ROCOv2: Radiology Objects in COntext Version 2, an Updated Multimodal Image Dataset.

Automated medical image analysis systems often require large amounts of training data with high quality labels, which are difficult and time consuming to generate. This paper introduces Radiology Object in COntext version 2 (ROCOv2), a multimodal dataset consisting of radiological images and associated medical concepts and captions extracted from the PMC Open Access subset. It is an updated version of the ROCO dataset published in 2018, and adds 35,705 new images added to PMC since 2018. It further provides manually curated concepts for imaging modalities with additional anatomical and directional concepts for X-rays. The dataset consists of 79,789 images and has been used, with minor modifications, in the concept detection and caption prediction tasks of ImageCLEFmedical Caption 2023. The dataset is suitable for training image annotation models based on image-caption pairs, or for multi-label image classification using Unified Medical Language System (UMLS) concepts provided with each image. In addition, it can serve for pre-training of medical domain models, and evaluation of deep learning models for multi-task learning.

Piximi - An Images to Discovery web tool for bioimages and beyond.

Deep learning has greatly accelerated research in biological image analysis yet it often requires programming skills and specialized tool installation. Here we present Piximi, a modern, no-programming image analysis tool leveraging deep learning. Implemented as a web application at Piximi.app, Piximi requires no installation and can be accessed by any modern web browser. Its client-only architecture preserves the security of researcher data by running all computation locally. Piximi offers four core modules: a deep learning classifier, an image annotator, measurement modules, and pre-trained deep learning segmentation modules. Piximi is interoperable with existing tools and workflows by supporting import and export of common data and model formats. The intuitive researcher interface and easy access to Piximi allows biological researchers to obtain insights into images within just a few minutes. Piximi aims to bring deep learning-powered image analysis to a broader community by eliminating barriers to entry.

Diabetic foot ulcers segmentation challenge report: Benchmark and analysis.

Monitoring the healing progress of diabetic foot ulcers is a challenging process. Accurate segmentation of foot ulcers can help podiatrists to quantitatively measure the size of wound regions to assist prediction of healing status. The main challenge in this field is the lack of publicly available manual delineation, which can be time consuming and laborious. Recently, methods based on deep learning have shown excellent results in automatic segmentation of medical images, however, they require large-scale datasets for training, and there is limited consensus on which methods perform the best. The 2022 Diabetic Foot Ulcers segmentation challenge was held in conjunction with the 2022 International Conference on Medical Image Computing and Computer Assisted Intervention, which sought to address these issues and stimulate progress in this research domain. A training set of 2000 images exhibiting diabetic foot ulcers was released with corresponding segmentation ground truth masks. Of the 72 (approved) requests from 47 countries, 26 teams used this data to develop fully automated systems to predict the true segmentation masks on a test set of 2000 images, with the corresponding ground truth segmentation masks kept private. Predictions from participating teams were scored and ranked according to their average Dice similarity coefficient of the ground truth masks and prediction masks. The winning team achieved a Dice of 0.7287 for diabetic foot ulcer segmentation. This challenge has now entered a live leaderboard stage where it serves as a challenging benchmark for diabetic foot ulcer segmentation.

Monitoring Flow-Forming Processes Using Design of Experiments and a Machine Learning Approach Based on Randomized-Supervised Time Series Forest and Recursive Feature Elimination.

