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Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated the microbiome study. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To this end, we propose a Bayesian stochastic block model to study the microbiome co-occurrence network based on the recently developed modified centered-log ratio transformation tailored for microbiome data analysis. Our model allows us to incorporate taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women, the first time the urinary microbiome co-occurrence network structure has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.

Initial orbit determination (IOD) is an important early step in the processing chain that makes sense of and reconciles the multiple optical observations of a resident space object. IOD methods generally operate on line-of-sight (LOS) vectors extracted from images of the object, hence the LOS vectors can be seen as discrete point samples of the raw optical measurements. Typically, the number of LOS vectors used by an IOD method is much smaller than the available measurements (\ie, the set of pixel intensity values), hence current IOD methods arguably under-utilize the rich information present in the data. In this paper, we propose a \emph{direct} IOD method called D-IOD that fits the orbital parameters directly on the observed streak images, without requiring LOS extraction. Since it does not utilize LOS vectors, D-IOD avoids potential inaccuracies or errors due to an imperfect LOS extraction step. Two innovations underpin our novel orbit-fitting paradigm: first, we introduce a novel non-linear least-squares objective function that computes the loss between the candidate-orbit-generated streak images and the observed streak images. Second, the objective function is minimized with a gradient descent approach that is embedded in our proposed optimization strategies designed for streak images. We demonstrate the effectiveness of D-IOD on a variety of simulated scenarios and challenging real streak images.

The prowess that makes few-shot learning desirable in medical image analysis is the efficient use of the support image data, which are labelled to classify or segment new classes, a task that otherwise requires substantially more training images and expert annotations. This work describes a fully 3D prototypical few-shot segmentation algorithm, such that the trained networks can be effectively adapted to clinically interesting structures that are absent in training, using only a few labelled images from a different institute. First, to compensate for the widely recognised spatial variability between institutions in episodic adaptation of novel classes, a novel spatial registration mechanism is integrated into prototypical learning, consisting of a segmentation head and an spatial alignment module. Second, to assist the training with observed imperfect alignment, support mask conditioning module is proposed to further utilise the annotation available from the support images. Extensive experiments are presented in an application of segmenting eight anatomical structures important for interventional planning, using a data set of 589 pelvic T2-weighted MR images, acquired at seven institutes. The results demonstrate the efficacy in each of the 3D formulation, the spatial registration, and the support mask conditioning, all of which made positive contributions independently or collectively. Compared with the previously proposed 2D alternatives, the few-shot segmentation performance was improved with statistical significance, regardless whether the support data come from the same or different institutes.

Block majorization-minimization (BMM) is a simple iterative algorithm for nonconvex constrained optimization that sequentially minimizes majorizing surrogates of the objective function in each block coordinate while the other coordinates are held fixed. BMM entails a large class of optimization algorithms such as block coordinate descent and its proximal-point variant, expectation-minimization, and block projected gradient descent. We establish that for general constrained nonconvex optimization, BMM with strongly convex surrogates can produce an $\epsilon$-stationary point within $O(\epsilon^{-2}(\log \epsilon^{-1})^{2})$ iterations and asymptotically converges to the set of stationary points. Furthermore, we propose a trust-region variant of BMM that can handle surrogates that are only convex and still obtain the same iteration complexity and asymptotic stationarity. These results hold robustly even when the convex sub-problems are inexactly solved as long as the optimality gaps are summable. As an application, we show that a regularized version of the celebrated multiplicative update algorithm for nonnegative matrix factorization by Lee and Seung has iteration complexity of $O(\epsilon^{-2}(\log \epsilon^{-1})^{2})$. The same result holds for a wide class of regularized nonnegative tensor decomposition algorithms as well as the classical block projected gradient descent algorithm. These theoretical results are validated through various numerical experiments.

Early sensory systems in the brain rapidly adapt to fluctuating input statistics, which requires recurrent communication between neurons. Mechanistically, such recurrent communication is often indirect and mediated by local interneurons. In this work, we explore the computational benefits of mediating recurrent communication via interneurons compared with direct recurrent connections. To this end, we consider two mathematically tractable recurrent linear neural networks that statistically whiten their inputs -- one with direct recurrent connections and the other with interneurons that mediate recurrent communication. By analyzing the corresponding continuous synaptic dynamics and numerically simulating the networks, we show that the network with interneurons is more robust to initialization than the network with direct recurrent connections in the sense that the convergence time for the synaptic dynamics in the network with interneurons (resp. direct recurrent connections) scales logarithmically (resp. linearly) with the spectrum of their initialization. Our results suggest that interneurons are computationally useful for rapid adaptation to changing input statistics. Interestingly, the network with interneurons is an overparameterized solution of the whitening objective for the network with direct recurrent connections, so our results can be viewed as a recurrent linear neural network analogue of the implicit acceleration phenomenon observed in overparameterized feedforward linear neural networks.

