gcn.