The machines of WF Maschinenbau process metal blanks into various workpieces using so-called flow-forming processes. The quality of these workpieces depends largely on the quality of the blanks and the condition of the machine. This creates an urgent need for automated monitoring of the forming processes and the condition of the machine. Since the complexity of the flow-forming processes makes physical modeling impossible, the present work deals with data-driven modeling using machine learning algorithms. The main contributions of this work lie in showcasing the feasibility of utilizing machine learning and sensor data to monitor flow-forming processes, along with developing a practical approach for this purpose. The approach includes an experimental design capable of providing the necessary data, as well as a procedure for preprocessing the data and extracting features that capture the information needed by the machine learning models to detect defects in the blank and the machine. To make efficient use of the small number of experiments available, the experimental design is generated using Design of Experiments methods. They consist of two parts. In the first part, a pre-selection of influencing variables relevant to the forming process is performed. In the second part of the design, the selected variables are investigated in more detail. The preprocessing procedure consists of feature engineering, feature extraction and feature selection. In the feature engineering step, the data set is augmented with time series variables that are meaningful in the domain. For feature extraction, an algorithm was developed based on the mechanisms of the r-STSF, a state-of-the-art algorithm for time series classification, extending them for multivariate time series and metric target variables. This feature extraction algorithm itself can be seen as an additional contribution of this work, because it is not tied to the application domain of monitoring flow-forming processes, but can be used as a feature extraction algorithm for multivariate time series classification in general. For feature selection, a Recursive Feature Elimination is employed. With the resulting features, random forests are trained to detect several quality features of the blank and defects of the machine. The trained models achieve good prediction accuracy for most of the target variables. This shows that the application of machine learning is a promising approach for the monitoring of flow-forming processes, which requires further investigation for confirmation.

Systematic comparison of 3D Deep learning and classical machine learning explanations for Alzheimer's Disease detection.

Black-box deep learning (DL) models trained for the early detection of Alzheimer's Disease (AD) often lack systematic model interpretation. This work computes the activated brain regions during DL and compares those with classical Machine Learning (ML) explanations. The architectures used for DL were 3D DenseNets, EfficientNets, and Squeeze-and-Excitation (SE) networks. The classical models include Random Forests (RFs), Support Vector Machines (SVMs), eXtreme Gradient Boosting (XGBoost), Light Gradient Boosting (LightGBM), Decision Trees (DTs), and Logistic Regression (LR). For explanations, SHapley Additive exPlanations (SHAP) values, Local Interpretable Model-agnostic Explanations (LIME), Gradient-weighted Class Activation Mapping (GradCAM), GradCAM++ and permutation-based feature importance were implemented. During interpretation, correlated features were consolidated into aspects. All models were trained on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. The validation includes internal and external validation on the Australian Imaging and Lifestyle flagship study of Ageing (AIBL) and the Open Access Series of Imaging Studies (OASIS). DL and ML models reached similar classification performances. Regarding the brain regions, both types focus on different regions. The ML models focus on the inferior and middle temporal gyri, and the hippocampus, and amygdala regions previously associated with AD. The DL models focus on a wider range of regions including the optical chiasm, the entorhinal cortices, the left and right vessels, and the 4th ventricle which were partially associated with AD. One explanation for the differences is the input features (textures vs. volumes). Both types show reasonable similarity to a ground truth Voxel-Based Morphometry (VBM) analysis. Slightly higher similarities were measured for ML models.

Optical Properties of MoSe2 Monolayer Implanted with Ultra-Low-Energy Cr Ions.

This paper explores the optical properties of an exfoliated MoSe2 monolayer implanted with Cr+ ions, accelerated to 25 eV. Photoluminescence of the implanted MoSe2 reveals an emission line from Cr-related defects that is present only under weak electron doping. Unlike band-to-band transition, the Cr-introduced emission is characterized by nonzero activation energy, long lifetimes, and weak response to the magnetic field. To rationalize the experimental results and get insights into the atomic structure of the defects, we modeled the Cr-ion irradiation process using ab initio molecular dynamics simulations followed by the electronic structure calculations of the system with defects. The experimental and theoretical results suggest that the recombination of electrons on the acceptors, which could be introduced by the Cr implantation-induced defects, with the valence band holes is the most likely origin of the low-energy emission. Our results demonstrate the potential of low-energy ion implantation as a tool to tailor the properties of two-dimensional (2D) materials by doping.

Medication event extraction in clinical notes: Contribution of the WisPerMed team to the n2c2 2022 challenge.

