arXiv research

SDSR reconstructs species trees from genetic markers efficiently.

Paper proposes an algorithm to reconstruct optimal model structure from graph adjacency matrix.

Uniform proof reconstructs spaces using cross ratio on boundary.

SNJ recovers latent tree models from similarity matrices.

We discuss an autoencoder model in which the encoding and decoding functions are implemented by decision trees. We use the soft decision tree where internal nodes realize soft multivariate splits given by a gating function and the overall output is the average of all leaves weighted by the gating values on their path. …

We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct from each other and from the underlying species tree, possibly confounding phyloge…

The tree reconstruction problem is to collect and analyze massive data at the $n$th level of the tree, to identify whether there is non-vanishing information of the root, as $n$ goes to infinity. Its connection to the clustering problem in the setting of the stochastic block model, which has wide applications in machin…

We propose a Bayesian expectation-maximization (EM) algorithm for reconstructing Markov-tree sparse signals via belief propagation. The measurements follow an underdetermined linear model where the regression-coefficient vector is the sum of an unknown approximately sparse signal and a zero-mean white Gaussian noise wi…

We propose and study a multi-scale approach to vector quantization. We develop an algorithm, dubbed reconstruction trees, inspired by decision trees. Here the objective is parsimonious reconstruction of unsupervised data, rather than classification. Contrasted to more standard vector quantization methods, such as K-mea…

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has …

We adopt data structure in the form of cover trees and iteratively apply approximate nearest neighbour (ANN) searches for fast compressed sensing reconstruction of signals living on discrete smooth manifolds. Levering on the recent stability results for the inexact Iterative Projected Gradient (IPG) algorithm and by us…

Auto-encoding is an important task which is typically realized by deep neural networks (DNNs) such as convolutional neural networks (CNN). In this paper, we propose EncoderForest (abbrv. eForest), the first tree ensemble based auto-encoder. We present a procedure for enabling forests to do backward reconstruction by ut…

In this article we extend the computational geometric curve reconstruction approach to curves in Riemannian manifolds. We prove that the minimal spanning tree, given a sufficiently dense sample, correctly reconstructs the smooth arcs and further closed and simple curves in Riemannian manifolds. The proof is based on th…

The paper proposes a method to infer differentiation trees from RNA velocity data.

We consider the classical sparse regression problem of recovering a sparse signal $x_0$ given a measurement vector $y = Φx_0+w$. We propose a tree search algorithm driven by the deep neural network for sparse regression (TSN). TSN improves the signal reconstruction performance of the deep neural network designed for sp…

Tree-AMP simplifies inference in complex tree-structured models.

The analysis of Belief Propagation and other algorithms for the {\em reconstruction problem} plays a key role in the analysis of community detection in inference on graphs, phylogenetic reconstruction in bioinformatics, and the cavity method in statistical physics. We prove a conjecture of Evans, Kenyon, Peres, and Sch…

Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the …

The paper tests properties of trees in graphical models using covariance queries.

Improved phylogenetic tree reconstruction using flexible branch length distributions.

Natural image statistics exhibit hierarchical dependencies across multiple scales. Representing such prior knowledge in non-factorial latent tree models can boost performance of image denoising, inpainting, deconvolution or reconstruction substantially, beyond standard factorial "sparse" methodology. We derive a large …

This work introduces novel methods to identify and compare cycles across topological objects.

We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method, the data is organized into a binary partition tree representing a multiscale structure. The dictionary atoms are defined ad…

High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the subclonal lineages of tumor cells present in the sample can be reconstructed from…

We present a syntax-infused variational autoencoder (SIVAE), that integrates sentences with their syntactic trees to improve the grammar of generated sentences. Distinct from existing VAE-based text generative models, SIVAE contains two separate latent spaces, for sentences and syntactic trees. The evidence lower bound…

New family of triangulated 3-spheres identified from trees.

In real-world and online social networks, individuals receive and transmit information in real time. Cascading information transmissions (e.g. phone calls, text messages, social media posts) may be understood as a realization of a diffusion process operating on the network, and its branching path can be represented by …

This work is the first step towards a description of the Gromov boundary of the free factor graph of a free product, with applications to subgroup classification for outer automorphisms. We extend the theory of algebraic laminations dual to trees, as developed by Coulbois, Hilion, Lustig and Reynolds, to the context of…

Study shows stability of travel time data reconstruction from closed subsets.

