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

Low-Rank Matrices on Graphs: Generalized Recovery & Applications

Many real world datasets subsume a linear or non-linear low-rank structure in a very low-dimensional space. Unfortunately, one often has very little or no information about the geometry of the space, resulting in a highly under-determined recovery problem. Under certain circumstances, state-of-the-art algorithms provide an exact recovery for linear low-rank structures but at the expense of highly inscalable algorithms which use nuclear norm. However, the case of non-linear structures remains unresolved. We revisit the problem of low-rank recovery from a totally different perspective, involving graphs which encode pairwise similarity between the data samples and features. Surprisingly, our analysis confirms that it is possible to recover many approximate linear and non-linear low-rank structures with recovery guarantees with a set of highly scalable and efficient algorithms. We call such data matrices as \textit{Low-Rank matrices on graphs} and show that many real world datasets satisfy this assumption approximately due to underlying stationarity. Our detailed theoretical and experimental analysis unveils the power of the simple, yet very novel recovery framework \textit{Fast Robust PCA on Graphs

KCRC-LCD: Discriminative Kernel Collaborative Representation with Locality Constrained Dictionary for Visual Categorization

We consider the image classification problem via kernel collaborative representation classification with locality constrained dictionary (KCRC-LCD). Specifically, we propose a kernel collaborative representation classification (KCRC) approach in which kernel method is used to improve the discrimination ability of collaborative representation classification (CRC). We then measure the similarities between the query and atoms in the global dictionary in order to construct a locality constrained dictionary (LCD) for KCRC. In addition, we discuss several similarity measure approaches in LCD and further present a simple yet effective unified similarity measure whose superiority is validated in experiments. There are several appealing aspects associated with LCD. First, LCD can be nicely incorporated under the framework of KCRC. The LCD similarity measure can be kernelized under KCRC, which theoretically links CRC and LCD under the kernel method. Second, KCRC-LCD becomes more scalable to both the training set size and the feature dimension. Example shows that KCRC is able to perfectly classify data with certain distribution, while conventional CRC fails completely. Comprehensive experiments on many public datasets also show that KCRC-LCD is a robust discriminative classifier with both excellent performance and good scalability, being comparable or outperforming many other state-of-the-art approaches

Unsupervised 2D dimensionality reduction with adaptive structure learning

© 2017 Massachusetts Institute of Technology. In recent years, unsupervised two-dimensional (2D) dimensionality reduction methods for unlabeled large-scale data have made progress. However, performance of these degrades when the learning of similarity matrix is at the beginning of the dimensionality reduction process.Asimilarity matrix is used to reveal the underlying geometry structure of data in unsupervised dimensionality reduction methods. Because of noise data, it is difficult to learn the optimal similarity matrix. In this letter, we propose a new dimensionality reduction model for 2D image matrices: unsupervised 2D dimensionality reductionwith adaptive structure learning (DRASL). Instead of using a predetermined similarity matrix to characterize the underlying geometry structure of the original2Dimage space, our proposed approach involves the learning of a similarity matrix in the procedure of dimensionality reduction. To realize a desirable neighbors assignment after dimensionality reduction, we add a constraint to our model such that there are exact c connected components in the final subspace. To accomplish these goals, we propose a unified objective function to integrate dimensionality reduction, the learning of the similarity matrix, and the adaptive learning of neighbors assignment into it. An iterative optimization algorithm is proposed to solve the objective function. We compare the proposed method with several 2D unsupervised dimensionality methods. K-means is used to evaluate the clustering performance. We conduct extensive experiments on Coil20, ATandT, FERET, USPS, and Yale data sets to verify the effectiveness of our proposed method

Robust PCA as Bilinear Decomposition with Outlier-Sparsity Regularization

Principal component analysis (PCA) is widely used for dimensionality reduction, with well-documented merits in various applications involving high-dimensional data, including computer vision, preference measurement, and bioinformatics. In this context, the fresh look advocated here permeates benefits from variable selection and compressive sampling, to robustify PCA against outliers. A least-trimmed squares estimator of a low-rank bilinear factor analysis model is shown closely related to that obtained from an $\ell_0$-(pseudo)norm-regularized criterion encouraging sparsity in a matrix explicitly modeling the outliers. This connection suggests robust PCA schemes based on convex relaxation, which lead naturally to a family of robust estimators encompassing Huber's optimal M-class as a special case. Outliers are identified by tuning a regularization parameter, which amounts to controlling sparsity of the outlier matrix along the whole robustification path of (group) least-absolute shrinkage and selection operator (Lasso) solutions. Beyond its neat ties to robust statistics, the developed outlier-aware PCA framework is versatile to accommodate novel and scalable algorithms to: i) track the low-rank signal subspace robustly, as new data are acquired in real time; and ii) determine principal components robustly in (possibly) infinite-dimensional feature spaces. Synthetic and real data tests corroborate the effectiveness of the proposed robust PCA schemes, when used to identify aberrant responses in personality assessment surveys, as well as unveil communities in social networks, and intruders from video surveillance data.Comment: 30 pages, submitted to IEEE Transactions on Signal Processin

Compressive Mining: Fast and Optimal Data Mining in the Compressed Domain

Real-world data typically contain repeated and periodic patterns. This suggests that they can be effectively represented and compressed using only a few coefficients of an appropriate basis (e.g., Fourier, Wavelets, etc.). However, distance estimation when the data are represented using different sets of coefficients is still a largely unexplored area. This work studies the optimization problems related to obtaining the \emph{tightest} lower/upper bound on Euclidean distances when each data object is potentially compressed using a different set of orthonormal coefficients. Our technique leads to tighter distance estimates, which translates into more accurate search, learning and mining operations \textit{directly} in the compressed domain. We formulate the problem of estimating lower/upper distance bounds as an optimization problem. We establish the properties of optimal solutions, and leverage the theoretical analysis to develop a fast algorithm to obtain an \emph{exact} solution to the problem. The suggested solution provides the tightest estimation of the $L_2$-norm or the correlation. We show that typical data-analysis operations, such as k-NN search or k-Means clustering, can operate more accurately using the proposed compression and distance reconstruction technique. We compare it with many other prevalent compression and reconstruction techniques, including random projections and PCA-based techniques. We highlight a surprising result, namely that when the data are highly sparse in some basis, our technique may even outperform PCA-based compression. The contributions of this work are generic as our methodology is applicable to any sequential or high-dimensional data as well as to any orthogonal data transformation used for the underlying data compression scheme.Comment: 25 pages, 20 figures, accepted in VLD