856 research outputs found
Deep Learning in Cardiology
The medical field is creating large amount of data that physicians are unable
to decipher and use efficiently. Moreover, rule-based expert systems are
inefficient in solving complicated medical tasks or for creating insights using
big data. Deep learning has emerged as a more accurate and effective technology
in a wide range of medical problems such as diagnosis, prediction and
intervention. Deep learning is a representation learning method that consists
of layers that transform the data non-linearly, thus, revealing hierarchical
relationships and structures. In this review we survey deep learning
application papers that use structured data, signal and imaging modalities from
cardiology. We discuss the advantages and limitations of applying deep learning
in cardiology that also apply in medicine in general, while proposing certain
directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table
CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples
Phylogenetic trees based on copy number alterations (CNAs) for multi-region samples of a single cancer patient are helpful to understand the spatio-temporal evolution of cancers, especially in tumours driven by chromosomal instability. Due to the high cost of deep sequencing data, low-coverage data are more accessible in practice, which only allow the calling of (relative) total copy numbers due to the lower resolution. However, methods to reconstruct sample phylogenies from CNAs often use allele-specific copy numbers and those using total copy number are mostly distance matrix or maximum parsimony methods which do not handle temporal data or estimate mutation rates. In this work, we developed a new maximum likelihood method based on a novel evolutionary model of CNAs, CNETML, to infer phylogenies from spatio-temporal samples taken within a single patient. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers when samples were taken at different time points. Our extensive simulations suggest CNETML performed well even on relative copy numbers with subclonal whole genome doubling events and under slight violation of model assumptions. The application of CNETML to real data from Barrett’s esophagus patients also generated consistent results with previous discoveries and novel early CNAs for further investigations
Modality Cycles with Masked Conditional Diffusion for Unsupervised Anomaly Segmentation in MRI
Unsupervised anomaly segmentation aims to detect patterns that are distinct
from any patterns processed during training, commonly called abnormal or
out-of-distribution patterns, without providing any associated manual
segmentations. Since anomalies during deployment can lead to model failure,
detecting the anomaly can enhance the reliability of models, which is valuable
in high-risk domains like medical imaging. This paper introduces Masked
Modality Cycles with Conditional Diffusion (MMCCD), a method that enables
segmentation of anomalies across diverse patterns in multimodal MRI. The method
is based on two fundamental ideas. First, we propose the use of cyclic modality
translation as a mechanism for enabling abnormality detection.
Image-translation models learn tissue-specific modality mappings, which are
characteristic of tissue physiology. Thus, these learned mappings fail to
translate tissues or image patterns that have never been encountered during
training, and the error enables their segmentation. Furthermore, we combine
image translation with a masked conditional diffusion model, which attempts to
`imagine' what tissue exists under a masked area, further exposing unknown
patterns as the generative model fails to recreate them. We evaluate our method
on a proxy task by training on healthy-looking slices of BraTS2021
multi-modality MRIs and testing on slices with tumors. We show that our method
compares favorably to previous unsupervised approaches based on image
reconstruction and denoising with autoencoders and diffusion models.Comment: Accepted in Multiscale Multimodal Medical Imaging workshop in MICCAI
202
An integrated Bayesian analysis of LOH and copy number data
Background: Cancer and other disorders are due to genomic lesions. SNP-microarrays are able to measure simultaneously both genotype and copy number (CN) at several Single Nucleotide Polymorphisms (SNPs) along the genome. CN is defined as the number of DNA copies, and the normal is two, since we have two copies of each chromosome. The genotype of a SNP is the status given by the nucleotides (alleles) which are present on the two copies of DNA. It is defined homozygous or heterozygous if the two alleles are the same or if they differ, respectively. Loss of heterozygosity (LOH) is the loss of the heterozygous status due to genomic events. Combining CN and LOH data, it is possible to better identify different types of genomic aberrations. For example, a long sequence of homozygous SNPs might be caused by either the physical loss of one copy or a uniparental disomy event (UPD), i.e. each SNP has two identical nucleotides both derived from only one parent. In this situation, the knowledge of the CN can help in distinguishing between these two events. Results: To better identify genomic aberrations, we propose a method (called gBPCR) which infers the type of aberration occurred, taking into account all the possible influence in the microarray detection of the homozygosity status of the SNPs, resulting from an altered CN level. Namely, we model the distributions of the detected genotype, given a specific genomic alteration and we estimate the parameters involved on public referenc
Multi-Scale Information, Network, Causality, and Dynamics: Mathematical Computation and Bayesian Inference to Cognitive Neuroscience and Aging
The human brain is estimated to contain 100 billion or so neurons and 10 thousand times as many connections. Neurons never function in isolation: each of them is connected to 10, 000 others and they interact extensively every millisecond. Brain cells are organized into neural circuits often in a dynamic way, processing specific types of information and providing th
Deep Causal Learning for Robotic Intelligence
This invited review discusses causal learning in the context of robotic
intelligence. The paper introduced the psychological findings on causal
learning in human cognition, then it introduced the traditional statistical
solutions on causal discovery and causal inference. The paper reviewed recent
deep causal learning algorithms with a focus on their architectures and the
benefits of using deep nets and discussed the gap between deep causal learning
and the needs of robotic intelligence
- …