In this work, we describe the findings of the 'WisPerMed' team from their participation in Track 1 (Contextualized Medication Event Extraction) of the n2c2 2022 challenge. We tackle two tasks: (i) medication extraction, which involves extracting all mentions of medications from the clinical notes, and (ii) event classification, which involves classifying the medication mentions based on whether a change in the medication has been discussed. To address the long lengths of clinical texts, which often exceed the maximum token length that models based on the transformer-architecture can handle, various approaches, such as the use of ClinicalBERT with a sliding window approach and Longformer-based models, are employed. In addition, domain adaptation through masked language modeling and preprocessing steps such as sentence splitting are utilized to improve model performance. Since both tasks were treated as named entity recognition (NER) problems, a sanity check was performed in the second release to eliminate possible weaknesses in the medication detection itself. This check used the medication spans to remove false positive predictions and replace missed tokens with the highest softmax probability of the disposition types. The effectiveness of these approaches is evaluated through multiple submissions to the tasks, as well as with post-challenge results, with a focus on the DeBERTa v3 model and its disentangled attention mechanism. Results show that the DeBERTa v3 model performs well in both the NER task and the event classification task.

NanoDefiner Framework and e-Tool Revisited According to the European Commission's Nanomaterial Definition 2022/C 229/01.

The new recommended definition of a nanomaterial, 2022/C 229/01, adopted by the European Commission in 2022, will have a considerable impact on European Union legislation addressing chemicals, and therefore tools to implement this new definition are urgently needed. The updated NanoDefiner framework and its e-tool implementation presented here are such instruments, which help stakeholders to find out in a straightforward way whether a material is a nanomaterial or not. They are two major outcomes of the NanoDefine project, which is explicitly referred to in the new definition. This work revisits the framework and e-tool, and elaborates necessary adjustments to make these outcomes applicable for the updated recommendation. A broad set of case studies on representative materials confirms the validity of these adjustments. To further foster the sustainability and applicability of the framework and e-tool, measures for the FAIRification of expert knowledge within the e-tool's knowledge base are elaborated as well. The updated framework and e-tool are now ready to be used in line with the updated recommendation. The presented approach may serve as an example for reviewing existing guidance and tools developed for the previous definition 2011/696/EU, particularly those adopting NanoDefine project outcomes.

Explainable AI in medical imaging: An overview for clinical practitioners - Saliency-based XAI approaches.

Since recent achievements of Artificial Intelligence (AI) have proven significant success and promising results throughout many fields of application during the last decade, AI has also become an essential part of medical research. The improving data availability, coupled with advances in high-performance computing and innovative algorithms, has increased AI's potential in various aspects. Because AI rapidly reshapes research and promotes the development of personalized clinical care, alongside its implementation arises an urgent need for a deep understanding of its inner workings, especially in high-stake domains. However, such systems can be highly complex and opaque, limiting the possibility of an immediate understanding of the system's decisions. Regarding the medical field, a high impact is attributed to these decisions as physicians and patients can only fully trust AI systems when reasonably communicating the origin of their results, simultaneously enabling the identification of errors and biases. Explainable AI (XAI), becoming an increasingly important field of research in recent years, promotes the formulation of explainability methods and provides a rationale allowing users to comprehend the results generated by AI systems. In this paper, we investigate the application of XAI in medical imaging, addressing a broad audience, especially healthcare professionals. The content focuses on definitions and taxonomies, standard methods and approaches, advantages, limitations, and examples representing the current state of research regarding XAI in medical imaging. This paper focuses on saliency-based XAI methods, where the explanation can be provided directly on the input data (image) and which naturally are of special importance in medical imaging.

Explainable AI in medical imaging: An overview for clinical practitioners - Beyond saliency-based XAI approaches.

Driven by recent advances in Artificial Intelligence (AI) and Computer Vision (CV), the implementation of AI systems in the medical domain increased correspondingly. This is especially true for the domain of medical imaging, in which the incorporation of AI aids several imaging-based tasks such as classification, segmentation, and registration. Moreover, AI reshapes medical research and contributes to the development of personalized clinical care. Consequently, alongside its extended implementation arises the need for an extensive understanding of AI systems and their inner workings, potentials, and limitations which the field of eXplainable AI (XAI) aims at. Because medical imaging is mainly associated with visual tasks, most explainability approaches incorporate saliency-based XAI methods. In contrast to that, in this article we would like to investigate the full potential of XAI methods in the field of medical imaging by specifically focusing on XAI techniques not relying on saliency, and providing diversified examples. We dedicate our investigation to a broad audience, but particularly healthcare professionals. Moreover, this work aims at establishing a common ground for cross-disciplinary understanding and exchange across disciplines between Deep Learning (DL) builders and healthcare professionals, which is why we aimed for a non-technical overview. Presented XAI methods are divided by a method's output representation into the following categories: Case-based explanations, textual explanations, and auxiliary explanations.

