arXiv subjects

Ariel Jaffe

Publications and source records attributed to Ariel Jaffe.

At least 19 recordsLinked to original sources

arXiv2026

SDSR: A Spectral Divide-and-Conquer Approach for Species Tree Reconstruction

Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance between the evolutionary history of individual genes and that of the species. The second challenge is computational, as contemporary studies involve thousands of species. Here we present SDSR, a scalable divide-and-conquer approach for species tree reconstruction based on spectral graph theory. The algorithm recursively partitions the species into subsets until their sizes are below a given threshold. The trees of these subsets are reconstructed by a user-chosen species tree algorithm. Finally, these subtrees are merged to form the full tree. On the theoretical front, we derive recovery guarantees for SDSR, under the multispecies coalescent (MSC) model. We also perform a runtime complexity analysis. We show that SDSR, when combined with a species tree reconstruction algorithm as a subroutine, yields substantial runtime savings as compared to applying the same algorithm on the full data. Empirically, we evaluate SDSR on synthetic benchmark datasets with incomplete lineage sorting and horizontal gene transfer. In accordance with our theoretical analysis, the simulations show that combining SDSR with common species tree methods, such as CA-ML or ASTRAL, yields up to 10-fold faster runtimes. In addition, SDSR achieves a comparable tree reconstruction accuracy to that obtained by applying these methods on the full data.

q-bio.PE↗

arXiv2026

Graph-based Semi-Supervised Learning via Maximum Discrimination

Semi-supervised learning (SSL) addresses the critical challenge of training accurate models when labeled data is scarce but unlabeled data is abundant. Graph-based SSL (GSSL) has emerged as a popular framework that captures data structure through graph representations. Classic graph SSL methods, such as Label Propagation and Label Spreading, aim to compute low-dimensional representations where points with the same labels are close in representation space. Although often effective, these methods can be suboptimal on data with complex label distributions. In our work, we develop AUC-spec, a graph approach that computes a low-dimensional representation that maximizes class separation. We compute this representation by optimizing the Area Under the ROC Curve (AUC) as estimated via the labeled points. We provide a detailed analysis of our approach under a product-of-manifold model, and show that the required number of labeled points for AUC-spec is polynomial in the model parameters. Empirically, we show that AUC-spec balances class separation with graph smoothness. It demonstrates competitive results on synthetic and real-world datasets while maintaining computational efficiency comparable to the field's classic and state-of-the-art methods.

stat.ML↗

arXiv2026

SpARCD: A Spectral Graph Framework for Revealing Differential Functional Connectivity in fMRI Data

Identifying brain regions that exhibit altered functional connectivity between cognitive or emotional states is a fundamental problem in neuroscience. We propose SpARCD (Spectral Analysis for Revealing Connectivity Differences), a statistical framework for detecting detecting condition-specific patterns of functional connectivity. SpARCD uses distance correlation, a dependence measure sensitive to both linear and nonlinear associations, to construct weighted region-wise connectivity graphs for each condition. A differential operator obtained through spectral filtering is then used to identify connectivity changes via its leading eigenvectors. To assess statistical significance, we develop a permutation-based testing procedure that yields interpretable region-level significance maps. We establish finite-sample validity of the permutation test and derive asymptotic guarantees for the stability of the resulting region rankings. Simulation studies demonstrate improved power relative to conventional edge-wise and univariate approaches, particularly in settings with nonlinear dependence structures. We applied SpARCD to fMRI data from 113 individuals with early-stage PTSD and 42 controls during emotional and neutral task conditions. The method identified distinct connectivity networks associated with visual processing in both PTSD and control participants. Resting-state comparisons between PTSD and control participants highlighted similar visual networks. SpARCD provides a statistically rigorous and computationally efficient framework for comparing high-dimensional connectivity patterns.

