22,475 research outputs found
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
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Translational research combining orthologous genes and human diseases with the OGOLOD dataset
OGOLOD is a Linked Open Data dataset derived from different biomedical resources by an automated pipeline, using a tailored ontology as a scaffold. The key contribution of OGOLOD is that it links, in new RDF triples, genetic human diseases and orthologous genes, paving the way for a more efficient translational biomedical research exploiting the Linked Open Data cloud
A Modified LeNet CNN for Breast Cancer Diagnosis in Ultrasound Images
Convolutional neural networks (CNNs) have been extensively utilized in medical image
processing to automatically extract meaningful features and classify various medical conditions,
enabling faster and more accurate diagnoses. In this paper, LeNet, a classic CNN architecture,
has been successfully applied to breast cancer data analysis. It demonstrates its ability to extract
discriminative features and classify malignant and benign tumors with high accuracy, thereby
supporting early detection and diagnosis of breast cancer. LeNet with corrected Rectified Linear Unit
(ReLU), a modification of the traditional ReLU activation function, has been found to improve the
performance of LeNet in breast cancer data analysis tasks via addressing the “dying ReLU” problem
and enhancing the discriminative power of the extracted features. This has led to more accurate,
reliable breast cancer detection and diagnosis and improved patient outcomes. Batch normalization
improves the performance and training stability of small and shallow CNN architecture like LeNet.
It helps to mitigate the effects of internal covariate shift, which refers to the change in the distribution
of network activations during training. This classifier will lessen the overfitting problem and reduce
the running time. The designed classifier is evaluated against the benchmarking deep learning
models, proving that this has produced a higher recognition rate. The accuracy of the breast image
recognition rate is 89.91%. This model will achieve better performance in segmentation, feature
extraction, classification, and breast cancer tumor detection
Translational Oncogenomics and Human Cancer Interactome Networks
An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general, ‘personalized medicine’. Several cancer detection techniques are currently under development both in the direction of improved detection sensitivity and increased time resolution of cellular events, with the limits of single molecule detection and picosecond time resolution already reached. The urgency for the complete mapping of a human cancer interactome with the help of such novel, high-efficiency / low-cost and ultra-sensitive techniques is also pointed out
Structured penalized regression for drug sensitivity prediction
Large-scale {\it in vitro} drug sensitivity screens are an important tool in
personalized oncology to predict the effectiveness of potential cancer drugs.
The prediction of the sensitivity of cancer cell lines to a panel of drugs is a
multivariate regression problem with high-dimensional heterogeneous multi-omics
data as input data and with potentially strong correlations between the outcome
variables which represent the sensitivity to the different drugs. We propose a
joint penalized regression approach with structured penalty terms which allow
us to utilize the correlation structure between drugs with group-lasso-type
penalties and at the same time address the heterogeneity between omics data
sources by introducing data-source-specific penalty factors to penalize
different data sources differently. By combining integrative penalty factors
(IPF) with tree-guided group lasso, we create the IPF-tree-lasso method. We
present a unified framework to transform more general IPF-type methods to the
original penalized method. Because the structured penalty terms have multiple
parameters, we demonstrate how the interval-search Efficient Parameter
Selection via Global Optimization (EPSGO) algorithm can be used to optimize
multiple penalty parameters efficiently. Simulation studies show that
IPF-tree-lasso can improve the prediction performance compared to other
lasso-type methods, in particular for heterogenous data sources. Finally, we
employ the new methods to analyse data from the Genomics of Drug Sensitivity in
Cancer project.Comment: Zhao Z, Zucknick M (2020). Structured penalized regression for drug
sensitivity prediction. Journal of the Royal Statistical Society, Series C.
19 pages, 6 figures and 2 table
Chasing a Better Decision Margin for Discriminative Histopathological Breast Cancer Image Classification
When considering a large dataset of histopathologic breast images captured at various magnification levels, the process of distinguishing between benign and malignant cancer from these images can be time-intensive. The automation of histopathological breast cancer image classification holds significant promise for expediting pathology diagnoses and reducing the analysis time. Convolutional neural networks (CNNs) have recently gained traction for their ability to more accurately classify histopathological breast cancer images. CNNs excel at extracting distinctive features that emphasize semantic information. However, traditional CNNs employing the softmax loss function often struggle to achieve the necessary discriminatory power for this task. To address this challenge, a set of angular margin-based softmax loss functions have emerged, including angular softmax (A-Softmax), large margin cosine loss (CosFace), and additive angular margin (ArcFace), each sharing a common objective: maximizing inter-class variation while minimizing intra-class variation. This study delves into these three loss functions and their potential to extract distinguishing features while expanding the decision boundary between classes. Rigorous experimentation on a well-established histopathological breast cancer image dataset, BreakHis, has been conducted. As per the results, it is evident that CosFace focuses on augmenting the differences between classes, while A-Softmax and ArcFace tend to emphasize augmenting within-class variations. These observations underscore the efficacy of margin penalties on angular softmax losses in enhancing feature discrimination within the embedding space. These loss functions consistently outperform softmax-based techniques, either by widening the gaps among classes or enhancing the compactness of individual classes
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