Tammy Riklin Raviv

Tal Ben-Haim, Ron Moshe Sofer, Gal Ben-Arie et al.

We present a novel deep learning approach to categorical segmentation of lung CTs of COVID-19 patients. Specifically, we partition the scans into healthy lung tissues, non-lung regions, and two different, yet visually similar, pathological lung tissues, namely, ground-glass opacity and consolidation. This is accomplished via a unique, end-to-end hierarchical network architecture and ensemble learning, which contribute to the segmentation and provide a measure for segmentation uncertainty. The proposed framework achieves competitive results and outstanding generalization capabilities for three COVID-19 datasets. Our method is ranked second in a public Kaggle competition for COVID-19 CT images segmentation. Moreover, segmentation uncertainty regions are shown to correspond to the disagreements between the manual annotations of two different radiologists. Finally, preliminary promising correspondence results are shown for our private dataset when comparing the patients' COVID-19 severity scores (based on clinical measures), and the segmented lung pathologies. Code and data are available at our repository: https://github.com/talbenha/covid-seg

Shira Karmi, Galia Avidan, Tammy Riklin Raviv

Understanding how large-scale brain networks represent visual categories is fundamental to linking perception and cortical organization. Using high-resolution 7T fMRI from the Natural Scenes Dataset, we construct parcel-level functional graphs and train a signed Graph Neural Network that models both positive and negative interactions, with a sparse edge mask and class-specific saliency. The model accurately decodes category-specific functional connectivity states (sports, food, vehicles) and reveals reproducible, biologically meaningful subnetworks along the ventral and dorsal visual pathways. This framework bridges machine learning and neuroscience by extending voxel-level category selectivity to a connectivity-based representation of visual processing.

Daniel Duenias, Brennan Nichyporuk, Tal Arbel et al.

The integration of diverse clinical modalities such as medical imaging and the tabular data extracted from patients' Electronic Health Records (EHRs) is a crucial aspect of modern healthcare. Integrative analysis of multiple sources can provide a comprehensive understanding of the clinical condition of a patient, improving diagnosis and treatment decision. Deep Neural Networks (DNNs) consistently demonstrate outstanding performance in a wide range of multimodal tasks in the medical domain. However, the complex endeavor of effectively merging medical imaging with clinical, demographic and genetic information represented as numerical tabular data remains a highly active and ongoing research pursuit. We present a novel framework based on hypernetworks to fuse clinical imaging and tabular data by conditioning the image processing on the EHR's values and measurements. This approach aims to leverage the complementary information present in these modalities to enhance the accuracy of various medical applications. We demonstrate the strength and generality of our method on two different brain Magnetic Resonance Imaging (MRI) analysis tasks, namely, brain age prediction conditioned by subject's sex and multi-class Alzheimer's Disease (AD) classification conditioned by tabular data. We show that our framework outperforms both single-modality models and state-of-the-art MRI tabular data fusion methods. A link to our code can be found at https://github.com/daniel4725/HyperFusion

Doron Serebro, Tammy Riklin-Raviv

Medical imaging datasets often vary due to differences in acquisition protocols, patient demographics, and imaging devices. These variations in data distribution, known as domain shift, present a significant challenge in adapting imaging analysis models for practical healthcare applications. Most current domain adaptation (DA) approaches aim either to align the distributions between the source and target domains or to learn an invariant feature space that generalizes well across all domains. However, both strategies require access to a sufficient number of examples, though not necessarily annotated, from the test domain during training. This limitation hinders the widespread deployment of models in clinical settings, where target domain data may only be accessible in real time. In this work, we introduce HyDA, a novel hypernetwork framework that leverages domain characteristics rather than suppressing them, enabling dynamic adaptation at inference time. Specifically, HyDA learns implicit domain representations and uses them to adjust model parameters on-the-fly, effectively interpolating to unseen domains. We validate HyDA on two clinically relevant applications - MRI brain age prediction and chest X-ray pathology classification - demonstrating its ability to generalize across tasks and modalities. Our code is available at TBD.

