相关论文: A Survival Copula Mixture Model for Comparing Two …
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
Undersampling can accelerate the signal acquisition but at the cost of bringing in artifacts. Removing these artifacts is a fundamental problem in signal processing and this task is also called signal reconstruction. Through modeling…
We propose a new copula model that can be used with replicated spatial data. Unlike the multivariate normal copula, the proposed copula is based on the assumption that a common factor exists and affects the joint dependence of all…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
We present a non-equilibrium statistical mechanics description of rank abundance relations (RAR) in random community models of ecology. Specifically, we study a multi-species replicator system with quenched random interaction matrices. We…
For a particular disease there may be two diagnostic tests developed, where each of the tests is subject to several studies. A quadrivariate generalized linear mixed model (GLMM) has been recently proposed to joint meta-analyse and compare…
Survival prediction is an important branch of cancer prognosis analysis. The model that predicts survival risk through TCGA genomics data can discover genes related to cancer and provide diagnosis and treatment recommendations based on…
Partial multi-label learning and complementary multi-label learning are two popular weakly supervised multi-label classification paradigms that aim to alleviate the high annotation costs of collecting precisely annotated multi-label data.…
Discrimination and calibration represent two important properties of survival analysis, with the former assessing the model's ability to accurately rank subjects and the latter evaluating the alignment of predicted outcomes with actual…
In genome wide association studies (GWAS), researchers are often dealing with non-normally distributed traits or a mixture of discrete-continuous traits. However, most of the current region-based methods rely on multivariate linear mixed…
We introduce Permutation and Structured Perturbation Inference (PSPI), a new problem formulation that abstracts many graph matching tasks that arise in systems biology. PSPI can be viewed as a robust formulation of the permutation inference…
In cancer biomarker development, a key objective is to evaluate whether a new biomarker, when combined with an established one, improves early cancer detection compared to using the established biomarker alone. Incremental value is often…
Background Study individuals may face repeated events overtime. However, there is no consensus around learning approaches to use in a high-dimensional framework for survival data (when the number of variables exceeds the number of…
A time-varying bivariate copula joint model, which models the repeatedly measured longitudinal outcome at each time point and the survival data jointly by both the random effects and time-varying bivariate copulas, is proposed in this…
Family studies provide an important tool for understanding etiology of diseases, with the key aim of discovering evidence of family aggregation and to determine if such aggregation can be attributed to genetic components. Heritability and…
Reconstruction of evolutionary relationships between species is an important topic in the field of computational biology. Pairwise compatibility graphs (PCGs) are used to model such relationships. A graph is a PCG if its edges can be…
The ability of homologous chromosomes (or selected chromosomal loci) to pair specifically in the apparent absence of DNA breakage and recombination represents a prominent feature of eukaryotic biology. The mechanism of homology recognition…
Phylogenetic data arising on two possibly different tree topologies might be mixed through several biological mechanisms, including incomplete lineage sorting or horizontal gene transfer in the case of different topologies, or simply…