Privacy Preserving Principal Component Analysis Clustering for Distributed Heterogeneous Gene Expression Datasets

2012 ◽  
pp. 238-271
Author(s):  
Xin Li
Keyword(s):  
Principal Component Analysis ◽  
Privacy Protection ◽  
Genomic Data ◽  
Principal Component ◽  
Original Data ◽  
Component Analysis ◽  
Privacy Preserving ◽  
Gene Clustering ◽  
Gene Profiles ◽  
Heterogeneous Datasets

In this paper, we present approaches to perform principal component analysis (PCA) clustering for distributed heterogeneous genomic datasets with privacy protection. The approaches allow data providers to collaborate together to identify gene profiles from a global viewpoint, and at the same time, protect the sensitive genomic data from possible privacy leaks. We then further develop a framework for privacy preserving PCA-based gene clustering, which includes two types of participants: data providers and a trusted central site (TCS). Two different methodologies are employed: Collective PCA (C-PCA) and Repeating PCA (R-PCA). The C-PCA requires local sites to transmit a sample of original data to the TCS and can be applied to any heterogeneous datasets. The R-PCA approach requires all local sites have the same or similar number of columns, but releases no original data. Experiments on five independent genomic datasets show that both C-PCA and R-PCA approaches maintain very good accuracy compared with the centralized scenario.

Privacy Preserving Principal Component Analysis Clustering for Distributed Heterogeneous Gene Expression Datasets

2011 ◽  
Vol 2 (4) ◽  
pp. 23-56
Author(s):  
Xin Li
Keyword(s):  
Principal Component Analysis ◽  
Privacy Protection ◽  
Good Accuracy ◽  
Principal Component ◽  
Original Data ◽  
Component Analysis ◽  
Privacy Preserving ◽  
Gene Clustering ◽  
Gene Profiles ◽  
Heterogeneous Datasets

In this paper, we present approaches to perform principal component analysis (PCA) clustering for distributed heterogeneous genomic datasets with privacy protection. The approaches allow data providers to collaborate together to identify gene profiles from a global viewpoint, and at the same time, protect the sensitive genomic data from possible privacy leaks. We then further develop a framework for privacy preserving PCA-based gene clustering, which includes two types of participants: data providers and a trusted central site (TCS). Two different methodologies are employed: Collective PCA (C-PCA) and Repeating PCA (R-PCA). The C-PCA requires local sites to transmit a sample of original data to the TCS and can be applied to any heterogeneous datasets. The R-PCA approach requires all local sites have the same or similar number of columns, but releases no original data. Experiments on five independent genomic datasets show that both C-PCA and R-PCA approaches maintain very good accuracy compared with the centralized scenario.

scholarly journals Laplace Input and Output Perturbation for Differentially Private Principal Components Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-10
Author(s):  
Yahong Xu ◽  
Geng Yang ◽  
Shuangjie Bai
Keyword(s):  
Principal Component Analysis ◽  
Data Analysis ◽  
Data Privacy ◽  
Differential Privacy ◽  
Approximation Error ◽  
Principal Component ◽  
Component Analysis ◽  
Privacy Preserving ◽  
Experimental Results ◽  
Widespread Application

With the widespread application of big data, privacy-preserving data analysis has become a topic of increasing significance. The current research studies mainly focus on privacy-preserving classification and regression. However, principal component analysis (PCA) is also an effective data analysis method which can be used to reduce the data dimensionality, commonly used in data processing, machine learning, and data mining. In order to implement approximate PCA while preserving data privacy, we apply the Laplace mechanism to propose two differential privacy principal component analysis algorithms: Laplace input perturbation (LIP) and Laplace output perturbation (LOP). We evaluate the performance of LIP and LOP in terms of noise magnitude and approximation error theoretically and experimentally. In addition, we explore the variation of performance of the two algorithms with different parameters such as number of samples, target dimension, and privacy parameter. Theoretical and experimental results show that algorithm LIP adds less noise and has lower approximation error than LOP. To verify the effectiveness of algorithm LIP, we compare our LIP with other algorithms. The experimental results show that algorithm LIP can provide strong privacy guarantee and good data utility.