Tal Ben-Haim, Tammy Riklin Raviv

We present a novel graph neural network (GNN) approach for cell tracking in high-throughput microscopy videos. By modeling the entire time-lapse sequence as a direct graph where cell instances are represented by its nodes and their associations by its edges, we extract the entire set of cell trajectories by looking for the maximal paths in the graph. This is accomplished by several key contributions incorporated into an end-to-end deep learning framework. We exploit a deep metric learning algorithm to extract cell feature vectors that distinguish between instances of different biological cells and assemble same cell instances. We introduce a new GNN block type which enables a mutual update of node and edge feature vectors, thus facilitating the underlying message passing process. The message passing concept, whose extent is determined by the number of GNN blocks, is of fundamental importance as it enables the `flow' of information between nodes and edges much behind their neighbors in consecutive frames. Finally, we solve an edge classification problem and use the identified active edges to construct the cells' tracks and lineage trees. We demonstrate the strengths of the proposed cell tracking approach by applying it to 2D and 3D datasets of different cell types, imaging setups, and experimental conditions. We show that our framework outperforms current state-of-the-art methods on most of the evaluated datasets. The code is available at our repository: https://github.com/talbenha/cell-tracker-gnn.

Assaf Arbelle, Eliav Elul, Tammy Riklin Raviv

We introduce a novel Deep Learning framework, which quantitatively estimates image segmentation quality without the need for human inspection or labeling. We refer to this method as a Quality Assurance Network -- QANet. Specifically, given an image and a `proposed' corresponding segmentation, obtained by any method including manual annotation, the QANet solves a regression problem in order to estimate a predefined quality measure with respect to the unknown ground truth. The QANet is by no means yet another segmentation method. Instead, it performs a multi-level, multi-feature comparison of an image-segmentation pair based on a unique network architecture, called the RibCage. To demonstrate the strength of the QANet, we addressed the evaluation of instance segmentation using two different datasets from different domains, namely, high throughput live cell microscopy images from the Cell Segmentation Benchmark and natural images of plants from the Leaf Segmentation Challenge. While synthesized segmentations were used to train the QANet, it was tested on segmentations obtained by publicly available methods that participated in the different challenges. We show that the QANet accurately estimates the scores of the evaluated segmentations with respect to the hidden ground truth, as published by the challenges' organizers. The code is available at: TBD.

Assaf Arbelle, Tammy Riklin Raviv

Live cell microscopy sequences exhibit complex spatial structures and complicated temporal behaviour, making their analysis a challenging task. Considering cell segmentation problem, which plays a significant role in the analysis, the spatial properties of the data can be captured using Convolutional Neural Networks (CNNs). Recent approaches show promising segmentation results using convolutional encoder-decoders such as the U-Net. Nevertheless, these methods are limited by their inability to incorporate temporal information, that can facilitate segmentation of individual touching cells or of cells that are partially visible. In order to exploit cell dynamics we propose a novel segmentation architecture which integrates Convolutional Long Short Term Memory (C-LSTM) with the U-Net. The network's unique architecture allows it to capture multi-scale, compact, spatio-temporal encoding in the C-LSTMs memory units. The method was evaluated on the Cell Tracking Challenge and achieved state-of-the-art results (1st on Fluo-N2DH-SIM+ and 2nd on DIC-C2DL-HeLa datasets) The code is freely available at: https://github.com/arbellea/LSTM-UNet.git

Assaf Arbelle, Tammy Riklin Raviv

We present a novel method for cell segmentation in microscopy images which is inspired by the Generative Adversarial Neural Network (GAN) approach. Our framework is built on a pair of two competitive artificial neural networks, with a unique architecture, termed Rib Cage, which are trained simultaneously and together define a min-max game resulting in an accurate segmentation of a given image. Our approach has two main strengths, similar to the GAN, the method does not require a formulation of a loss function for the optimization process. This allows training on a limited amount of annotated data in a weakly supervised manner. Promising segmentation results on real fluorescent microscopy data are presented. The code is freely available at: https://github.com/arbellea/DeepCellSeg.git

