Related papers: YFitter: Maximum likelihood assignment of Y chromo…

Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…

We propose an algorithm for solving nonlinear convex programs defined in terms of a symmetric positive semidefinite matrix variable $X$. This algorithm rests on the factorization $X=Y Y^T$, where the number of columns of Y fixes the rank of…

DNA samples are often pooled, either by experimental design, or because the sample itself is a mixture. For example, when population allele frequencies are of primary interest, individual samples may be pooled together to lower the cost of…

Accurate segmentation and classification of nuclei in histology images is critical but challenging due to nuclei heterogeneity, staining variations, and tissue complexity. Existing methods often struggle with limited dataset variability,…

We consider the problem of selecting confounders for adjustment from a potentially large set of covariates, when estimating a causal effect. Recently, the high-dimensional Propensity Score (hdPS) method was developed for this task; hdPS…

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…

Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically…

Comprehensive discovery of structural variation (SV) in human genomes from DNA sequencing requires the integration of multiple alignment signals including read-pair, split-read and read-depth. However, owing to inherent technical…

Most successful machine intelligence systems rely on gradient-based learning, which is made possible by backpropagation. Some systems are designed to aid us in interpreting data when explicit goals cannot be provided. These unsupervised…

Prior work has shown that Visual Recognition datasets frequently underrepresent bias groups $B$ (\eg Female) within class labels $Y$ (\eg Programmers). This dataset bias can lead to models that learn spurious correlations between class…

The Nystr\"om method is a convenient heuristic method to obtain low-rank approximations to kernel matrices in nearly linear complexity. Existing studies typically use the method to approximate positive semidefinite matrices with low or…

We develop a highly scalable optimization method called "hierarchical group-thresholding" for solving a multi-task regression model with complex structured sparsity constraints on both input and output spaces. Despite the recent emergence…

Outcomes of data-driven AI models cannot be assumed to be always correct. To estimate the uncertainty in these outcomes, the uncertainty wrapper framework has been proposed, which considers uncertainties related to model fit, input quality,…

Identifying galaxy groups from redshift surveys of galaxies plays an important role in connecting galaxies with the underlying dark matter distribution. Current and future high-$z$ spectroscopic surveys, usually incomplete in redshift…

We here introduce a novel classification approach adopted from the nonlinear model identification framework, which jointly addresses the feature selection and classifier design tasks. The classifier is constructed as a polynomial expansion…

Indefinite similarity measures can be frequently found in bio-informatics by means of alignment scores, but are also common in other fields like shape measures in image retrieval. Lacking an underlying vector space, the data are given as…

In this paper a hybrid feature selection method is proposed which takes advantages of wrapper subset evaluation with a lower cost and improves the performance of a group of classifiers. The method uses combination of sample domain filtering…

We consider the problem of setting confidence intervals on a parameter of interest from the maximum-likelihood fit of a physics model to a binned data set with a large number of bins, large event-counts per bin, and in the presence of…

For extremely weak-supervised text classification, pioneer research generates pseudo labels by mining texts similar to the class names from the raw corpus, which may end up with very limited or even no samples for the minority classes.…

B-cell repertoires are characterized by a diverse set of receptors of distinct specificities generated through two processes of somatic diversification: V(D)J recombination and somatic hypermutations. B cell clonal families stem from the…