arXiv research

New method infers centromere locations in yeast using Hi-C data.

In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping chromosomes. A segmentation solution that is fast and automated will enable scaling of co…

Genetic algorithms are a well-known method for tackling the problem of variable selection. As they are non-parametric and can use a large variety of fitness functions, they are well-suited as a variable selection wrapper that can be applied to many different models. In almost all cases, the chromosome formulation used …

Phase segregation, the process by which the components of a binary mixture spontaneously separate, is a key process in the evolution and design of many chemical, mechanical, and biological systems. In this work, we present a data-driven approach for the learning, modeling, and prediction of phase segregation. A direct …

Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid organisms, including humans, are organized into homologous pairs of chromosomes that d…

A Bayesian Boolean Matrix Factorization for cancer genomics

Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled markers, offer an alternative approach. As these technologies mature towards becom…

Controversies around race and machine learning have sparked debate among computer scientists over how to design machine learning systems that guarantee fairness. These debates rarely engage with how racial identity is embedded in our social experience, making for sociological and psychological complexity. This complexi…

New model values equity-linked securities with guaranteed return.

Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self tran…

Bayesian MS-VAR model for pricing equity-linked life insurance products.

Loyal buyer-seller relationships can arise by design, e.g. when a seller tailors a product to a specific market niche to accomplish the best possible returns, and buyers respond to the dedicated efforts the seller makes to meet their needs. We ask whether it is possible, instead, for loyalty to arise spontaneously, and…

Study explores how wealth dynamics change with preferential interactions in kinetic exchange models.

A method for estimating the cross-correlation $C_{xy}(τ)$ of long-range correlated series $x(t)$ and $y(t)$, at varying lags $τ$ and scales $n$, is proposed. For fractional Brownian motions with Hurst exponents $H_1$ and $H_2$, the asymptotic expression of $C_{xy}(τ)$ depends only on the lag $τ$ (wide-sense stationarit…

We introduce the Genetic-Gated Networks (G2Ns), simple neural networks that combine a gate vector composed of binary genetic genes in the hidden layer(s) of networks. Our method can take both advantages of gradient-free optimization and gradient-based optimization methods, of which the former is effective for problems …

By incorporating market impact and asymmetric sensitivity into the evolutionary minority game, we study the coevolutionary dynamics of stock prices and investment strategies in financial markets. Both the stock price movement and the investors' global behavior are found to be closely related to the phase region they fa…

We developed a perturbation model for affine gravity theories.

Model shows partial compliance can lead to less fair outcomes than expected.

Unsupervised two-view learning, or detection of dependencies between two paired data sets, is typically done by some variant of canonical correlation analysis (CCA). CCA searches for a linear projection for each view, such that the correlations between the projections are maximized. The solution is invariant to any lin…

A genetic algorithm improves multivariate kernel density estimation.

Cash collateral is perfect in that it provides simultaneous counterparty credit risk protection and derivatives funding. Securities are imperfect collateral, because of collateral segregation or differences in CSA haircuts and repo haircuts. Moreover, the collateral rate term structure is not observable in the repo mar…

DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment organizations on a given locus where contigs containing rearranged segments represent ver…

Bayesian optimization has recently attracted the attention of the automatic machine learning community for its excellent results in hyperparameter tuning. BO is characterized by the sample efficiency with which it can optimize expensive black-box functions. The efficiency is achieved in a similar fashion to the learnin…

Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture methods such as HiC have recently been employed. However, computational methods…

We describe a novel non-parametric statistical hypothesis test of relative dependence between a source variable and two candidate target variables. Such a test enables us to determine whether one source variable is significantly more dependent on a first target variable or a second. Dependence is measured via the Hilbe…

Generates new human genomic sequences for LAI training.

Proposes a novel SAM operator for separate item and relational memories.

CN-SBM clusters cancer samples and regions based on copy number variants.

Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated expression of modules (and module groups) of functionally related genes across the gen…

Study on optimal fees in hedge funds with first-loss compensation.

Model shows how confidence feedback can lead to different crisis outcomes.

DFMM automates market making with adaptive pricing and risk management.

Novel CNN array for sign language recognition using wearable IMUs.

Study uses TV news to measure climate risks affecting clean energy firms.

The functional significance of resting state networks and their abnormal manifestations in psychiatric disorders are firmly established, as is the importance of the cortical rhythms in mediating these networks. Resting state networks are known to undergo substantial reorganization from childhood to adulthood, but wheth…

This paper addresses the problem of localizing audio sources using binaural measurements. We propose a supervised formulation that simultaneously localizes multiple sources at different locations. The approach is intrinsically efficient because, contrary to prior work, it relies neither on source separation, nor on mon…

The paper characterizes brain states and transitions using functional MRI data.

Bayesian framework for model uncertainty identifies complex heterogeneity without strong assumptions.

Ventricular Fibrillation (VF), one of the most dangerous arrhythmias, is responsible for sudden cardiac arrests. Thus, various algorithms have been developed to predict VF from Electrocardiogram (ECG), which is a binary classification problem. In the literature, we find a number of algorithms based on signal processing…

Estimates network causal effects considering contagion and latent confounding.

Study multi-currency markets with multiple interest rates and collateral.

Humans perceive the seemingly chaotic world in a structured and compositional way with the prerequisite of being able to segregate conceptual entities from the complex visual scenes. The mechanism of grouping basic visual elements of scenes into conceptual entities is termed as perceptual grouping. In this work, we pro…

Topological surgery is a mathematical technique used for creating new manifolds out of known ones. We observe that it occurs in natural phenomena where a sphere of dimension 0 or 1 is selected, forces are applied and the manifold in which they occur changes type. For example, 1-dimensional surgery happens during chromo…

Study of urban lifestyles from mobility data of 1.2M people in 11 U.S. cities.

Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized data sets that facilitate fair assessment of new methods and lower the barrier to …

The paper uses GIS data to predict urban sprawl.

The paper tackles interpreting DCM with image data by addressing data isomorphism.

Model forecasts natural gas consumption with Fourier series and feedback.