Related papers: A network approach to analyzing highly recombinant…
We consider the community detection problem in sparse random hypergraphs under the non-uniform hypergraph stochastic block model (HSBM), a general model of random networks with community structure and higher-order interactions. When the…
Malaria microscopy, microscopic examination of stained blood slides to detect parasite Plasmodium, is considered to be a gold-standard for detecting life-threatening disease malaria. Detecting the plasmodium parasite requires a skilled…
Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost has led to an exponential…
Inferring genetic networks from gene expression data is one of the most challenging work in the post-genomic era, partly due to the vast space of possible networks and the relatively small amount of data available. In this field, Gaussian…
A key public health problem during an outbreak is to reconstruct the disease cascade from a partial set of confirmed infections. This has been studied extensively under the Maximum Likelihood Estimation (MLE) formulation, which reduces the…
Accurate prediction and identification of variables associated with outcomes or disease states are critical for advancing diagnosis, prognosis, and precision medicine in biomedical research. Regularized regression techniques, such as lasso,…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…
Chronic viral infections can persist in an infected person for decades. From the perspective of the virus, a single infection can span thousands of generations, leading to a highly diverse population of viruses with its own complex…
Reconstructing the evolutionary history relating a collection of molecular sequences is the main subject of modern Bayesian phylogenetic inference. However, the commonly used Markov chain Monte Carlo methods can be inefficient due to the…
Resting-state fMRI has been shown to provide surrogate biomarkers for the analysis of various diseases. In addition, fMRI data helps in understanding the brain's functional working during resting state and task-induced activity. To improve…
Malaria parasites pose a significant global health burden, causing widespread suffering and mortality. Detecting malaria infection accurately is crucial for effective treatment and control. However, existing automated detection techniques…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
Malware detection is an interesting and valuable domain to work in because it has significant real-world impact and unique machine-learning challenges. We investigate existing long-range techniques and benchmarks and find that they're not…
Malaria is a serious infectious disease that is responsible for over half million deaths yearly worldwide. The major cause of these mortalities is late or inaccurate diagnosis. Manual microscopy is currently considered as the dominant…
A key aim of systems biology is the reconstruction of molecular networks, however we do not yet have networks that integrate information from all datasets available for a particular clinical condition. This is in part due to the limited…
Accurate detection of Plasmodium falciparum in Giemsa-stained blood smears is an essential component of reliable malaria diagnosis, especially in developing countries. Deep learning-based object detection methods have demonstrated strong…
Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced…
Malaria, which primarily spreads with the bite of female anopheles mosquitos, often leads to death of people - specifically children in the age-group of 0-5 years. Clinical experts identify malaria by observing RBCs in blood smeared images…
Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities.…