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

Discovering semantic features in the literature: a foundation for building functional associations

BACKGROUND: Experimental techniques such as DNA microarray, serial analysis of gene expression (SAGE) and mass spectrometry proteomics, among others, are generating large amounts of data related to genes and proteins at different levels. As in any other experimental approach, it is necessary to analyze these data in the context of previously known information about the biological entities under study. The literature is a particularly valuable source of information for experiment validation and interpretation. Therefore, the development of automated text mining tools to assist in such interpretation is one of the main challenges in current bioinformatics research. RESULTS: We present a method to create literature profiles for large sets of genes or proteins based on common semantic features extracted from a corpus of relevant documents. These profiles can be used to establish pair-wise similarities among genes, utilized in gene/protein classification or can be even combined with experimental measurements. Semantic features can be used by researchers to facilitate the understanding of the commonalities indicated by experimental results. Our approach is based on non-negative matrix factorization (NMF), a machine-learning algorithm for data analysis, capable of identifying local patterns that characterize a subset of the data. The literature is thus used to establish putative relationships among subsets of genes or proteins and to provide coherent justification for this clustering into subsets. We demonstrate the utility of the method by applying it to two independent and vastly different sets of genes. CONCLUSION: The presented method can create literature profiles from documents relevant to sets of genes. The representation of genes as additive linear combinations of semantic features allows for the exploration of functional associations as well as for clustering, suggesting a valuable methodology for the validation and interpretation of high-throughput experimental data

Feature Extraction and Duplicate Detection for Text Mining: A Survey

Text mining, also known as Intelligent Text Analysis is an important research area. It is very difficult to focus on the most appropriate information due to the high dimensionality of data. Feature Extraction is one of the important techniques in data reduction to discover the most important features. Proce- ssing massive amount of data stored in a unstructured form is a challenging task. Several pre-processing methods and algo- rithms are needed to extract useful features from huge amount of data. The survey covers different text summarization, classi- fication, clustering methods to discover useful features and also discovering query facets which are multiple groups of words or phrases that explain and summarize the content covered by a query thereby reducing time taken by the user. Dealing with collection of text documents, it is also very important to filter out duplicate data. Once duplicates are deleted, it is recommended to replace the removed duplicates. Hence we also review the literature on duplicate detection and data fusion (remove and replace duplicates).The survey provides existing text mining techniques to extract relevant features, detect duplicates and to replace the duplicate data to get fine grained knowledge to the user

Multimodal music information processing and retrieval: survey and future challenges

Towards improving the performance in various music information processing tasks, recent studies exploit different modalities able to capture diverse aspects of music. Such modalities include audio recordings, symbolic music scores, mid-level representations, motion, and gestural data, video recordings, editorial or cultural tags, lyrics and album cover arts. This paper critically reviews the various approaches adopted in Music Information Processing and Retrieval and highlights how multimodal algorithms can help Music Computing applications. First, we categorize the related literature based on the application they address. Subsequently, we analyze existing information fusion approaches, and we conclude with the set of challenges that Music Information Retrieval and Sound and Music Computing research communities should focus in the next years

An Analytical Performance Evaluation on Multiview Clustering Approaches

The concept of machine learning encompasses a wide variety of different approaches, one of which is called clustering. The data points are grouped together in this approach to the problem. Using a clustering method, it is feasible, given a collection of data points, to classify each data point as belonging to a specific group. This can be done if the algorithm is given the collection of data points. In theory, data points that constitute the same group ought to have attributes and characteristics that are equivalent to one another, however data points that belong to other groups ought to have properties and characteristics that are very different from one another. The generation of multiview data is made possible by recent developments in information collecting technologies. The data were collected from à variety of sources and were analysed using a variety of perspectives. The data in question are what are known as multiview data. On a single view, the conventional clustering algorithms are applied. In spite of this, real-world data are complicated and can be clustered in a variety of different ways, depending on how the data are interpreted. In practise, the real-world data are messy. In recent years, Multiview Clustering, often known as MVC, has garnered an increasing amount of attention due to its goal of utilising complimentary and consensus information derived from different points of view. On the other hand, the vast majority of the systems that are currently available only enable the single-clustering scenario, whereby only makes utilization of a single cluster to split the data. This is the case since there is only one cluster accessible. In light of this, it is absolutely necessary to carry out investigation on the multiview data format. The study work is centred on multiview clustering and how well it performs compared to these other strategies

Multi-Target Prediction: A Unifying View on Problems and Methods

Multi-target prediction (MTP) is concerned with the simultaneous prediction of multiple target variables of diverse type. Due to its enormous application potential, it has developed into an active and rapidly expanding research field that combines several subfields of machine learning, including multivariate regression, multi-label classification, multi-task learning, dyadic prediction, zero-shot learning, network inference, and matrix completion. In this paper, we present a unifying view on MTP problems and methods. First, we formally discuss commonalities and differences between existing MTP problems. To this end, we introduce a general framework that covers the above subfields as special cases. As a second contribution, we provide a structured overview of MTP methods. This is accomplished by identifying a number of key properties, which distinguish such methods and determine their suitability for different types of problems. Finally, we also discuss a few challenges for future research

Asymmetric double-winged multi-view clustering network for exploring Diverse and Consistent Information

In unsupervised scenarios, deep contrastive multi-view clustering (DCMVC) is becoming a hot research spot, which aims to mine the potential relationships between different views. Most existing DCMVC algorithms focus on exploring the consistency information for the deep semantic features, while ignoring the diverse information on shallow features. To fill this gap, we propose a novel multi-view clustering network termed CodingNet to explore the diverse and consistent information simultaneously in this paper. Specifically, instead of utilizing the conventional auto-encoder, we design an asymmetric structure network to extract shallow and deep features separately. Then, by aligning the similarity matrix on the shallow feature to the zero matrix, we ensure the diversity for the shallow features, thus offering a better description of multi-view data. Moreover, we propose a dual contrastive mechanism that maintains consistency for deep features at both view-feature and pseudo-label levels. Our framework's efficacy is validated through extensive experiments on six widely used benchmark datasets, outperforming most state-of-the-art multi-view clustering algorithms