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Bayesian neural networks (BNNs) have recently regained a significant amount of attention in the deep learning community due to the development of scalable approximate Bayesian inference techniques. There are several advantages of using a Bayesian approach: Parameter and prediction uncertainties become easily available, facilitating rigorous statistical analysis. Furthermore, prior knowledge can be incorporated. However, so far, there have been no scalable techniques capable of combining both structural and parameter uncertainty. In this paper, we apply the concept of model uncertainty as a framework for structural learning in BNNs and hence make inference in the joint space of structures/models and parameters. Moreover, we suggest an adaptation of a scalable variational inference approach with reparametrization of marginal inclusion probabilities to incorporate the model space constraints. Experimental results on a range of benchmark datasets show that we obtain comparable accuracy results with the competing models, but based on methods that are much more sparse than ordinary BNNs.

Integer linear programming models a wide range of practical combinatorial optimization problems and has significant impacts in industry and management sectors. This work develops the first standalone local search solver for general integer linear programming validated on a large heterogeneous problem dataset. We propose a local search framework that switches in three modes, namely Search, Improve, and Restore modes, and design tailored operators adapted to different modes, thus improve the quality of the current solution according to different situations. For the Search and Restore modes, we propose an operator named tight move, which adaptively modifies variables' values trying to make some constraint tight. For the Improve mode, an efficient operator lift move is proposed to improve the quality of the objective function while maintaining feasibility. Putting these together, we develop a local search solver for integer linear programming called Local-ILP. Experiments conducted on the MIPLIB dataset show the effectiveness of our solver in solving large-scale hard integer linear programming problems within a reasonably short time. Local-ILP is competitive and complementary to the state-of-the-art commercial solver Gurobi and significantly outperforms the state-of-the-art non-commercial solver SCIP. Moreover, our solver establishes new records for 6 MIPLIB open instances.

The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [ICALP '19]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of $1-1/e-\epsilon$ and both generalize and accelerate the results of Ene and Nguyen [ICALP '19]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondr\'ak [SODA '14]. To achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel FREEZE operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [TALG '05] that maintains the maximum weight basis under insertions and deletions of elements in $O(\log n)$ time. For the transversal matroid the FREEZE operation corresponds to requiring the data structure to keep a certain set $S$ of vertices matched, a property that we call $S$-stability.

The Naive Bayesian classifier is a popular classification method employing the Bayesian paradigm. The concept of having conditional dependence among input variables sounds good in theory but can lead to a majority vote style behaviour. Achieving conditional independence is often difficult, and they introduce decision biases in the estimates. In Naive Bayes, certain features are called independent features as they have no conditional correlation or dependency when predicting a classification. In this paper, we focus on the optimal partition of features by proposing a novel technique called the Comonotone-Independence Classifier (CIBer) which is able to overcome the challenges posed by the Naive Bayes method. For different datasets, we clearly demonstrate the efficacy of our technique, where we achieve lower error rates and higher or equivalent accuracy compared to models such as Random Forests and XGBoost.

Matrix functions play an increasingly important role in many areas of scientific computing and engineering disciplines. In such real-world applications, algorithms working in floating-point arithmetic are used for computing matrix functions and additionally, input data might be unreliable, e.g., due to measurement errors. Therefore, it is crucial to understand the sensitivity of matrix functions to perturbations, which is measured by condition numbers. However, the condition number itself might not be computed exactly as well due to round-off and errors in the input. The sensitivity of the condition number is measured by the so-called level-2 condition number. For the usual (level-1) condition number, it is well-known that structured condition numbers (i.e., where only perturbations are taken into account that preserve the structure of the input matrix) might be much smaller than unstructured ones, which, e.g., suggests that structure-preserving algorithms for matrix functions might yield much more accurate results than general-purpose algorithms. In this work, we examine structured level-2 condition numbers in the particular case of restricting the perturbation matrix to an automorphism group, a Lie or Jordan algebra or the space of quasi-triangular matrices. In numerical experiments, we then compare the unstructured level-2 condition number with the structured one for some specific matrix functions such as the matrix logarithm, matrix square root, and matrix exponential.

We introduce a new computational framework for estimating parameters in generalized generalized linear models (GGLM), a class of models that extends the popular generalized linear models (GLM) to account for dependencies among observations in spatio-temporal data. The proposed approach uses a monotone operator-based variational inequality method to overcome non-convexity in parameter estimation and provide guarantees for parameter recovery. The results can be applied to GLM and GGLM, focusing on spatio-temporal models. We also present online instance-based bounds using martingale concentrations inequalities. Finally, we demonstrate the performance of the algorithm using numerical simulations and a real data example for wildfire incidents.

In many regression settings the unknown coefficients may have some known structure, for instance they may be ordered in space or correspond to a vectorized matrix or tensor. At the same time, the unknown coefficients may be sparse, with many nearly or exactly equal to zero. However, many commonly used priors and corresponding penalties for coefficients do not encourage simultaneously structured and sparse estimates. In this paper we develop structured shrinkage priors that generalize multivariate normal, Laplace, exponential power and normal-gamma priors. These priors allow the regression coefficients to be correlated a priori without sacrificing elementwise sparsity or shrinkage. The primary challenges in working with these structured shrinkage priors are computational, as the corresponding penalties are intractable integrals and the full conditional distributions that are needed to approximate the posterior mode or simulate from the posterior distribution may be non-standard. We overcome these issues using a flexible elliptical slice sampling procedure, and demonstrate that these priors can be used to introduce structure while preserving sparsity.

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, if not better than, the original dense networks. Sparsity can reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field.

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.