stat.ME↗

arXiv2024

Spectral Self-supervised Feature Selection

Choosing a meaningful subset of features from high-dimensional observations in unsupervised settings can greatly enhance the accuracy of downstream analysis, such as clustering or dimensionality reduction, and provide valuable insights into the sources of heterogeneity in a given dataset. In this paper, we propose a self-supervised graph-based approach for unsupervised feature selection. Our method's core involves computing robust pseudo-labels by applying simple processing steps to the graph Laplacian's eigenvectors. The subset of eigenvectors used for computing pseudo-labels is chosen based on a model stability criterion. We then measure the importance of each feature by training a surrogate model to predict the pseudo-labels from the observations. Our approach is shown to be robust to challenging scenarios, such as the presence of outliers and complex substructures. We demonstrate the effectiveness of our method through experiments on real-world datasets, showing its robustness across multiple domains, particularly its effectiveness on biological datasets.

cs.LG↗

arXiv2024

Spectral Graph Filtering for Modality-Specific Representation Learning

Multimodal datasets, where measurements are obtained from multiple sensors, have become central to many scientific domains. In unsupervised settings, most representation learning methods focus on identifying shared latent structures, such as clusters or continuous processes that appear across modalities. However, some aspects of the data may be observed only through a single modality. For example, in computational biology, certain cell-subtypes may appear in genetic profiles but not in epigenetic markers. In this paper, we present DELVE, a spectral method for extracting modality-specific (differential) latent variables. Our approach constructs a graph for each modality and leverages differences in their connectivity patterns to design a graph filter that attenuates shared signals while preserving modality-specific components. We provide an asymptotic convergence analysis for our method under a product manifold model. To evaluate the performance of our method, we test its ability to recover differential latent structures in several synthetic and real datasets.

stat.ME↗

arXiv2023

Multi-modal Differentiable Unsupervised Feature Selection

Multi-modal high throughput biological data presents a great scientific opportunity and a significant computational challenge. In multi-modal measurements, every sample is observed simultaneously by two or more sets of sensors. In such settings, many observed variables in both modalities are often nuisance and do not carry information about the phenomenon of interest. Here, we propose a multi-modal unsupervised feature selection framework: identifying informative variables based on coupled high-dimensional measurements. Our method is designed to identify features associated with two types of latent low-dimensional structures: (i) shared structures that govern the observations in both modalities and (ii) differential structures that appear in only one modality. To that end, we propose two Laplacian-based scoring operators. We incorporate the scores with differentiable gates that mask nuisance features and enhance the accuracy of the structure captured by the graph Laplacian. The performance of the new scheme is illustrated using synthetic and real datasets, including an extended biological application to single-cell multi-omics.

cs.LG↗

arXiv2022

DiSC: Differential Spectral Clustering of Features

Selecting subsets of features that differentiate between two conditions is a key task in a broad range of scientific domains. In many applications, the features of interest form clusters with similar effects on the data at hand. To recover such clusters we develop DiSC, a data-driven approach for detecting groups of features that differentiate between conditions. For each condition, we construct a graph whose nodes correspond to the features and whose weights are functions of the similarity between them for that condition. We then apply a spectral approach to compute subsets of nodes whose connectivity differs significantly between the condition-specific feature graphs. On the theoretical front, we analyze our approach with a toy example based on the stochastic block model. We evaluate DiSC on a variety of datasets, including MNIST, hyperspectral imaging, simulated scRNA-seq and task fMRI, and demonstrate that DiSC uncovers features that better differentiate between conditions compared to competing methods.

cs.LG↗

arXiv2022

Weakly Supervised Indoor Localization via Manifold Matching

Inferring the location of a mobile device in an indoor setting is an open problem of utmost significance. A leading approach that does not require the deployment of expensive infrastructure is fingerprinting, where a classifier is trained to predict the location of a device based on its captured signal. The main caveat of this approach is that acquiring a sufficiently large and accurate training set may be prohibitively expensive. Here, we propose a weakly supervised method that only requires the location of a small number of devices. The localization is done by matching a low-dimensional spectral representation of the signals to a given sketch of the indoor environment. We test our approach on simulated and real data and show that it yields an accuracy of a few meters, which is on par with fully supervised approaches. The simplicity of our method and its accuracy with minimal supervision makes it ideal for implementation in indoor localization systems.

