Deep Learning for Genomics: A Concise Overview

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning since we are expecting from deep learning a superhuman intelligence that explores beyond our knowledge to interpret the genome. A powerful deep learning model should rely on insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with a proper deep architecture, and remark on practical considerations of developing modern deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research, as well as pointing out potential opportunities and obstacles for future genomics applications.Comment: Invited chapter for Springer Book: Handbook of Deep Learning Application

Automatic segmentation and classification methods using optical coherence tomography angiography (Octa): A review and handbook

Optical coherence tomography angiography (OCTA) is a promising technology for the non-invasive imaging of vasculature. Many studies in literature present automated algorithms to quantify OCTA images, but there is a lack of a review on the most common methods and their comparison considering multiple clinical applications (e.g., ophthalmology and dermatology). Here, we aim to provide readers with a useful review and handbook for automatic segmentation and classification methods using OCTA images, presenting a comparison of techniques found in the literature based on the adopted segmentation or classification method and on the clinical application. Another goal of this study is to provide insight into the direction of research in automated OCTA image analysis, especially in the current era of deep learning

Migrating Knowledge between Physical Scenarios based on Artificial Neural Networks

Deep learning is known to be data-hungry, which hinders its application in many areas of science when datasets are small. Here, we propose to use transfer learning methods to migrate knowledge between different physical scenarios and significantly improve the prediction accuracy of artificial neural networks trained on a small dataset. This method can help reduce the demand for expensive data by making use of additional inexpensive data. First, we demonstrate that in predicting the transmission from multilayer photonic film, the relative error rate is reduced by 46.8% (26.5%) when the source data comes from 10-layer (8-layer) films and the target data comes from 8-layer (10-layer) films. Second, we show that the relative error rate is decreased by 22% when knowledge is transferred between two very different physical scenarios: transmission from multilayer films and scattering from multilayer nanoparticles. Finally, we propose a multi-task learning method to improve the performance of different physical scenarios simultaneously in which each task only has a small dataset

A Boxology of Design Patterns for Hybrid Learning and Reasoning Systems

We propose a set of compositional design patterns to describe a large variety of systems that combine statistical techniques from machine learning with symbolic techniques from knowledge representation. As in other areas of computer science (knowledge engineering, software engineering, ontology engineering, process mining and others), such design patterns help to systematize the literature, clarify which combinations of techniques serve which purposes, and encourage re-use of software components. We have validated our set of compositional design patterns against a large body of recent literature.Comment: 12 pages,55 reference

A Review on the Application of Natural Computing in Environmental Informatics

Natural computing offers new opportunities to understand, model and analyze the complexity of the physical and human-created environment. This paper examines the application of natural computing in environmental informatics, by investigating related work in this research field. Various nature-inspired techniques are presented, which have been employed to solve different relevant problems. Advantages and disadvantages of these techniques are discussed, together with analysis of how natural computing is generally used in environmental research.Comment: Proc. of EnviroInfo 201

Customer purchase behavior prediction in E-commerce: a conceptual framework and research agenda

Digital retailers are experiencing an increasing number of transactions coming from their consumers online, a consequence of the convenience in buying goods via E-commerce platforms. Such interactions compose complex behavioral patterns which can be analyzed through predictive analytics to enable businesses to understand consumer needs. In this abundance of big data and possible tools to analyze them, a systematic review of the literature is missing. Therefore, this paper presents a systematic literature review of recent research dealing with customer purchase prediction in the E-commerce context. The main contributions are a novel analytical framework and a research agenda in the field. The framework reveals three main tasks in this review, namely, the prediction of customer intents, buying sessions, and purchase decisions. Those are followed by their employed predictive methodologies and are analyzed from three perspectives. Finally, the research agenda provides major existing issues for further research in the field of purchase behavior prediction online