Dataset Information

A technical review of canonical correlation analysis for neuroscience applications.

ABSTRACT: Collecting comprehensive data sets of the same subject has become a standard in neuroscience research and uncovering multivariate relationships among collected data sets have gained significant attentions in recent years. Canonical correlation analysis (CCA) is one of the powerful multivariate tools to jointly investigate relationships among multiple data sets, which can uncover disease or environmental effects in various modalities simultaneously and characterize changes during development, aging, and disease progressions comprehensively. In the past 10?years, despite an increasing number of studies have utilized CCA in multivariate analysis, simple conventional CCA dominates these applications. Multiple CCA-variant techniques have been proposed to improve the model performance; however, the complicated multivariate formulations and not well-known capabilities have delayed their wide applications. Therefore, in this study, a comprehensive review of CCA and its variant techniques is provided. Detailed technical formulation with analytical and numerical solutions, current applications in neuroscience research, and advantages and limitations of each CCA-related technique are discussed. Finally, a general guideline in how to select the most appropriate CCA-related technique based on the properties of available data sets and particularly targeted neuroscience questions is provided.

SUBMITTER: Zhuang X

PROVIDER: S-EPMC7416047 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A technical review of canonical correlation analysis for neuroscience applications.

Zhuang Xiaowei X Yang Zhengshi Z Cordes Dietmar D

Human brain mapping 20200627 13

Collecting comprehensive data sets of the same subject has become a standard in neuroscience research and uncovering multivariate relationships among collected data sets have gained significant attentions in recent years. Canonical correlation analysis (CCA) is one of the powerful multivariate tools to jointly investigate relationships among multiple data sets, which can uncover disease or environmental effects in various modalities simultaneously and characterize changes during development, agi ...[more]

PMID: 32592530

Similar Datasets

Project description:BackgroundChatbots are applications that can conduct natural language conversations with users. In the medical field, chatbots have been developed and used to serve different purposes. They provide patients with timely information that can be critical in some scenarios, such as access to mental health resources. Since the development of the first chatbot, ELIZA, in the late 1960s, much effort has followed to produce chatbots for various health purposes developed in different ways.ObjectiveThis study aimed to explore the technical aspects and development methodologies associated with chatbots used in the medical field to explain the best methods of development and support chatbot development researchers on their future work.MethodsWe searched for relevant articles in 8 literature databases (IEEE, ACM, Springer, ScienceDirect, Embase, MEDLINE, PsycINFO, and Google Scholar). We also performed forward and backward reference checking of the selected articles. Study selection was performed by one reviewer, and 50% of the selected studies were randomly checked by a second reviewer. A narrative approach was used for result synthesis. Chatbots were classified based on the different technical aspects of their development. The main chatbot components were identified in addition to the different techniques for implementing each module.ResultsThe original search returned 2481 publications, of which we identified 45 studies that matched our inclusion and exclusion criteria. The most common language of communication between users and chatbots was English (n=23). We identified 4 main modules: text understanding module, dialog management module, database layer, and text generation module. The most common technique for developing text understanding and dialogue management is the pattern matching method (n=18 and n=25, respectively). The most common text generation is fixed output (n=36). Very few studies relied on generating original output. Most studies kept a medical knowledge base to be used by the chatbot for different purposes throughout the conversations. A few studies kept conversation scripts and collected user data and previous conversations.ConclusionsMany chatbots have been developed for medical use, at an increasing rate. There is a recent, apparent shift in adopting machine learning-based approaches for developing chatbot systems. Further research can be conducted to link clinical outcomes to different chatbot development techniques and technical characteristics.

Project description:The emergence of high-throughput genomic datasets from different sources and platforms (e.g., gene expression, single nucleotide polymorphisms (SNP), and copy number variation (CNV)) has greatly enhanced our understandings of the interplay of these genomic factors as well as their influences on the complex diseases. It is challenging to explore the relationship between these different types of genomic data sets. In this paper, we focus on a multivariate statistical method, canonical correlation analysis (CCA) method for this problem. Conventional CCA method does not work effectively if the number of data samples is significantly less than that of biomarkers, which is a typical case for genomic data (e.g., SNPs). Sparse CCA (sCCA) methods were introduced to overcome such difficulty, mostly using penalizations with l-1 norm (CCA-l1) or the combination of l-1and l-2 norm (CCA-elastic net). However, they overlook the structural or group effect within genomic data in the analysis, which often exist and are important (e.g., SNPs spanning a gene interact and work together as a group).We propose a new group sparse CCA method (CCA-sparse group) along with an effective numerical algorithm to study the mutual relationship between two different types of genomic data (i.e., SNP and gene expression). We then extend the model to a more general formulation that can include the existing sCCA models. We apply the model to feature/variable selection from two data sets and compare our group sparse CCA method with existing sCCA methods on both simulation and two real datasets (human gliomas data and NCI60 data). We use a graphical representation of the samples with a pair of canonical variates to demonstrate the discriminating characteristic of the selected features. Pathway analysis is further performed for biological interpretation of those features.The CCA-sparse group method incorporates group effects of features into the correlation analysis while performs individual feature selection simultaneously. It outperforms the two sCCA methods (CCA-l1 and CCA-group) by identifying the correlated features with more true positives while controlling total discordance at a lower level on the simulated data, even if the group effect does not exist or there are irrelevant features grouped with true correlated features. Compared with our proposed CCA-group sparse models, CCA-l1 tends to select less true correlated features while CCA-group inclines to select more redundant features.

Dataset Information

A technical review of canonical correlation analysis for neuroscience applications.

Publications

A technical review of canonical correlation analysis for neuroscience applications.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets