A Transformer-Based Pipeline for German Clinical Document De-Identification.

Objective:  Commercially available large language models such as Chat Generative Pre-Trained Transformer (ChatGPT) cannot be applied to real patient data for data protection reasons. At the same time, de-identification of clinical unstructured data is a tedious and time-consuming task when done manually. Since transformer models can efficiently process and analyze large amounts of text data, our study aims to explore the impact of a large training dataset on the performance of this task.

BioKGrapher: Initial evaluation of automated knowledge graph construction from biomedical literature.

The growth of biomedical literature presents challenges in extracting and structuring knowledge. Knowledge Graphs (KGs) offer a solution by representing relationships between biomedical entities. However, manual construction of KGs is labor-intensive and time-consuming, highlighting the need for automated methods.

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.

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.

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.

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.

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.

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

This paper explores the optical properties of an exfoliated MoSe monolayer implanted with Cr ions, accelerated to 25 eV. Photoluminescence of the implanted MoSe 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.

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.

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.

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.

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.

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.

Quasiparticle Self-Consistent 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.

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.

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.

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.

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.

Sociodemographic data and APOE-ε4 augmentation for MRI-based detection of amnestic mild cognitive impairment using deep learning systems.

Detection and diagnosis of early and subclinical stages of Alzheimer's Disease (AD) play an essential role in the implementation of intervention and prevention strategies. Neuroimaging techniques predominantly provide insight into anatomic structure changes associated with AD. Deep learning methods have been extensively applied towards creating and evaluating models capable of differentiating between cognitively unimpaired, patients with Mild Cognitive Impairment (MCI) and AD dementia.

Nano or Not Nano? A Structured Approach for Identifying Nanomaterials According to the European Commission's Definition.

Identifying nanomaterials (NMs) according to European Union legislation is challenging, as there is an enormous variety of materials, with different physico-chemical properties. The NanoDefiner Framework and its Decision Support Flow Scheme (DSFS) allow choosing the optimal method to measure the particle size distribution by matching the material properties and the performance of the particular measurement techniques. The DSFS leads to a reliable and economic decision whether a material is an NM or not based on scientific criteria and respecting regulatory requirements.

Mimicking the radiologists' workflow: Estimating pediatric hand bone age with stacked deep neural networks.

Pediatric endocrinologists regularly order radiographs of the left hand to estimate the degree of bone maturation in order to assess their patients for advanced or delayed growth, physical development, and to monitor consecutive therapeutic measures. The reading of such images is a labor-intensive task that requires a lot of experience and is normally performed by highly trained experts like pediatric radiologists. In this paper we build an automated system for pediatric bone age estimation that mimics and accelerates the workflow of the radiologist without breaking it.

Plasmons in MoS studied via experimental and theoretical correlation of energy loss spectra.

This paper takes a fundamental view of the electron energy loss spectra of monolayer and few layer MoS . The dielectric function of monolayer MoS is compared to the experimental spectra to give clear criteria for the nature of different signals. Kramers-Krönig analysis allows a direct extraction of the dielectric function from the experimental data.