scholarly journals Deep learning in systems medicine

2020 ◽  
Author(s):  
Haiying Wang ◽  
Estelle Pujos-Guillot ◽  
Blandine Comte ◽  
Joao Luis de Miranda ◽  
Vojtech Spiwok ◽  
...  
Keyword(s):  
Deep Learning ◽  
Precision Medicine ◽  
Human Body ◽  
Review Paper ◽  
Heterogeneous Data ◽  
Clinical Impact ◽  
High Dimensional ◽  
Great Promise ◽  
Systems Medicine ◽  
Prevention And Treatment

Abstract Systems medicine (SM) has emerged as a powerful tool for studying the human body at the systems level with the aim of improving our understanding, prevention and treatment of complex diseases. Being able to automatically extract relevant features needed for a given task from high-dimensional, heterogeneous data, deep learning (DL) holds great promise in this endeavour. This review paper addresses the main developments of DL algorithms and a set of general topics where DL is decisive, namely, within the SM landscape. It discusses how DL can be applied to SM with an emphasis on the applications to predictive, preventive and precision medicine. Several key challenges have been highlighted including delivering clinical impact and improving interpretability. We used some prototypical examples to highlight the relevance and significance of the adoption of DL in SM, one of them is involving the creation of a model for personalized Parkinson’s disease. The review offers valuable insights and informs the research in DL and SM.

scholarly journals Precision Therapy of Head and Neck Squamous Cell Carcinoma

2018 ◽  
Vol 97 (6) ◽  
pp. 614-621 ◽  
Author(s):  
P.J. Polverini ◽  
N.J. D’Silva ◽  
Y.L. Lei
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Precision Medicine ◽  
Squamous Cell ◽  
Response To Therapy ◽  
Neck Squamous Cell Carcinoma ◽  
Great Promise ◽  
Prevention And Treatment ◽  
Precision Therapy

Precision medicine is an approach to disease prevention and treatment that takes into account genetic variability and environmental and lifestyle influences that are unique to each patient. It facilitates stratification of patient populations that vary in their susceptibility to disease and response to therapy. Shared databases and the implementation of new technology systems designed to advance the integration of this information will enable health care providers to more accurately predict and customize prevention and treatment strategies for patients. Although precision medicine has had a limited impact in most areas of medicine, it has been shown to be an increasingly successful approach to cancer therapy. Despite early promising results targeting aberrant signaling pathways or inhibitors designed to block tumor-driven processes such as angiogenesis, limited success emphasizes the need to discover new biomarkers and treatment targets that are more reliable in predicting response to therapy and result in better health outcomes. Recent successes in the use of immunity-inducing antibodies have stimulated increased interest in the use of precision immunotherapy of head and neck squamous cell carcinoma. Using next-generation sequencing, the precise profiling of tumor-infiltrating lymphocytes has great promise to identify hypoimmunogenic cancer that would benefit from a rationally designed combinatorial approach. Continued interrogation of tumors will reveal new actionable targets with increasing therapeutic efficacy and fulfill the promise of precision therapy of head and neck cancer.

Deep Learning in the Study of Protein-Related Interactions

2020 ◽  
Vol 27 (5) ◽  
pp. 359-369 ◽  
Author(s):  
Cheng Shi ◽  
Jiaxing Chen ◽  
Xinyue Kang ◽  
Guiling Zhao ◽  
Xingzhen Lao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Physiological Data ◽  
Great Promise ◽  
Complex Data ◽  
Protein Protein Interactions ◽  
Learning Patterns ◽  
Introductory Overview ◽  
Protein Research ◽  
Neural Network Theory

: Protein-related interaction prediction is critical to understanding life processes, biological functions, and mechanisms of drug action. Experimental methods used to determine proteinrelated interactions have always been costly and inefficient. In recent years, advances in biological and medical technology have provided us with explosive biological and physiological data, and deep learning-based algorithms have shown great promise in extracting features and learning patterns from complex data. At present, deep learning in protein research has emerged. In this review, we provide an introductory overview of the deep neural network theory and its unique properties. Mainly focused on the application of this technology in protein-related interactions prediction over the past five years, including protein-protein interactions prediction, protein-RNA\DNA, Protein– drug interactions prediction, and others. Finally, we discuss some of the challenges that deep learning currently faces.

