scholarly journals A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Audrey Hulot ◽  
Denis Laloë ◽  
Florence Jaffrézic
Keyword(s):  
Breast Cancer ◽  
Simple Procedure ◽  
Data Sets ◽  
Integration Step ◽  
Visual Interpretation ◽  
Data Types ◽  
Unified Framework ◽  
Real World Data ◽  
Multiple Factor Analysis ◽  
Data Set

Abstract Background Integrating data from different sources is a recurring question in computational biology. Much effort has been devoted to the integration of data sets of the same type, typically multiple numerical data tables. However, data types are generally heterogeneous: it is a common place to gather data in the form of trees, networks or factorial maps, as these representations all have an appealing visual interpretation that helps to study grouping patterns and interactions between entities. The question we aim to answer in this paper is that of the integration of such representations. Results To this end, we provide a simple procedure to compare data with various types, in particular trees or networks, that relies essentially on two steps: the first step projects the representations into a common coordinate system; the second step then uses a multi-table integration approach to compare the projected data. We rely on efficient and well-known methodologies for each step: the projection step is achieved by retrieving a distance matrix for each representation form and then applying multidimensional scaling to provide a new set of coordinates from all the pairwise distances. The integration step is then achieved by applying a multiple factor analysis to the multiple tables of the new coordinates. This procedure provides tools to integrate and compare data available, for instance, as tree or network structures. Our approach is complementary to kernel methods, traditionally used to answer the same question. Conclusion Our approach is evaluated on simulation and used to analyze two real-world data sets: first, we compare several clusterings for different cell-types obtained from a transcriptomics single-cell data set in mouse embryos; second, we use our procedure to aggregate a multi-table data set from the TCGA breast cancer database, in order to compare several protein networks inferred for different breast cancer subtypes.

Auto-sharing parameters for transfer learning based on multi-objective optimization

2021 ◽  
pp. 1-13
Author(s):  
Hailin Liu ◽  
Fangqing Gu ◽  
Zixian Lin
Keyword(s):  
Transfer Learning ◽  
Optimization Problem ◽  
Data Sets ◽  
Multi Objective Optimization ◽  
Particle Swarm Optimizer ◽  
Real World Data ◽  
Data Set ◽  
Target Task ◽  
Main Research ◽  
Multi Objective

Transfer learning methods exploit similarities between different datasets to improve the performance of the target task by transferring knowledge from source tasks to the target task. “What to transfer” is a main research issue in transfer learning. The existing transfer learning method generally needs to acquire the shared parameters by integrating human knowledge. However, in many real applications, an understanding of which parameters can be shared is unknown beforehand. Transfer learning model is essentially a special multi-objective optimization problem. Consequently, this paper proposes a novel auto-sharing parameter technique for transfer learning based on multi-objective optimization and solves the optimization problem by using a multi-swarm particle swarm optimizer. Each task objective is simultaneously optimized by a sub-swarm. The current best particle from the sub-swarm of the target task is used to guide the search of particles of the source tasks and vice versa. The target task and source task are jointly solved by sharing the information of the best particle, which works as an inductive bias. Experiments are carried out to evaluate the proposed algorithm on several synthetic data sets and two real-world data sets of a school data set and a landmine data set, which show that the proposed algorithm is effective.

scholarly journals Data Fusion Using a Multi-Sensor Sparse-Based Clustering Algorithm

2020 ◽  
Vol 12 (23) ◽  
pp. 4007
Author(s):  
Kasra Rafiezadeh Shahi ◽  
Pedram Ghamisi ◽  
Behnood Rasti ◽  
Robert Jackisch ◽  
Paul Scheunders ◽  
...  
Keyword(s):  
Clustering Algorithm ◽  
Spatial Information ◽  
Clustering Algorithms ◽  
Hyperspectral Data ◽  
Sensor Data ◽  
Data Sets ◽  
Data Types ◽  
Data Set ◽  
Multiple Data Sets ◽  
Imaging Sensors

The increasing amount of information acquired by imaging sensors in Earth Sciences results in the availability of a multitude of complementary data (e.g., spectral, spatial, elevation) for monitoring of the Earth’s surface. Many studies were devoted to investigating the usage of multi-sensor data sets in the performance of supervised learning-based approaches at various tasks (i.e., classification and regression) while unsupervised learning-based approaches have received less attention. In this paper, we propose a new approach to fuse multiple data sets from imaging sensors using a multi-sensor sparse-based clustering algorithm (Multi-SSC). A technique for the extraction of spatial features (i.e., morphological profiles (MPs) and invariant attribute profiles (IAPs)) is applied to high spatial-resolution data to derive the spatial and contextual information. This information is then fused with spectrally rich data such as multi- or hyperspectral data. In order to fuse multi-sensor data sets a hierarchical sparse subspace clustering approach is employed. More specifically, a lasso-based binary algorithm is used to fuse the spectral and spatial information prior to automatic clustering. The proposed framework ensures that the generated clustering map is smooth and preserves the spatial structures of the scene. In order to evaluate the generalization capability of the proposed approach, we investigate its performance not only on diverse scenes but also on different sensors and data types. The first two data sets are geological data sets, which consist of hyperspectral and RGB data. The third data set is the well-known benchmark Trento data set, including hyperspectral and LiDAR data. Experimental results indicate that this novel multi-sensor clustering algorithm can provide an accurate clustering map compared to the state-of-the-art sparse subspace-based clustering algorithms.

