ADAPT: Multimodal Learning for Detecting Physiological Changes under Missing Modalities

Multimodality has recently gained attention in the medical domain, where imaging or video modalities may be integrated with biomedical signals or health records. Yet, two challenges remain: balancing the contributions of modalities, especially in cases with a limited amount of data available, and tackling missing modalities. To address both issues, in this paper, we introduce the AnchoreD multimodAl Physiological Transformer (ADAPT), a multimodal, scalable framework with two key components: (i) aligning all modalities in the space of the strongest, richest modality (called anchor) to learn a joint embedding space, and (ii) a Masked Multimodal Transformer, leveraging both inter- and intra-modality correlations while handling missing modalities. We focus on detecting physiological changes in two real-life scenarios: stress in individuals induced by specific triggers and fighter pilots' loss of consciousness induced by $g$-forces. We validate the generalizability of ADAPT through extensive experiments on two datasets for these tasks, where we set the new state of the art while demonstrating its robustness across various modality scenarios and its high potential for real-life applications.

You Don't Need Data-Augmentation in Self-Supervised Learning

Self-Supervised learning (SSL) with Joint-Embedding Architectures (JEA) has led to outstanding performances. All instantiations of this paradigm were trained using strong and well-established hand-crafted data augmentations, leading to the general belief that they are required for the proper training and performance of such models. On the other hand, generative reconstruction-based models such as BEIT and MAE or Joint-Embedding Predictive Architectures such as I-JEPA have shown strong performance without using data augmentations except masking. In this work, we challenge the importance of invariance and data-augmentation in JEAs at scale. By running a case-study on a recent SSL foundation model - DINOv2 - we show that strong image representations can be obtained with JEAs and only cropping without resizing provided the training data is large enough, reaching state-of-the-art results and using the least amount of augmentation in the literature. Through this study, we also discuss the impact of compute constraints on the outcomes of experimental deep learning research, showing that they can lead to very different conclusions.

Advancing human-centric AI for robust X-ray analysis through holistic self-supervised learning

AI Foundation models are gaining traction in various applications, including medical fields like radiology. However, medical foundation models are often tested on limited tasks, leaving their generalisability and biases unexplored. We present RayDINO, a large visual encoder trained by self-supervision on 873k chest X-rays. We compare RayDINO to previous state-of-the-art models across nine radiology tasks, from classification and dense segmentation to text generation, and provide an in depth analysis of population, age and sex biases of our model. Our findings suggest that self-supervision allows patient-centric AI proving useful in clinical workflows and interpreting X-rays holistically. With RayDINO and small task-specific adapters, we reach state-of-the-art results and improve generalization to unseen populations while mitigating bias, illustrating the true promise of foundation models: versatility and robustness.

SI-MIL: Taming Deep MIL for Self-Interpretability in Gigapixel Histopathology

Introducing interpretability and reasoning into Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) analysis is challenging, given the complexity of gigapixel slides. Traditionally, MIL interpretability is limited to identifying salient regions deemed pertinent for downstream tasks, offering little insight to the end-user (pathologist) regarding the rationale behind these selections. To address this, we propose Self-Interpretable MIL (SI-MIL), a method intrinsically designed for interpretability from the very outset. SI-MIL employs a deep MIL framework to guide an interpretable branch grounded on handcrafted pathological features, facilitating linear predictions. Beyond identifying salient regions, SI-MIL uniquely provides feature-level interpretations rooted in pathological insights for WSIs. Notably, SI-MIL, with its linear prediction constraints, challenges the prevalent myth of an inevitable trade-off between model interpretability and performance, demonstrating competitive results compared to state-of-the-art methods on WSI-level prediction tasks across three cancer types. In addition, we thoroughly benchmark the local- and global-interpretability of SI-MIL in terms of statistical analysis, a domain expert study, and desiderata of interpretability, namely, user-friendliness and faithfulness.

Data-Centric Machine Learning for Geospatial Remote Sensing Data

Recent developments and research in modern machine learning have led to substantial improvements in the geospatial field. Although numerous deep learning models have been proposed, the majority of them have been developed on benchmark datasets that lack strong real-world relevance. Furthermore, the performance of many methods has already saturated on these datasets. We argue that shifting the focus towards a complementary data-centric perspective is necessary to achieve further improvements in accuracy, generalization ability, and real impact in end-user applications. This work presents a definition and precise categorization of automated data-centric learning approaches for geospatial data. It highlights the complementary role of data-centric learning with respect to model-centric in the larger machine learning deployment cycle. We review papers across the entire geospatial field and categorize them into different groups. A set of representative experiments shows concrete implementation examples. These examples provide concrete steps to act on geospatial data with data-centric machine learning approaches.

Certification of Deep Learning Models for Medical Image Segmentation

In medical imaging, segmentation models have known a significant improvement in the past decade and are now used daily in clinical practice. However, similar to classification models, segmentation models are affected by adversarial attacks. In a safety-critical field like healthcare, certifying model predictions is of the utmost importance. Randomized smoothing has been introduced lately and provides a framework to certify models and obtain theoretical guarantees. In this paper, we present for the first time a certified segmentation baseline for medical imaging based on randomized smoothing and diffusion models. Our results show that leveraging the power of denoising diffusion probabilistic models helps us overcome the limits of randomized smoothing. We conduct extensive experiments on five public datasets of chest X-rays, skin lesions, and colonoscopies, and empirically show that we are able to maintain high certified Dice scores even for highly perturbed images. Our work represents the first attempt to certify medical image segmentation models, and we aspire for it to set a foundation for future benchmarks in this crucial and largely uncharted area.

