Abstract Motivation Multimodal profiling strategies promise to produce more informative insights into biomedical cohorts via the integration of the information each modality contributes. To perform ...this integration, however, the development of novel analytical strategies is needed. Multimodal profiling strategies often come at the expense of lower sample numbers, which can challenge methods to uncover shared signals across a cohort. Thus, factor analysis approaches are commonly used for the analysis of high-dimensional data in molecular biology, however, they typically do not yield representations that are directly interpretable, whereas many research questions often center around the analysis of pathways associated with specific observations. Results We develop PathFA, a novel approach for multimodal factor analysis over the space of pathways. PathFA produces integrative and interpretable views across multimodal profiling technologies, which allow for the derivation of concrete hypotheses. PathFA combines a pathway-learning approach with integrative multimodal capability under a Bayesian procedure that is efficient, hyper-parameter free, and able to automatically infer observation noise from the data. We demonstrate strong performance on small sample sizes within our simulation framework and on matched proteomics and transcriptomics profiles from real tumor samples taken from the Swiss Tumor Profiler consortium. On a subcohort of melanoma patients, PathFA recovers pathway activity that has been independently associated with poor outcome. We further demonstrate the ability of this approach to identify pathways associated with the presence of specific cell-types as well as tumor heterogeneity. Our results show that we capture known biology, making it well suited for analyzing multimodal sample cohorts. Availability and implementation The tool is implemented in python and available at https://github.com/ratschlab/path-fa
Abstract
Gaining knowledge and actionable insights from complex, high-dimensional and heterogeneous biomedical data remains a key challenge in transforming health care. Various types of data have ...been emerging in modern biomedical research, including electronic health records, imaging, -omics, sensor data and text, which are complex, heterogeneous, poorly annotated and generally unstructured. Traditional data mining and statistical learning approaches typically need to first perform feature engineering to obtain effective and more robust features from those data, and then build prediction or clustering models on top of them. There are lots of challenges on both steps in a scenario of complicated data and lacking of sufficient domain knowledge. The latest advances in deep learning technologies provide new effective paradigms to obtain end-to-end learning models from complex data. In this article, we review the recent literature on applying deep learning technologies to advance the health care domain. Based on the analyzed work, we suggest that deep learning approaches could be the vehicle for translating big biomedical data into improved human health. However, we also note limitations and needs for improved methods development and applications, especially in terms of ease-of-understanding for domain experts and citizen scientists. We discuss such challenges and suggest developing holistic and meaningful interpretable architectures to bridge deep learning models and human interpretability.
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Machine learning has become a pivotal tool for many projects in computational biology, bioinformatics, and health informatics. Nevertheless, beginners and biomedical researchers often do not have ...enough experience to run a data mining project effectively, and therefore can follow incorrect practices, that may lead to common mistakes or over-optimistic results. With this review, we present ten quick tips to take advantage of machine learning in any computational biology context, by avoiding some common errors that we observed hundreds of times in multiple bioinformatics projects. We believe our ten suggestions can strongly help any machine learning practitioner to carry on a successful project in computational biology and related sciences.
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The birth of wireless communication systems nearly 1 century ago has transformed and redefined the way humans communicate and interact. This transformation, which has opened boundaries between ...societies and eliminated cultural barriers, has evolved from the original paradigm of wireless electromagnetic communication systems. This paradigm has experienced numerous evolutionary developments that have not only brought along seamless connectivity for human interactions but also communication between machines and devices.
COVID-19 outbreak has put the whole world in an unprecedented difficult situation bringing life around the world to a frightening halt and claiming thousands of lives. Due to COVID-19's spread in 212 ...countries and territories and increasing numbers of infected cases and death tolls mounting to 5,212,172 and 334,915 (as of May 22 2020), it remains a real threat to the public health system. This paper renders a response to combat the virus through Artificial Intelligence (AI). Some Deep Learning (DL) methods have been illustrated to reach this goal, including Generative Adversarial Networks (GANs), Extreme Learning Machine (ELM), and Long/Short Term Memory (LSTM). It delineates an integrated bioinformatics approach in which different aspects of information from a continuum of structured and unstructured data sources are put together to form the user-friendly platforms for physicians and researchers. The main advantage of these AI-based platforms is to accelerate the process of diagnosis and treatment of the COVID-19 disease. The most recent related publications and medical reports were investigated with the purpose of choosing inputs and targets of the network that could facilitate reaching a reliable Artificial Neural Network-based tool for challenges associated with COVID-19. Furthermore, there are some specific inputs for each platform, including various forms of the data, such as clinical data and medical imaging which can improve the performance of the introduced approaches toward the best responses in practical applications.
Deep Learning and Its Applications in Biomedicine Cao, Chensi; Liu, Feng; Tan, Hai ...
