scholarly journals Variational autoencoders for cancer data integration: design principles and computational practice

2019 ◽  
Author(s):  
Nikola Simidjievski ◽  
Cristian Bodnar ◽  
Ifrah Tariq ◽  
Paul Scherer ◽  
Helena Andres-Terre ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Clinical Data ◽  
Molecular Taxonomy ◽  
Patient Data ◽  
Data Sets ◽  
Data Types ◽  
Cancer Data ◽  
Learning Framework ◽  
Multiple Data ◽  
Multiple Data Sets

ABSTRACTInternational initiatives such as the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) are collecting multiple data sets at different genome-scales with the aim to identify novel cancer bio-markers and predict patient survival. To analyse such data, several machine learning, bioinformatics and statistical methods have been applied, among them neural networks such as autoencoders. Although these models provide a good statistical learning framework to analyse multi-omic and/or clinical data, there is a distinct lack of work on how to integrate diverse patient data and identify the optimal design best suited to the available data.In this paper, we investigate several autoencoder architectures that integrate a variety of cancer patient data types (e.g., multi-omics and clinical data). We perform extensive analyses of these approaches and provide a clear methodological and computational framework for designing systems that enable clinicians to investigate cancer traits and translate the results into clinical applications. We demonstrate how these networks can be designed, built and, in particular, applied to tasks of integrative analyses of heterogeneous breast cancer data. The results show that these approaches yield relevant data representations that, in turn, lead to accurate and stable diagnosis.

scholarly journals Coupled Co-clustering-based Unsupervised Transfer Learning for the Integrative Analysis of Single-Cell Genomic Data

2020 ◽  
Author(s):  
Pengcheng Zeng ◽  
Jiaxuan WangWu ◽  
Zhixiang Lin
Keyword(s):  
Single Cell ◽  
Transfer Learning ◽  
Learning Algorithm ◽  
Genomic Data ◽  
Integrative Analysis ◽  
Data Sets ◽  
Clustering Methods ◽  
Data Types ◽  
Multiple Data ◽  
Multiple Data Sets

AbstractUnsupervised methods, such as clustering methods, are essential to the analysis of single-cell genomic data. Most current clustering methods are designed for one data type only, such as scRNA-seq, scATAC-seq or sc-methylation data alone, and a few are developed for the integrative analysis of multiple data types. Integrative analysis of multimodal single-cell genomic data sets leverages the power in multiple data sets and can deepen the biological insight. We propose a coupled co-clustering-based unsupervised transfer learning algorithm (coupleCoC) for the integrative analysis of multimodal single-cell data. Our proposed coupleCoC builds upon the information theoretic co-clustering framework. We applied coupleCoC for the integrative analysis of scATAC-seq and scRNA-seq data, sc-methylation and scRNA-seq data, and scRNA-seq data from mouse and human. We demonstrate that coupleCoC improves the overall clustering performance and matches the cell subpopulations across multimodal single-cell genomic data sets. The software and data sets are available at https://github.com/cuhklinlab/coupleCoC.

The development of nurses’ foundational values

2021 ◽  
pp. 096973302110032
Author(s):  
Sastrawan Sastrawan ◽  
Jennifer Weller-Newton ◽  
Gabrielle Brand ◽  
Gulzar Malik
Keyword(s):  
Professional Training ◽  
Reference Points ◽  
Constructivist Grounded Theory ◽  
Professional Values ◽  
Data Sets ◽  
Value System ◽  
Institutional Values ◽  
Multiple Data ◽  
Human Ethics ◽  
Multiple Data Sets

Background: In the ever-changing and complex healthcare environment, nurses encounter challenging situations that may involve a clash between their personal and professional values resulting in a profound impact on their practice. Nevertheless, there is a dearth of literature on how nurses develop their personal–professional values. Aim: The aim of this study was to understand how nurses develop their foundational values as the base for their value system. Research design: A constructivist grounded theory methodology was employed to collect multiple data sets, including face-to-face focus group and individual interviews, along with anecdote and reflective stories. Participants and research context: Fifty-four nurses working across various nursing settings in Indonesia were recruited to participate. Ethical considerations: Ethics approval was obtained from the Monash University Human Ethics Committee, project approval number 1553. Findings: Foundational values acquisition was achieved through family upbringing, professional nurse education and organisational/institutional values reinforcement. These values are framed through three reference points: religious lens, humanity perspective and professionalism. This framing results in a unique combination of personal–professional values that comprise nurses’ values system. Values are transferred to other nurses either in a formal or informal way as part of one’s professional responsibility and customary social interaction via telling and sharing in person or through social media. Discussion: Values and ethics are inherently interweaved during nursing practice. Ethical and moral values are part of professional training, but other values are often buried in a hidden curriculum, and attained and activated through interactions during nurses’ training. Conclusion: Developing a value system is a complex undertaking that involves basic social processes of attaining, enacting and socialising values. These processes encompass several intertwined entities such as the sources of values, the pool of foundational values, value perspectives and framings, initial value structures, and methods of value transference.

