Classification of Keratitis from Eye Corneal Photographs using Deep Learning

Keratitis is an inflammatory corneal condition responsible for 10% of visual impairment in low- and middle-income countries (LMICs), with bacteria, fungi, or amoeba as the most common infection etiologies. While an accurate and timely diagnosis is crucial for the selected treatment and the patients' sight outcomes, due to the high cost and limited availability of laboratory diagnostics in LMICs, diagnosis is often made by clinical observation alone, despite its lower accuracy. In this study, we investigate and compare different deep learning approaches to diagnose the source of infection: 1) three separate binary models for infection type predictions; 2) a multitask model with a shared backbone and three parallel classification layers (Multitask V1); and, 3) a multitask model with a shared backbone and a multi-head classification layer (Multitask V2). We used a private Brazilian cornea dataset to conduct the empirical evaluation. We achieved the best results with Multitask V2, with an area under the receiver operating characteristic curve (AUROC) confidence intervals of 0.7413-0.7740 (bacteria), 0.8395-0.8725 (fungi), and 0.9448-0.9616 (amoeba). A statistical analysis of the impact of patient features on models' performance revealed that sex significantly affects amoeba infection prediction, and age seems to affect fungi and bacteria predictions.

MST-KD: Multiple Specialized Teachers Knowledge Distillation for Fair Face Recognition

As in school, one teacher to cover all subjects is insufficient to distill equally robust information to a student. Hence, each subject is taught by a highly specialised teacher. Following a similar philosophy, we propose a multiple specialized teacher framework to distill knowledge to a student network. In our approach, directed at face recognition use cases, we train four teachers on one specific ethnicity, leading to four highly specialized and biased teachers. Our strategy learns a project of these four teachers into a common space and distill that information to a student network. Our results highlighted increased performance and reduced bias for all our experiments. In addition, we further show that having biased/specialized teachers is crucial by showing that our approach achieves better results than when knowledge is distilled from four teachers trained on balanced datasets. Our approach represents a step forward to the understanding of the importance of ethnicity-specific features.

Evaluating the Impact of Pulse Oximetry Bias in Machine Learning under Counterfactual Thinking

Algorithmic bias in healthcare mirrors existing data biases. However, the factors driving unfairness are not always known. Medical devices capture significant amounts of data but are prone to errors; for instance, pulse oximeters overestimate the arterial oxygen saturation of darker-skinned individuals, leading to worse outcomes. The impact of this bias in machine learning (ML) models remains unclear. This study addresses the technical challenges of quantifying the impact of medical device bias in downstream ML. Our experiments compare a "perfect world", without pulse oximetry bias, using SaO2 (blood-gas), to the "actual world", with biased measurements, using SpO2 (pulse oximetry). Under this counterfactual design, two models are trained with identical data, features, and settings, except for the method of measuring oxygen saturation: models using SaO2 are a "control" and models using SpO2 a "treatment". The blood-gas oximetry linked dataset was a suitable test-bed, containing 163,396 nearly-simultaneous SpO2 - SaO2 paired measurements, aligned with a wide array of clinical features and outcomes. We studied three classification tasks: in-hospital mortality, respiratory SOFA score in the next 24 hours, and SOFA score increase by two points. Models using SaO2 instead of SpO2 generally showed better performance. Patients with overestimation of O2 by pulse oximetry of > 3% had significant decreases in mortality prediction recall, from 0.63 to 0.59, P < 0.001. This mirrors clinical processes where biased pulse oximetry readings provide clinicians with false reassurance of patients' oxygen levels. A similar degradation happened in ML models, with pulse oximetry biases leading to more false negatives in predicting adverse outcomes.

Learning Ordinality in Semantic Segmentation

Semantic segmentation consists of predicting a semantic label for each image pixel. Conventional deep learning models do not take advantage of ordinal relations that might exist in the domain at hand. For example, it is known that the pupil is inside the iris, and the lane markings are inside the road. Such domain knowledge can be employed as constraints to make the model more robust. The current literature on this topic has explored pixel-wise ordinal segmentation methods, which treat each pixel as an independent observation and promote ordinality in its representation. This paper proposes novel spatial ordinal segmentation methods, which take advantage of the structured image space by considering each pixel as an observation dependent on its neighborhood context to also promote ordinal spatial consistency. When evaluated with five biomedical datasets and multiple configurations of autonomous driving datasets, ordinal methods resulted in more ordinally-consistent models, with substantial improvements in ordinal metrics and some increase in the Dice coefficient. It was also shown that the incorporation of ordinal consistency results in models with better generalization abilities.