On the detection of Out-Of-Distribution samples in Multiple Instance Learning

The deployment of machine learning solutions in real-world scenarios often involves addressing the challenge of out-of-distribution (OOD) detection. While significant efforts have been devoted to OOD detection in classical supervised settings, the context of weakly supervised learning, particularly the Multiple Instance Learning (MIL) framework, remains under-explored. In this study, we tackle this challenge by adapting post-hoc OOD detection methods to the MIL setting while introducing a novel benchmark specifically designed to assess OOD detection performance in weakly supervised scenarios. Extensive experiments based on diverse public datasets do not reveal a single method with a clear advantage over the others. Although DICE emerges as the best-performing method overall, it exhibits significant shortcomings on some datasets, emphasizing the complexity of this under-explored and challenging topic. Our findings shed light on the complex nature of OOD detection under the MIL framework, emphasizing the importance of developing novel, robust, and reliable methods that can generalize effectively in a weakly supervised context. The code for the paper is available here: https://github.com/loic-lb/OOD_MIL.

Spatio-Temporal Analysis of Patient-Derived Organoid Videos Using Deep Learning for the Prediction of Drug Efficacy

Over the last ten years, Patient-Derived Organoids (PDOs) emerged as the most reliable technology to generate ex-vivo tumor avatars. PDOs retain the main characteristics of their original tumor, making them a system of choice for pre-clinical and clinical studies. In particular, PDOs are attracting interest in the field of Functional Precision Medicine (FPM), which is based upon an ex-vivo drug test in which living tumor cells (such as PDOs) from a specific patient are exposed to a panel of anti-cancer drugs. Currently, the Adenosine Triphosphate (ATP) based cell viability assay is the gold standard test to assess the sensitivity of PDOs to drugs. The readout is measured at the end of the assay from a global PDO population and therefore does not capture single PDO responses and does not provide time resolution of drug effect. To this end, in this study, we explore for the first time the use of powerful large foundation models for the automatic processing of PDO data. In particular, we propose a novel imaging-based high-throughput screening method to assess real-time drug efficacy from a time-lapse microscopy video of PDOs. The recently proposed SAM algorithm for segmentation and DINOv2 model are adapted in a comprehensive pipeline for processing PDO microscopy frames. Moreover, an attention mechanism is proposed for fusing temporal and spatial features in a multiple instance learning setting to predict ATP. We report better results than other non-time-resolved methods, indicating that the temporality of data is an important factor for the prediction of ATP. Extensive ablations shed light on optimizing the experimental setting and automating the prediction both in real-time and for forecasting.

SAM-Path: A Segment Anything Model for Semantic Segmentation in Digital Pathology

Semantic segmentations of pathological entities have crucial clinical value in computational pathology workflows. Foundation models, such as the Segment Anything Model (SAM), have been recently proposed for universal use in segmentation tasks. SAM shows remarkable promise in instance segmentation on natural images. However, the applicability of SAM to computational pathology tasks is limited due to the following factors: (1) lack of comprehensive pathology datasets used in SAM training and (2) the design of SAM is not inherently optimized for semantic segmentation tasks. In this work, we adapt SAM for semantic segmentation by introducing trainable class prompts, followed by further enhancements through the incorporation of a pathology encoder, specifically a pathology foundation model. Our framework, SAM-Path enhances SAM's ability to conduct semantic segmentation in digital pathology without human input prompts. Through experiments on two public pathology datasets, the BCSS and the CRAG datasets, we demonstrate that the fine-tuning with trainable class prompts outperforms vanilla SAM with manual prompts and post-processing by 27.52% in Dice score and 71.63% in IOU. On these two datasets, the proposed additional pathology foundation model further achieves a relative improvement of 5.07% to 5.12% in Dice score and 4.50% to 8.48% in IOU.

Structured State Space Models for Multiple Instance Learning in Digital Pathology

Multiple instance learning is an ideal mode of analysis for histopathology data, where vast whole slide images are typically annotated with a single global label. In such cases, a whole slide image is modelled as a collection of tissue patches to be aggregated and classified. Common models for performing this classification include recurrent neural networks and transformers. Although powerful compression algorithms, such as deep pre-trained neural networks, are used to reduce the dimensionality of each patch, the sequences arising from whole slide images remain excessively long, routinely containing tens of thousands of patches. Structured state space models are an emerging alternative for sequence modelling, specifically designed for the efficient modelling of long sequences. These models invoke an optimal projection of an input sequence into memory units that compress the entire sequence. In this paper, we propose the use of state space models as a multiple instance learner to a variety of problems in digital pathology. Across experiments in metastasis detection, cancer subtyping, mutation classification, and multitask learning, we demonstrate the competitiveness of this new class of models with existing state of the art approaches. Our code is available at https://github.com/MICS-Lab/s4_digital_pathology.