We exhibit a 5-uniform hypergraph that has no polychromatic 3-coloring, but all its restricted subhypergraphs with edges of size at least 3 are 2-colorable. This disproves a bold conjecture of Keszegh and the author, and can be considered as the first step to understand polychromatic colorings of hereditary hypergraph families better since the seminal work of Berge. We also show that our method cannot give hypergraphs of arbitrary high uniformity, and mention some connections to panchromatic colorings.
An increasingly common viewpoint is that protein dynamics data sets reside in a non-linear subspace of low conformational energy. Ideal data analysis tools for such data sets should therefore account for such non-linear geometry. The Riemannian geometry setting can be suitable for a variety of reasons. First, it comes with a rich structure to account for a wide range of geometries that can be modelled after an energy landscape. Second, many standard data analysis tools initially developed for data in Euclidean space can also be generalised to data on a Riemannian manifold. In the context of protein dynamics, a conceptual challenge comes from the lack of a suitable smooth manifold and the lack of guidelines for constructing a smooth Riemannian structure based on an energy landscape. In addition, computational feasibility in computing geodesics and related mappings poses a major challenge. This work considers these challenges. The first part of the paper develops a novel local approximation technique for computing geodesics and related mappings on Riemannian manifolds in a computationally feasible manner. The second part constructs a smooth manifold of point clouds modulo rigid body group actions and a Riemannian structure that is based on an energy landscape for protein conformations. The resulting Riemannian geometry is tested on several data analysis tasks relevant for protein dynamics data. It performs exceptionally well on coarse-grained molecular dynamics simulated data. In particular, the geodesics with given start- and end-points approximately recover corresponding molecular dynamics trajectories for proteins that undergo relatively ordered transitions with medium sized deformations. The Riemannian protein geometry also gives physically realistic summary statistics and retrieves the underlying dimension even for large-sized deformations within seconds on a laptop.
Whittle-Mat\'ern fields are a recently introduced class of Gaussian processes on metric graphs, which are specified as solutions to a fractional-order stochastic differential equation. Unlike earlier covariance-based approaches for specifying Gaussian fields on metric graphs, the Whittle-Mat\'ern fields are well-defined for any compact metric graph and can provide Gaussian processes with differentiable sample paths. We derive the main statistical properties of the model class, particularly the consistency and asymptotic normality of maximum likelihood estimators of model parameters and the necessary and sufficient conditions for asymptotic optimality properties of linear prediction based on the model with misspecified parameters. The covariance function of the Whittle-Mat\'ern fields is generally unavailable in closed form, and they have therefore been challenging to use for statistical inference. However, we show that for specific values of the fractional exponent, when the fields have Markov properties, likelihood-based inference and spatial prediction can be performed exactly and computationally efficiently. This facilitates using the Whittle-Mat\'ern fields in statistical applications involving big datasets without the need for any approximations. The methods are illustrated via an application to modeling of traffic data, where allowing for differentiable processes dramatically improves the results.
The life-cycle of electric batteries depends on a complex system of interacting electrochemical and growth phenomena that produce dendritic structures during the discharge cycle. We study herein a system of 3 partial differential equations combining an Allen--Cahn phase-field model (simulating the dendrite-electrolyte interface) with the Poisson--Nernst--Planck systems simulating the electrodynamics and leading to the formation of such dendritic structures. We prove novel existence, uniqueness and stability results for this system and use it to produce simulations based on a finite element code.
This paper presents a new algorithm for generating random inverse-Wishart matrices that directly generates the Cholesky factor of the matrix without computing the factorization. Whenever parameterized in terms of a precision matrix $\Omega=\Sigma^{-1}$, or its Cholesky factor, instead of a covariance matrix $\Sigma$, the new algorithm is more efficient than the current standard algorithm.
We give the explicit equations for a P^3 x P^3 embedding of the Jacobian of a curve of genus 2, which gives a natural analog for abelian surfaces of the Edwards curve model of elliptic curves. This gives a much more succinct description of the Jacobian variety than the standard version in P^{15}. We also give a condition under which, as for the Edwards curve, the abelian surfaces have a universal group law.
