arXiv subjects

Robert Harb

Publications and source records attributed to Robert Harb.

4 recordsLinked to original sources

arXiv2025

From slides to AI-ready maps: Standardized multi-layer tissue maps as metadata for artificial intelligence in digital pathology

A Whole Slide Image (WSI) is a high-resolution digital image created by scanning an entire glass slide containing a biological specimen, such as tissue sections or cell samples, at multiple magnifications. These images are digitally viewable, analyzable, and shareable, and are widely used for Artificial Intelligence (AI) algorithm development. WSIs play an important role in pathology for disease diagnosis and oncology for cancer research, but are also applied in neurology, veterinary medicine, hematology, microbiology, dermatology, pharmacology, toxicology, immunology, and forensic science. When assembling cohorts for AI training or validation, it is essential to know the content of a WSI. However, no standard currently exists for this metadata, and such a selection has largely relied on manual inspection, which is not suitable for large collections with millions of objects. We propose a general framework to generate 2D index maps (tissue maps) that describe the morphological content of WSIs using common syntax and semantics to achieve interoperability between catalogs. The tissue maps are structured in three layers: source, tissue type, and pathological alterations. Each layer assigns WSI segments to specific classes, providing AI-ready metadata. We demonstrate the advantages of this standard by applying AI-based metadata extraction from WSIs to generate tissue maps and integrating them into a WSI archive. This integration enhances search capabilities within WSI archives, thereby facilitating the accelerated assembly of high-quality, balanced, and more targeted datasets for AI training, validation, and cancer research.

cs.CV↗

arXiv2023

Diffusion-based generation of Histopathological Whole Slide Images at a Gigapixel scale

We present a novel diffusion-based approach to generate synthetic histopathological Whole Slide Images (WSIs) at an unprecedented gigapixel scale. Synthetic WSIs have many potential applications: They can augment training datasets to enhance the performance of many computational pathology applications. They allow the creation of synthesized copies of datasets that can be shared without violating privacy regulations. Or they can facilitate learning representations of WSIs without requiring data annotations. Despite this variety of applications, no existing deep-learning-based method generates WSIs at their typically high resolutions. Mainly due to the high computational complexity. Therefore, we propose a novel coarse-to-fine sampling scheme to tackle image generation of high-resolution WSIs. In this scheme, we increase the resolution of an initial low-resolution image to a high-resolution WSI. Particularly, a diffusion model sequentially adds fine details to images and increases their resolution. In our experiments, we train our method with WSIs from the TCGA-BRCA dataset. Additionally to quantitative evaluations, we also performed a user study with pathologists. The study results suggest that our generated WSIs resemble the structure of real WSIs.

eess.IV↗

arXiv2021

InfoSeg: Unsupervised Semantic Image Segmentation with Mutual Information Maximization

We propose a novel method for unsupervised semantic image segmentation based on mutual information maximization between local and global high-level image features. The core idea of our work is to leverage recent progress in self-supervised image representation learning. Representation learning methods compute a single high-level feature capturing an entire image. In contrast, we compute multiple high-level features, each capturing image segments of one particular semantic class. To this end, we propose a novel two-step learning procedure comprising a segmentation and a mutual information maximization step. In the first step, we segment images based on local and global features. In the second step, we maximize the mutual information between local features and high-level features of their respective class. For training, we provide solely unlabeled images and start from random network initialization. For quantitative and qualitative evaluation, we use established benchmarks, and COCO-Persons, whereby we introduce the latter in this paper as a challenging novel benchmark. InfoSeg significantly outperforms the current state-of-the-art, e.g., we achieve a relative increase of 26% in the Pixel Accuracy metric on the COCO-Stuff dataset.

cs.CV↗

arXiv2018

Sound event detection using weakly-labeled semi-supervised data with GCRNNS, VAT and Self-Adaptive Label Refinement

In this paper, we present a gated convolutional recurrent neural network based approach to solve task 4, large-scale weakly labelled semi-supervised sound event detection in domestic environments, of the DCASE 2018 challenge. Gated linear units and a temporal attention layer are used to predict the onset and offset of sound events in 10s long audio clips. Whereby for training only weakly-labelled data is used. Virtual adversarial training is used for regularization, utilizing both labelled and unlabeled data. Furthermore, we introduce self-adaptive label refinement, a method which allows unsupervised adaption of our trained system to refine the accuracy of frame-level class predictions. The proposed system reaches an overall macro averaged event-based F-score of 34.6%, resulting in a relative improvement of 20.5% over the baseline system.

cs.SD↗