Say My Name: a Model's Bias Discovery Framework

In the last few years, due to the broad applicability of deep learning to downstream tasks and end-to-end training capabilities, increasingly more concerns about potential biases to specific, non-representative patterns have been raised. Many works focusing on unsupervised debiasing usually leverage the tendency of deep models to learn ``easier'' samples, for example by clustering the latent space to obtain bias pseudo-labels. However, the interpretation of such pseudo-labels is not trivial, especially for a non-expert end user, as it does not provide semantic information about the bias features. To address this issue, we introduce ``Say My Name'' (SaMyNa), the first tool to identify biases within deep models semantically. Unlike existing methods, our approach focuses on biases learned by the model. Our text-based pipeline enhances explainability and supports debiasing efforts: applicable during either training or post-hoc validation, our method can disentangle task-related information and proposes itself as a tool to analyze biases. Evaluation on traditional benchmarks demonstrates its effectiveness in detecting biases and even disclaiming them, showcasing its broad applicability for model diagnosis.

Anatomical Foundation Models for Brain MRIs

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for pretraining DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information with a weakly contrastive learning approach and ii.) achieves state-of-the-art performances in many different downstream tasks. To validate our approach we consider 12 different downstream tasks for diagnosis classification, and prediction of 10 different clinical assessment scores.

Unsupervised Contrastive Analysis for Salient Pattern Detection using Conditional Diffusion Models

Contrastive Analysis (CA) regards the problem of identifying patterns in images that allow distinguishing between a background (BG) dataset (i.e. healthy subjects) and a target (TG) dataset (i.e. unhealthy subjects). Recent works on this topic rely on variational autoencoders (VAE) or contrastive learning strategies to learn the patterns that separate TG samples from BG samples in a supervised manner. However, the dependency on target (unhealthy) samples can be challenging in medical scenarios due to their limited availability. Also, the blurred reconstructions of VAEs lack utility and interpretability. In this work, we redefine the CA task by employing a self-supervised contrastive encoder to learn a latent representation encoding only common patterns from input images, using samples exclusively from the BG dataset during training, and approximating the distribution of the target patterns by leveraging data augmentation techniques. Subsequently, we exploit state-of-the-art generative methods, i.e. diffusion models, conditioned on the learned latent representation to produce a realistic (healthy) version of the input image encoding solely the common patterns. Thorough validation on a facial image dataset and experiments across three brain MRI datasets demonstrate that conditioning the generative process of state-of-the-art generative methods with the latent representation from our self-supervised contrastive encoder yields improvements in the generated image quality and in the accuracy of image classification. The code is available at https://github.com/CristianoPatricio/unsupervised-contrastive-cond-diff.

Multi-target stain normalization for histology slides

Traditional staining normalization approaches, e.g. Macenko, typically rely on the choice of a single representative reference image, which may not adequately account for the diverse staining patterns of datasets collected in practical scenarios. In this study, we introduce a novel approach that leverages multiple reference images to enhance robustness against stain variation. Our method is parameter-free and can be adopted in existing computational pathology pipelines with no significant changes. We evaluate the effectiveness of our method through experiments using a deep-learning pipeline for automatic nuclei segmentation on colorectal images. Our results show that by leveraging multiple reference images, better results can be achieved when generalizing to external data, where the staining can widely differ from the training set.

AI-Assisted Diagnosis for Covid-19 CXR Screening: From Data Collection to Clinical Validation

In this paper, we present the major results from the Covid Radiographic imaging System based on AI (Co.R.S.A.) project, which took place in Italy. This project aims to develop a state-of-the-art AI-based system for diagnosing Covid-19 pneumonia from Chest X-ray (CXR) images. The contributions of this work are manyfold: the release of the public CORDA dataset, a deep learning pipeline for Covid-19 detection, and the clinical validation of the developed solution by expert radiologists. The proposed detection model is based on a two-step approach that, paired with state-of-the-art debiasing, provides reliable results. Most importantly, our investigation includes the actual usage of the diagnosis aid tool by radiologists, allowing us to assess the real benefits in terms of accuracy and time efficiency. Project homepage: https://corsa.di.unito.it/

Detection of subclinical atherosclerosis by image-based deep learning on chest x-ray

