We investigate image segmentation of cells under the lens of scalar fields. Our goal is to learn a continuous scalar field on image domains such that its segmentation produces robust instances for cells present in images. This field is a function parameterized by the trained network, and its segmentation is realized by the watershed method. The fields we experiment with are solutions to the Poisson partial differential equation and a diffusion mimicking the steady-state solution of the heat equation. These solutions are obtained by minimizing just the field residuals, no regularization is needed, providing a robust regression capable of diminishing the adverse impacts of outliers in the training data and allowing for sharp cell boundaries. A single tensor is all that is needed to train a \unet\ thus simplifying implementation, lowering training and inference times, hence reducing energy consumption, and requiring a small memory footprint, all attractive features in edge computing. We present competitive results on public datasets from the literature and show that our novel, simple yet geometrically insightful approach can achieve excellent cell segmentation results.

Age-related macular degeneration (AMD) is one of the leading causes of irreversible vision impairment in people over the age of 60. This research focuses on semantic segmentation for AMD lesion detection in RGB fundus images, a non-invasive and cost-effective imaging technique. The results of the ADAM challenge - the most comprehensive AMD detection from RGB fundus images research competition and open dataset to date - serve as a benchmark for our evaluation. Taking the U-Net connectivity as a base of our framework, we evaluate and compare several approaches to improve the segmentation model's architecture and training pipeline, including pre-processing techniques, encoder (backbone) deep network types of varying complexity, and specialized loss functions to mitigate class imbalances on image and pixel levels. The main outcome of this research is the final configuration of the AMD detection framework, which outperforms all the prior ADAM challenge submissions on the multi-class segmentation of different AMD lesion types in non-invasive RGB fundus images. The source code used to conduct the experiments presented in this paper is made freely available.

Counterfactual explanations (CFs) offer human-centric insights into machine learning predictions by highlighting minimal changes required to alter an outcome. Therefore, CFs can be used as (i) interventions for abnormality prevention and (ii) augmented data for training robust models. In this work, we explore large language models (LLMs), specifically GPT-4o-mini, for generating CFs in a zero-shot and three-shot setting. We evaluate our approach on two datasets: the AI-Readi flagship dataset for stress prediction and a public dataset for heart disease detection. Compared to traditional methods such as DiCE, CFNOW, and NICE, our few-shot LLM-based approach achieves high plausibility (up to 99%), strong validity (up to 0.99), and competitive sparsity. Moreover, using LLM-generated CFs as augmented samples improves downstream classifier performance (an average accuracy gain of 5%), especially in low-data regimes. This demonstrates the potential of prompt-based generative techniques to enhance explainability and robustness in clinical and physiological prediction tasks. Code base: github.com/shovito66/SenseCF.

Prompting and Multiple Choices Questions (MCQ) have become the preferred approach to assess the capabilities of Large Language Models (LLMs), due to their ease of manipulation and evaluation. Such experimental appraisals have pointed toward the LLMs' apparent ability to perform causal reasoning or to grasp uncertainty. In this paper, we investigate whether these abilities are measurable outside of tailored prompting and MCQ by reformulating these issues as direct text completion - the foundation of LLMs. To achieve this goal, we define scenarios with multiple possible outcomes and we compare the prediction made by the LLM through prompting (their Stated Answer) to the probability distributions they compute over these outcomes during next token prediction (their Revealed Belief). Our findings suggest that the Revealed Belief of LLMs significantly differs from their Stated Answer and hint at multiple biases and misrepresentations that their beliefs may yield in many scenarios and outcomes. As text completion is at the core of LLMs, these results suggest that common evaluation methods may only provide a partial picture and that more research is needed to assess the extent and nature of their capabilities.

The prevailing deep learning-based methods of predicting cardiac segmentation involve reconstructed magnetic resonance (MR) images. The heavy dependency of segmentation approaches on image quality significantly limits the acceleration rate in fast MR reconstruction. Moreover, the practice of treating reconstruction and segmentation as separate sequential processes leads to artifact generation and information loss in the intermediate stage. These issues pose a great risk to achieving high-quality outcomes. To leverage the redundant k-space information overlooked in this dual-step pipeline, we introduce a novel approach to directly deriving segmentations from sparse k-space samples using a transformer (DiSK). DiSK operates by globally extracting latent features from 2D+time k-space data with attention blocks and subsequently predicting the segmentation label of query points. We evaluate our model under various acceleration factors (ranging from 4 to 64) and compare against two image-based segmentation baselines. Our model consistently outperforms the baselines in Dice and Hausdorff distances across foreground classes for all presented sampling rates.

