Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

From patterned response dependency to structured covariate dependency: categorical-pattern-matching

Data generated from a system of interest typically consists of measurements from an ensemble of subjects across multiple response and covariate features, and is naturally represented by one response-matrix against one covariate-matrix. Likely each of these two matrices simultaneously embraces heterogeneous data types: continuous, discrete and categorical. Here a matrix is used as a practical platform to ideally keep hidden dependency among/between subjects and features intact on its lattice. Response and covariate dependency is individually computed and expressed through mutliscale blocks via a newly developed computing paradigm named Data Mechanics. We propose a categorical pattern matching approach to establish causal linkages in a form of information flows from patterned response dependency to structured covariate dependency. The strength of an information flow is evaluated by applying the combinatorial information theory. This unified platform for system knowledge discovery is illustrated through five data sets. In each illustrative case, an information flow is demonstrated as an organization of discovered knowledge loci via emergent visible and readable heterogeneity. This unified approach fundamentally resolves many long standing issues, including statistical modeling, multiple response, renormalization and feature selections, in data analysis, but without involving man-made structures and distribution assumptions. The results reported here enhance the idea that linking patterns of response dependency to structures of covariate dependency is the true philosophical foundation underlying data-driven computing and learning in sciences.Comment: 32 pages, 10 figures, 3 box picture

Definition of MV Load Diagrams via Weighted Evidence Accumulation Clustering using Subsampling

A definition of medium voltage (MV) load diagrams was made, based on the data base knowledge discovery process. Clustering techniques were used as support for the agents of the electric power retail markets to obtain specific knowledge of their customers’ consumption habits. Each customer class resulting from the clustering operation is represented by its load diagram. The Two-step clustering algorithm and the WEACS approach based on evidence accumulation (EAC) were applied to an electricity consumption data from a utility client’s database in order to form the customer’s classes and to find a set of representative consumption patterns. The WEACS approach is a clustering ensemble combination approach that uses subsampling and that weights differently the partitions in the co-association matrix. As a complementary step to the WEACS approach, all the final data partitions produced by the different variations of the method are combined and the Ward Link algorithm is used to obtain the final data partition. Experiment results showed that WEACS approach led to better accuracy than many other clustering approaches. In this paper the WEACS approach separates better the customer’s population than Two-step clustering algorithm

Determination of electricity consumers’ load profiles via weighted evidence accumulation clustering using subsampling

With the electricity market liberalization, the distribution and retail companies are looking for better market strategies based on adequate information upon the consumption patterns of its electricity consumers. A fair insight on the consumers’ behavior will permit the definition of specific contract aspects based on the different consumption patterns. In order to form the different consumers’ classes, and find a set of representative consumption patterns we use electricity consumption data from a utility client’s database and two approaches: Two-step clustering algorithm and the WEACS approach based on evidence accumulation (EAC) for combining partitions in a clustering ensemble. While EAC uses a voting mechanism to produce a co-association matrix based on the pairwise associations obtained from N partitions and where each partition has equal weight in the combination process, the WEACS approach uses subsampling and weights differently the partitions. As a complementary step to the WEACS approach, we combine the partitions obtained in the WEACS approach with the ALL clustering ensemble construction method and we use the Ward Link algorithm to obtain the final data partition. The characterization of the obtained consumers’ clusters was performed using the C5.0 classification algorithm. Experiment results showed that the WEACS approach leads to better results than many other clustering approaches

The Consensus Clustering as a Contribution to Parental Recognition Problem Based on Hand Biometrics

The clustering analysis is a subject that has been interesting researchers from several areas, such as health (medical diagnosis, clustering of proteins and genes), marketing (market analysis and image segmentation), information management (clustering of web pages). The clustering algorithms are usually applied in Data Mining, allowing the identification of natural groups for a given data set. The use of different clustering methods for the same data set can produce different groups. So, several studies have been led to validate the resulting clusters. There has been an increasing interest on how to determine a consensus clustering that combines the different individual clusterings, reflecting the main structure in clusters inherent to each of them, as a perspective to get a higher quality clustering. As several techniques of consensus clustering have been researched, the present work focuses on problem of finding the best partition in the consensus clustering. We analyze the most referred techniques in literature, the consensus clustering techniques with different mechanisms to achieve the consensus, i.e.; Voting mechanisms; Co-association matrix; Mutual Information and hyper-graphs; and a multi-objective consensus clustering existing on literature. In this paper we discuss these approaches and a comparative study is presented, that considers a set of experiments using two-dimensional synthetic data sets with different characteristics, as number of clusters, their cardinality, shape, homogeneity and separability, and a real-world data set based on hand\u27s biometrics shape, in context of people parental recognition. With this data we intend to investigate the ability of the consensus clustering algorithms in correctly cluster a child and her/his parents. This has an enormous business potential leading to a great economic value, since that with this technology a website can match data, as hand\u27s photographs, and say if A and B are related somehow. We conclude that, in some cases, the multi-objective technique proved to outperform the other techniques, and unlike the other techniques, is little influenced by poor clustering even in situations like noise introduction and clusters with different homogeneity or overlapped. Furthermore, shows that can capture the performance of the best base clustering and still outperform it. Regarding to real data, no technique was capable of identifying a person\u27s mother/father. However, the research of distances between hands from a person and its father, mother, siblings, can retrieve the probability of that person being his/her familiar. This doesn\u27t enable the identification of relatives but instead, decreases the size of database for seeking the matches