Aims. To develop a deep-learning based system for recognition of subclinical atherosclerosis on a plain frontal chest x-ray. Methods and Results. A deep-learning algorithm to predict coronary artery calcium (CAC) score (the AI-CAC model) was developed on 460 chest x-ray (80% training cohort, 20% internal validation cohort) of primary prevention patients (58.4% male, median age 63 [51-74] years) with available paired chest x-ray and chest computed tomography (CT) indicated for any clinical reason and performed within 3 months. The CAC score calculated on chest CT was used as ground truth. The model was validated on an temporally-independent cohort of 90 patients from the same institution (external validation). The diagnostic accuracy of the AI-CAC model assessed by the area under the curve (AUC) was the primary outcome. Overall, median AI-CAC score was 35 (0-388) and 28.9% patients had no AI-CAC. AUC of the AI-CAC model to identify a CAC>0 was 0.90 in the internal validation cohort and 0.77 in the external validation cohort. Sensitivity was consistently above 92% in both cohorts. In the overall cohort (n=540), among patients with AI-CAC=0, a single ASCVD event occurred, after 4.3 years. Patients with AI-CAC>0 had significantly higher Kaplan Meier estimates for ASCVD events (13.5% vs. 3.4%, log-rank=0.013). Conclusion. The AI-CAC model seems to accurately detect subclinical atherosclerosis on chest x-ray with elevated sensitivity, and to predict ASCVD events with elevated negative predictive value. Adoption of the AI-CAC model to refine CV risk stratification or as an opportunistic screening tool requires prospective evaluation.

Contrastive learning for regression in multi-site brain age prediction

Building accurate Deep Learning (DL) models for brain age prediction is a very relevant topic in neuroimaging, as it could help better understand neurodegenerative disorders and find new biomarkers. To estimate accurate and generalizable models, large datasets have been collected, which are often multi-site and multi-scanner. This large heterogeneity negatively affects the generalization performance of DL models since they are prone to overfit site-related noise. Recently, contrastive learning approaches have been shown to be more robust against noise in data or labels. For this reason, we propose a novel contrastive learning regression loss for robust brain age prediction using MRI scans. Our method achieves state-of-the-art performance on the OpenBHB challenge, yielding the best generalization capability and robustness to site-related noise.

Unbiased Supervised Contrastive Learning

Many datasets are biased, namely they contain easy-to-learn features that are highly correlated with the target class only in the dataset but not in the true underlying distribution of the data. For this reason, learning unbiased models from biased data has become a very relevant research topic in the last years. In this work, we tackle the problem of learning representations that are robust to biases. We first present a margin-based theoretical framework that allows us to clarify why recent contrastive losses (InfoNCE, SupCon, etc.) can fail when dealing with biased data. Based on that, we derive a novel formulation of the supervised contrastive loss (epsilon-SupInfoNCE), providing more accurate control of the minimal distance between positive and negative samples. Furthermore, thanks to our theoretical framework, we also propose FairKL, a new debiasing regularization loss, that works well even with extremely biased data. We validate the proposed losses on standard vision datasets including CIFAR10, CIFAR100, and ImageNet, and we assess the debiasing capability of FairKL with epsilon-SupInfoNCE, reaching state-of-the-art performance on a number of biased datasets, including real instances of biases in the wild.

Rethinking Positive Sampling for Contrastive Learning with Kernel

Data augmentation is a crucial component in unsupervised contrastive learning (CL). It determines how positive samples are defined and, ultimately, the quality of the representation. While efficient augmentations have been found for standard vision datasets, such as ImageNet, it is still an open problem in other applications, such as medical imaging, or in datasets with easy-to-learn but irrelevant imaging features. In this work, we propose a new way to define positive samples using kernel theory along with a novel loss called decoupled uniformity. We propose to integrate prior information, learnt from generative models or given as auxiliary attributes, into contrastive learning, to make it less dependent on data augmentation. We draw a connection between contrastive learning and the conditional mean embedding theory to derive tight bounds on the downstream classification loss. In an unsupervised setting, we empirically demonstrate that CL benefits from generative models, such as VAE and GAN, to less rely on data augmentations. We validate our framework on vision datasets including CIFAR10, CIFAR100, STL10 and ImageNet100 and a brain MRI dataset. In the weakly supervised setting, we demonstrate that our formulation provides state-of-the-art results.

Unsupervised Learning of Unbiased Visual Representations

Deep neural networks are known for their inability to learn robust representations when biases exist in the dataset. This results in a poor generalization to unbiased datasets, as the predictions strongly rely on peripheral and confounding factors, which are erroneously learned by the network. Many existing works deal with this issue by either employing an explicit supervision on the bias attributes, or assuming prior knowledge about the bias. In this work we study this problem in a more difficult scenario, in which no explicit annotation about the bias is available, and without any prior knowledge about its nature. We propose a fully unsupervised debiasing framework, consisting of three steps: first, we exploit the natural preference for learning malignant biases, obtaining a bias-capturing model; then, we perform a pseudo-labelling step to obtain bias labels; finally we employ state-of-the-art supervised debiasing techniques to obtain an unbiased model. We also propose a theoretical framework to assess the biasness of a model, and provide a detailed analysis on how biases affect the training of neural networks. We perform experiments on synthetic and real-world datasets, showing that our method achieves state-of-the-art performance in a variety of settings, sometimes even higher than fully supervised debiasing approaches.