Beginning with Witkowski et al. (2023), recent work on forecasting competitions has addressed incentive problems with the common winner-take-all mechanism. Frongillo et al. (2021) propose a competition mechanism based on Multiplicative Weights, an online learning algorithm. They show that their mechanism selects an epsilon-optimal forecaster with high probability using only O(log(n)/epsilon^2) events. These works, together with all prior work on this problem thus far, assume that events are independent. We prove the first accuracy and approximate truthfulness guarantees for forecasting competitions with correlated events. To quantify correlation, we introduce a notion of block correlation, which allows each event to be strongly correlated with up to b others and weakly correlated with the rest. We show that under distributions with this correlation, the Multiplicative Weights mechanism retains its epsilon-optimal guarantee using O(b^2 log(n)/epsilon^2) events. Our proof involves a novel concentration bound for correlated random variables which may be of broader interest.

Consider a tree T = (V,E) with root ∘ and an edge length function 𝓁:E → ℝ_+. The phylogenetic covariance matrix of T is the matrix C with rows and columns indexed by L, the leaf set of T, with entries C(i,j): = ∑_{e ∈ [i∧ j,o]}𝓁(e), for each i,j ∈ L. Recent work [Gorman & Lladser 2023] has shown that the phylogenetic covariance matrix of a large but random binary tree T is significantly sparsified, with overwhelmingly high probability, under a change-of-basis to the so-called Haar-like wavelets of T. Notably, this finding enables manipulating the spectrum of covariance matrices of large binary trees without the necessity to store them in computer memory but instead performing two post-order traversals of the tree [Gorman & Lladser 2023]. Building on the methods of the aforesaid paper, this manuscript further advances their sparsification result to encompass the broader class of k-regular trees, for any given k ≥ 2. This extension is achieved by refining existing asymptotic formulas for the mean and variance of the internal path length of random k-regular trees, utilizing hypergeometric function properties and identities.

Random forests have emerged as a promising tool in comparative metagenomics because they can predict environmental characteristics based on microbial composition in datasets where β-diversity metrics fall short of revealing meaningful relationships between samples. Nevertheless, despite this efficacy, they lack biological insight in tandem with their predictions, potentially hindering scientific advancement. To overcome this limitation, we leverage a geometric characterization of random forests to introduce a data-driven phylogenetic β-diversity metric, the adaptive Haar-like distance. This new metric assigns a weight to each internal node (i.e., split or bifurcation) of a reference phylogeny, indicating the relative importance of that node in discerning environmental samples based on their microbial composition. Alongside this, a weighted nearest-neighbors classifier, constructed using the adaptive metric, can be used as a proxy for the random forest while maintaining accuracy on par with that of the original forest and another state-of-the-art classifier, CoDaCoRe. As shown in datasets from diverse microbial environments, however, the new metric and classifier significantly enhance the biological interpretability and visualization of high-dimensional metagenomic samples.

We describe a novel way to represent the probability distribution of a random binary string as a mixture having a maximally weighted component associated with independent (though not necessarily identically distributed) Bernoulli characters. We refer to this as the latent independent weight of the probabilistic source producing the string, and derive a combinatorial algorithm to compute it. The decomposition we propose may serve as an alternative to the Boolean paradigm of hypothesis testing, or to assess the fraction of uncorrupted samples originating from a source with independent marginals. In this sense, the latent independent weight quantifies the maximal amount of independence contained within a probabilistic source, which, properly speaking, may not have independent marginals.

A subset of vertices in a graph is called resolving when the geodesic distances to those vertices uniquely distinguish every vertex in the graph. Here, we characterize the resolvability of Hamming graphs in terms of a constrained linear system and deduce a novel but straightforward characterization of resolvability for hypercubes. We propose an integer linear programming method to assess resolvability rapidly and provide a more costly but definite method based on Gröbner bases to determine whether or not a set of vertices resolves an arbitrary Hamming graph. As proof of concept, we identify a resolving set of size 77 in the metric space of all octapeptides (i.e., proteins composed of eight amino acids) with respect to the Hamming distance; in particular, any octamer may be readily represented as a 77-dimensional real vector. Representing $k$-mers as low-dimensional numerical vectors may enable new applications of machine learning algorithms to symbolic sequences.