scholarly journals Data segmentation based on the local intrinsic dimension

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Michele Allegra ◽  
Elena Facco ◽  
Francesco Denti ◽  
Alessandro Laio ◽  
Antonietta Mira
Keyword(s):  
High Dimensional Data ◽  
Large Data ◽  
Large Data Sets ◽  
High Dimensional ◽  
Data Sets ◽  
Imaging Data ◽  
Unsupervised Segmentation ◽  
Real World Data ◽  
Data Set ◽  
Intrinsic Dimension

Abstract One of the founding paradigms of machine learning is that a small number of variables is often sufficient to describe high-dimensional data. The minimum number of variables required is called the intrinsic dimension (ID) of the data. Contrary to common intuition, there are cases where the ID varies within the same data set. This fact has been highlighted in technical discussions, but seldom exploited to analyze large data sets and obtain insight into their structure. Here we develop a robust approach to discriminate regions with different local IDs and segment the points accordingly. Our approach is computationally efficient and can be proficiently used even on large data sets. We find that many real-world data sets contain regions with widely heterogeneous dimensions. These regions host points differing in core properties: folded versus unfolded configurations in a protein molecular dynamics trajectory, active versus non-active regions in brain imaging data, and firms with different financial risk in company balance sheets. A simple topological feature, the local ID, is thus sufficient to achieve an unsupervised segmentation of high-dimensional data, complementary to the one given by clustering algorithms.

scholarly journals Structure Identification-Based Clustering According to Density Consistency

2011 ◽  
Vol 2011 ◽  
pp. 1-14 ◽  
Author(s):  
Chunzhong Li ◽  
Zongben Xu
Keyword(s):  
High Dimension ◽  
Real World ◽  
Clustering Algorithm ◽  
Density Difference ◽  
Structure Identification ◽  
Data Sets ◽  
Critical Importance ◽  
Real World Data ◽  
Data Set ◽  
High Dimension Data

Structure of data set is of critical importance in identifying clusters, especially the density difference feature. In this paper, we present a clustering algorithm based on density consistency, which is a filtering process to identify same structure feature and classify them into same cluster. This method is not restricted by the shapes and high dimension data set, and meanwhile it is robust to noises and outliers. Extensive experiments on synthetic and real world data sets validate the proposed the new clustering algorithm.

Enhancing Recommender Diversity Using Gaussian Cloud Transformation

2015 ◽  
Vol 23 (04) ◽  
pp. 521-544 ◽  
Author(s):  
Jinpeng Chen ◽  
Yu Liu ◽  
Deyi Li
Keyword(s):  
Recommender Systems ◽  
Recommendation System ◽  
Data Sets ◽  
Complete Spectrum ◽  
Unified Framework ◽  
Real World Data ◽  
Balance Accuracy ◽  
Average Accuracy ◽  
Novel Method ◽  
Attention To Diversity

The recommender systems community is paying great attention to diversity as key qualities beyond accuracy in real recommendation scenarios. Multifarious diversity-increasing approaches have been developed to enhance recommendation diversity in the related literature while making personalized recommendations to users. In this work, we present Gaussian Cloud Recommendation Algorithm (GCRA), a novel method designed to balance accuracy and diversity personalized top-N recommendation lists in order to capture the user's complete spectrum of tastes. Our proposed algorithm does not require semantic information. Meanwhile we propose a unified framework to extend the traditional CF algorithms via utilizing GCRA for improving the recommendation system performance. Our work builds upon prior research on recommender systems. Though being detrimental to average accuracy, we show that our method can capture the user's complete spectrum of interests. Systematic experiments on three real-world data sets have demonstrated the effectiveness of our proposed approach in learning both accuracy and diversity.

