Zohar Yakhini

Tomer Cohen, Zhiying Wang, Eitan Yaakobi et al.

This paper studies two problems that are motivated by combining two novel approaches, namely DNA composite and rank modulation. The recent approach of composite DNA takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm, every composite symbols does not store a single nucleotide but a mixture of the four DNA nucleotides. Instead of considering all the possible composite symbols we are interested only in the rank of the motifs in the symbol. The first problem in this paper addresses the capacity of a channel that uses such symbols, while in the second, bounds and construction of such codes are studied.

Ben Vardi, Dana Schonberger, Yuval Friedmann et al.

Pathology foundation models (PFMs) have advanced rapidly in recent years and support training classifiers for a range of histopathology tasks. However, their robustness across hospitals remains limited: performance often degrades when training a classifier on data from one hospital and evaluating it on another target hospital. We address this challenge by fine-tuning PFMs with a local maximum mean discrepancy (LMMD) objective that applies to two settings: domain adaptation, where unlabeled target-hospital data is available, and domain generalization, where target-hospital data is unavailable at all. Experiments at both the patch- and slide-level show consistent improvements across multiple PFMs and tasks.

Tomer Cohen, Eitan Yaakobi, Zohar Yakhini

We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single nucleotide, but rather a designed mixture of DNA nucleotides. Using the high multiplicity that is intrinsic to synthesis and sequencing a composite symbol consists of frequencies in the mixture. Rank modulation codes use permutations to represent information. Combining the two, we construct encoding that uses permutations of nucleotide frequencies rather than the exact frequency values. Codes for this approach were addressed in previous work, under Kendall's tau distances. In this work we study deletion and insertion codes. We present bounds and constructions of efficient codes defined over partial permutations.

Alona Levy-Jurgenson, Zohar Yakhini

Generative methods have recently seen significant improvements by generating in a lower-dimensional latent representation of the data. However, many of the generative methods applied in the latent space remain complex and difficult to train. Further, it is not entirely clear why transitioning to a lower-dimensional latent space can improve generative quality. In this work, we introduce a new and simple generative method grounded in topology theory -- Generative Topological Networks (GTNs) -- which also provides insights into why lower-dimensional latent-space representations might be better-suited for data generation. GTNs are simple to train -- they employ a standard supervised learning approach and do not suffer from common generative pitfalls such as mode collapse, posterior collapse or the need to pose constraints on the neural network architecture. We demonstrate the use of GTNs on several datasets, including MNIST, CelebA, CIFAR-10 and the Hands and Palm Images dataset by training GTNs on a lower-dimensional latent representation of the data. We show that GTNs can improve upon VAEs and that they are quick to converge, generating realistic samples in early epochs. Further, we use the topological considerations behind the development of GTNs to offer insights into why generative models may benefit from operating on a lower-dimensional latent space, highlighting the important link between the intrinsic dimension of the data and the dimension in which the data is generated. Particularly, we demonstrate that generating in high dimensional ambient spaces may be a contributing factor to out-of-distribution samples generated by diffusion models. We also highlight other topological properties that are important to consider when using and designing generative models. Our code is available at: https://github.com/alonalj/GTN

Nir Weingarten, Zohar Yakhini, Moshe Butman et al.

Deep Neural Nets (DNNs) learn latent representations induced by their downstream task, objective function, and other parameters. The quality of the learned representations impacts the DNN's generalization ability and the coherence of the emerging latent space. The Information Bottleneck (IB) provides a hypothetically optimal framework for data modeling, yet it is often intractable. Recent efforts combined DNNs with the IB by applying VAE-inspired variational methods to approximate bounds on mutual information, resulting in improved robustness to adversarial attacks. This work introduces a new and tighter variational bound for the IB, improving performance of previous IB-inspired DNNs. These advancements strengthen the case for the IB and its variational approximations as a data modeling framework, and provide a simple method to significantly enhance the adversarial robustness of classifier DNNs.

Alon Oring, Zohar Yakhini, Yacov Hel-Or

Autoencoders represent an effective approach for computing the underlying factors characterizing datasets of different types. The latent representation of autoencoders have been studied in the context of enabling interpolation between data points by decoding convex combinations of latent vectors. This interpolation, however, often leads to artifacts or produces unrealistic results during reconstruction. We argue that these incongruities are due to the structure of the latent space and because such naively interpolated latent vectors deviate from the data manifold. In this paper, we propose a regularization technique that shapes the latent representation to follow a manifold that is consistent with the training images and that drives the manifold to be smooth and locally convex. This regularization not only enables faithful interpolation between data points, as we show herein, but can also be used as a general regularization technique to avoid overfitting or to produce new samples for data augmentation.

Nir Friedman, Zohar Yakhini

In recent years there has been an increasing interest in learning Bayesian networks from data. One of the most effective methods for learning such networks is based on the minimum description length (MDL) principle. Previous work has shown that this learning procedure is asymptotically successful: with probability one, it will converge to the target distribution, given a sufficient number of samples. However, the rate of this convergence has been hitherto unknown. In this work we examine the sample complexity of MDL based learning procedures for Bayesian networks. We show that the number of samples needed to learn an epsilon-close approximation (in terms of entropy distance) with confidence delta is O((1/epsilon)^(4/3)log(1/epsilon)log(1/delta)loglog (1/delta)). This means that the sample complexity is a low-order polynomial in the error threshold and sub-linear in the confidence bound. We also discuss how the constants in this term depend on the complexity of the target distribution. Finally, we address questions of asymptotic minimality and propose a method for using the sample complexity results to speed up the learning process.

Ari Frank, Dan Geiger, Zohar Yakhini

There is no known efficient method for selecting k Gaussian features from n which achieve the lowest Bayesian classification error. We show an example of how greedy algorithms faced with this task are led to give results that are not optimal. This motivates us to propose a more robust approach. We present a Branch and Bound algorithm for finding a subset of k independent Gaussian features which minimizes the naive Bayesian classification error. Our algorithm uses additive monotonic distance measures to produce bounds for the Bayesian classification error in order to exclude many feature subsets from evaluation, while still returning an optimal solution. We test our method on synthetic data as well as data obtained from gene expression profiling.