We present a fast and simple algorithm to detect nascent RNA transcription in global nuclear run-on sequencing (GRO-seq). GRO-seq is a relatively new protocol that captures nascent transcripts from actively engaged polymerase, providing a direct read-out on bona fide transcription. Most traditional assays, such as RNA-seq, measure steady state RNA levels which are affected by transcription, post-transcriptional processing, and RNA stability. GRO-seq data, however, presents unique analysis challenges that are only beginning to be addressed. Here, we describe a new algorithm, Fast Read Stitcher (FStitch), that takes advantage of two popular machine-learning techniques, hidden Markov models and logistic regression, to classify which regions of the genome are transcribed. Given a small user-defined training set, our algorithm is accurate, robust to varying read depth, annotation agnostic, and fast. Analysis of GRO-seq data without a priori need for annotation uncovers surprising new insights into several aspects of the transcription process.

The role of a distance metric in many supervised and semi-supervised learning applications is central in the success of clustering algorithms. Since existing metrics like Euclidean do not necessarily reflect the true structure (clusters or manifolds) in the data, it becomes imperative that an appropriate metric be somehow learned from training or labeled data. Metric learning has been a relatively new topic in data mining and machine learning, though most work that deals with this topic learns a suitable linear transformation of the original data. This transformation is usually learned using training data and has been shown to improve test data classification accuracy. In this paper we present a Markov random walk based semi-supervised method for metric learning. Our method differs from the aforementioned techniques in that we use minimal labeled data and we do not assume any Mahalanobis type metric structure on the data. We create a computationally efficient nearest neighbor graph representation of the data and pose a semidefinite program that learns the random walk on the associated graph. This is used to generate a distance measure between all unlabeled points and the performance is compared against other important metrics using the k-NN classification rule.

BACKGROUND: The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differences and taking the log of the resulting probability matrices, methods based on Markov triples, and maximum likelihood methods that infer the substitution probabilities that lead to the most likely model of evolution. However, the speed and accuracy of these methods has not been compared. RESULTS: Different methods differ in performance by orders of magnitude (ranging from 1 ms to 10 s per matrix), but differences in accuracy of rate matrix reconstruction appear to be relatively small. Encouragingly, relatively simple and fast methods can provide results at least as accurate as far more complex and computationally intensive methods, especially when the sequences to be compared are relatively short. CONCLUSION: Based on the conditions tested, we recommend the use of method of Gojobori et al. (1982) for long sequences (> 600 nucleotides), and the method of Goldman et al. (1996) for shorter sequences (< 600 nucleotides). The method of Barry and Hartigan (1987) can provide somewhat more accuracy, measured as the Euclidean distance between the true and inferred matrices, on long sequences (> 2000 nucleotides) at the expense of substantially longer computation time. The availability of methods that are both fast and accurate will allow us to gain a global picture of change in the nucleotide substitution rate matrix on a genomewide scale across the tree of life.

Uniform asymptotic formulae for arrays of complex numbers of the form $(f_{r,s})$, with r and s nonnegative integers, are provided as r and s converge to infinity at a comparable rate. Our analysis is restricted to the case in which the generating function $F(z,w):=\sum f_{r,s} z^r w^s$ is meromorphic in a neighborhood of the origin. We provide uniform asymptotic formulae for the coefficients $f_{r,s}$ along directions in the $(r,s)$‐lattice determined by regular points of the singular variety of F. Our main result derives from the analysis of a one dimensional parameter‐varying integral describing the asymptotic behavior of $f_{r,s}$. We specifically consider the case in which the phase term of this integral has a unique stationary point; however, we allow the possibility that one or more stationary points of the amplitude term coalesce with this. Our results find direct application in certain problems associated to the Lagrange inversion formula as well as bivariate generating functions of the form $v(z)/(1-w\cdot u(z))$.