Itay Benou, Tammy Riklin-Raviv

Modern deep neural networks have now reached human-level performance across a variety of tasks. However, unlike humans they lack the ability to explain their decisions by showing where and telling what concepts guided them. In this work, we present a unified framework for transforming any vision neural network into a spatially and conceptually interpretable model. We introduce a spatially-aware concept bottleneck layer that projects "black-box" features of pre-trained backbone models into interpretable concept maps, without requiring human labels. By training a classification layer over this bottleneck, we obtain a self-explaining model that articulates which concepts most influenced its prediction, along with heatmaps that ground them in the input image. Accordingly, we name this method "Spatially-Aware and Label-Free Concept Bottleneck Model" (SALF-CBM). Our results show that the proposed SALF-CBM: (1) Outperforms non-spatial CBM methods, as well as the original backbone, on a variety of classification tasks; (2) Produces high-quality spatial explanations, outperforming widely used heatmap-based methods on a zero-shot segmentation task; (3) Facilitates model exploration and debugging, enabling users to query specific image regions and refine the model's decisions by locally editing its concept maps.

Itzik Waizman, Yakov Gusakov, Itay Benou et al.

White matter tractography is an advanced neuroimaging technique that reconstructs the 3D white matter pathways of the brain from diffusion MRI data. It can be framed as a pathfinding problem aiming to infer neural fiber trajectories from noisy and ambiguous measurements, facing challenges such as crossing, merging, and fanning white-matter configurations. In this paper, we propose a novel tractography method that leverages Transformers to model the sequential nature of white matter streamlines, enabling the prediction of fiber directions by integrating both the trajectory context and current diffusion MRI measurements. To incorporate spatial information, we utilize CNNs that extract microstructural features from local neighborhoods around each voxel. By combining these complementary sources of information, our approach improves the precision and completeness of neural pathway mapping compared to traditional tractography models. We evaluate our method with the Tractometer toolkit, achieving competitive performance against state-of-the-art approaches, and present qualitative results on the TractoInferno dataset, demonstrating strong generalization to real-world data.

Yael Ben-Guigui, Jacob Goldberger, Tammy Riklin-Raviv

The pressing need to reduce the capacity of deep neural networks has stimulated the development of network dilution methods and their analysis. While the ability of $L_1$ and $L_0$ regularization to encourage sparsity is often mentioned, $L_2$ regularization is seldom discussed in this context. We present a novel framework for weight pruning by sampling from a probability function that favors the zeroing of smaller weights. In addition, we examine the contribution of $L_1$ and $L_2$ regularization to the dynamics of node pruning while optimizing for weight pruning. We then demonstrate the effectiveness of the proposed stochastic framework when used together with a weight decay regularizer on popular classification models in removing 50% of the nodes in an MLP for MNIST classification, 60% of the filters in VGG-16 for CIFAR10 classification, and on medical image models in removing 60% of the channels in a U-Net for instance segmentation and 50% of the channels in CNN model for COVID-19 detection. For these node-pruned networks, we also present competitive weight pruning results that are only slightly less accurate than the original, dense networks.

Mor Avi-Aharon, Assaf Arbelle, Tammy Riklin Raviv

We present the DeepHist - a novel Deep Learning framework for augmenting a network by histogram layers and demonstrate its strength by addressing image-to-image translation problems. Specifically, given an input image and a reference color distribution we aim to generate an output image with the structural appearance (content) of the input (source) yet with the colors of the reference. The key idea is a new technique for a differentiable construction of joint and color histograms of the output images. We further define a color distribution loss based on the Earth Mover's Distance between the output's and the reference's color histograms and a Mutual Information loss based on the joint histograms of the source and the output images. Promising results are shown for the tasks of color transfer, image colorization and edges $\rightarrow$ photo, where the color distribution of the output image is controlled. Comparison to Pix2Pix and CyclyGANs are shown.