Blood vessel segmentation in medical imaging is one of the essential steps for vascular disease diagnosis and interventional planning in a broad spectrum of clinical scenarios in image-based medicine and interventional medicine. Unfortunately, manual annotation of the vessel masks is challenging and resource-intensive due to subtle branches and complex structures. To overcome this issue, this paper presents a self-supervised vessel segmentation method, dubbed the contrastive diffusion adversarial representation learning (C-DARL) model. Our model is composed of a diffusion module and a generation module that learns the distribution of multi-domain blood vessel data by generating synthetic vessel images from diffusion latent. Moreover, we employ contrastive learning through a mask-based contrastive loss so that the model can learn more realistic vessel representations. To validate the efficacy, C-DARL is trained using various vessel datasets, including coronary angiograms, abdominal digital subtraction angiograms, and retinal imaging. Experimental results confirm that our model achieves performance improvement over baseline methods with noise robustness, suggesting the effectiveness of C-DARL for vessel segmentation.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

To increase the adoption of counterfactual explanations in practice, several criteria that these should adhere to have been put forward in the literature. We propose counterfactual explanations using optimization with constraint learning (CE-OCL), a generic and flexible approach that addresses all these criteria and allows room for further extensions. Specifically, we discuss how we can leverage an optimization with constraint learning framework for the generation of counterfactual explanations, and how components of this framework readily map to the criteria. We also propose two novel modeling approaches to address data manifold closeness and diversity, which are two key criteria for practical counterfactual explanations. We test CE-OCL on several datasets and present our results in a case study. Compared against the current state-of-the-art methods, CE-OCL allows for more flexibility and has an overall superior performance in terms of several evaluation metrics proposed in related work.

Deep learning methods are the de-facto solutions to a multitude of medical image analysis tasks. Cardiac MRI segmentation is one such application which, like many others, requires a large number of annotated data so a trained network can generalize well. Unfortunately, the process of having a large number of manually curated images by medical experts is both slow and utterly expensive. In this paper, we set out to explore whether expert knowledge is a strict requirement for the creation of annotated datasets that machine learning can successfully train on. To do so, we gauged the performance of three segmentation models, namely U-Net, Attention U-Net, and ENet, trained with different loss functions on expert and non-expert groundtruth for cardiac cine-MRI segmentation. Evaluation was done with classic segmentation metrics (Dice index and Hausdorff distance) as well as clinical measurements, such as the ventricular ejection fractions and the myocardial mass. Results reveal that generalization performances of a segmentation neural network trained on non-expert groundtruth data is, to all practical purposes, as good as on expert groundtruth data, in particular when the non-expert gets a decent level of training, highlighting an opportunity for the efficient and cheap creation of annotations for cardiac datasets.

-- Translation of fully automated deep learning based medical image segmentation technologies to clinical workflows face two main algorithmic challenges. The first, is the collection and archival of large quantities of manually annotated ground truth data for both training and validation. The second is the relative inability of the majority of deep learning based segmentation techniques to alert physicians to a likely segmentation failure. Here we propose a novel algorithm, named'Eigenrank' which addresses both of these challenges. Eigenrank can select for manual labeling, a subset of medical images from a large database, such that a U-Net trained on this subset is superior to one trained on a randomly selected subset of the same size. Eigenrank can also be used to pick out, cases in a large database, where deep learning segmentation will fail. We present our algorithm, followed by results and a discussion of how Eigenrank exploits the V on Neumann information to perform both data subset selection and failure prediction for medical image segmentation using deep learning. I. INTRODUCTION A. Significance Deep learning methods have become the mainstay of fully automatic medical image segmentation. These methods play a key role in the development of quantitative imaging biomarkers for a number of pathologies. However, training and deploying deep learning segmentation in practice is beset by a number of challenges. Failure Prediction (FP) - the ability to predict on which cases a deep learning based segmentation model will fail. Both problems are significant in medical image segmentation, more than natural image segmentation. This is because, availability of expert annotated data for training medical image segmentation models is severely constrained.