Lung Pattern Analysis using Artificial Intelligence for the Diagnosis Support of Interstitial Lung Diseases

Interstitial lung diseases (ILDs) is a group of more than 200 chronic lung disorders characterized by inflammation and scarring of the lung tissue that leads to respiratory failure. Although ILD is a heterogeneous group of histologically distinct diseases, most of them exhibit similar clinical presentations and their diagnosis often presents a diagnostic dilemma. Early diagnosis is crucial for making treatment decisions, while misdiagnosis may lead to life-threatening complications. If a final diagnosis cannot be reached with the high resolution computed tomography scan, additional invasive procedures are required (e.g. bronchoalveolar lavage, surgical biopsy). The aim of this PhD thesis was to investigate the components of a computational system that will assist radiologists with the diagnosis of ILDs, while avoiding the dangerous, expensive and time-consuming invasive biopsies. The appropriate interpretation of the available radiological data combined with clinical/biochemical information can provide a reliable diagnosis, able to improve the diagnostic accuracy of the radiologists. In this thesis, we introduce two convolutional neural networks particularly designed for ILDs and a training scheme that employs knowledge transfer from the similar domain of general texture classification for performance enhancement. Moreover, we investigate the clinical relevance of breathing information for disease classification. The breathing information is quantified as a deformation field between inhale-exhale lung images using a novel 3D convolutional neural network for medical image registration. Finally, we design and evaluate the final end-to-end computational system for ILD classification using lung anatomy segmentation algorithms from the literature and the proposed ILD quantification neural networks. Deep learning approaches have been mostly investigated for all the aforementioned steps, while the results demonstrated their potential in analyzing lung images

Semantic Segmentation of Pathological Lung Tissue with Dilated Fully Convolutional Networks

Early and accurate diagnosis of interstitial lung diseases (ILDs) is crucial for making treatment decisions, but can be challenging even for experienced radiologists. The diagnostic procedure is based on the detection and recognition of the different ILD pathologies in thoracic CT scans, yet their manifestation often appears similar. In this study, we propose the use of a deep purely convolutional neural network for the semantic segmentation of ILD patterns, as the basic component of a computer aided diagnosis (CAD) system for ILDs. The proposed CNN, which consists of convolutional layers with dilated filters, takes as input a lung CT image of arbitrary size and outputs the corresponding label map. We trained and tested the network on a dataset of 172 sparsely annotated CT scans, within a cross-validation scheme. The training was performed in an end-to-end and semi-supervised fashion, utilizing both labeled and non-labeled image regions. The experimental results show significant performance improvement with respect to the state of the art

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

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

Perspectives and Preferences of Adult Smartphone Users Regarding Nutrition and Diet Apps: Web-Based Survey Study

BACKGROUND: Digital technologies have evolved dramatically in the recent years finding applications in a variety of aspects of everyday life. Smartphones and mobile apps are steadily used for more and more tasks including health monitoring. A large amount of "Nutrition and Diet" apps are available with some of them being very popular in terms of user downloads highlighting a trend towards diet monitoring and assessment. OBJECTIVE: We sought to explore the perspectives of end-users on the features, current use, and acceptance of "Nutrition and Diet" mHealth apps with a survey. We expect that such a study can provide user insights, assisting researchers and developers towards innovative dietary assessment. METHODS: A multidisciplinary team designed and compiled the survey. Before its release, it has been pilot-tested by 18 end-users. A 19-question survey was finally developed which has been translated into six languages: EN, DE, FR, ES, IT, EL. The participants were mainly recruited via social media and mailing lists of universities, university hospitals and patient associations. RESULTS: Respondents (n=2382) (79.4% female, 19.9% male, 0.7% neither) with a mean age of 27.2 (SD: 8.5) completed the survey. Around half of the participants (51.5%, 1227 out of 2382) have used a "Nutrition and Diet" app. The primary criteria for selecting such an app were to be easy to use (65.9%, 1570 out of 2382), free of charge (59.3%, 1413 out of 2382) and also produce automatic readings of caloric (51.7%, 1231 out of 2382) and macronutrient content (46.9%, 1117 out of 2382) (i.e., food type and/or the portion size are estimated by the system without any contribution by the user). An app is less likely to be selected if it incorrectly estimates portion size, calories or nutrient content (33.5%, 798 out of 2382). Moreover, other important limitations include the use of a database that comprises of non-local foods (27.5%, 655 out of 2382) and which may omit major foods (41%, 977 out of 2382). CONCLUSIONS: This comprehensive study in a mostly European population assessed the preferences and perspectives of (potential) "Nutrition and Diet" app users. Understanding user needs will benefit both researchers who work on tools for innovative dietary assessment, as well as those who assist research on behavioural changes related to nutrition

Influence of Lung Reconstruction Algorithms on Interstitial Lung Pattern Recognition on CT.