As quantum theory allows for information processing and computing tasks that otherwise are not possible with classical systems, there is a need and use of quantum Internet beyond existing network systems. At the same time, the realization of a desirably functional quantum Internet is hindered by fundamental and practical challenges such as high loss during transmission of quantum systems, decoherence due to interaction with the environment, fragility of quantum states, etc. We study the implications of these constraints by analyzing the limitations on the scaling and robustness of quantum Internet. Considering quantum networks, we present practical bottlenecks for secure communication, delegated computing, and resource distribution among end nodes. Motivated by the power of abstraction in graph theory (in association with quantum information theory), we consider graph-theoretic quantifiers to assess network robustness and provide critical values of communication lines for viable communication over quantum Internet. In particular, we begin by discussing limitations on usefulness of isotropic states as device-independent quantum key repeaters which otherwise could be useful for device-independent quantum key distribution. We consider some quantum networks of practical interest, ranging from satellite-based networks connecting far-off spatial locations to currently available quantum processor architectures within computers, and analyze their robustness to perform quantum information processing tasks. Some of these tasks form primitives for delegated quantum computing, e.g., entanglement distribution and quantum teleportation. For some examples of quantum networks, we present algorithms to perform different quantum network tasks of interest such as constructing the network structure, finding the shortest path between a pair of end nodes, and optimizing the flow of resources at a node.

Consider the following prediction problem. Assume that there is a block box that produces bits according to some unknown computable distribution on the binary tree. We know first $n$ bits $x_1 x_2 \ldots x_n$. We want to know the probability of the event that that the next bit is equal to $1$. Solomonoff suggested to use universal semimeasure $m$ for solving this task. He proved that for every computable distribution $P$ and for every $b \in \{0,1\}$ the following holds: $$\sum_{n=1}^{\infty}\sum_{x: l(x)=n} P(x) (P(b | x) - m(b | x))^2 < \infty\ .$$ However, Solomonoff's method has a negative aspect: Hutter and Muchnik proved that there are an universal semimeasure $m$, computable distribution $P$ and a random (in Martin-L{\"o}f sense) sequence $x_1 x_2\ldots$ such that $\lim_{n \to \infty} P(x_{n+1} | x_1\ldots x_n) - m(x_{n+1} | x_1\ldots x_n) \nrightarrow 0$. We suggest a new way for prediction. For every finite string $x$ we predict the new bit according to the best (in some sence) distribution for $x$. We prove the similar result as Solomonoff theorem for our way of prediction. Also we show that our method of prediction has no that negative aspect as Solomonoff's method.

The expectation is an example of a descriptive statistic that is monotone with respect to stochastic dominance, and additive for sums of independent random variables. We provide a complete characterization of such statistics, and explore a number of applications to models of individual and group decision-making. These include a representation of stationary monotone time preferences, extending the work of Fishburn and Rubinstein (1982) to time lotteries. This extension offers a new perspective on risk attitudes toward time, as well as on the aggregation of multiple discount factors.

Data-driven modeling is useful for reconstructing nonlinear dynamical systems when the underlying process is unknown or too expensive to compute. Having reliable uncertainty assessment of the forecast enables tools to be deployed to predict new scenarios unobserved before. In this work, we first extend parallel partial Gaussian processes for predicting the vector-valued transition function that links the observations between the current and next time points, and quantify the uncertainty of predictions by posterior sampling. Second, we show the equivalence between the dynamic mode decomposition and the maximum likelihood estimator of the linear mapping matrix in the linear state space model. The connection provides a data generating model of dynamic mode decomposition and thus, uncertainty of predictions can be obtained. Furthermore, we draw close connections between different data-driven models for approximating nonlinear dynamics, through a unified view of data generating models. We study two numerical examples, where the inputs of the dynamics are assumed to be known in the first example and the inputs are unknown in the second example. The examples indicate that uncertainty of forecast can be properly quantified, whereas model or input misspecification can degrade the accuracy of uncertainty quantification.

The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.