A German version of the Intermittent Claudication Questionnaire (ICQ): cultural adaptation and validation

VASA ◽  
2012 ◽  
Vol 41 (5) ◽  
pp. 333-342 ◽  
Author(s):  
Kirchberger ◽  
Finger ◽  
Müller-Bühl
Keyword(s):  
Principal Component Analysis ◽  
Intermittent Claudication ◽  
Completion Time ◽  
Short Form ◽  
Principal Component ◽  
Component Analysis ◽  
German Version ◽  
Average Completion Time ◽  
Sf 36 ◽  
Related Quality

Background: The Intermittent Claudication Questionnaire (ICQ) is a short questionnaire for the assessment of health-related quality of life (HRQOL) in patients with intermittent claudication (IC). The objective of this study was to translate the ICQ into German and to investigate the psychometric properties of the German ICQ version in patients with IC. Patients and methods: The original English version was translated using a forward-backward method. The resulting German version was reviewed by the author of the original version and an experienced clinician. Finally, it was tested for clarity with 5 German patients with IC. A sample of 81 patients were administered the German ICQ. The sample consisted of 58.0 % male patients with a median age of 71 years and a median IC duration of 36 months. Test of feasibility included completeness of questionnaires, completion time, and ratings of clarity, length and relevance. Reliability was assessed through a retest in 13 patients at 14 days, and analysis of Cronbach’s alpha for internal consistency. Construct validity was investigated using principal component analysis. Concurrent validity was assessed by correlating the ICQ scores with the Short Form 36 Health Survey (SF-36) as well as clinical measures. Results: The ICQ was completely filled in by 73 subjects (90.1 %) with an average completion time of 6.3 minutes. Cronbach’s alpha coefficient reached 0.75. Intra-class correlation for test-retest reliability was r = 0.88. Principal component analysis resulted in a 3 factor solution. The first factor explained 51.5 of the total variation and all items had loadings of at least 0.65 on it. The ICQ was significantly associated with the SF-36 and treadmill-walking distances whereas no association was found for resting ABPI. Conclusions: The German version of the ICQ demonstrated good feasibility, satisfactory reliability and good validity. Responsiveness should be investigated in further validation studies.

Multifactorial analysis of clinical laboratory signs, the levels of IL-17A, IL-23, IL-33, IL-35, and specific antibodies in the serum of patients with Lyme borreliosis without erythema migrans

2020 ◽  
Vol 4 (11) ◽  
pp. 676-681
Author(s):  
V.V. Sapozhnikova ◽  
◽  
A.L. Bondarenko ◽  
Keyword(s):  
Principal Component Analysis ◽  
Lyme Borreliosis ◽  
Clinical Laboratory ◽  
Acute Infection ◽  
Erythema Migrans ◽  
Principal Component ◽  
Component Analysis ◽  
Control Group ◽  
Multifactorial Analysis ◽  
Specific Antibodies

Aim: to determine the association between clinical laboratory parameters, the production of cytokines (IL-17A, -23, -33, -35), and specific IgM and IgG in the serum of patients with Lyme borreliosis without erythema migrans. Patients and Methods: complete blood count, the concentrations of IL-17A, -23, -33, -35, and the levels of specific IgM and IgG were measured during acute infection and convalescence (n=30). The control group included age- and sex-matched healthy individuals (n=30). Statistical analysis was performed using the StatSoft Statistica v 10.0 software (parametric and non-parametric methods and multifactorial analysis, i.e., principal component analysis). Results: most (80%) patients with Lyme borreliosis without erythema migrans are the people of working age. In most patients, the combination of the specific antibodies against Borrelia afzelii and Borrelia garinii (76.7%) and severe intoxication and inflammatory process (100%) were detected. Moderate and severe disease associated with meningism was diagnosed in 90% and 10%, respectively. The mean duration of hectic period was 8.3±1.27 days. Abnormal ECG was reported in 40% of patients, i.e., conduction abnormalities in 20%, sinus bradycardia in 16.7%,and sinus tachycardia in 3.3%. The clinical laboratory signs of hepatitis without jaundice were identified in 26.7%. During treatment, the significant reduction in band and segmented neutrophil counts as well as the significant increase in platelet count were revealed compared to these parameters at admission. Abnormal cytokine levels (i.e., the increase in IL-17A, -23, -33 and the deficiency of IL-35) were detected. Conclusions: multifactorial analysis has demonstrated that the severity of immunological abnormalities in patients with Lyme borreliosis without erythema migrans is associated with fever, cardiac and liver disorders, the high levels of IL-23 and IL-33, and the lack of IL-35 and specific IgM and IgG. KEYWORDS: tick-borne borreliosis, Lyme disease without erythema migrans, clinical laboratory signs, cytokines, specific antibodies, multifactorial analysis, principal component analysis. FOR CITATION: Sapozhnikova V.V., Bondarenko A.L. Multifactorial analysis of clinical laboratory signs, the levels of IL-17A, IL-23, IL-33, IL-35, and specific antibodies in the serum of patients with Lyme borreliosis without erythema migrans. Russian Medical Inquiry. 2020;4(11):676–681. DOI: 10.32364/2587-6821-2020-4-11-676-681.

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