There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees. These tools rely on several inference methods available to produce phylogenetic trees, with resulting trees not being unique. Thus, methods for comparing phylogenies that are capable of revealing where two phylogenetic trees agree or differ are required. An approach is then to compute a similarity or dissimilarity measure between trees, with the Robinson- Foulds distance being one of the most used, and which can be computed in linear time and space. Nevertheless, given the large and increasing volume of phylogenetic data, phylogenetic trees are becoming very large with hundreds of thousands of leafs. In this context, space requirements become an issue both while computing tree distances and while storing trees. We propose then an efficient implementation of the Robinson-Foulds distance over trees succinct representations. Our implementation generalizes also the Robinson-Foulds distances to labelled phylogenetic trees, i.e., trees containing labels on all nodes, instead of only on leaves. Experimental results show that we are able to still achieve linear time while requiring less space. Our implementation is available as an open-source tool at //github.com/pedroparedesbranco/TreeDiff.
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We propose a novel neural network architecture based on conformer transducer that adds contextual information flow to the ASR systems. Our method improves the accuracy of recognizing uncommon words while not harming the word error rate of regular words. We explore the uncommon words accuracy improvement when we use the new model and/or shallow fusion with context language model. We found that combination of both provides cumulative gain in uncommon words recognition accuracy.
The stochastic simulation algorithm (SSA) and the corresponding Monte Carlo (MC) method are among the most common approaches for studying stochastic processes. They rely on knowledge of interevent probability density functions (PDFs) and on information about dependencies between all possible events. Analytical representations of a PDF are difficult to specify in advance, in many real life applications. Knowing the shapes of PDFs, and using experimental data, different optimization schemes can be applied in order to evaluate probability density functions and, therefore, the properties of the studied system. Such methods, however, are computationally demanding, and often not feasible. We show that, in the case where experimentally accessed properties are directly related to the frequencies of events involved, it may be possible to replace the heavy Monte Carlo core of optimization schemes with an analytical solution. Such a replacement not only provides a more accurate estimation of the properties of the process, but also reduces the simulation time by a factor of order of the sample size (at least $\approx 10^4$). The proposed analytical approach is valid for any choice of PDF. The accuracy, computational efficiency, and advantages of the method over MC procedures are demonstrated in the exactly solvable case and in the evaluation of branching fractions in controlled radical polymerization (CRP) of acrylic monomers. This polymerization can be modeled by a constrained stochastic process. Constrained systems are quite common, and this makes the method useful for various applications.
We introduce a random recursive tree model with two communities, called balanced community modulated random recursive tree, or BCMRT in short. In this setting, pairs of nodes of different type appear sequentially. Each node of the pair decides independently to attach to their own type with probability 1-q, or to the other type with probability q, and then chooses its parent uniformly within the set of existing nodes with the selected type. We find that the limiting degree distributions coincide for different q. Therefore, as far as inference is concerned, other statistics have to be studied. We first consider the setting where the time-labels of the nodes, i.e., their time of arrival, are observed but their type is not. In this setting, we design a consistent estimator for q and provide bounds for the feasibility of testing between two different values of q. Moreover, we show that if q is small enough, then it is possible to cluster the nodes in a way correlated with the true partition, even though the algorithm is exponential in time (in passing, we show that our clustering procedure is intimately connected to the NP-hard problem of minimum fair bisection). In the unlabelled setting, i.e., when only the tree structure is observed, we show that it is possible to test between different values of q in a strictly better way than by random guessing. This follows from a delicate analysis of the sum-of-distances statistic.
Liquid droplet dynamics are widely used in biological and engineering applications, which contain complex interfacial instabilities and pattern formulation such as droplet merging, splitting, and transport. This paper studies a class of mean field control formulation towards these droplet dynamics. They are used to control and maintain the manipulation of droplets in applications. We first formulate the droplet dynamics as gradient flows of free energies in modified optimal transport metrics with nonlinear mobilities. We then design an optimal control problem for these gradient flows. We lastly apply the primal-dual hybrid gradient algorithm with high-order finite element methods to simulate the proposed mean field control problems. Numerical examples, including droplet formation, bead-up/spreading, transport, and merging/splitting on a two-dimensional spatial domain, demonstrate the effectiveness of the proposed mean field control mechanism.