Multiclass Contour-Preserving Classification with Support Vector Machine (SVM)

2017 ◽  
Vol 26 (2) ◽  
pp. 323-334 ◽  
Author(s):  
Piyabute Fuangkhon
Keyword(s):  
Support Vector Machine ◽  
Classification Accuracy ◽  
University Of California ◽  
Support Vector ◽  
Data Sets ◽  
Feed Forward Neural Network ◽  
Real World Data ◽  
Data Set ◽  
The University ◽  
Training Sets

AbstractMulticlass contour-preserving classification (MCOV) has been used to preserve the contour of the data set and improve the classification accuracy of a feed-forward neural network. It synthesizes two types of new instances, called fundamental multiclass outpost vector (FMCOV) and additional multiclass outpost vector (AMCOV), in the middle of the decision boundary between consecutive classes of data. This paper presents a comparison on the generalization of an inclusion of FMCOVs, AMCOVs, and both MCOVs on the final training sets with support vector machine (SVM). The experiments were carried out using MATLAB R2015a and LIBSVM v3.20 on seven types of the final training sets generated from each of the synthetic and real-world data sets from the University of California Irvine machine learning repository and the ELENA project. The experimental results confirm that an inclusion of FMCOVs on the final training sets having raw data can improve the SVM classification accuracy significantly.

scholarly journals A Spatial Biosurveillance Synthetic Data Generator in R

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Drew Levin ◽  
Patrick Finley
Keyword(s):  
Power Law ◽  
Real World ◽  
Degree Distribution ◽  
Transportation Network ◽  
Synthetic Data ◽  
Data Sets ◽  
Real World Data ◽  
Data Set ◽  
Scale Free ◽  
Data Generator

ObjectiveTo develop a spatially accurate biosurveillance synthetic datagenerator for the testing, evaluation, and comparison of new outbreakdetection techniques.IntroductionDevelopment of new methods for the rapid detection of emergingdisease outbreaks is a research priority in the field of biosurveillance.Because real-world data are often proprietary in nature, scientists mustutilize synthetic data generation methods to evaluate new detectionmethodologies. Colizza et. al. have shown that epidemic spread isdependent on the airline transportation network [1], yet current datagenerators do not operate over network structures.Here we present a new spatial data generator that models thespread of contagion across a network of cities connected by airlineroutes. The generator is developed in the R programming languageand produces data compatible with the popular `surveillance’ softwarepackage.MethodsColizza et. al. demonstrate the power-law relationships betweencity population, air traffic, and degree distribution [1]. We generate atransportation network as a Chung-Lu random graph [2] that preservesthese scale-free relationships (Figure 1).First, given a power-law exponent and a desired number of cities,a probability mass function (PMF) is generated that mirrors theexpected degree distribution for the given power-law relationship.Values are then sampled from this PMF to generate an expecteddegree (number of connected cities) for each city in the network.Edges (airline connections) are added to the network probabilisticallyas described in [2]. Unconnected graph components are each joinedto the largest component using linear preferential attachment. Finally,city sizes are calculated based on an observed three-quarter power-law scaling relationship with the sampled degree distribution.Each city is represented as a customizable stochastic compartmentalSIR model. Transportation between cities is modeled similar to [2].An infection is initialized in a single random city and infection countsare recorded in each city for a fixed period of time. A consistentfraction of the modeled infection cases are recorded as daily clinicvisits. These counts are then added onto statically generated baselinedata for each city to produce a full synthetic data set. Alternatively,data sets can be generated using real-world networks, such as the onemaintained by the International Air Transport Association.ResultsDynamics such as the number of cities, degree distribution power-law exponent, traffic flow, and disease kinetics can be customized.In the presented example (Figure 2) the outbreak spreads over a 20city transportation network. Infection spreads rapidly once the morepopulated hub cities are infected. Cities that are multiple flights awayfrom the initially infected city are infected late in the process. Thegenerator is capable of creating data sets of arbitrary size, length, andconnectivity to better mirror a diverse set of observed network types.ConclusionsNew computational methods for outbreak detection andsurveillance must be compared to established approaches. Outbreakmitigation strategies require a realistic model of human transportationbehavior to best evaluate impact. These actions require test data thataccurately reflect the complexity of the real-world data they wouldbe applied to. The outbreak data generated here represents thecomplexity of modern transportation networks and are made to beeasily integrated with established software packages to allow for rapidtesting and deployment.Randomly generated scale-free transportation network with a power-lawdegree exponent ofλ=1.8. City and link sizes are scaled to reflect their weight.An example of observed daily outbreak-related clinic visits across a randomlygenerated network of 20 cities. Each city is colored by the number of flightsrequired to reach the city from the initial infection location. These generatedcounts are then added onto baseline data to create a synthetic data set forexperimentation.KeywordsSimulation; Network; Spatial; Synthetic; Data

scholarly journals Providing Data With High Utility And No Disclosure Risk For The Public and Researchers: An Evaluation By Advanced Statistical Disclosure Risk Methods