BACKGROUND  Despite current recommendations, there is no recent scientific study comparing the influence of CT reconstruction kernels on lung pattern recognition in interstitial lung disease (ILD). PURPOSE  To evaluate the sensitivity of lung (i70) and soft (i30) CT kernel algorithms for the diagnosis of ILD patterns. MATERIALS AND METHODS  We retrospectively extracted between 15-25 pattern annotations per case (1 annotation = 15 slices of 1 mm) from 23 subjects resulting in 408 annotation stacks per lung kernel and soft kernel reconstructions. Two subspecialized chest radiologists defined the ground truth in consensus. 4 residents, 2 fellows, and 2 general consultants in radiology with 3 to 13 years of experience in chest imaging performed a blinded readout. In order to account for data clustering, a generalized linear mixed model (GLMM) with random intercept for reader and nested for patient and image and a kernel/experience interaction term was used to analyze the results. RESULTS  The results of the GLMM indicated, that the odds of correct pattern recognition is 12 % lower with lung kernel compared to soft kernel; however, this was not statistically significant (OR 0.88; 95%-CI, 0.73-1.06; p = 0.187). Furthermore, the consultants' odds of correct pattern recognition was 78 % higher than the residents' odds, although this finding did not reach statistical significance either (OR 1.78; 95%-CI, 0.62-5.06; p = 0.283). There was no significant interaction between the two fixed terms kernel and experience. Intra-rater agreement between lung and soft kernel was substantial (κ = 0.63 ± 0.19). The mean inter-rater agreement for lung/soft kernel was κ = 0.37 ± 0.17/κ = 0.38 ± 0.17. CONCLUSION  There is no significant difference between lung and soft kernel reconstructed CT images for the correct pattern recognition in ILD. There are non-significant trends indicating that the use of soft kernels and a higher level of experience lead to a higher probability of correct pattern identification. KEY POINTS   · There is no significant difference between lung and soft kernel reconstructed CT images for the correct pattern recognition in interstitial lung disease.. · There are even non-significant tendencies that the use of soft kernels lead to a higher probability of correct pattern identification.. · These results challenge the current recommendations and the routinely performed separate lung kernel reconstructions for lung parenchyma analysis.. CITATION FORMAT · Klaus JB, Christodoulidis S, Peters AA et al. Influence of Lung Reconstruction Algorithms on Interstitial Lung Pattern Recognition on CT. Fortschr Röntgenstr 2022; DOI: 10.1055/a-1901-7814

Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment.

The prognosis of early breast cancer (BC) relies on cell autonomous and immune parameters. The impact of the intestinal microbiome on clinical outcome has not yet been evaluated. Shotgun metagenomics was used to determine the composition of the fecal microbiota in 121 specimens from 76 early BC patients, 45 of whom were paired before and after chemotherapy. These patients were enrolled in the CANTO prospective study designed to record the side effects associated with the clinical management of BC. We analyzed associations between baseline or post-chemotherapy fecal microbiota and plasma metabolomics with BC prognosis, as well as with therapy-induced side effects. We examined the clinical relevance of these findings in immunocompetent mice colonized with BC patient microbiota that were subsequently challenged with histo-compatible mouse BC and chemotherapy. We conclude that specific gut commensals that are overabundant in BC patients compared with healthy individuals negatively impact BC prognosis, are modulated by chemotherapy, and may influence weight gain and neurological side effects of BC therapies. These findings obtained in adjuvant and neoadjuvant settings warrant prospective validation

Self-Attention and Ingredient-Attention Based Model for Recipe Retrieval from Image Queries

Direct computer vision based-nutrient content estimation is a demanding task, due to deformation and occlusions of ingredients, as well as high intra-class and low inter-class variability between meal classes. In order to tackle these issues, we propose a system for recipe retrieval from images. The recipe information can subsequently be used to estimate the nutrient content of the meal. In this study, we utilize the multi-modal Recipe1M dataset, which contains over 1 million recipes accompanied by over 13 million images. The proposed model can operate as a first step in an automatic pipeline for the estimation of nutrition content by supporting hints related to ingredient and instruction. Through self-attention, our model can directly process raw recipe text, making the upstream instruction sentence embedding process redundant and thus reducing training time, while providing desirable retrieval results. Furthermore, we propose the use of an ingredient attention mechanism, in order to gain insight into which instructions, parts of instructions or single instruction words are of importance for processing a single ingredient within a certain recipe. Attention-based recipe text encoding contributes to solving the issue of high intra-class/low inter-class variability by focusing on preparation steps specific to the meal. The experimental results demonstrate the potential of such a system for recipe retrieval from images. A comparison with respect to two baseline methods is also presented