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Gaussian process (GP) is a Bayesian model which provides several advantages for regression tasks in machine learning such as reliable quantitation of uncertainty and improved interpretability. Their adoption has been precluded by their excessive computational cost and by the difficulty in adapting them for analyzing sequences (e.g. amino acid and nucleotide sequences) and graphs (e.g. ones representing small molecules). In this study, we develop efficient and scalable approaches for fitting GP models as well as fast convolution kernels which scale linearly with graph or sequence size. We implement these improvements by building an open-source Python library called xGPR. We compare the performance of xGPR with the reported performance of various deep learning models on 20 benchmarks, including small molecule, protein sequence and tabular data. We show that xGRP achieves highly competitive performance with much shorter training time. Furthermore, we also develop new kernels for sequence and graph data and show that xGPR generally outperforms convolutional neural networks on predicting key properties of proteins and small molecules. Importantly, xGPR provides uncertainty information not available from typical deep learning models. Additionally, xGPR provides a representation of the input data that can be used for clustering and data visualization. These results demonstrate that xGPR provides a powerful and generic tool that can be broadly useful in protein engineering and drug discovery.

Collecting and leveraging data with good coverage properties plays a crucial role in different aspects of reinforcement learning (RL), including reward-free exploration and offline learning. However, the notion of "good coverage" really depends on the application at hand, as data suitable for one context may not be so for another. In this paper, we formalize the problem of active coverage in episodic Markov decision processes (MDPs), where the goal is to interact with the environment so as to fulfill given sampling requirements. This framework is sufficiently flexible to specify any desired coverage property, making it applicable to any problem that involves online exploration. Our main contribution is an instance-dependent lower bound on the sample complexity of active coverage and a simple game-theoretic algorithm, CovGame, that nearly matches it. We then show that CovGame can be used as a building block to solve different PAC RL tasks. In particular, we obtain a simple algorithm for PAC reward-free exploration with an instance-dependent sample complexity that, in certain MDPs which are "easy to explore", is lower than the minimax one. By further coupling this exploration algorithm with a new technique to do implicit eliminations in policy space, we obtain a computationally-efficient algorithm for best-policy identification whose instance-dependent sample complexity scales with gaps between policy values.

Gaussianization is a simple generative model that can be trained without backpropagation. It has shown compelling performance on low dimensional data. As the dimension increases, however, it has been observed that the convergence speed slows down. We show analytically that the number of required layers scales linearly with the dimension for Gaussian input. We argue that this is because the model is unable to capture dependencies between dimensions. Empirically, we find the same linear increase in cost for arbitrary input $p(x)$, but observe favorable scaling for some distributions. We explore potential speed-ups and formulate challenges for further research.

We improve the Solovay-Kitaev theorem and algorithm for a general finite, inverse-closed generating set acting on a qudit. Prior versions of the algorithm can efficiently find a word of length $O((\log 1/\epsilon)^{3+\delta})$ to approximate an arbitrary target gate to within $\epsilon$. Using two new ideas, each of which reduces the exponent separately, our new bound on the world length is $O((\log 1/\epsilon)^{1.44042\ldots+\delta})$. Our result holds more generally for any finite set that densely generates any connected, semisimple real Lie group, with an extra length term in the non-compact case to reach group elements far away from the identity.

We propose a logic-informed knowledge-driven modeling framework for human movements by analyzing their trajectories. Our approach is inspired by the fact that human actions are usually driven by their intentions or desires, and are influenced by environmental factors such as the spatial relationships with surrounding objects. In this paper, we introduce a set of spatial-temporal logic rules as knowledge to explain human actions. These rules will be automatically discovered from observational data. To learn the model parameters and the rule content, we design an expectation-maximization (EM) algorithm, which treats the rule content as latent variables. The EM algorithm alternates between the E-step and M-step: in the E-step, the posterior distribution over the latent rule content is evaluated; in the M-step, the rule generator and model parameters are jointly optimized by maximizing the current expected log-likelihood. Our model may have a wide range of applications in areas such as sports analytics, robotics, and autonomous cars, where understanding human movements are essential. We demonstrate the model's superior interpretability and prediction performance on pedestrian and NBA basketball player datasets, both achieving promising results.

