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Beyond identifying genetic variants, we introduce a set of Boolean relations that allows for a comprehensive classification of the relation for every pair of variants by taking all minimal alignments into account. We present an efficient algorithm to compute these relations, including a novel way of efficiently computing all minimal alignments within the best theoretical complexity bounds. We show that for all variants of the CFTR gene in dbSNP these relations are common and many non-trivial. Ultimately, we present an approach for the storing and indexing of variants in the context of a database that enables the efficient querying for all these relations.

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Spectral independence is a recently-developed framework for obtaining sharp bounds on the convergence time of the classical Glauber dynamics. This new framework has yielded optimal $O(n \log n)$ sampling algorithms on bounded-degree graphs for a large class of problems throughout the so-called uniqueness regime, including, for example, the problems of sampling independent sets, matchings, and Ising-model configurations. Our main contribution is to relax the bounded-degree assumption that has so far been important in establishing and applying spectral independence. Previous methods for avoiding degree bounds rely on using $L^p$-norms to analyse contraction on graphs with bounded connective constant (Sinclair, Srivastava, Yin; FOCS'13). The non-linearity of $L^p$-norms is an obstacle to applying these results to bound spectral independence. Our solution is to capture the $L^p$-analysis recursively by amortising over the subtrees of the recurrence used to analyse contraction. Our method generalises previous analyses that applied only to bounded-degree graphs. As a main application of our techniques, we consider the random graph $G(n,d/n)$, where the previously known algorithms run in time $n^{O(\log d)}$ or applied only to large $d$. We refine these algorithmic bounds significantly, and develop fast $n^{1+o(1)}$ algorithms based on Glauber dynamics that apply to all $d$, throughout the uniqueness regime.

Differential privacy is a mathematical concept that provides an information-theoretic security guarantee. While differential privacy has emerged as a de facto standard for guaranteeing privacy in data sharing, the known mechanisms to achieve it come with some serious limitations. Utility guarantees are usually provided only for a fixed, a priori specified set of queries. Moreover, there are no utility guarantees for more complex - but very common - machine learning tasks such as clustering or classification. In this paper we overcome some of these limitations. Working with metric privacy, a powerful generalization of differential privacy, we develop a polynomial-time algorithm that creates a private measure from a data set. This private measure allows us to efficiently construct private synthetic data that are accurate for a wide range of statistical analysis tools. Moreover, we prove an asymptotically sharp min-max result for private measures and synthetic data for general compact metric spaces. A key ingredient in our construction is a new superregular random walk, whose joint distribution of steps is as regular as that of independent random variables, yet which deviates from the origin logarithmicaly slowly.

This paper explores formalizing Geometric (or Clifford) algebras into the Lean 3 theorem prover, building upon the substantial body of work that is the Lean mathematics library, mathlib. As we use Lean source code to demonstrate many of our ideas, we include a brief introduction to the Lean language targeted at a reader with no prior experience with Lean or theorem provers in general. We formalize the multivectors as the quotient of the tensor algebra by a suitable relation, which provides the ring structure automatically, then go on to establish the universal property of the Clifford algebra. We show that this is quite different to the approach taken by existing formalizations of Geometric algebra in other theorem provers; most notably, our approach does not require a choice of basis. We go on to show how operations and structure such as involutions, versors, and the $\mathbb{Z}_2$-grading can be defined using the universal property alone, and how to recover an induction principle from the universal property suitable for proving statements about these definitions. We outline the steps needed to formalize the wedge product and $\mathbb{N}$-grading, and some of the gaps in mathlib that currently make this challenging.

We study approaches for compressing the empirical measure in the context of finite dimensional reproducing kernel Hilbert spaces (RKHSs).In this context, the empirical measure is contained within a natural convex set and can be approximated using convex optimization methods. Such an approximation gives under certain conditions rise to a coreset of data points. A key quantity that controls how large such a coreset has to be is the size of the largest ball around the empirical measure that is contained within the empirical convex set. The bulk of our work is concerned with deriving high probability lower bounds on the size of such a ball under various conditions. We complement this derivation of the lower bound by developing techniques that allow us to apply the compression approach to concrete inference problems such as kernel ridge regression. We conclude with a construction of an infinite dimensional RKHS for which the compression is poor, highlighting some of the difficulties one faces when trying to move to infinite dimensional RKHSs.

