This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network. Moreover, we characterize when this is possible and show that, in such instances, the resulting directed nonbinary phylogenetic network is unique. In addition, without being given the location of the root and the reticulation vertices, we describe an algorithm for deciding whether an undirected binary phylogenetic network $N$ can be oriented as a directed binary phylogenetic network of a certain class. The algorithm is fixed-parameter tractable (FPT) when the parameter is the level of $N$ and is applicable to classes of directed phylogenetic networks that satisfy certain conditions. As an example, we show that the well-studied class of binary tree-child networks satisfies these conditions.
In sampling-based Bayesian models of brain function, neural activities are assumed to be samples from probability distributions that the brain uses for probabilistic computation. However, a comprehensive understanding of how mechanistic models of neural dynamics can sample from arbitrary distributions is still lacking. We use tools from functional analysis and stochastic differential equations to explore the minimum architectural requirements for $\textit{recurrent}$ neural circuits to sample from complex distributions. We first consider the traditional sampling model consisting of a network of neurons whose outputs directly represent the samples (sampler-only network). We argue that synaptic current and firing-rate dynamics in the traditional model have limited capacity to sample from a complex probability distribution. We show that the firing rate dynamics of a recurrent neural circuit with a separate set of output units can sample from an arbitrary probability distribution. We call such circuits reservoir-sampler networks (RSNs). We propose an efficient training procedure based on denoising score matching that finds recurrent and output weights such that the RSN implements Langevin sampling. We empirically demonstrate our model's ability to sample from several complex data distributions using the proposed neural dynamics and discuss its applicability to developing the next generation of sampling-based brain models.
Feedforward neural networks (FNNs) are typically viewed as pure prediction algorithms, and their strong predictive performance has led to their use in many machine-learning applications. However, their flexibility comes with an interpretability trade-off; thus, FNNs have been historically less popular among statisticians. Nevertheless, classical statistical theory, such as significance testing and uncertainty quantification, is still relevant. Supplementing FNNs with methods of statistical inference, and covariate-effect visualisations, can shift the focus away from black-box prediction and make FNNs more akin to traditional statistical models. This can allow for more inferential analysis, and, hence, make FNNs more accessible within the statistical-modelling context.
During the last decades macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full understanding of the dynamical processes behind them. In particular, abundance fluctuations of different species are found to be correlated, both across time and across communities in metagenomic samples. Reproducing such correlations through appropriate population models remains an open challenge. The present paper tackles this problem and points to sparse species interactions as a necessary mechanism to account for them. Specifically, we discuss several possibilities to include interactions in population models and recognize Lotka-Volterra constants as a successful ansatz. For this, we design a Bayesian inference algorithm to extract sets of interaction constants able to reproduce empirical probability distributions of pairwise correlations for diverse biomes. Importantly, the inferred models still reproduce well-known single-species macroecological patterns concerning abundance fluctuations across both species and communities. Endorsed by the agreement with the empirically observed phenomenology, our analyses provide insights on the properties of the networks of microbial interactions, revealing that sparsity is a crucial feature.
Physics-informed neural networks and operator networks have shown promise for effectively solving equations modeling physical systems. However, these networks can be difficult or impossible to train accurately for some systems of equations. We present a novel multifidelity framework for stacking physics-informed neural networks and operator networks that facilitates training. We successively build a chain of networks, where the output at one step can act as a low-fidelity input for training the next step, gradually increasing the expressivity of the learned model. The equations imposed at each step of the iterative process can be the same or different (akin to simulated annealing). The iterative (stacking) nature of the proposed method allows us to progressively learn features of a solution that are hard to learn directly. Through benchmark problems including a nonlinear pendulum, the wave equation, and the viscous Burgers equation, we show how stacking can be used to improve the accuracy and reduce the required size of physics-informed neural networks and operator networks.
The concept of Rao-Blackwellization is employed to improve predictions of artificial neural networks by physical information. The error norm and the proof of improvement are transferred from the original statistical concept to a deterministic one, using sufficient information on physics-based conditions. The proposed strategy is applied to material modeling and illustrated by examples of the identification of a yield function, elasto-plastic steel simulations, the identification of driving forces for quasi-brittle damage and rubber experiments. Sufficient physical information is employed, e.g., in the form of invariants, parameters of a minimization problem, dimensional analysis, isotropy and differentiability. It is proven how intuitive accretion of information can yield improvement if it is physically sufficient, but also how insufficient or superfluous information can cause impairment. Opportunities for the improvement of artificial neural networks are explored in terms of the training data set, the networks' structure and output filters. Even crude initial predictions are remarkably improved by reducing noise, overfitting and data requirements.
We investigate how shallow ReLU networks interpolate between known regions. Our analysis shows that empirical risk minimizers converge to a minimum norm interpolant as the number of data points and parameters tends to infinity when a weight decay regularizer is penalized with a coefficient which vanishes at a precise rate as the network width and the number of data points grow. With and without explicit regularization, we numerically study the implicit bias of common optimization algorithms towards known minimum norm interpolants.
We investigate the use of multilevel Monte Carlo (MLMC) methods for estimating the expectation of discretized random fields. Specifically, we consider a setting in which the input and output vectors of the numerical simulators have inconsistent dimensions across the multilevel hierarchy. This requires the introduction of grid transfer operators borrowed from multigrid methods. Starting from a simple 1D illustration, we demonstrate numerically that the resulting MLMC estimator deteriorates the estimation of high-frequency components of the discretized expectation field compared to a Monte Carlo (MC) estimator. By adapting mathematical tools initially developed for multigrid methods, we perform a theoretical spectral analysis of the MLMC estimator of the expectation of discretized random fields, in the specific case of linear, symmetric and circulant simulators. This analysis provides a spectral decomposition of the variance into contributions associated with each scale component of the discretized field. We then propose improved MLMC estimators using a filtering mechanism similar to the smoothing process of multigrid methods. The filtering operators improve the estimation of both the small- and large-scale components of the variance, resulting in a reduction of the total variance of the estimator. These improvements are quantified for the specific class of simulators considered in our spectral analysis. The resulting filtered MLMC (F-MLMC) estimator is applied to the problem of estimating the discretized variance field of a diffusion-based covariance operator, which amounts to estimating the expectation of a discretized random field. The numerical experiments support the conclusions of the theoretical analysis even with non-linear simulators, and demonstrate the improvements brought by the proposed F-MLMC estimator compared to both a crude MC and an unfiltered MLMC estimator.
It is well known that artificial neural networks initialized from independent and identically distributed priors converge to Gaussian processes in the limit of large number of neurons per hidden layer. In this work we prove an analogous result for Quantum Neural Networks (QNNs). Namely, we show that the outputs of certain models based on Haar random unitary or orthogonal deep QNNs converge to Gaussian processes in the limit of large Hilbert space dimension $d$. The derivation of this result is more nuanced than in the classical case due to the role played by the input states, the measurement observable, and the fact that the entries of unitary matrices are not independent. An important consequence of our analysis is that the ensuing Gaussian processes cannot be used to efficiently predict the outputs of the QNN via Bayesian statistics. Furthermore, our theorems imply that the concentration of measure phenomenon in Haar random QNNs is worse than previously thought, as we prove that expectation values and gradients concentrate as $\mathcal{O}\left(\frac{1}{e^d \sqrt{d}}\right)$. Finally, we discuss how our results improve our understanding of concentration in $t$-designs.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.