Static and Dynamic Accuracy and Occlusion Robustness of SteamVR Tracking 2.0 in Multi-Base Station Setups.

The tracking of objects and person position, orientation, and movement is relevant for various medical use cases, e.g., practical training of medical staff or patient rehabilitation. However, these demand high tracking accuracy and occlusion robustness. Expensive professional tracking systems fulfill these demands, however, cost-efficient and potentially adequate alternatives can be found in the gaming industry, e.g., SteamVR Tracking. This work presents an evaluation of SteamVR Tracking in its latest version 2.0 in two experimental setups, involving two and four base stations. Tracking accuracy, both static and dynamic, and occlusion robustness are investigated using a VIVE Tracker (3.0). A dynamic analysis further compares three different velocities. An error evaluation is performed using a Universal Robots UR10 robotic arm as ground-truth system under nonlaboratory conditions. Results are presented using the Root Mean Square Error. For static experiments, tracking errors in the submillimeter and subdegree range are achieved by both setups. Dynamic experiments achieved errors in the submillimeter range as well, yet tracking accuracy suffers from increasing velocity. Four base stations enable generally higher accuracy and robustness, especially in the dynamic experiments. Both setups enable adequate accuracy for diverse medical use cases. However, use cases demanding very high accuracy should primarily rely on SteamVR Tracking 2.0 with four base stations.

Quasiparticle Self-Consistent GW Study of Simple Metals.

The GW method is a standard method to calculate the electronic band structure from first principles. It has been applied to a large variety of semiconductors and insulators but less often to metallic systems, in particular, with respect to a self-consistent employment of the method. In this work, we take a look at all-electron quasiparticle self-consistent GW (QSGW) calculations for simple metals (alkali and alkaline earth metals) based on the full-potential linearized augmented-plane-wave approach and compare the results to single-shot (i.e., non-selfconsistent) G0W0 calculations, density-functional theory (DFT) calculations in the local-density approximation, and experimental measurements. We show that, while DFT overestimates the bandwidth of most of the materials, the GW quasiparticle renormalization corrects the bandwidths in the right direction, but a full self-consistent calculation is needed to consistently achieve good agreement with photoemission data. The results mainly confirm the common belief that simple metals can be regarded as nearly free electron gases with weak electronic correlation. The finding is particularly important in light of a recent debate in which this seemingly established view has been contested.

Intracranial Aneurysm Classifier Using Phenotypic Factors: An International Pooled Analysis.

Intracranial aneurysms (IAs) are usually asymptomatic with a low risk of rupture, but consequences of aneurysmal subarachnoid hemorrhage (aSAH) are severe. Identifying IAs at risk of rupture has important clinical and socio-economic consequences. The goal of this study was to assess the effect of patient and IA characteristics on the likelihood of IA being diagnosed incidentally versus ruptured. Patients were recruited at 21 international centers. Seven phenotypic patient characteristics and three IA characteristics were recorded. The analyzed cohort included 7992 patients. Multivariate analysis demonstrated that: (1) IA location is the strongest factor associated with IA rupture status at diagnosis; (2) Risk factor awareness (hypertension, smoking) increases the likelihood of being diagnosed with unruptured IA; (3) Patients with ruptured IAs in high-risk locations tend to be older, and their IAs are smaller; (4) Smokers with ruptured IAs tend to be younger, and their IAs are larger; (5) Female patients with ruptured IAs tend to be older, and their IAs are smaller; (6) IA size and age at rupture correlate. The assessment of associations regarding patient and IA characteristics with IA rupture allows us to refine IA disease models and provide data to develop risk instruments for clinicians to support personalized decision-making.

Bayesian network analysis reveals the interplay of intracranial aneurysm rupture risk factors.