eess.SP↗

arXiv2021

Spectral Top-Down Recovery of Latent Tree Models

Modeling the distribution of high dimensional data by a latent tree graphical model is a prevalent approach in multiple scientific domains. A common task is to infer the underlying tree structure, given only observations of its terminal nodes. Many algorithms for tree recovery are computationally intensive, which limits their applicability to trees of moderate size. For large trees, a common approach, termed divide-and-conquer, is to recover the tree structure in two steps. First, recover the structure separately of multiple, possibly random subsets of the terminal nodes. Second, merge the resulting subtrees to form a full tree. Here, we develop Spectral Top-Down Recovery (STDR), a deterministic divide-and-conquer approach to infer large latent tree models. Unlike previous methods, STDR partitions the terminal nodes in a non random way, based on the Fiedler vector of a suitable Laplacian matrix related to the observed nodes. We prove that under certain conditions, this partitioning is consistent with the tree structure. This, in turn, leads to a significantly simpler merging procedure of the small subtrees. We prove that STDR is statistically consistent and bound the number of samples required to accurately recover the tree with high probability. Using simulated data from several common tree models in phylogenetics, we demonstrate that STDR has a significant advantage in terms of runtime, with improved or similar accuracy.

stat.ML↗

arXiv2020

Super-resolution multi-reference alignment

We study super-resolution multi-reference alignment, the problem of estimating a signal from many circularly shifted, down-sampled, and noisy observations. We focus on the low SNR regime, and show that a signal in $\mathbb{R}^M$ is uniquely determined when the number $L$ of samples per observation is of the order of the square root of the signal's length $(L=O(\sqrt{M}))$. Phrased more informally, one can square the resolution. This result holds if the number of observations is proportional to at least 1/SNR$^3$. In contrast, with fewer observations recovery is impossible even when the observations are not down-sampled ($L=M$). The analysis combines tools from statistical signal processing and invariant theory. We design an expectation-maximization algorithm and demonstrate that it can super-resolve the signal in challenging SNR regimes.

cs.IT↗

arXiv2020

Spectral neighbor joining for reconstruction of latent tree models

A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a set of observed organisms. Given a set of independent realizations of the random variables at the leaves of the tree, a key challenge is to infer the underlying tree topology. In this work we develop Spectral Neighbor Joining (SNJ), a novel method to recover the structure of latent tree graphical models. Given a matrix that contains a measure of similarity between all pairs of observed variables, SNJ computes a spectral measure of cohesion between groups of observed variables. We prove that SNJ is consistent, and derive a sufficient condition for correct tree recovery from an estimated similarity matrix. Combining this condition with a concentration of measure result on the similarity matrix, we bound the number of samples required to recover the tree with high probability. We illustrate via extensive simulations that in comparison to several other reconstruction methods, SNJ requires fewer samples to accurately recover trees with a large number of leaves or long edges.

stat.ML↗

arXiv2020

The Spectral Underpinning of word2vec

word2vec due to Mikolov \textit{et al.} (2013) is a word embedding method that is widely used in natural language processing. Despite its great success and frequent use, theoretical justification is still lacking. The main contribution of our paper is to propose a rigorous analysis of the highly nonlinear functional of word2vec. Our results suggest that word2vec may be primarily driven by an underlying spectral method. This insight may open the door to obtaining provable guarantees for word2vec. We support these findings by numerical simulations. One fascinating open question is whether the nonlinear properties of word2vec that are not captured by the spectral method are beneficial and, if so, by what mechanism.

cs.LG↗

arXiv2018

Learning Binary Latent Variable Models: A Tensor Eigenpair Approach

Latent variable models with hidden binary units appear in various applications. Learning such models, in particular in the presence of noise, is a challenging computational problem. In this paper we propose a novel spectral approach to this problem, based on the eigenvectors of both the second order moment matrix and third order moment tensor of the observed data. We prove that under mild non-degeneracy conditions, our method consistently estimates the model parameters at the optimal parametric rate. Our tensor-based method generalizes previous orthogonal tensor decomposition approaches, where the hidden units were assumed to be either statistically independent or mutually exclusive. We illustrate the consistency of our method on simulated data and demonstrate its usefulness in learning a common model for population mixtures in genetics.