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

scholarly journals Unsupervised Multi-Level Feature Extraction for Improvement of Hyperspectral Classification

2021 ◽  
Vol 13 (8) ◽  
pp. 1602
Author(s):  
Qiaoqiao Sun ◽  
Xuefeng Liu ◽  
Salah Bourennane
Keyword(s):  
Feature Extraction ◽  
Deep Learning ◽  
Spatial Information ◽  
Hyperspectral Data ◽  
Great Promise ◽  
Learning Models ◽  
Single Level ◽  
Multiple Networks ◽  
Multi Level ◽  
Hyperspectral Classification

Deep learning models have strong abilities in learning features and they have been successfully applied in hyperspectral images (HSIs). However, the training of most deep learning models requires labeled samples and the collection of labeled samples are labor-consuming in HSI. In addition, single-level features from a single layer are usually considered, which may result in the loss of some important information. Using multiple networks to obtain multi-level features is a solution, but at the cost of longer training time and computational complexity. To solve these problems, a novel unsupervised multi-level feature extraction framework that is based on a three dimensional convolutional autoencoder (3D-CAE) is proposed in this paper. The designed 3D-CAE is stacked by fully 3D convolutional layers and 3D deconvolutional layers, which allows for the spectral-spatial information of targets to be mined simultaneously. Besides, the 3D-CAE can be trained in an unsupervised way without involving labeled samples. Moreover, the multi-level features are directly obtained from the encoded layers with different scales and resolutions, which is more efficient than using multiple networks to get them. The effectiveness of the proposed multi-level features is verified on two hyperspectral data sets. The results demonstrate that the proposed method has great promise in unsupervised feature learning and can help us to further improve the hyperspectral classification when compared with single-level features.

scholarly journals Interpretable deep learning for the remote characterisation of ambulation in multiple sclerosis using smartphones

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrew P. Creagh ◽  
Florian Lipsmeier ◽  
Michael Lindemann ◽  
Maarten De Vos
Keyword(s):  
Multiple Sclerosis ◽  
Deep Learning ◽  
Inertial Sensor ◽  
Heterogeneous Data ◽  
Fine Tuning ◽  
Sensor Data ◽  
Support Vector ◽  
Deep Convolutional Neural Networks ◽  
Healthcare Applications ◽  
Feature Based

AbstractThe emergence of digital technologies such as smartphones in healthcare applications have demonstrated the possibility of developing rich, continuous, and objective measures of multiple sclerosis (MS) disability that can be administered remotely and out-of-clinic. Deep Convolutional Neural Networks (DCNN) may capture a richer representation of healthy and MS-related ambulatory characteristics from the raw smartphone-based inertial sensor data than standard feature-based methodologies. To overcome the typical limitations associated with remotely generated health data, such as low subject numbers, sparsity, and heterogeneous data, a transfer learning (TL) model from similar large open-source datasets was proposed. Our TL framework leveraged the ambulatory information learned on human activity recognition (HAR) tasks collected from wearable smartphone sensor data. It was demonstrated that fine-tuning TL DCNN HAR models towards MS disease recognition tasks outperformed previous Support Vector Machine (SVM) feature-based methods, as well as DCNN models trained end-to-end, by upwards of 8–15%. A lack of transparency of “black-box” deep networks remains one of the largest stumbling blocks to the wider acceptance of deep learning for clinical applications. Ensuing work therefore aimed to visualise DCNN decisions attributed by relevance heatmaps using Layer-Wise Relevance Propagation (LRP). Through the LRP framework, the patterns captured from smartphone-based inertial sensor data that were reflective of those who are healthy versus people with MS (PwMS) could begin to be established and understood. Interpretations suggested that cadence-based measures, gait speed, and ambulation-related signal perturbations were distinct characteristics that distinguished MS disability from healthy participants. Robust and interpretable outcomes, generated from high-frequency out-of-clinic assessments, could greatly augment the current in-clinic assessment picture for PwMS, to inform better disease management techniques, and enable the development of better therapeutic interventions.