Clinical decision making regarding the treatment of unruptured intracranial aneurysms (IA) benefits from a better understanding of the interplay of IA rupture risk factors. Probabilistic graphical models can capture and graphically display potentially causal relationships in a mechanistic model. In this study, Bayesian networks (BN) were used to estimate IA rupture risk factors influences. From 1248 IA patient records, a retrospective, single-cohort, patient-level data set with 9 phenotypic rupture risk factors (n=790 complete entries) was extracted. Prior knowledge together with score-based structure learning algorithms estimated rupture risk factor interactions. Two approaches, discrete and mixed-data additive BN, were implemented and compared. The corresponding graphs were learned using non-parametric bootstrapping and Markov chain Monte Carlo, respectively. The BN models were compared to standard descriptive and regression analysis methods. Correlation and regression analyses showed significant associations between IA rupture status and patient's sex, familial history of IA, age at IA diagnosis, IA location, IA size and IA multiplicity. BN models confirmed the findings from standard analysis methods. More precisely, they directly associated IA rupture with familial history of IA, IA size and IA location in a discrete framework. Additive model formulation, enabling mixed-data, found that IA rupture was directly influenced by patient age at diagnosis besides additional mutual influences of the risk factors. This study establishes a data-driven methodology for mechanistic disease modelling of IA rupture and shows the potential to direct clinical decision-making in IA treatment, allowing personalised prediction.

Extracorporeal membrane oxygenation and inhaled sedation in coronavirus disease 2019-related acute respiratory distress syndrome.

Coronavirus disease 2019 (COVID-19) related acute respiratory distress syndrome (ARDS) is a severe complication of infection with severe acute respiratory syndrome coronavirus 2, and the primary cause of death in the current pandemic. Critically ill patients often undergo extracorporeal membrane oxygenation (ECMO) therapy as the last resort over an extended period. ECMO therapy requires sedation of the patient, which is usually achieved by intravenous administration of sedatives. The shortage of intravenous sedative drugs due to the ongoing pandemic, and attempts to improve treatment outcome for COVID-19 patients, drove the application of inhaled sedation as a promising alternative for sedation during ECMO therapy. Administration of volatile anesthetics requires an appropriate delivery. Commercially available ones are the anesthetic gas reflection systems AnaConDa® and MIRUSTM, and each should be combined with a gas scavenging system. In this review, we describe respiratory management in COVID-19 patients and the procedures for inhaled sedation during ECMO therapy of COVID-19 related ARDS. We focus particularly on the technical details of administration of volatile anesthetics. Furthermore, we describe the advantages of inhaled sedation and volatile anesthetics, and we discuss the limitations as well as the requirements for safe application in the clinical setting.

Data analysis with Shapley values for automatic subject selection in Alzheimer's disease data sets using interpretable machine learning.

BACKGROUND: For the recruitment and monitoring of subjects for therapy studies, it is important to predict whether mild cognitive impaired (MCI) subjects will prospectively develop Alzheimer's disease (AD). Machine learning (ML) is suitable to improve early AD prediction. The etiology of AD is heterogeneous, which leads to high variability in disease patterns. Further variability originates from multicentric study designs, varying acquisition protocols, and errors in the preprocessing of magnetic resonance imaging (MRI) scans. The high variability makes the differentiation between signal and noise difficult and may lead to overfitting. This article examines whether an automatic and fair data valuation method based on Shapley values can identify the most informative subjects to improve ML classification. METHODS: An ML workflow was developed and trained for a subset of the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. The validation was executed for an independent ADNI test set and for the Australian Imaging, Biomarker and Lifestyle Flagship Study of Ageing (AIBL) cohort. The workflow included volumetric MRI feature extraction, feature selection, sample selection using Data Shapley, random forest (RF), and eXtreme Gradient Boosting (XGBoost) for model training as well as Kernel SHapley Additive exPlanations (SHAP) values for model interpretation. RESULTS: The RF models, which excluded 134 of the 467 training subjects based on their RF Data Shapley values, outperformed the base models that reached a mean accuracy of 62.64% by 5.76% (3.61 percentage points) for the independent ADNI test set. The XGBoost base models reached a mean accuracy of 60.00% for the AIBL data set. The exclusion of those 133 subjects with the smallest RF Data Shapley values could improve the classification accuracy by 2.98% (1.79 percentage points). The cutoff values were calculated using an independent validation set. CONCLUSION: The Data Shapley method was able to improve the mean accuracies for the test sets. The most informative subjects were associated with the number of ApolipoproteinE ε4 (ApoE ε4) alleles, cognitive test results, and volumetric MRI measurements.