scholarly journals Evaluation of daily precipitation statistics and monsoon onset/retreat over western Sahel in multiple data sets

2014 ◽  
Vol 45 (5-6) ◽  
pp. 1325-1354 ◽  
Author(s):  
Emilia Paula Diaconescu ◽  
Philippe Gachon ◽  
John Scinocca ◽  
René Laprise
Keyword(s):  
Daily Precipitation ◽  
Monsoon Onset ◽  
Data Sets ◽  
Multiple Data ◽  
Western Sahel ◽  
Multiple Data Sets

Can earning much lead to doing good? Firm performance implications for corporate social responsibility

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Siyu Hou ◽  
Zhaoyang Guo ◽  
Chuangneng Cai ◽  
Xiaobo Jiao
Keyword(s):  
Corporate Social Responsibility ◽  
Firm Performance ◽  
Social Responsibility ◽  
State Ownership ◽  
Data Sets ◽  
Content Type ◽  
Multiple Data ◽  
Instrumental Variable Regression ◽  
Multiple Data Sets ◽  
Corporate Social

Purpose The purpose of this study is to examine the influence of firm performance on corporate social responsibility (CSR) and its possible moderating effect. Despite the significance of CSR, there remains an extensive debate about how it is affected by firm performance. Design/methodology/approach The conceptual model is mainly built on goal-setting theory. Based on archival data from multiple data sets on 1,650 companies, collected from 2010 to 2017, the hypotheses are tested using the two-stage instrumental variable regression method. Findings There is an inverted U-shaped relationship between firm performance and CSR that first increases and then decreases. In addition, considering the boundary conditions, state ownership makes the inverted U-shaped curve steeper, while high executive wage concentration makes the inverted U-shaped curve flatter. Research limitations/implications This study harmonizes the traditional contradictory findings of the influence of firm performance on CSR, that is, it supports a positive, negative or neutral relationship between the two. Originality/value This research provides a necessary structure for the CSR literature. By delving deeply into the relationship between firm performance and CSR, it enables scholars to better address the critical management question of whether earning more will lead to doing good.

Assimilation of multiple data sets with the ensemble Kalman filter to improve forecasts of forest carbon dynamics

2011 ◽  
Vol 21 (5) ◽  
pp. 1461-1473 ◽  
Author(s):  
Chao Gao ◽  
Han Wang ◽  
Ensheng Weng ◽  
S. Lakshmivarahan ◽  
Yanfen Zhang ◽  
...  
Keyword(s):  
Kalman Filter ◽  
Ensemble Kalman Filter ◽  
Carbon Dynamics ◽  
Forest Carbon ◽  
Data Sets ◽  
Multiple Data ◽  
Multiple Data Sets

scholarly journals Approaches to improve the robustness of the Comparison Model Method for the inverse problem of groundwater hydrology

2021 ◽  
Author(s):  
Alessandro Comunian ◽  
Mauro Giudici
Keyword(s):  
Geometric Mean ◽  
Optimization Methods ◽  
Forward Problem ◽  
Data Sets ◽  
Direct Inversion ◽  
Model Method ◽  
Comparison Model ◽  
Multiple Data ◽  
Hydraulic Gradients ◽  
Multiple Data Sets

<p>Indirect inversion approaches are widely used in Geosciences, and in particular also for the identification of the hydraulic properties of aquifers. Nevertheless, their application requires a substantial number of model evaluation (forward problem) runs, a task that for complex problems can be computationally intensive. Reducing this computational burden is an active research topic, and many solutions, including the use of hybrid optimization methods, the use of physical proxies or again machine-learning tools <span>allow to avoid</span> considering the full physics of the problem when running a numerical implementation of the forward problem.</p><p>Direct inversion approaches represent computationally frugal alternatives to indirect approaches, because in general they require a smaller number of runs of the forward problem. The classical drawbacks of these methods can be alleviated by some implementation approaches and in particular by using multiple sets of data, when available.</p><p>This work is an effort to improve the robustness of the Comparison Model Method (CMM), a direct inversion approach aimed at the identification of the hydraulic transmissivity of a confined aquifer. The robustness of the CMM is here ameliorated by (i) improving the parameterization required to handle small hydraulic gradients; (ii) investigating the role of different criteria aimed at merging multiple data-sets corresponding to different flow conditions.</p><p>On a synthetic case study, it is demonstrated that correcting a small percentage of the small hydraulic gradients (about 10%) allows to obtain reliable results, and that a criteria based on the geometric mean is adequate to merge the results coming from multiple data-sets. In addition, the use of multiple-data sets allows to noticeably improve the robustness of the CMM when the input data are affected by noise.</p><p>All the tests are performed by using open source and widely <span>used</span> tools like the USGS Modflow6 and its Python interface flopy to foster the application of the <span>CMM. The scripts and corresponding package</span>, named <em>cmmpy</em>, is available on the Python Package Index (PyPI) and on bitbucket at the following address: https://bitbucket.org/alecomunian/cmmpy.</p>

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