MMIST-ccRCC: A Real World Medical Dataset for the Development of Multi-Modal Systems

The acquisition of different data modalities can enhance our knowledge and understanding of various diseases, paving the way for a more personalized healthcare. Thus, medicine is progressively moving towards the generation of massive amounts of multi-modal data (\emph{e.g,} molecular, radiology, and histopathology). While this may seem like an ideal environment to capitalize data-centric machine learning approaches, most methods still focus on exploring a single or a pair of modalities due to a variety of reasons: i) lack of ready to use curated datasets; ii) difficulty in identifying the best multi-modal fusion strategy; and iii) missing modalities across patients. In this paper we introduce a real world multi-modal dataset called MMIST-CCRCC that comprises 2 radiology modalities (CT and MRI), histopathology, genomics, and clinical data from 618 patients with clear cell renal cell carcinoma (ccRCC). We provide single and multi-modal (early and late fusion) benchmarks in the task of 12-month survival prediction in the challenging scenario of one or more missing modalities for each patient, with missing rates that range from 26$\%$ for genomics data to more than 90$\%$ for MRI. We show that even with such severe missing rates the fusion of modalities leads to improvements in the survival forecasting. Additionally, incorporating a strategy to generate the latent representations of the missing modalities given the available ones further improves the performance, highlighting a potential complementarity across modalities. Our dataset and code are available here: https://multi-modal-ist.github.io/datasets/ccRCC

Key Patches Are All You Need: A Multiple Instance Learning Framework For Robust Medical Diagnosis

Deep learning models have revolutionized the field of medical image analysis, due to their outstanding performances. However, they are sensitive to spurious correlations, often taking advantage of dataset bias to improve results for in-domain data, but jeopardizing their generalization capabilities. In this paper, we propose to limit the amount of information these models use to reach the final classification, by using a multiple instance learning (MIL) framework. MIL forces the model to use only a (small) subset of patches in the image, identifying discriminative regions. This mimics the clinical procedures, where medical decisions are based on localized findings. We evaluate our framework on two medical applications: skin cancer diagnosis using dermoscopy and breast cancer diagnosis using mammography. Our results show that using only a subset of the patches does not compromise diagnostic performance for in-domain data, compared to the baseline approaches. However, our approach is more robust to shifts in patient demographics, while also providing more detailed explanations about which regions contributed to the decision. Code is available at: https://github.com/diogojpa99/MedicalMultiple-Instance-Learning.

Extending 3D body pose estimation for robotic-assistive therapies of autistic children

Robotic-assistive therapy has demonstrated very encouraging results for children with Autism. Accurate estimation of the child's pose is essential both for human-robot interaction and for therapy assessment purposes. Non-intrusive methods are the sole viable option since these children are sensitive to touch. While depth cameras have been used extensively, existing methods face two major limitations: (i) they are usually trained with adult-only data and do not correctly estimate a child's pose, and (ii) they fail in scenarios with a high number of occlusions. Therefore, our goal was to develop a 3D pose estimator for children, by adapting an existing state-of-the-art 3D body modelling method and incorporating a linear regression model to fine-tune one of its inputs, thereby correcting the pose of children's 3D meshes. In controlled settings, our method has an error below $0.3m$, which is considered acceptable for this kind of application and lower than current state-of-the-art methods. In real-world settings, the proposed model performs similarly to a Kinect depth camera and manages to successfully estimate the 3D body poses in a much higher number of frames.

XAI for Skin Cancer Detection with Prototypes and Non-Expert Supervision

Skin cancer detection through dermoscopy image analysis is a critical task. However, existing models used for this purpose often lack interpretability and reliability, raising the concern of physicians due to their black-box nature. In this paper, we propose a novel approach for the diagnosis of melanoma using an interpretable prototypical-part model. We introduce a guided supervision based on non-expert feedback through the incorporation of: 1) binary masks, obtained automatically using a segmentation network; and 2) user-refined prototypes. These two distinct information pathways aim to ensure that the learned prototypes correspond to relevant areas within the skin lesion, excluding confounding factors beyond its boundaries. Experimental results demonstrate that, even without expert supervision, our approach achieves superior performance and generalization compared to non-interpretable models.

Test-Time Selection for Robust Skin Lesion Analysis

Skin lesion analysis models are biased by artifacts placed during image acquisition, which influence model predictions despite carrying no clinical information. Solutions that address this problem by regularizing models to prevent learning those spurious features achieve only partial success, and existing test-time debiasing techniques are inappropriate for skin lesion analysis due to either making unrealistic assumptions on the distribution of test data or requiring laborious annotation from medical practitioners. We propose TTS (Test-Time Selection), a human-in-the-loop method that leverages positive (e.g., lesion area) and negative (e.g., artifacts) keypoints in test samples. TTS effectively steers models away from exploiting spurious artifact-related correlations without retraining, and with less annotation requirements. Our solution is robust to a varying availability of annotations, and different levels of bias. We showcase on the ISIC2019 dataset (for which we release a subset of annotated images) how our model could be deployed in the real-world for mitigating bias.

Even Small Correlation and Diversity Shifts Pose Dataset-Bias Issues

Distribution shifts are common in real-world datasets and can affect the performance and reliability of deep learning models. In this paper, we study two types of distribution shifts: diversity shifts, which occur when test samples exhibit patterns unseen during training, and correlation shifts, which occur when test data present a different correlation between seen invariant and spurious features. We propose an integrated protocol to analyze both types of shifts using datasets where they co-exist in a controllable manner. Finally, we apply our approach to a real-world classification problem of skin cancer analysis, using out-of-distribution datasets and specialized bias annotations. Our protocol reveals three findings: 1) Models learn and propagate correlation shifts even with low-bias training; this poses a risk of accumulating and combining unaccountable weak biases; 2) Models learn robust features in high- and low-bias scenarios but use spurious ones if test samples have them; this suggests that spurious correlations do not impair the learning of robust features; 3) Diversity shift can reduce the reliance on spurious correlations; this is counter intuitive since we expect biased models to depend more on biases when invariant features are missing. Our work has implications for distribution shift research and practice, providing new insights into how models learn and rely on spurious correlations under different types of shifts.

Artifact-Based Domain Generalization of Skin Lesion Models

Deep Learning failure cases are abundant, particularly in the medical area. Recent studies in out-of-distribution generalization have advanced considerably on well-controlled synthetic datasets, but they do not represent medical imaging contexts. We propose a pipeline that relies on artifacts annotation to enable generalization evaluation and debiasing for the challenging skin lesion analysis context. First, we partition the data into levels of increasingly higher biased training and test sets for better generalization assessment. Then, we create environments based on skin lesion artifacts to enable domain generalization methods. Finally, after robust training, we perform a test-time debiasing procedure, reducing spurious features in inference images. Our experiments show our pipeline improves performance metrics in biased cases, and avoids artifacts when using explanation methods. Still, when evaluating such models in out-of-distribution data, they did not prefer clinically-meaningful features. Instead, performance only improved in test sets that present similar artifacts from training, suggesting models learned to ignore the known set of artifacts. Our results raise a concern that debiasing models towards a single aspect may not be enough for fair skin lesion analysis.

A Survey on Deep Learning for Skin Lesion Segmentation

Skin cancer is a major public health problem that could benefit from computer-aided diagnosis to reduce the burden of this common disease. Skin lesion segmentation from images is an important step toward achieving this goal. However, the presence of natural and artificial artifacts (e.g., hair and air bubbles), intrinsic factors (e.g., lesion shape and contrast), and variations in image acquisition conditions make skin lesion segmentation a challenging task. Recently, various researchers have explored the applicability of deep learning models to skin lesion segmentation. In this survey, we cross-examine 134 research papers that deal with deep learning based segmentation of skin lesions. We analyze these works along several dimensions, including input data (datasets, preprocessing, and synthetic data generation), model design (architecture, modules, and losses), and evaluation aspects (data annotation requirements and segmentation performance). We discuss these dimensions both from the viewpoint of select seminal works, and from a systematic viewpoint, examining how those choices have influenced current trends, and how their limitations should be addressed. We summarize all examined works in a comprehensive table to facilitate comparisons.