Deep learning in diabetic foot ulcers detection: A comprehensive evaluation.

There has been a substantial amount of research involving computer methods and technology for the detection and recognition of diabetic foot ulcers (DFUs), but there is a lack of systematic comparisons of state-of-the-art deep learning object detection frameworks applied to this problem. DFUC2020 provided participants with a comprehensive dataset consisting of 2,000 images for training and 2,000 images for testing. This paper summarizes the results of DFUC2020 by comparing the deep learning-based algorithms proposed by the winning teams: Faster R-CNN, three variants of Faster R-CNN and an ensemble method; YOLOv3; YOLOv5; EfficientDet; and a new Cascade Attention Network. For each deep learning method, we provide a detailed description of model architecture, parameter settings for training and additional stages including pre-processing, data augmentation and post-processing. We provide a comprehensive evaluation for each method. All the methods required a data augmentation stage to increase the number of images available for training and a post-processing stage to remove false positives. The best performance was obtained from Deformable Convolution, a variant of Faster R-CNN, with a mean average precision (mAP) of 0.6940 and an F1-Score of 0.7434. Finally, we demonstrate that the ensemble method based on different deep learning methods can enhance the F1-Score but not the mAP.

Patient assessment and feasibility of treatment in older patients with cancer: results from the IN-GHO® Registry.

PURPOSE: Predicting feasibility of treatment in older patients with cancer is a major clinical task. The Initiative Geriatrische Hämatologie und Onkologie (IN-GHO®) registry prospectively collected data on the comprehensive geriatric assessment (CGA), physician's and patient's-self assessment of fitness for treatment, and the course of treatment in patients within a treatment decision aged ≥ 70 years. PATIENTS AND METHODS: The registry included 3169 patients from 93 centres and evaluated clinical course and treatment outcomes 2-3 and 6 months after initial assessment. Fitness for treatment was classified as fit, compromised and frail according to results of a CGA, and in addition by an experienced physician's and by patient's itself. Feasibility of treatment (termed IN-GHO®-FIT) was defined as a composite endpoint, including willingness to undergo the same treatment again in retrospect, no modification or unplanned termination of treatment, and no early mortality (within 90 days). RESULTS: CGA classified 30.0% as fit, 35.8% as compromised, and 34.2% as frail. Physician's and patient's-self assessment classified 61.8%/52.3% as fit, 34.2%/42.4% as compromised, and 3.9%/5.3%, as frail, respectively. Survival status at day 180 was available in 2072 patients, of which 625 (30.2%) had died. After 2-3 months, feasibility of treatment could be assessed in 1984 patients. 62.8% fulfilled IN-GHO®-FIT criteria. Multivariable analysis identified physician's assessment as the single most important item regarding feasibility of treatment. CONCLUSION: Geriatricians were involved in 2% of patients only. Classification of fitness for treatment by CGA, and physician's or patient's-self assessment showed marked discrepancies. For the prediction of feasibility of treatment no single item was superior to physician's assessment. However CGA was not performed by trained geriatricians.

Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors.

Rupture of an intracranial aneurysm leads to subarachnoid hemorrhage, a severe type of stroke. To discover new risk loci and the genetic architecture of intracranial aneurysms, we performed a cross-ancestry, genome-wide association study in 10,754 cases and 306,882 controls of European and East Asian ancestry. We discovered 17 risk loci, 11 of which are new. We reveal a polygenic architecture and explain over half of the disease heritability. We show a high genetic correlation between ruptured and unruptured intracranial aneurysms. We also find a suggestive role for endothelial cells by using gene mapping and heritability enrichment. Drug-target enrichment shows pleiotropy between intracranial aneurysms and antiepileptic and sex hormone drugs, providing insights into intracranial aneurysm pathophysiology. Finally, genetic risks for smoking and high blood pressure, the two main clinical risk factors, play important roles in intracranial aneurysm risk, and drive most of the genetic correlation between intracranial aneurysms and other cerebrovascular traits.