The algebraic degree is an important parameter of Boolean functions used in cryptography. When a function in a large number of variables is not given explicitly in algebraic normal form, it might not be feasible to compute its degree. Instead, one can try to estimate the degree using probabilistic tests. We propose a probabilistic test for deciding whether the algebraic degree of a Boolean function $f$ is below a certain value $k$. The test involves picking an affine space of dimension $k$ and testing whether the values on $f$ on that space sum up to zero. If $deg(f)<k$, then $f$ will always pass the test, otherwise it will sometimes pass and sometimes fail the test, depending on which affine space was chosen. The probability of failing the proposed test is closely related to the number of monomials of degree $k$ in a polynomial $g$, averaged over all the polynomials $g$ which are affine equivalent to $f$. We initiate the study of the probability of failing the proposed ``$deg(f)<k$'' test. We show that in the particular case when the degree of $f$ is actually equal to $k$, the probability will be in the interval $(0.288788, 0.5]$, and therefore a small number of runs of the test is sufficient to give, with very high probability, the correct answer. Exact values of this probability for all the polynomials in 8 variables were computed using the representatives listed by Hou and by Langevin and Leander.

We employ a toolset -- dubbed Dr. Frankenstein -- to analyse the similarity of representations in deep neural networks. With this toolset, we aim to match the activations on given layers of two trained neural networks by joining them with a stitching layer. We demonstrate that the inner representations emerging in deep convolutional neural networks with the same architecture but different initializations can be matched with a surprisingly high degree of accuracy even with a single, affine stitching layer. We choose the stitching layer from several possible classes of linear transformations and investigate their performance and properties. The task of matching representations is closely related to notions of similarity. Using this toolset, we also provide a novel viewpoint on the current line of research regarding similarity indices of neural network representations: the perspective of the performance on a task.

Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.

In order to overcome the expressive limitations of graph neural networks (GNNs), we propose the first method that exploits vector flows over graphs to develop globally consistent directional and asymmetric aggregation functions. We show that our directional graph networks (DGNs) generalize convolutional neural networks (CNNs) when applied on a grid. Whereas recent theoretical works focus on understanding local neighbourhoods, local structures and local isomorphism with no global information flow, our novel theoretical framework allows directional convolutional kernels in any graph. First, by defining a vector field in the graph, we develop a method of applying directional derivatives and smoothing by projecting node-specific messages into the field. Then we propose the use of the Laplacian eigenvectors as such vector field, and we show that the method generalizes CNNs on an n-dimensional grid, and is provably more discriminative than standard GNNs regarding the Weisfeiler-Lehman 1-WL test. Finally, we bring the power of CNN data augmentation to graphs by providing a means of doing reflection, rotation and distortion on the underlying directional field. We evaluate our method on different standard benchmarks and see a relative error reduction of 8\% on the CIFAR10 graph dataset and 11% to 32% on the molecular ZINC dataset. An important outcome of this work is that it enables to translate any physical or biological problems with intrinsic directional axes into a graph network formalism with an embedded directional field.

In structure learning, the output is generally a structure that is used as supervision information to achieve good performance. Considering the interpretation of deep learning models has raised extended attention these years, it will be beneficial if we can learn an interpretable structure from deep learning models. In this paper, we focus on Recurrent Neural Networks (RNNs) whose inner mechanism is still not clearly understood. We find that Finite State Automaton (FSA) that processes sequential data has more interpretable inner mechanism and can be learned from RNNs as the interpretable structure. We propose two methods to learn FSA from RNN based on two different clustering methods. We first give the graphical illustration of FSA for human beings to follow, which shows the interpretability. From the FSA's point of view, we then analyze how the performance of RNNs are affected by the number of gates, as well as the semantic meaning behind the transition of numerical hidden states. Our results suggest that RNNs with simple gated structure such as Minimal Gated Unit (MGU) is more desirable and the transitions in FSA leading to specific classification result are associated with corresponding words which are understandable by human beings.