A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Test assesses if a linear classifier is random or significant.
Unified framework improves gene prioritization in disease studies.
The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In order to develop early diagnostics of cancer-causing methylations and to develop a…
Model predicts anti-cancer drug responses using gene and molecular data.
ERICA assesses reproducibility in cluster analysis.
Deep learning model explains breast cancer subtypes using logistic regression.
ERICA assesses replicability of cluster analysis results.
iDeepViewLearn combines deep learning and feature selection for multiview learning.
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we de…
Global optimization approach for MAP clustering under Gaussian mixtures.
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of phenotypes makes high-throughput phenotype profiling a very difficult and labor…
Copula-based fusion improves breast cancer risk stratification.
Paper proposes scalable method for analyzing multi-omic data.
Motivation : Molecular signatures for diagnosis or prognosis estimated from large-scale gene expression data often lack robustness and stability, rendering their biological interpretation challenging. Increasing the signature's interpretability and stability across perturbations of a given dataset and, if possible, acr…
Cancer is one of the leading cause of death, worldwide. Many believe that genomic data will enable us to better predict the survival time of these patients, which will lead to better, more personalized treatment options and patient care. As standard survival prediction models have a hard time coping with the high-dimen…
Gene expression data represents a unique challenge in predictive model building, because of the small number of samples compared to the huge amount of features . This "" property has hampered application of deep learning techniques for disease outcome classification. Sparse learning by incorporating ex…
Survival month for non-small lung cancer patients depend upon which stage of lung cancer is present. Our aim is to identify smoking specific gene expression biomarkers in the prognosis of lung cancer patients. In this paper, we introduce the network elastic net, a generalization of network lasso that allows for simulta…
Sparse Canonical Correlation Analysis (CCA) has received considerable attention in high-dimensional data analysis to study the relationship between two sets of random variables. However, there has been remarkably little theoretical statistical foundation on sparse CCA in high-dimensional settings despite active methodo…
We consider the problem of high-dimensional classification between the two groups with unequal covariance matrices. Rather than estimating the full quadratic discriminant rule, we propose to perform simultaneous variable selection and linear dimension reduction on original data, with the subsequent application of quadr…
We consider the analysis of high dimensional data given in the form of a matrix with columns consisting of observations and rows consisting of features. Often the data is such that the observations do not reside on a regular grid, and the given order of the features is arbitrary and does not convey a notion of locality…
With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis using gene expression data continues to pose challenges due to the high dimensio…
Microarray cancer gene expression data comprise of very high dimensions. Reducing the dimensions helps in improving the overall analysis and classification performance. We propose two hybrid techniques, Biogeography - based Optimization - Random Forests (BBO - RF) and BBO - SVM (Support Vector Machines) with gene ranki…
Study predicts 10-year survival rates for breast cancer patients.
Study improves cancer classification using gene selection and projection methods.
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks …
We study a norm for structured sparsity which leads to sparse linear predictors whose supports are unions of prede ned overlapping groups of variables. We call the obtained formulation latent group Lasso, since it is based on applying the usual group Lasso penalty on a set of latent variables. A detailed analysis of th…
The method integrates survival constraints into NMF for identifying survival-associated gene clusters.
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa…
Among American women, the rate of breast cancer is only second to lung cancer. An estimated 12.4% women will develop breast cancer over the course of their lifetime. The widespread use of social media across the socio-economic spectrum offers unparalleled ways to facilitate information sharing, in particular as it pert…
Method uses network biology to construct gene expression models for cancer.
Boosting strategies for merging vs. ensembling studies analyzed.
As much as data science is playing a pivotal role everywhere, healthcare also finds it prominent application. Breast Cancer is the top rated type of cancer amongst women; which took away 627,000 lives alone. This high mortality rate due to breast cancer does need attention, for early detection so that prevention can be…
LogGENE uses log-cosh loss for deep learning in gene expression datasets, improving accuracy and interpretability.
A hybrid method clusters and characterizes cancer data efficiently.
Kernel testing compares cell states in single-cell data.
New method groups genetic data into coherent topics for disease insights.
Neural networks improve cancer risk prediction from family history data.
The availability of large microarray data has led to a growing interest in biclustering methods in the past decade. Several algorithms have been proposed to identify subsets of genes and conditions according to different similarity measures and under varying constraints. In this paper we focus on the exclusive row bicl…
Breast cancer is the most frequently reported cancer type among the women around the globe and beyond that it has the second highest female fatality rate among all cancer types. Despite all the progresses made in prevention and early intervention, early prognosis and survival prediction rates are still unsatisfactory. …
Study identifies biomarkers for lung cancer in female non-smokers.
Develops a model for RNA-seq data clustering.
We trained and evaluated a localization-based deep CNN for breast cancer screening exam classification on over 200,000 exams (over 1,000,000 images). Our model achieves an AUC of 0.919 in predicting malignancy in patients undergoing breast cancer screening, reducing the error rate of the baseline (Wu et al., 2019a) by …
Non-synonymous single nucleotide polymorphisms (nsSNPs) are single nucleotide substitution occurring in the coding region of a gene and leads to a change in amino-acid sequence of protein. The studies have shown these variations may be associated with disease. Thus, investigating the effects of nsSNPs on protein functi…
Microwave-based breast cancer detection has been proposed as a complementary approach to compensate for some drawbacks of existing breast cancer detection techniques. Among the existing microwave breast cancer detection methods, machine learning-type algorithms have recently become more popular. These focus on detectin…
Deep learning network matches radiologists in breast cancer segmentation.
Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an opportunity to apply machine learning methods for this purpose. In addition to cytotoxi…
Paper presents a breast cancer detection model using ELM-RBF.
Motivation: Biomarker discovery from high-dimensional data is a crucial problem with enormous applications in biology and medicine. It is also extremely challenging from a statistical viewpoint, but surprisingly few studies have investigated the relative strengths and weaknesses of the plethora of existing feature sele…