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.

AVAILABILITY AND IMPLEMENTATION

The documentation is available at https://chromax.readthedocs.io. The code is available at https://github.com/kora-labs/chromax.

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.

Design, Settings, and Participants

This cohort study included clinical data and transthoracic echocardiogram results of patients with AMI from the Zurich Acute Coronary Syndrome Registry and patients with TTS obtained from 7 cardiovascular centers in the International Takotsubo Registry. Data from the validation cohort were obtained from April 2011 to February 2017. Data from the training cohort were obtained from March 2017 to May 2019. Data were analyzed from September 2019 to June 2021.

Exposure

Transthoracic echocardiograms of 224 patients with TTS and 224 patients with AMI were analyzed.

Main Outcomes and Measures

Area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity of the machine learning system evaluated on an independent data set and 4 practicing cardiologists for comparison. Echocardiography videos of 228 patients were used in the development and training of a deep learning model. The performance of the automated echocardiogram video analysis method was evaluated on an independent data set consisting of 220 patients. Data were matched according to age, sex, and ST-segment elevation/non-ST-segment elevation (1 patient with AMI for each patient with TTS). Predictions were compared with echocardiographic-based interpretations from 4 practicing cardiologists in terms of sensitivity, specificity, and AUC calculated from confidence scores concerning their binary diagnosis.

Results

In this cohort study, apical 2-chamber and 4-chamber echocardiographic views of 110 patients with TTS (mean [SD] age, 68.4 [12.1] years; 103 [90.4%] were female) and 110 patients with AMI (mean [SD] age, 69.1 [12.2] years; 103 [90.4%] were female) from an independent data set were evaluated. This approach achieved a mean (SD) AUC of 0.79 (0.01) with an overall accuracy of 74.8 (0.7%). In comparison, cardiologists achieved a mean (SD) AUC of 0.71 (0.03) and accuracy of 64.4 (3.5%) on the same data set. In a subanalysis based on 61 patients with apical TTS and 56 patients with AMI due to occlusion of the left anterior descending coronary artery, the model achieved a mean (SD) AUC score of 0.84 (0.01) and an accuracy of 78.6 (1.6%), outperforming the 4 practicing cardiologists (mean [SD] AUC, 0.72 [0.02]) and accuracy of 66.9 (2.8%).

Conclusions and Relevance

In this cohort study, a real-time system for fully automated interpretation of echocardiogram videos was established and trained to differentiate TTS from AMI. While this system was more accurate than cardiologists in echocardiography-based disease classification, further studies are warranted for clinical application.

Artificial intelligence in echocardiography diagnostics – detection of takotsubo syndrome

Background

Machine learning allows classifying diseases based only on raw echocardiographic imaging data and is therefore a landmark in the development of computer-assisted decision support systems in echocardiography.

Purpose

The present study sought to determine the value of deep (machine) learning systems for automatic discrimination of takotsubo syndrome and acute myocardial infarction.

Methods

Apical 2- and 4-chamber echocardiographic views of 110 patients with takotsubo syndrome and 110 patients with acute myocardial infarction were used in the development, training and validation of a deep learning approach, i.e. a convolutional autoencoder (CAE) for feature extraction followed by classical machine learning models for classification of the diseases.

Results

The deep learning model achieved an area under the receiver operating curve (AUC) of 0.801 with an overall accuracy of 74.5% for 5-fold cross validation evaluated on a clinically relevant dataset. In comparison, experienced cardiologists achieved AUCs in the range 0.678–0.740 and an average accuracy of 64.5% on the same dataset.

Conclusions

A real-time system for fully automated interpretation of echocardiographic videos was established and trained to differentiate takotsubo syndrome from acute myocardial infarction. The framework provides insight into the algorithms' decision process for physicians and yields new and valuable information on the manifestation of disease patterns in echocardiographic data. While our system was superior to cardiologists in echocardiography-based disease classification, further studies should be conducted in a larger patient population to prove its clinical application.

Funding Acknowledgement

Type of funding source: None