Genomics, Proteomics & Bioinformatics/Genomics, proteomics and bioinformatics,
02/2018, Volume:
16, Issue:
1
Journal Article
Peer reviewed
Open access
Advances in biological and medical technologies have been providing us explosive volumes of biological and physiological data, such as medical images, electroencephalography, genomic and protein ...sequences. Learning from these data facilitates the understanding of human health and disease. Developed from artificial neural networks, deep learning-based algorithms show great promise in extracting features and learning patterns from complex data. The aim of this paper is to provide an overview of deep learning techniques and some of the state-of-the-art applications in the biomedical field. We first introduce the development of artificial neural network and deep learning. We then describe two main components of deep learning, i.e., deep learning architectures and model optimization. Subsequently, some examples are demonstrated for deep learning applications, including medical image classification, genomic sequence analysis, as well as protein structure classification and prediction. Finally, we offer our perspectives for the future directions in the field of deep learning.
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Cardiovascular diseases kill approximately 17 million people globally every year, and they mainly exhibit as myocardial infarctions and heart failures. Heart failure (HF) occurs when the heart cannot ...pump enough blood to meet the needs of the body.Available electronic medical records of patients quantify symptoms, body features, and clinical laboratory test values, which can be used to perform biostatistics analysis aimed at highlighting patterns and correlations otherwise undetectable by medical doctors. Machine learning, in particular, can predict patients' survival from their data and can individuate the most important features among those included in their medical records.
In this paper, we analyze a dataset of 299 patients with heart failure collected in 2015. We apply several machine learning classifiers to both predict the patients survival, and rank the features corresponding to the most important risk factors. We also perform an alternative feature ranking analysis by employing traditional biostatistics tests, and compare these results with those provided by the machine learning algorithms. Since both feature ranking approaches clearly identify serum creatinine and ejection fraction as the two most relevant features, we then build the machine learning survival prediction models on these two factors alone.
Our results of these two-feature models show not only that serum creatinine and ejection fraction are sufficient to predict survival of heart failure patients from medical records, but also that using these two features alone can lead to more accurate predictions than using the original dataset features in its entirety. We also carry out an analysis including the follow-up month of each patient: even in this case, serum creatinine and ejection fraction are the most predictive clinical features of the dataset, and are sufficient to predict patients' survival.
This discovery has the potential to impact on clinical practice, becoming a new supporting tool for physicians when predicting if a heart failure patient will survive or not. Indeed, medical doctors aiming at understanding if a patient will survive after heart failure may focus mainly on serum creatinine and ejection fraction.
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•A summary of clinical background of MDD and BD, Brain structure and EEG based brain activity,•EEG experimental protocols study for mental disorders diagnosis,•An extensive study of state-of-the-art ...shallow and deep neural networks models for EEG based clinical depression detection,•An extensive study of neural networks based approaches for Biploar Disorder diagnosis using EEG signals,•A discussion of state-of-the-art methods limitations and giving valuable recommendations for future research
Mental disorders represent critical public health challenges as they are leading contributors to the global burden of disease and intensely influence social and financial welfare of individuals. The present comprehensive review concentrate on the two mental disorders: Major depressive Disorder (MDD) and Bipolar Disorder (BD) with noteworthy publications during the last ten years. There is a big need nowadays for phenotypic characterization of psychiatric disorders with biomarkers. Electroencephalography (EEG) signals could offer a rich signature for MDD and BD and then they could improve understanding of pathophysiological mechanisms underling these mental disorders. In this review, we focus on the literature works adopting neural networks fed by EEG signals. Among those studies using EEG and neural networks, we have discussed a variety of EEG based protocols, biomarkers and public datasets for depression and bipolar disorder detection. We conclude with a discussion and valuable recommendations that will help to improve the reliability of developed models and for more accurate and more deterministic computational intelligence based systems in psychiatry. This review will prove to be a structured and valuable initial point for the researchers working on depression and bipolar disorders recognition by using EEG signals.
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Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic ...health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10−16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.
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•Analyzing “big data” can be extremely challenging, especially in biomedical fields.•TDA approaches may uncover insights from data missed by traditional analysis.•TDA converts large, ...complex data sets into simple summaries of their key features.•Applications of TDA include precision medicine, structural biology, cell phenotyping.
Significant technological advances made in recent years have shepherded a dramatic increase in utilization of digital technologies for biomedicine– everything from the widespread use of electronic health records to improved medical imaging capabilities and the rising ubiquity of genomic sequencing contribute to a “digitization” of biomedical research and clinical care. With this shift toward computerized tools comes a dramatic increase in the amount of available data, and current tools for data analysis capable of extracting meaningful knowledge from this wealth of information have yet to catch up. This article seeks to provide an overview of emerging mathematical methods with the potential to improve the abilities of clinicians and researchers to analyze biomedical data, but may be hindered from doing so by a lack of conceptual accessibility and awareness in the life sciences research community. In particular, we focus on topological data analysis (TDA), a set of methods grounded in the mathematical field of algebraic topology that seeks to describe and harness features related to the “shape” of data. We aim to make such techniques more approachable to non-mathematicians by providing a conceptual discussion of their theoretical foundations followed by a survey of their published applications to scientific research. Finally, we discuss the limitations of these methods and suggest potential avenues for future work integrating mathematical tools into clinical care and biomedical informatics.
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