2014 ◽  
Vol 43 (4) ◽  
pp. 247-254
Author(s):  
Matthias Templ
Keyword(s):  
Data Privacy ◽  
Data Sets ◽  
Real World Data ◽  
Data Set ◽  
The Public ◽  
Disclosure Control ◽  
High Data ◽  
Disclosure Risk ◽  
Statistical Disclosure ◽  
High Utility

The demand of data from surveys, registers or other data sets containing sensibleinformation on people or enterprises have been increased significantly over the last years.However, before providing data to the public or to researchers, confidentiality has to berespected for any data set containing sensible individual information. Confidentiality canbe achieved by applying statistical disclosure control (SDC) methods to the data. Theresearch on SDC methods becomes more and more important in the last years because ofan increase of the awareness on data privacy and because of the fact that more and moredata are provided to the public or to researchers. However, for legal reasons this is onlyvisible when the released data has (very) low disclosure risk.In this contribution existing disclosure risk methods are review and summarized. Thesemethods are finally applied on a popular real-world data set - the Structural EarningsSurvey (SES) of Austria. It is shown that the application of few selected anonymisationmethods leads to well-protected anonymised data with high data utility and low informationloss.

scholarly journals Construction of competing endogenous RNA networks from paired RNA-seq data sets by pointwise mutual information

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Chaowang Lan ◽  
Hui Peng ◽  
Gyorgy Hutvagner ◽  
Jinyan Li
Keyword(s):  
Breast Cancer ◽  
Mutual Information ◽  
Noncoding Rna ◽  
Regulation Mechanism ◽  
Data Sets ◽  
Rna Seq ◽  
Competing Endogenous Rna ◽  
Data Set ◽  
Cerna Network ◽  
Pointwise Mutual Information

Abstract Background A long noncoding RNA (lncRNA) can act as a competing endogenous RNA (ceRNA) to compete with an mRNA for binding to the same miRNA. Such an interplay between the lncRNA, miRNA, and mRNA is called a ceRNA crosstalk. As an miRNA may have multiple lncRNA targets and multiple mRNA targets, connecting all the ceRNA crosstalks mediated by the same miRNA forms a ceRNA network. Methods have been developed to construct ceRNA networks in the literature. However, these methods have limits because they have not explored the expression characteristics of total RNAs. Results We proposed a novel method for constructing ceRNA networks and applied it to a paired RNA-seq data set. The first step of the method takes a competition regulation mechanism to derive candidate ceRNA crosstalks. Second, the method combines a competition rule and pointwise mutual information to compute a competition score for each candidate ceRNA crosstalk. Then, ceRNA crosstalks which have significant competition scores are selected to construct the ceRNA network. The key idea, pointwise mutual information, is ideally suitable for measuring the complex point-to-point relationships embedded in the ceRNA networks. Conclusion Computational experiments and results demonstrate that the ceRNA networks can capture important regulatory mechanism of breast cancer, and have also revealed new insights into the treatment of breast cancer. The proposed method can be directly applied to other RNA-seq data sets for deeper disease understanding.

scholarly journals Scalable Micro-planned Generation of Discourse from Structured Data

2020 ◽  
Vol 45 (4) ◽  
pp. 737-763 ◽  
Author(s):  
Anirban Laha ◽  
Parag Jain ◽  
Abhijit Mishra ◽  
Karthik Sankaranarayanan
Keyword(s):  
Natural Language ◽  
Structured Data ◽  
Data Sets ◽  
Data Types ◽  
Data Set ◽  
Language Generation ◽  
Parallel Data ◽  
Simple Sentences ◽  
Diverse Data ◽  
Existing Data

We present a framework for generating natural language description from structured data such as tables; the problem comes under the category of data-to-text natural language generation (NLG). Modern data-to-text NLG systems typically use end-to-end statistical and neural architectures that learn from a limited amount of task-specific labeled data, and therefore exhibit limited scalability, domain-adaptability, and interpretability. Unlike these systems, ours is a modular, pipeline-based approach, and does not require task-specific parallel data. Rather, it relies on monolingual corpora and basic off-the-shelf NLP tools. This makes our system more scalable and easily adaptable to newer domains. Our system utilizes a three-staged pipeline that: (i) converts entries in the structured data to canonical form, (ii) generates simple sentences for each atomic entry in the canonicalized representation, and (iii) combines the sentences to produce a coherent, fluent, and adequate paragraph description through sentence compounding and co-reference replacement modules. Experiments on a benchmark mixed-domain data set curated for paragraph description from tables reveals the superiority of our system over existing data-to-text approaches. We also demonstrate the robustness of our system in accepting other popular data sets covering diverse data types such as knowledge graphs and key-value maps.

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