We investigate active learning by pairwise similarity over the leaves of trees originating from hierarchical clustering procedures. In the realizable setting, we provide a full characterization of the number of queries needed to achieve perfect reconstruction of the tree cut. In the non-realizable setting, we rely on k…

Statistical dependencies among wavelet coefficients are commonly represented by graphical models such as hidden Markov trees(HMTs). However, in linear inverse problems such as deconvolution, tomography, and compressed sensing, the presence of a sensing or observation matrix produces a linear mixing of the simple Markov…

This work introduces a method for visualizing high-dimensional posteriors using hierarchical tree-valued predictions.

Many iterative and non-iterative methods have been developed for inverse problems associated with Ising models. Aiming to derive an accurate non-iterative method for the inverse problems, we employ the tree-reweighted approximation. Using the tree-reweighted approximation, we can optimize the rigorous lower bound of th…

The paper deals with the problem of reconstructing the topological structure of a network of dynamical systems. A distance function is defined in order to evaluate the "closeness" of two processes and a few useful mathematical properties are derived. Theoretical results to guarantee the correctness of the identificatio…

We study the problem of distinguishing between two distributions on a metric space; i.e., given metric measure spaces $({\mathbb X}, d, μ_1)$ and $({\mathbb X}, d, μ_2)$, we are interested in the problem of determining from finite data whether or not $μ_1$ is $μ_2$. The key is to use pairwise distances between observat…

Efficiently learns tree-structured Ising models with minimal samples.

Objects are composed of a set of geometrically organized parts. We introduce an unsupervised capsule autoencoder (SCAE), which explicitly uses geometric relationships between parts to reason about objects. Since these relationships do not depend on the viewpoint, our model is robust to viewpoint changes. SCAE consists …

One of the most important problems of data processing in high energy and nuclear physics is the event reconstruction. Its main part is the track reconstruction procedure which consists in looking for all tracks that elementary particles leave when they pass through a detector among a huge number of points, so-called hi…

Convex clustering refers, for given $\left\{x_1, \dots, x_n\right\} \subset \mathbb{R}^p$, to the minimization of \begin{eqnarray*} u(γ) & = & \underset{u_1, \dots, u_n }{\arg\min}\;\sum_{i=1}^{n}{\lVert x_i - u_i \rVert^2} + γ\sum_{i,j=1}^{n}{w_{ij} \lVert u_i - u_j\rVert},\\ \end{eqnarray*} where $w_{ij} \geq 0$ is a…

Ensemble methods are among the state-of-the-art predictive modeling approaches. Applied to modern big data, these methods often require a large number of sub-learners, where the complexity of each learner typically grows with the size of the dataset. This phenomenon results in an increasing demand for storage space, wh…

Unified framework for inference in complex nonlinear processes.

Distribution grid is the medium and low voltage part of a large power system. Structurally, the majority of distribution networks operate radially, such that energized lines form a collection of trees, i.e. forest, with a substation being at the root of any tree. The operational topology/forest may change from time to …

Sparse coding consists in representing signals as sparse linear combinations of atoms selected from a dictionary. We consider an extension of this framework where the atoms are further assumed to be embedded in a tree. This is achieved using a recently introduced tree-structured sparse regularization norm, which has pr…

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons …

Gradient estimation techniques applied to programs with randomness in high energy physics.

An axiomatic approach to signal reconstruction is formulated, involving a sample consistent set and a guiding set, describing desired reconstructions. New frame-less reconstruction methods are proposed, based on a novel concept of a reconstruction set, defined as a shortest pathway between the sample consistent set and…

There is a recent surge of interest in identifying the sharp recovery thresholds for cluster recovery under the stochastic block model. In this paper, we address the more refined question of how many vertices that will be misclassified on average. We consider the binary form of the stochastic block model, where $n$ ver…

One of the most important problems of data processing in high energy and nuclear physics is the event reconstruction. Its main part is the track reconstruction procedure which consists in looking for all tracks that elementary particles leave when they pass through a detector among a huge number of points, so-called hi…