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Ziv Yaniv

Publications and source records attributed to Ziv Yaniv.

8 recordsLinked to original sources
arXiv2026

Training Neural Networks with Optimal Double-Bayesian Learning

Backpropagation with gradient descent is a common optimization strategy employed by most neural network architectures in machine learning. However, finding optimal hyperparameters to guide training has proven challenging. While it is widely acknowledged that selecting appropriate parameters is crucial for avoiding overfitting and achieving unbiased outcomes, this choice remains largely based on empirical experiments and experience. This paper presents a new probabilistic framework for the learning rate, a key parameter in stochastic gradient descent. The framework develops classic Bayesian statistics into a double-Bayesian decision mechanism involving two antagonistic Bayesian processes. A theoretically optimal learning rate can be derived from these two processes and used for stochastic gradient descent. Experiments across various classification, segmentation, and detection tasks corroborate the practical significance of the theoretically derived learning rate. The paper also discusses the ramifications of the proposed double-Bayesian framework for network training and model performance.

cs.LG↗
arXiv2024

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, such as primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.

q-bio.TO↗
arXiv2024

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

Alongside molecular insights into genes and proteins, biological imaging holds great promise for deepening scientific understanding of complex cellular systems and advancing predictive, personalized therapies for human health. To realize this potential, quality-assured image data must be shared globally across laboratories to enable comparison, pooling, and reanalysis-unlocking value far beyond the original purpose of data collection. Two broad sets of requirements are essential to enable image data sharing in the life sciences. The companion article Enabling Global Image Data Sharing in the Life Sciences outlines the need to develop cyberinfrastructure for sharing bioimage data. In this manuscript, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse bioimage data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges and democratize access to everyday practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.

q-bio.OT↗
arXiv2021

IBEX: An open and extensible method for high content multiplex imaging of diverse tissues

High content imaging is needed to catalogue the variety of cellular phenotypes and multi-cellular ecosystems present in metazoan tissues. We recently developed Iterative Bleaching Extends multi-pleXity (IBEX), an iterative immunolabeling and chemical bleaching method that enables multiplexed imaging (>65 parameters) in diverse tissues, including human organs relevant for international consortia efforts. IBEX is compatible with over 250 commercially available antibodies, 16 unique fluorophores, and can be easily adopted to different imaging platforms using slides and non-proprietary imaging chambers. The overall protocol consists of iterative cycles of antibody labelling, imaging, and chemical bleaching that can be completed at relatively low cost in 2-5 days by biologists with basic laboratory skills. To support widespread adoption, we provide extensive details on tissue processing, curated lists of validated antibodies, and tissue-specific panels for multiplex imaging. Furthermore, instructions are included on how to automate the method using competitively priced instruments and reagents. Finally, we present a software solution for image alignment that can be executed by individuals without programming experience using open source software and freeware. In summary, IBEX is an open and versatile method that can be readily implemented by academic laboratories and scaled to achieve high content mapping of diverse tissues in support of a Human Reference Atlas or other such applications.

q-bio.TO↗
arXiv2019

A Distance Map Regularized CNN for Cardiac Cine MR Image Segmentation

Cardiac image segmentation is a critical process for generating personalized models of the heart and for quantifying cardiac performance parameters. Several convolutional neural network (CNN) architectures have been proposed to segment the heart chambers from cardiac cine MR images. Here we propose a multi-task learning (MTL)-based regularization framework for cardiac MR image segmentation. The network is trained to perform the main task of semantic segmentation, along with a simultaneous, auxiliary task of pixel-wise distance map regression. The proposed distance map regularizer is a decoder network added to the bottleneck layer of an existing CNN architecture, facilitating the network to learn robust global features. The regularizer block is removed after training, so that the original number of network parameters does not change. We show that the proposed regularization method improves both binary and multi-class segmentation performance over the corresponding state-of-the-art CNN architectures on two publicly available cardiac cine MRI datasets, obtaining average dice coefficient of 0.84$\pm$0.03 and 0.91$\pm$0.04, respectively. Furthermore, we also demonstrate improved generalization performance of the distance map regularized network on cross-dataset segmentation, showing as much as 42% improvement in myocardium Dice coefficient from 0.56$\pm$0.28 to 0.80$\pm$0.14.

cs.CV↗
arXiv2018

Left Ventricle Segmentation and Quantification from Cardiac Cine MR Images via Multi-task Learning

Segmentation of the left ventricle and quantification of various cardiac contractile functions is crucial for the timely diagnosis and treatment of cardiovascular diseases. Traditionally, the two tasks have been tackled independently. Here we propose a convolutional neural network based multi-task learning approach to perform both tasks simultaneously, such that, the network learns better representation of the data with improved generalization performance. Probabilistic formulation of the problem enables learning the task uncertainties during the training, which are used to automatically compute the weights for the tasks. We performed a five fold cross-validation of the myocardium segmentation obtained from the proposed multi-task network on 97 patient 4-dimensional cardiac cine-MRI datasets available through the STACOM LV segmentation challenge against the provided gold-standard myocardium segmentation, obtaining a Dice overlap of $0.849 \pm 0.036$ and mean surface distance of $0.274 \pm 0.083$ mm, while simultaneously estimating the myocardial area with mean absolute difference error of $205\pm198$ mm$^2$.

cs.CV↗
arXiv2018

Scalable Simple Linear Iterative Clustering (SSLIC) Using a Generic and Parallel Approach

Superpixel algorithms have proven to be a useful initial step for segmentation and subsequent processing of images, reducing computational complexity by replacing the use of expensive per-pixel primitives with a higher-level abstraction, superpixels. They have been successfully applied both in the context of traditional image analysis and deep learning based approaches. In this work, we present a generalized implementation of the simple linear iterative clustering (SLIC) superpixel algorithm that has been generalized for n-dimensional scalar and multi-channel images. Additionally, the standard iterative implementation is replaced by a parallel, multi-threaded one. We describe the implementation details and analyze its scalability using a strong scaling formulation. Quantitative evaluation is performed using a 3D image, the Visible Human cryosection dataset, and a 2D image from the same dataset. Results show good scalability with runtime gains even when using a large number of threads that exceeds the physical number of available cores (hyperthreading).

cs.CV↗