stat.ML↗

arXiv2017

Newton correction methods for computing real eigenpairs of symmetric tensors

Real eigenpairs of symmetric tensors play an important role in multiple applications. In this paper we propose and analyze a fast iterative Newton-based method to compute real eigenpairs of symmetric tensors. We derive sufficient conditions for a real eigenpair to be a stable fixed point for our method, and prove that given a sufficiently close initial guess, the convergence rate is quadratic. Empirically, our method converges to a significantly larger number of eigenpairs compared to previously proposed iterative methods, and with enough random initializations typically finds all real eigenpairs. In particular, for a generic symmetric tensor, the sufficient conditions for local convergence of our Newton-based method hold simultaneously for all its real eigenpairs.

math.NA↗

arXiv2016

Minimax-optimal semi-supervised regression on unknown manifolds

We consider semi-supervised regression when the predictor variables are drawn from an unknown manifold. A simple two step approach to this problem is to: (i) estimate the manifold geodesic distance between any pair of points using both the labeled and unlabeled instances; and (ii) apply a k nearest neighbor regressor based on these distance estimates. We prove that given sufficiently many unlabeled points, this simple method of geodesic kNN regression achieves the optimal finite-sample minimax bound on the mean squared error, as if the manifold were known. Furthermore, we show how this approach can be efficiently implemented, requiring only O(k N log N) operations to estimate the regression function at all N labeled and unlabeled points. We illustrate this approach on two datasets with a manifold structure: indoor localization using WiFi fingerprints and facial pose estimation. In both cases, geodesic kNN is more accurate and much faster than the popular Laplacian eigenvector regressor.

stat.ML↗

arXiv2016

The discrete sign problem: uniqueness, recovery algorithms and phase retrieval applications

In this paper we consider the following real-valued and finite dimensional specific instance of the 1-D classical phase retrieval problem. Let ${\bf F}\in\mathbb{R}^N$ be an $N$-dimensional vector, whose discrete Fourier transform has a compact support. The sign problem is to recover ${\bf F}$ from its magnitude $|{\bf F}|$. First, in contrast to the classical 1-D phase problem which in general has multiple solutions, we prove that with sufficient over-sampling, the sign problem admits a unique solution. Next, we show that the sign problem can be viewed as a special case of a more general piecewise constant phase problem. Relying on this result, we derive a computationally efficient and robust to noise sign recovery algorithm. In the noise-free case and with a sufficiently high sampling rate, our algorithm is guaranteed to recover the true sign pattern. Finally, we present two phase retrieval applications of the sign problem: (i) vectorial phase retrieval with three measurement vectors; and (ii) recovery of two well separated 1-D objects.

math.NA↗

arXiv2016

A Deep Learning Approach to Unsupervised Ensemble Learning

We show how deep learning methods can be applied in the context of crowdsourcing and unsupervised ensemble learning. First, we prove that the popular model of Dawid and Skene, which assumes that all classifiers are conditionally independent, is {\em equivalent} to a Restricted Boltzmann Machine (RBM) with a single hidden node. Hence, under this model, the posterior probabilities of the true labels can be instead estimated via a trained RBM. Next, to address the more general case, where classifiers may strongly violate the conditional independence assumption, we propose to apply RBM-based Deep Neural Net (DNN). Experimental results on various simulated and real-world datasets demonstrate that our proposed DNN approach outperforms other state-of-the-art methods, in particular when the data violates the conditional independence assumption.

stat.ML↗

arXiv2015

Unsupervised Ensemble Learning with Dependent Classifiers

In unsupervised ensemble learning, one obtains predictions from multiple sources or classifiers, yet without knowing the reliability and expertise of each source, and with no labeled data to assess it. The task is to combine these possibly conflicting predictions into an accurate meta-learner. Most works to date assumed perfect diversity between the different sources, a property known as conditional independence. In realistic scenarios, however, this assumption is often violated, and ensemble learners based on it can be severely sub-optimal. The key challenges we address in this paper are:\ (i) how to detect, in an unsupervised manner, strong violations of conditional independence; and (ii) construct a suitable meta-learner. To this end we introduce a statistical model that allows for dependencies between classifiers. Our main contributions are the development of novel unsupervised methods to detect strongly dependent classifiers, better estimate their accuracies, and construct an improved meta-learner. Using both artificial and real datasets, we showcase the importance of taking classifier dependencies into account and the competitive performance of our approach.

cs.LG↗