2D echocardiography video to 3D heart shape reconstruction for clinical application.

Transthoracic Echocardiography (TTE) is a crucial tool for assessing cardiac morphology and function quickly and non-invasively without ionising radiation. However, the examination is subject to intra- and inter-user variability and recordings are often limited to 2D imaging and assessments of end-diastolic and end-systolic volumes. We have developed a novel, fully automated machine learning-based framework to generate a personalised 4D (3D plus time) model of the left ventricular (LV) blood pool with high temporal resolution.

A unified generation-registration framework for improved MR-based CT synthesis in proton therapy.

Background: The use of magnetic resonance (MR) imaging for proton therapy treatment planning is gaining attention as a highly effective method for guidance. At the core of this approach is the generation of computed tomography (CT) images from MR scans. However, the critical issue in this process is accurately aligning the MR and CT images, a task that becomes particularly challenging in frequently moving body areas, such as the head-and-neck.

Fundamentals of Arthroscopic Surgery Training and beyond: a reinforcement learning exploration and benchmark.

Purpose: This work presents FASTRL, a benchmark set of instrument manipulation tasks adapted to the domain of reinforcement learning and used in simulated surgical training. This benchmark enables and supports the design and training of human-centric reinforcement learning agents which assist and evaluate human trainees in surgical practice.

Methods: Simulation tasks from the Fundamentals of Arthroscopic Surgery Training (FAST) program are adapted to the reinforcement learning setting for the purpose of training virtual agents that are capable of providing assistance and scoring to the surgical trainees.

Uncertainty-aware MR-based CT synthesis for robust proton therapy planning of brain tumour.

Background And Purpose: Deep learning techniques excel in MR-based CT synthesis, but missing uncertainty prediction limits its clinical use in proton therapy. We developed an uncertainty-aware framework and evaluated its efficiency in robust proton planning.

Materials And Methods: A conditional generative-adversarial network was trained on 64 brain tumour patients with paired MR-CT images to generate synthetic CTs (sCT) from combined T1-T2 MRs of three orthogonal planes.

ChromaX: a fast and scalable breeding program simulator.

Summary: ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two orders of magnitude faster than existing tools with standard hardware. This offers breeders and scientists new opportunities to simulate genetic gain and optimize breeding schemes.

Weakly supervised inference of personalized heart meshes based on echocardiography videos.

Echocardiography provides recordings of the heart chamber size and function and is a central tool for non-invasive diagnosis of heart diseases. It produces high-dimensional video data with substantial stochasticity in the measurements, which frequently prove difficult to interpret. To address this challenge, we propose an automated framework to enable the inference of a high resolution personalized 4D (3D plus time) surface mesh of the cardiac structures from 2D echocardiography video data.

Natural Age-Related Slow-Wave Sleep Alterations Onset Prematurely in the Tg2576 Mouse Model of Alzheimer's Disease.

Introduction: Sleep insufficiency or decreased quality have been associated with Alzheimer's disease (AD) already in its preclinical stages. Whether such traits are also present in rodent models of the disease has been poorly addressed, somewhat disabling the preclinical exploration of sleep-based therapeutic interventions for AD.

Methods: We investigated age-dependent sleep-wake phenotype of a widely used mouse model of AD, the Tg2576 line.

Automatic Detection of Atrial Fibrillation from Single-Lead ECG Using Deep Learning of the Cardiac Cycle.

. Atrial fibrillation (AF) is a serious medical condition that requires effective and timely treatment to prevent stroke. We explore deep neural networks (DNNs) for learning cardiac cycles and reliably detecting AF from single-lead electrocardiogram (ECG) signals.

Assessment of Artificial Intelligence in Echocardiography Diagnostics in Differentiating Takotsubo Syndrome From Myocardial Infarction.

Importance: Machine learning algorithms enable the automatic classification of cardiovascular diseases based on raw cardiac ultrasound imaging data. However, the utility of machine learning in distinguishing between takotsubo syndrome (TTS) and acute myocardial infarction (AMI) has not been studied.

Objectives: To assess the utility of machine learning systems for automatic discrimination of TTS and AMI.

Rapid and reversible control of human metabolism by individual sleep states.

Sleep is crucial to restore body functions and metabolism across nearly all tissues and cells, and sleep restriction is linked to various metabolic dysfunctions in humans. Using exhaled breath analysis by secondary electrospray ionization high-resolution mass spectrometry, we measured the human exhaled metabolome at 10-s resolution across a night of sleep in combination with conventional polysomnography. Our subsequent analysis of almost 2,000 metabolite features demonstrates rapid, reversible control of major metabolic pathways by the individual vigilance states.

Self-supervised representation learning for surgical activity recognition.

Purpose: Virtual reality-based simulators have the potential to become an essential part of surgical education. To make full use of this potential, they must be able to automatically recognize activities performed by users and assess those. Since annotations of trajectories by human experts are expensive, there is a need for methods that can learn to recognize surgical activities in a data-efficient way.

Improving 1-year mortality prediction in ACS patients using machine learning.

Background: The Global Registry of Acute Coronary Events (GRACE) score is an established clinical risk stratification tool for patients with acute coronary syndromes (ACS). We developed and internally validated a model for 1-year all-cause mortality prediction in ACS patients.

Methods: Between 2009 and 2012, 2'168 ACS patients were enrolled into the Swiss SPUM-ACS Cohort.