scholarly journals A Review of Recent Deep Learning Approaches in Human-Centered Machine Learning

Sensors ◽  
2021 ◽  
Vol 21 (7) ◽  
pp. 2514
Author(s):  
Tharindu Kaluarachchi ◽  
Andrew Reis ◽  
Suranga Nanayakkara
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Review Paper ◽  
Learning Systems ◽  
Learning Approaches ◽  
Application Development ◽  
Research Gaps ◽  
Domain Experts ◽  
Working Definition ◽  
Real World Application

After Deep Learning (DL) regained popularity recently, the Artificial Intelligence (AI) or Machine Learning (ML) field is undergoing rapid growth concerning research and real-world application development. Deep Learning has generated complexities in algorithms, and researchers and users have raised concerns regarding the usability and adoptability of Deep Learning systems. These concerns, coupled with the increasing human-AI interactions, have created the emerging field that is Human-Centered Machine Learning (HCML). We present this review paper as an overview and analysis of existing work in HCML related to DL. Firstly, we collaborated with field domain experts to develop a working definition for HCML. Secondly, through a systematic literature review, we analyze and classify 162 publications that fall within HCML. Our classification is based on aspects including contribution type, application area, and focused human categories. Finally, we analyze the topology of the HCML landscape by identifying research gaps, highlighting conflicting interpretations, addressing current challenges, and presenting future HCML research opportunities.

No Gain, No Pain: Ethics and the Genomic Revolution

2008 ◽  
Vol 89 (4) ◽  
pp. 562-570 ◽  
Author(s):  
Martin T. Hall ◽  
Anna Scheyett ◽  
Kimberly Strom-Gottfried
Keyword(s):  
Social Workers ◽  
Ethical Issues ◽  
Continuing Professional Development ◽  
Self Determination ◽  
Great Promise ◽  
Prevention And Treatment ◽  
Genetics Knowledge ◽  
Genetic Science ◽  
Genetic Contributions ◽  
Genomic Revolution

The mapping of the human genome and scientific discoveries regarding genetic contributions to disease hold great promise for the prevention and treatment of an array of conditions. Social workers and other professionals must keep abreast of these developments and the ethical dimensions of such progress. Familiar ethical provisions such as confidentiality, informed consent, self-determination, and social justice take on new meaning in light of innovations in genetic science. This article reviews ethical issues and practice implications emerging from advances in genetics knowledge, and it suggests mechanisms for continuing professional development and involvement in this important area.

scholarly journals Nesting Monte Carlo for high-dimensional non-linear PDEs

2018 ◽  
Vol 24 (4) ◽  
pp. 225-247 ◽  
Author(s):  
Xavier Warin
Keyword(s):  
Monte Carlo ◽  
Deep Learning ◽  
High Dimension ◽  
Analytical Solutions ◽  
New Method ◽  
Computational Time ◽  
High Dimensional ◽  
Learning Methods ◽  
Lipschitz Constants ◽  
Linear Pdes

Abstract A new method based on nesting Monte Carlo is developed to solve high-dimensional semi-linear PDEs. Depending on the type of non-linearity, different schemes are proposed and theoretically studied: variance error are given and it is shown that the bias of the schemes can be controlled. The limitation of the method is that the maturity or the Lipschitz constants of the non-linearity should not be too high in order to avoid an explosion of the computational time. Many numerical results are given in high dimension for cases where analytical solutions are available or where some solutions can be computed by deep-learning methods.

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