Mor Avi-Aharon, Assaf Arbelle, Tammy Riklin Raviv

We present the Hue-Net - a novel Deep Learning framework for Intensity-based Image-to-Image Translation. The key idea is a new technique termed network augmentation which allows a differentiable construction of intensity histograms from images. We further introduce differentiable representations of (1D) cyclic and joint (2D) histograms and use them for defining loss functions based on cyclic Earth Mover's Distance (EMD) and Mutual Information (MI). While the Hue-Net can be applied to several image-to-image translation tasks, we choose to demonstrate its strength on color transfer problems, where the aim is to paint a source image with the colors of a different target image. Note that the desired output image does not exist and therefore cannot be used for supervised pixel-to-pixel learning. This is accomplished by using the HSV color-space and defining an intensity-based loss that is built on the EMD between the cyclic hue histograms of the output and the target images. To enforce color-free similarity between the source and the output images, we define a semantic-based loss by a differentiable approximation of the MI of these images. The incorporation of histogram loss functions in addition to an adversarial loss enables the construction of semantically meaningful and realistic images. Promising results are presented for different datasets.

Or Shwartzman, Harel Gazit, Ilan Shelef et al.

The problem of inter-rater variability is often discussed in the context of manual labeling of medical images. The emergence of data-driven approaches such as Deep Neural Networks (DNNs) brought this issue of raters' disagreement to the front-stage. In this paper, we highlight the issue of inter-rater bias as opposed to random inter-observer variability and demonstrate its influence on DNN training, leading to different segmentation results for the same input images. In fact, lower overlap scores are obtained between the outputs of a DNN trained on annotations of one rater and tested on another. Moreover, we demonstrate that inter-rater bias in the training examples is amplified and becomes more consistent, considering the segmentation predictions of the DNNs' test data. We support our findings by showing that a classifier-DNN trained to distinguish between raters based on their manual annotations performs better when the automatic segmentation predictions rather than the actual raters' annotations were tested. For this study, we used two different datasets: the ISBI 2015 Multiple Sclerosis (MS) challenge dataset, including MRI scans each with annotations provided by two raters with different levels of expertise; and Intracerebral Hemorrhage (ICH) CT scans with manual and semi-manual segmentations. The results obtained allow us to underline a worrisome clinical implication of a DNN bias induced by an inter-rater bias during training. Specifically, we present a consistent underestimate of MS-lesion loads when calculated from segmentation predictions of a DNN trained on input provided by the less experienced rater. In the same manner, the differences in ICH volumes calculated based on outputs of identical DNNs, each trained on annotations from a different source are more consistent and larger than the differences in volumes between the manual and semi-manual annotations used for training.

Itay Benou, Ronel Veksler, Alon Friedman et al.

We present the concept of fiber-flux density for locally quantifying white matter (WM) fiber bundles. By combining scalar diffusivity measures (e.g., fractional anisotropy) with fiber-flux measurements, we define new local descriptors called Fiber-Flux Diffusion Density (FFDD) vectors. Applying each descriptor throughout fiber bundles allows along-tract coupling of a specific diffusion measure with geometrical properties, such as fiber orientation and coherence. A key step in the proposed framework is the construction of an FFDD dissimilarity measure for sub-voxel alignment of fiber bundles, based on the fast marching method (FMM). The obtained aligned WM tract-profiles enable meaningful inter-subject comparisons and group-wise statistical analysis. We demonstrate our method using two different datasets of contact sports players. Along-tract pairwise comparison as well as group-wise analysis, with respect to non-player healthy controls, reveal significant and spatially-consistent FFDD anomalies. Comparing our method with along-tract FA analysis shows improved sensitivity to subtle structural anomalies in football players over standard FA measurements.