Estimating the structure of directed acyclic graphs (DAGs) from observational data remains a significant challenge in machine learning. Most research in this area concentrates on learning a single DAG for the entire population. This paper considers an alternative setting where the graph structure varies across individuals based on available "contextual" features. We tackle this contextual DAG problem via a neural network that maps the contextual features to a DAG, represented as a weighted adjacency matrix. The neural network is equipped with a novel projection layer that ensures the output matrices are sparse and satisfy a recently developed characterization of acyclicity. We devise a scalable computational framework for learning contextual DAGs and provide a convergence guarantee and an analytical gradient for backpropagating through the projection layer. Our experiments suggest that the new approach can recover the true context-specific graph where existing approaches fail.
Forced alignment systems automatically determine boundaries between segments in speech data, given an orthographic transcription. These tools are commonplace in phonetics to facilitate the use of speech data that would be infeasible to manually transcribe and segment. In the present paper, we describe a new neural network-based forced alignment system, the Mason-Alberta Phonetic Segmenter (MAPS). The MAPS aligner serves as a testbed for two possible improvements we pursue for forced alignment systems. The first is treating the acoustic model in a forced aligner as a tagging task, rather than a classification task, motivated by the common understanding that segments in speech are not truly discrete and commonly overlap. The second is an interpolation technique to allow boundaries more precise than the common 10 ms limit in modern forced alignment systems. We compare configurations of our system to a state-of-the-art system, the Montreal Forced Aligner. The tagging approach did not generally yield improved results over the Montreal Forced Aligner. However, a system with the interpolation technique had a 27.92% increase relative to the Montreal Forced Aligner in the amount of boundaries within 10 ms of the target on the test set. We also reflect on the task and training process for acoustic modeling in forced alignment, highlighting how the output targets for these models do not match phoneticians' conception of similarity between phones and that reconciliation of this tension may require rethinking the task and output targets or how speech itself should be segmented.
Suppose a finite, unweighted, combinatorial graph $G = (V,E)$ is the union of several (degree-)regular graphs which are then additionally connected with a few additional edges. $G$ will then have only a small number of vertices $v \in V$ with the property that one of their neighbors $(v,w) \in E$ has a higher degree $\mbox{deg}(w) > \mbox{deg}(v)$. We prove the converse statement: if a graph has few vertices having a neighbor with higher degree and satisfies a mild regularity condition, then, via adding and removing a few edges, the graph can be turned into a disjoint union of (distance-)regular graphs. The number of edge operations depends on the maximum degree and number of vertices with a higher degree neighbor but is independent of the size of $|V|$.
The linear varying coefficient models posits a linear relationship between an outcome and covariates in which the covariate effects are modeled as functions of additional effect modifiers. Despite a long history of study and use in statistics and econometrics, state-of-the-art varying coefficient modeling methods cannot accommodate multivariate effect modifiers without imposing restrictive functional form assumptions or involving computationally intensive hyperparameter tuning. In response, we introduce VCBART, which flexibly estimates the covariate effect in a varying coefficient model using Bayesian Additive Regression Trees. With simple default settings, VCBART outperforms existing varying coefficient methods in terms of covariate effect estimation, uncertainty quantification, and outcome prediction. We illustrate the utility of VCBART with two case studies: one examining how the association between later-life cognition and measures of socioeconomic position vary with respect to age and socio-demographics and another estimating how temporal trends in urban crime vary at the neighborhood level. An R package implementing VCBART is available at //github.com/skdeshpande91/VCBART
Hashing has been widely used in approximate nearest search for large-scale database retrieval for its computation and storage efficiency. Deep hashing, which devises convolutional neural network architecture to exploit and extract the semantic information or feature of images, has received increasing attention recently. In this survey, several deep supervised hashing methods for image retrieval are evaluated and I conclude three main different directions for deep supervised hashing methods. Several comments are made at the end. Moreover, to break through the bottleneck of the existing hashing methods, I propose a Shadow Recurrent Hashing(SRH) method as a try. Specifically, I devise a CNN architecture to extract the semantic features of images and design a loss function to encourage similar images projected close. To this end, I propose a concept: shadow of the CNN output. During optimization process, the CNN output and its shadow are guiding each other so as to achieve the optimal solution as much as possible. Several experiments on dataset CIFAR-10 show the satisfying performance of SRH.