We give a fast algorithm for sampling uniform solutions of general constraint satisfaction problems (CSPs) in a local lemma regime. The expected running time of our algorithm is near-linear in $n$ and a fixed polynomial in $\Delta$, where $n$ is the number of variables and $\Delta$ is the max degree of constraints. Previously, up to similar conditions, sampling algorithms with running time polynomial in both $n$ and $\Delta$, only existed for the almost atomic case, where each constraint is violated by a small number of forbidden local configurations. Our sampling approach departs from all previous fast algorithms for sampling LLL, which were based on Markov chains. A crucial step of our algorithm is a recursive marginal sampler that is of independent interests. Within a local lemma regime, this marginal sampler can draw a random value for a variable according to its marginal distribution, at a local cost independent of the size of the CSP.

Stochastic Gradient Descent (SGD) is a central tool in machine learning. We prove that SGD converges to zero loss, even with a fixed (non-vanishing) learning rate - in the special case of homogeneous linear classifiers with smooth monotone loss functions, optimized on linearly separable data. Previous works assumed either a vanishing learning rate, iterate averaging, or loss assumptions that do not hold for monotone loss functions used for classification, such as the logistic loss. We prove our result on a fixed dataset, both for sampling with or without replacement. Furthermore, for logistic loss (and similar exponentially-tailed losses), we prove that with SGD the weight vector converges in direction to the $L_2$ max margin vector as $O(1/\log(t))$ for almost all separable datasets, and the loss converges as $O(1/t)$ - similarly to gradient descent. Lastly, we examine the case of a fixed learning rate proportional to the minibatch size. We prove that in this case, the asymptotic convergence rate of SGD (with replacement) does not depend on the minibatch size in terms of epochs, if the support vectors span the data. These results may suggest an explanation to similar behaviors observed in deep networks, when trained with SGD.

There has been an arising trend of adopting deep learning methods to study partial differential equations (PDEs). This article is to propose a Deep Learning Galerkin Method (DGM) for the closed-loop geothermal system, which is a new coupled multi-physics PDEs and mainly consists of a framework of underground heat exchange pipelines to extract the geothermal heat from the geothermal reservoir. This method is a natural combination of Galerkin Method and machine learning with the solution approximated by a neural network instead of a linear combination of basis functions. We train the neural network by randomly sampling the spatiotemporal points and minimize loss function to satisfy the differential operators, initial condition, boundary and interface conditions. Moreover, the approximate ability of the neural network is proved by the convergence of the loss function and the convergence of the neural network to the exact solution in L^2 norm under certain conditions. Finally, some numerical examples are carried out to demonstrate the approximation ability of the neural networks intuitively.

In this work, we study the transfer learning problem under high-dimensional generalized linear models (GLMs), which aim to improve the fit on target data by borrowing information from useful source data. Given which sources to transfer, we propose a transfer learning algorithm on GLM, and derive its $\ell_1/\ell_2$-estimation error bounds as well as a bound for a prediction error measure. The theoretical analysis shows that when the target and source are sufficiently close to each other, these bounds could be improved over those of the classical penalized estimator using only target data under mild conditions. When we don't know which sources to transfer, an algorithm-free transferable source detection approach is introduced to detect informative sources. The detection consistency is proved under the high-dimensional GLM transfer learning setting. We also propose an algorithm to construct confidence intervals of each coefficient component, and the corresponding theories are provided. Extensive simulations and a real-data experiment verify the effectiveness of our algorithms. We implement the proposed GLM transfer learning algorithms in a new R package glmtrans, which is available on CRAN.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

Recently, ensemble has been applied to deep metric learning to yield state-of-the-art results. Deep metric learning aims to learn deep neural networks for feature embeddings, distances of which satisfy given constraint. In deep metric learning, ensemble takes average of distances learned by multiple learners. As one important aspect of ensemble, the learners should be diverse in their feature embeddings. To this end, we propose an attention-based ensemble, which uses multiple attention masks, so that each learner can attend to different parts of the object. We also propose a divergence loss, which encourages diversity among the learners. The proposed method is applied to the standard benchmarks of deep metric learning and experimental results show that it outperforms the state-of-the-art methods by a significant margin on image retrieval tasks.

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