Related papers: A Mutagenetic Tree Hidden Markov Model for Longitu…
Hidden Markov models are widely used for modeling sequential data but typically have limited applicability in observational causal inference due to their strong conditional independence assumptions. I introduce feedback-augmented…
In this study, we address the interpretability issue in complex, black-box Machine Learning models applied to sequence data. We introduce the Model-Based tree Hidden Semi-Markov Model (MOB-HSMM), an inherently interpretable model aimed at…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
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,…
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the…
Development of resistance limits efficiency of present anticancer therapies and preventing it remains big challenge in cancer research. It is accepted, at intuitive level, that the resistance emerges as a consequence of cancer cells…
People are living longer than ever before, and with this arises new complications and challenges for humanity. Among the most pressing of these challenges is of understanding the role of aging in the development of dementia. This paper is…
We discuss a cancer hallmark network framework for modelling genome-sequencing data to predict cancer clonal evolution and associated clinical phenotypes. Strategies of using this framework in conjunction with genome sequencing data in an…
The article presents an application of Hidden Markov Models (HMMs) for pattern recognition on genome sequences. We apply HMM for identifying genes encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma brucei (T.…
We develop a modeling framework for cancer progression that distinguishes the order of two possible mutations. Recent observations and information on myeloproliferative neoplasms are analyzed within our framework. In some patients with…
In this work, we present two defective regression models for the analysis of interval-censored competing risk data in the presence of cured individuals, viz., defective Gompertz and defective inverse Gaussian regression models. The proposed…
Reversibility of state transitions is intensively studied topic in many scientific disciplines over many years. In cell biology, it plays an important role in epigenetic variation of phenotypes, known as phenotypic plasticity. More…
We use a cellular automata model to study the evolution of HIV infection and the onset of AIDS. The model takes into account the global features of the immune response to any pathogen, the fast mutation rate of the HIV and a fair amount of…
Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, because the higher resolution of these data compared to standard Sanger sequencing provide evidence into the direction of infectious…
It is now evident that the commonly accepted strategy for treatment of HIV/AIDS by highly active antiretroviral therapy (HAART) will not lead to eradication of HIV in a reasonable time. This is straightforward from the typical exponential…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a real-valued…
Retaining persons living with HIV (PLWH) in medical care is paramount to preventing new transmissions of the virus and allowing PLWH to live normal and healthy lifespans. Maintaining regular appointments with an HIV provider and taking…
Identifying a patient's key problems over time is a common task for providers at the point care, yet a complex and time-consuming activity given current electric health records. To enable a problem-oriented summarizer to identify a…
We analyze the convergence rate of a simplified version of a popular Gibbs sampling method used for statistical discovery of gene regulatory binding motifs in DNA sequences. This sampler satisfies a very strong form of ergodicity (uniform).…