The comparison of frequency distributions is a common statistical task with broad applications and a long history of methodological development. However, existing measures do not quantify the magnitude and direction by which one distribution is shifted relative to another. In the present study, we define distributional shift (DS) as the concentration of frequencies away from the greatest discrete class, e.g., a histogram's right-most bin. We derive a measure of DS based on the sum of cumulative frequencies, intuitively quantifying shift as a statistical moment. We then define relative distributional shift (RDS) as the difference in DS between distributions. Using simulated random sampling, we demonstrate that RDS is highly related to measures that are popularly used to compare frequency distributions. Focusing on a specific use case, i.e., simulated healthcare Evaluation and Management coding profiles, we show how RDS can be used to examine many pairs of empirical and expected distributions via shift-significance plots. In comparison to other measures, RDS has the unique advantage of being a signed (directional) measure based on a simple difference in an intuitive property.
We propose a new loss function for supervised and physics-informed training of neural networks and operators that incorporates a posteriori error estimate. More specifically, during the training stage, the neural network learns additional physical fields that lead to rigorous error majorants after a computationally cheap postprocessing stage. Theoretical results are based upon the theory of functional a posteriori error estimates, which allows for the systematic construction of such loss functions for a diverse class of practically relevant partial differential equations. From the numerical side, we demonstrate on a series of elliptic problems that for a variety of architectures and approaches (physics-informed neural networks, physics-informed neural operators, neural operators, and classical architectures in the regression and physics-informed settings), we can reach better or comparable accuracy and in addition to that cheaply recover high-quality upper bounds on the error after training.
We formulate a uniform tail bound for empirical processes indexed by a class of functions, in terms of the individual deviations of the functions rather than the worst-case deviation in the considered class. The tail bound is established by introducing an initial "deflation" step to the standard generic chaining argument. The resulting tail bound is the sum of the complexity of the "deflated function class" in terms of a generalization of Talagrand's $\gamma$ functional, and the deviation of the function instance, both of which are formulated based on the natural seminorm induced by the corresponding Cram\'{e}r functions. We also provide certain approximations for the mentioned seminorm when the function class lies in a given (exponential type) Orlicz space, that can be used to make the complexity term and the deviation term more explicit.
We study the problem of training diffusion models to sample from a distribution with a given unnormalized density or energy function. We benchmark several diffusion-structured inference methods, including simulation-based variational approaches and off-policy methods (continuous generative flow networks). Our results shed light on the relative advantages of existing algorithms while bringing into question some claims from past work. We also propose a novel exploration strategy for off-policy methods, based on local search in the target space with the use of a replay buffer, and show that it improves the quality of samples on a variety of target distributions. Our code for the sampling methods and benchmarks studied is made public at //github.com/GFNOrg/gfn-diffusion as a base for future work on diffusion models for amortized inference.
The methodological contribution in this paper is motivated by biomechanical studies where data characterizing human movement are waveform curves representing joint measures such as flexion angles, velocity, acceleration, and so on. In many cases the aim consists of detecting differences in gait patterns when several independent samples of subjects walk or run under different conditions (repeated measures). Classic kinematic studies often analyse discrete summaries of the sample curves discarding important information and providing biased results. As the sample data are obviously curves, a Functional Data Analysis approach is proposed to solve the problem of testing the equality of the mean curves of a functional variable observed on several independent groups under different treatments or time periods. A novel approach for Functional Analysis of Variance (FANOVA) for repeated measures that takes into account the complete curves is introduced. By assuming a basis expansion for each sample curve, two-way FANOVA problem is reduced to Multivariate ANOVA for the multivariate response of basis coefficients. Then, two different approaches for MANOVA with repeated measures are considered. Besides, an extensive simulation study is developed to check their performance. Finally, two applications with gait data are developed.
Researchers would often like to leverage data from a collection of sources (e.g., primary studies in a meta-analysis) to estimate causal effects in a target population of interest. However, traditional meta-analytic methods do not produce causally interpretable estimates for a well-defined target population. In this paper, we present the CausalMetaR R package, which implements efficient and robust methods to estimate causal effects in a given internal or external target population using multi-source data. The package includes estimators of average and subgroup treatment effects for the entire target population. To produce efficient and robust estimates of causal effects, the package implements doubly robust and non-parametric efficient estimators and supports using flexible data-adaptive (e.g., machine learning techniques) methods and cross-fitting techniques to estimate the nuisance models (e.g., the treatment model, the outcome model). We describe the key features of the package and demonstrate how to use the package through an example.
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