Context dependent prediction in DNA sequence using neural networks.

One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural network that obtained an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, the neural network performed significantly better than any of the alternative models by a large margin. We report on where the accuracy was obtained, first observing that the performance appeared to be uniform over the chromosomes. The models performed best in repetitive sequences, as expected, although their performance far from random in the more difficult coding sections, the proportions being ~70:40%. We further explored the sources of the accuracy, Fourier transforming the predictions revealed weak but clear periodic signals. In the human genome the characteristic periods hinted at connections to nucleosome positioning. We found similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before. On other large genomes similarly high accuracy was found, while lower predictive accuracy was observed on smaller genomes. Only in the mouse genome did we see periodic signals in the same range as in the human genome, though weaker and of a different type. This indicates that the sources of these signals are other or more than nucleosome arrangement. Interestingly, applying a model trained on the mouse genome to the human genome resulted in a performance far below that of the human model, except in the difficult coding regions. Despite the clear outcomes of the likelihood-ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.

The Added Effect of Artificial Intelligence on Physicians' Performance in Detecting Thoracic Pathologies on CT and Chest X-ray: A Systematic Review.

Our systematic review investigated the additional effect of artificial intelligence-based devices on human observers when diagnosing and/or detecting thoracic pathologies using different diagnostic imaging modalities, such as chest X-ray and CT. Peer-reviewed, original research articles from EMBASE, PubMed, Cochrane library, SCOPUS, and Web of Science were retrieved. Included articles were published within the last 20 years and used a device based on artificial intelligence (AI) technology to detect or diagnose pulmonary findings. The AI-based device had to be used in an observer test where the performance of human observers with and without addition of the device was measured as sensitivity, specificity, accuracy, AUC, or time spent on image reading. A total of 38 studies were included for final assessment. The quality assessment tool for diagnostic accuracy studies (QUADAS-2) was used for bias assessment. The average sensitivity increased from 67.8% to 74.6%; specificity from 82.2% to 85.4%; accuracy from 75.4% to 81.7%; and Area Under the ROC Curve (AUC) from 0.75 to 0.80. Generally, a faster reading time was reported when radiologists were aided by AI-based devices. Our systematic review showed that performance generally improved for the physicians when assisted by AI-based devices compared to unaided interpretation.