A Survey on Cell Nuclei Instance Segmentation and Classification: Leveraging Context and Attention

Manually annotating nuclei from the gigapixel Hematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs) is a laborious and costly task, meaning automated algorithms for cell nuclei instance segmentation and classification could alleviate the workload of pathologists and clinical researchers and at the same time facilitate the automatic extraction of clinically interpretable features. But due to high intra- and inter-class variability of nuclei morphological and chromatic features, as well as H&E-stains susceptibility to artefacts, state-of-the-art algorithms cannot correctly detect and classify instances with the necessary performance. In this work, we hypothesise context and attention inductive biases in artificial neural networks (ANNs) could increase the generalization of algorithms for cell nuclei instance segmentation and classification. We conduct a thorough survey on context and attention methods for cell nuclei instance segmentation and classification from H&E-stained microscopy imaging, while providing a comprehensive discussion of the challenges being tackled with context and attention. Besides, we illustrate some limitations of current approaches and present ideas for future research. As a case study, we extend both a general instance segmentation and classification method (Mask-RCNN) and a tailored cell nuclei instance segmentation and classification model (HoVer-Net) with context- and attention-based mechanisms, and do a comparative analysis on a multi-centre colon nuclei identification and counting dataset. Although pathologists rely on context at multiple levels while paying attention to specific Regions of Interest (RoIs) when analysing and annotating WSIs, our findings suggest translating that domain knowledge into algorithm design is no trivial task, but to fully exploit these mechanisms, the scientific understanding of these methods should be addressed.

Deep Learning-based Prediction of Breast Cancer Tumor and Immune Phenotypes from Histopathology

The interactions between tumor cells and the tumor microenvironment (TME) dictate therapeutic efficacy of radiation and many systemic therapies in breast cancer. However, to date, there is not a widely available method to reproducibly measure tumor and immune phenotypes for each patient's tumor. Given this unmet clinical need, we applied multiple instance learning (MIL) algorithms to assess activity of ten biologically relevant pathways from the hematoxylin and eosin (H&E) slide of primary breast tumors. We employed different feature extraction approaches and state-of-the-art model architectures. Using binary classification, our models attained area under the receiver operating characteristic (AUROC) scores above 0.70 for nearly all gene expression pathways and on some cases, exceeded 0.80. Attention maps suggest that our trained models recognize biologically relevant spatial patterns of cell sub-populations from H&E. These efforts represent a first step towards developing computational H&E biomarkers that reflect facets of the TME and hold promise for augmenting precision oncology.

Second Edition FRCSyn Challenge at CVPR 2024: Face Recognition Challenge in the Era of Synthetic Data

Synthetic data is gaining increasing relevance for training machine learning models. This is mainly motivated due to several factors such as the lack of real data and intra-class variability, time and errors produced in manual labeling, and in some cases privacy concerns, among others. This paper presents an overview of the 2nd edition of the Face Recognition Challenge in the Era of Synthetic Data (FRCSyn) organized at CVPR 2024. FRCSyn aims to investigate the use of synthetic data in face recognition to address current technological limitations, including data privacy concerns, demographic biases, generalization to novel scenarios, and performance constraints in challenging situations such as aging, pose variations, and occlusions. Unlike the 1st edition, in which synthetic data from DCFace and GANDiffFace methods was only allowed to train face recognition systems, in this 2nd edition we propose new sub-tasks that allow participants to explore novel face generative methods. The outcomes of the 2nd FRCSyn Challenge, along with the proposed experimental protocol and benchmarking contribute significantly to the application of synthetic data to face recognition.

Anonymizing medical case-based explanations through disentanglement

Case-based explanations are an intuitive method to gain insight into the decision-making process of deep learning models in clinical contexts. However, medical images cannot be shared as explanations due to privacy concerns. To address this problem, we propose a novel method for disentangling identity and medical characteristics of images and apply it to anonymize medical images. The disentanglement mechanism replaces some feature vectors in an image while ensuring that the remaining features are preserved, obtaining independent feature vectors that encode the images' identity and medical characteristics. We also propose a model to manufacture synthetic privacy-preserving identities to replace the original image's identity and achieve anonymization. The models are applied to medical and biometric datasets, demonstrating their capacity to generate realistic-looking anonymized images that preserve their original medical content. Additionally, the experiments show the network's inherent capacity to generate counterfactual images through the replacement of medical features.

Compressed Models Decompress Race Biases: What Quantized Models Forget for Fair Face Recognition

With the ever-growing complexity of deep learning models for face recognition, it becomes hard to deploy these systems in real life. Researchers have two options: 1) use smaller models; 2) compress their current models. Since the usage of smaller models might lead to concerning biases, compression gains relevance. However, compressing might be also responsible for an increase in the bias of the final model. We investigate the overall performance, the performance on each ethnicity subgroup and the racial bias of a State-of-the-Art quantization approach when used with synthetic and real data. This analysis provides a few more details on potential benefits of performing quantization with synthetic data, for instance, the reduction of biases on the majority of test scenarios. We tested five distinct architectures and three different training datasets. The models were evaluated on a fourth dataset which was collected to infer and compare the performance of face recognition models on different ethnicity.

Unveiling the Two-Faced Truth: Disentangling Morphed Identities for Face Morphing Detection

Morphing attacks keep threatening biometric systems, especially face recognition systems. Over time they have become simpler to perform and more realistic, as such, the usage of deep learning systems to detect these attacks has grown. At the same time, there is a constant concern regarding the lack of interpretability of deep learning models. Balancing performance and interpretability has been a difficult task for scientists. However, by leveraging domain information and proving some constraints, we have been able to develop IDistill, an interpretable method with state-of-the-art performance that provides information on both the identity separation on morph samples and their contribution to the final prediction. The domain information is learnt by an autoencoder and distilled to a classifier system in order to teach it to separate identity information. When compared to other methods in the literature it outperforms them in three out of five databases and is competitive in the remaining.