Or Zuk

Ortal Reshef, Ofer Glassman, Or Zuk et al.

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.

Ori Meidler, Shaul Tolkovsky, Or Zuk

Generative models are powerful tools for sampling from a learned distribution $\mathcal{P}(Y \mid X)$, and inverse-design methods invert this map to find an input $x$ that produces a desired point output $y^*$. However, many design goals are naturally distributional rather than pointwise, incorporating the inherent uncertainty of $Y$ and targeting a specific form for it, a task not addressed by standard inverse design. To address this issue we introduce Conditional Distribution Matching (CDM), a new inverse-design problem class in generative modeling: given a joint distribution $\mathcal{P}(X, Y)$ and a target distribution $\mathcal{G}(Y)$, find an input $x^*$ whose induced conditional distribution $\mathcal{P}(Y \mid X = x^*)$ matches $\mathcal{G}$. We formally define two variants: Conditional Distribution Matching Sampling (CDMS) and Conditional Distribution Matching Optimization (CDMO). To solve these problems, we propose MLGD-F (Matching-Loss Guided Diffusion with a Fast inner sampler), a plug-and-play inference-time algorithm that combines a pretrained score-based diffusion model with a pretrained fast conditional sampler, requiring no additional training or fine-tuning. By leveraging single-step conditional sampling, MLGD-F enables tractable gradient computation, making the estimation of $\mathcal{P}(Y \mid X)$ both memory-efficient and computationally lightweight. We validate MLGD-F on synthetic benchmarks, structured image transformations, and generative editing optimization, demonstrating reliable recovery of inputs whose conditional distributions match diverse user-specified targets, including discrete mixtures and continuous low-rank supports.

Shaul Tolkovsky, Ori Meidler, Or Zuk

Mode separation, namely how sharply a distribution fragments into barrier-separated clusters, is a fundamental geometric property of densities, difficult to quantify in high dimensions. It is structurally distinct from dispersion, yet existing tools fall short: differential entropy rises with spread regardless of fragmentation, PCA orders directions by variance regardless of barriers, and mutual information requires a mixture decomposition one usually does not have. We measure mode separation through a single stochastic process intrinsic to the density: a unique reversible diffusion with $f$ as its stationary distribution and constant scalar diffusion coefficient. We extract two readouts from its autocovariance matrix: SSA (Sum of Squared Autocorrelations), a scalar barrier-sensitive measure; and DA (Dominant Autocorrelation directions), linear projections ordered by metastability rather than variance. Under an isotropic-Gaussian null, we derive a closed-form spectrum for the empirical autocovariance that generalizes Marchenko--Pastur, with an analytic upper edge that selects the lag at which DA is read off. Both readouts use only samples and a score function, scaling to high dimensions through pretrained score-based generative models via Tweedie's identity. We apply our framework to three settings: (i) synthetic Gaussian mixtures, where SSA tracks mutual information; (ii) SDXL text-to-image generations, where SSA and DA capture structure that entropy and PCA miss; and (iii) molecular dynamics of alanine dipeptide, where DA recovers the known slow backbone dihedrals from static samples alone.

Tom Hope, Avishai Wagner, Or Zuk

We propose a simple and efficient time-series clustering framework particularly suited for low Signal-to-Noise Ratio (SNR), by simultaneous smoothing and dimensionality reduction aimed at preserving clustering information. We extend the sparse K-means algorithm by incorporating structured sparsity, and use it to exploit the multi-scale property of wavelets and group structure in multivariate signals. Finally, we extract features invariant to translation and scaling with the scattering transform, which corresponds to a convolutional network with filters given by a wavelet operator, and use the network's structure in sparse clustering. By promoting sparsity, this transform can yield a low-dimensional representation of signals that gives improved clustering results on several real datasets.

Avishai Wagner, Or Zuk

We propose and study a row-and-column affine measurement scheme for low-rank matrix recovery. Each measurement is a linear combination of elements in one row or one column of a matrix $X$. This setting arises naturally in applications from different domains. However, current algorithms developed for standard matrix recovery problems do not perform well in our case, hence the need for developing new algorithms and theory for our problem. We propose a simple algorithm for the problem based on Singular Value Decomposition ($SVD$) and least-squares ($LS$), which we term \alg. We prove that (a simplified version of) our algorithm can recover $X$ exactly with the minimum possible number of measurements in the noiseless case. In the general noisy case, we prove performance guarantees on the reconstruction accuracy under the Frobenius norm. In simulations, our row-and-column design and \alg algorithm show improved speed, and comparable and in some cases better accuracy compared to standard measurements designs and algorithms. Our theoretical and experimental results suggest that the proposed row-and-column affine measurements scheme, together with our recovery algorithm, may provide a powerful framework for affine matrix reconstruction.

Or Zuk, Shiri Margel, Eytan Domany

Bayesian Networks (BNs) are useful tools giving a natural and compact representation of joint probability distributions. In many applications one needs to learn a Bayesian Network (BN) from data. In this context, it is important to understand the number of samples needed in order to guarantee a successful learning. Previous work have studied BNs sample complexity, yet it mainly focused on the requirement that the learned distribution will be close to the original distribution which generated the data. In this work, we study a different aspect of the learning, namely the number of samples needed in order to learn the correct structure of the network. We give both asymptotic results, valid in the large sample limit, and experimental results, demonstrating the learning behavior for feasible sample sizes. We show that structure learning is a more difficult task, compared to approximating the correct distribution, in the sense that it requires a much larger number of samples, regardless of the computational power available for the learner.

Or Zuk, Liat Ein-Dor, Eytan Domany

Ranking objects is a simple and natural procedure for organizing data. It is often performed by assigning a quality score to each object according to its relevance to the problem at hand. Ranking is widely used for object selection, when resources are limited and it is necessary to select a subset of most relevant objects for further processing. In real world situations, the object's scores are often calculated from noisy measurements, casting doubt on the ranking reliability. We introduce an analytical method for assessing the influence of noise levels on the ranking reliability. We use two similarity measures for reliability evaluation, Top-K-List overlap and Kendall's tau measure, and show that the former is much more sensitive to noise than the latter. We apply our method to gene selection in a series of microarray experiments of several cancer types. The results indicate that the reliability of the lists obtained from these experiments is very poor, and that experiment sizes which are necessary for attaining reasonably stable Top-K-Lists are much larger than those currently available. Simulations support our analytical results.