Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

A survey on deep learning in medical image analysis

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.

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Attention U-Net: Learning Where to Look for the Pancreas

In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies.

Deep learning in bioinformatics

Attention gated networks: Learning to leverage salient regions in medical images.

Imaging of cancer with 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) has become a standard component of diagnosis and staging in oncology, and is becoming more important as a quantitative monitor of individual response to therapy. In this article we investigate the challenging problem of predicting a patient's response to neoadjuvant chemotherapy from a single 18F-FDG PET scan taken prior to treatment. We take a "radiomics" approach whereby a large amount of quantitative features is automatically extracted from pretherapy PET images in order to build a comprehensive quantification of the tumor phenotype. While the dominant methodology relies on hand-crafted texture features, we explore the potential of automatically learning low- to high-level features directly from PET scans. We report on a study that compares the performance of two competing radiomics strategies: an approach based on state-of-the-art statistical classifiers using over 100 quantitative imaging descriptors, including texture features as well as standardized uptake values, and a convolutional neural network, 3S-CNN, trained directly from PET scans by taking sets of adjacent intra-tumor slices. Our experimental results, based on a sample of 107 patients with esophageal cancer, provide initial evidence that convolutional neural networks have the potential to extract PET imaging representations that are highly predictive of response to therapy. On this dataset, 3S-CNN achieves an average 80.7% sensitivity and 81.6% specificity in predicting non-responders, and outperforms other competing predictive models.

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Predicting Response to Neoadjuvant Chemotherapy with PET Imaging Using Convolutional Neural Networks.

Learning to detect chest radiographs containing pulmonary lesions using visual attention networks

Background 
There are no widely used models in clinical care to predict outcome in acute lower gastro-intestinal bleeding (ALGIB). If available these could help triage patients at presentation to appropriate levels of care/intervention and improve medical resource utilisation. We aimed to apply a state-of-the-art machine learning classifier, gradient boosting (GB), to predict outcome in ALGIB using non-endoscopic measurements as predictors.


Methods 
Non-endoscopic variables from patients with ALGIB attending the emergency departments of two teaching hospitals were analysed retrospectively for training/internal validation (n=170) and external validation (n=130) of the GB model. The performance of the GB algorithm in predicting recurrent bleeding, clinical intervention and severe bleeding was compared to a multiple logic regression (MLR) model and two published MLR-based prediction algorithms (BLEED and Strate prediction rule).


Results 
The GB algorithm had the best negative predictive values for the chosen outcomes (>88%). On internal validation the accuracy of the GB algorithm for predicting recurrent bleeding, therapeutic intervention and severe bleeding were (88%, 88% and 78% respectively) and superior to the BLEED classification (64%, 68% and 63%), Strate prediction rule (78%, 78%, 67%) and conventional MLR (74%, 74% 62%). On external validation the accuracy was similar to conventional MLR for recurrent bleeding (88% vs. 83%) and therapeutic intervention (91% vs. 87%) but superior for severe bleeding (83% vs. 71%).


Conclusion 
The gradient boosting algorithm accurately predicts outcome in patients with acute lower gastrointestinal bleeding and outperforms multiple logistic regression based models. These may be useful for risk stratification of patients on presentation to the emergency department.

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Prediction of Outcome in Acute Lower Gastrointestinal Bleeding Using Gradient Boosting

X-rays are commonly performed imaging tests that use small amounts of radiation to produce pictures of the organs, tissues, and bones of the body. X-rays of the chest are used to detect abnormalities or diseases of the airways, blood vessels, bones, heart, and lungs. In this work we present a stochastic attention-based model that is capable of learning what regions within a chest X-ray scan should be visually explored in order to conclude that the scan contains a specific radiological abnormality. The proposed model is a recurrent neural network (RNN) that learns to sequentially sample the entire X-ray and focus only on informative areas that are likely to contain the relevant information. We report on experiments carried out with more than $100,000$ X-rays containing enlarged hearts or medical devices. The model has been trained using reinforcement learning methods to learn task-specific policies.

Learning what to look in chest X-rays with a recurrent visual attention model

Computed tomography (CT) generates a stack of cross-sectional images covering a region of the body. The visual assessment of these images for the identification of potential abnormalities is a challenging and time consuming task due to the large amount of information that needs to be processed. In this article we propose a deep artificial neural network architecture, ReCTnet, for the fully-automated detection of pulmonary nodules in CT scans. The architecture learns to distinguish nodules and normal structures at the pixel level and generates three-dimensional probability maps highlighting areas that are likely to harbour the objects of interest. Convolutional and recurrent layers are combined to learn expressive image representations exploiting the spatial dependencies across axial slices. We demonstrate that leveraging intra-slice dependencies substantially increases the sensitivity to detect pulmonary nodules without inflating the false positive rate. On the publicly available LIDC/IDRI dataset consisting of 1,018 annotated CT scans, ReCTnet reaches a detection sensitivity of 90.5% with an average of 4.5 false positives per scan. Comparisons with a competing multi-channel convolutional neural network for multi-slice segmentation and other published methodologies using the same dataset provide evidence that ReCTnet offers significant performance gains.

Petros-Pavlos Ypsilantis

Papers

Predicting Response to Neoadjuvant Chemotherapy with PET Imaging Using Convolutional Neural Networks.

Learning to detect chest radiographs containing pulmonary lesions using visual attention networks

Prediction of Outcome in Acute Lower Gastrointestinal Bleeding Using Gradient Boosting

Learning what to look in chest X-rays with a recurrent visual attention model

Recurrent Convolutional Networks for Pulmonary Nodule Detection in CT Imaging.