Prognostic value of inflammatory biomarkers and GRACE score for cardiac death and acute kidney injury after acute coronary syndromes.

Aims: The aim of this study was to analyse the role of inflammation and established clinical scores in predicting acute kidney injury (AKI) after acute coronary syndromes (ACS).

Methods And Results: In a prospective multicentre cohort including 2034 patients with ACS undergoing percutaneous coronary intervention, high-sensitivity C-reactive protein (hsCRP), neutrophil count, neutrophil-to-lymphocyte ratio (NL-ratio), and creatinine were measured at the index procedure. AKI (n = 39, defined according to RIFLE criteria) and major cardiovascular and cerebrovascular events were adjudicated after 1 year.

Neural collaborative filtering for unsupervised mitral valve segmentation in echocardiography.

The segmentation of the mitral valve annulus and leaflets specifies a crucial first step to establish a machine learning pipeline that can support physicians in performing multiple tasks, e.g. diagnosis of mitral valve diseases, surgical planning, and intraoperative procedures.

Automatic Human Sleep Stage Scoring Using Deep Neural Networks.

The classification of sleep stages is the first and an important step in the quantitative analysis of polysomnographic recordings. Sleep stage scoring relies heavily on visual pattern recognition by a human expert and is time consuming and subjective. Thus, there is a need for automatic classification.

Pipeline validation for connectivity-based cortex parcellation.

Structural connectivity plays a dominant role in brain function and arguably lies at the core of understanding the structure-function relationship in the cerebral cortex. Connectivity-based cortex parcellation (CCP), a framework to process structural connectivity information gained from diffusion MRI and diffusion tractography, identifies cortical subunits that furnish functional inference. The underlying pipeline of algorithms interprets similarity in structural connectivity as a segregation criterion.

A generative model of whole-brain effective connectivity.

The development of whole-brain models that can infer effective (directed) connection strengths from fMRI data represents a central challenge for computational neuroimaging. A recently introduced generative model of fMRI data, regression dynamic causal modeling (rDCM), moves towards this goal as it scales gracefully to very large networks. However, large-scale networks with thousands of connections are difficult to interpret; additionally, one typically lacks information (data points per free parameter) for precise estimation of all model parameters.

Semiautomatic Assessment of the Terminal Ileum and Colon in Patients with Crohn Disease Using MRI (the VIGOR++ Project).

Rationale And Objectives: The objective of this study was to develop and validate a predictive magnetic resonance imaging (MRI) activity score for ileocolonic Crohn disease activity based on both subjective and semiautomatic MRI features.

Materials And Methods: An MRI activity score (the "virtual gastrointestinal tract [VIGOR]" score) was developed from 27 validated magnetic resonance enterography datasets, including subjective radiologist observation of mural T2 signal and semiautomatic measurements of bowel wall thickness, excess volume, and dynamic contrast enhancement (initial slope of increase). A second subjective score was developed based on only radiologist observations.

Regression DCM for fMRI.

The development of large-scale network models that infer the effective (directed) connectivity among neuronal populations from neuroimaging data represents a key challenge for computational neuroscience. Dynamic causal models (DCMs) of neuroimaging and electrophysiological data are frequently used for inferring effective connectivity but are presently restricted to small graphs (typically up to 10 regions) in order to keep model inversion computationally feasible. Here, we present a novel variant of DCM for functional magnetic resonance imaging (fMRI) data that is suited to assess effective connectivity in large (whole-brain) networks.

Glaucoma detection using entropy sampling and ensemble learning for automatic optic cup and disc segmentation.

We present a novel method to segment retinal images using ensemble learning based convolutional neural network (CNN) architectures. An entropy sampling technique is used to select informative points thus reducing computational complexity while performing superior to uniform sampling. The sampled points are used to design a novel learning framework for convolutional filters based on boosting.

Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity.

Recent large-scale genome analyses of human tissue samples have uncovered a high degree of genetic alterations and tumour heterogeneity in most tumour entities, independent of morphological phenotypes and histopathological characteristics. Assessment of genetic copy-number variation (CNV) and tumour heterogeneity by fluorescence in situ hybridization (ISH) provides additional tissue morphology at single-cell resolution, but it is labour intensive with limited throughput and high inter-observer variability. We present an integrative method combining bright-field dual-colour chromogenic and silver ISH assays with an image-based computational workflow (ISHProfiler), for accurate detection of molecular signals, high-throughput evaluation of CNV, expressive visualization of multi-level heterogeneity (cellular, inter- and intra-tumour heterogeneity), and objective quantification of heterogeneous genetic deletions (PTEN) and amplifications (19q12, HER2) in diverse human tumours (prostate, endometrial, ovarian and gastric), using various tissue sizes and different scanners, with unprecedented throughput and reproducibility.

Active learning based segmentation of Crohns disease from abdominal MRI.

This paper proposes a novel active learning (AL) framework, and combines it with semi supervised learning (SSL) for segmenting Crohns disease (CD) tissues from abdominal magnetic resonance (MR) images. Robust fully supervised learning (FSL) based classifiers require lots of labeled data of different disease severities. Obtaining such data is time consuming and requires considerable expertise.

Visual saliency-based active learning for prostate magnetic resonance imaging segmentation.

We propose an active learning (AL) approach for prostate segmentation from magnetic resonance images. Our label query strategy is inspired from the principles of visual saliency that have similar considerations for choosing the most salient region. These similarities are encoded in a graph using classification maps and low-level features.