Related papers: Selecting ChIP-seq Normalization Methods from the …
We investigate saddlepoint approximations applied to the score test statistic in genome-wide association studies with binary phenotypes. The inaccuracy in the normal approximation of the score test statistic increases with increasing sample…
In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…
Two-sample inference for the difference of population means typically relies upon a Central Limit Theorem approximation. When data are drawn from a Negative Binomial distribution, previous work of Shilane et al. (2010) showed that a Normal…
Disjoint sampling is critical for rigorous and unbiased evaluation of state-of-the-art (SOTA) models. When training, validation, and test sets overlap or share data, it introduces a bias that inflates performance metrics and prevents…
Histopathology-based survival modelling has two major hurdles. Firstly, a well-performing survival model has minimal clinical application if it does not contribute to the stratification of a cancer patient cohort into different risk groups,…
Motivation: Researchers need a rich trove of genomic datasets that they can leverage to gain a better understanding of the genetic basis of the human genome and identify associations between phenotypes and specific parts of DNA. However,…
Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work we present a probabilistic…
Although a vast body of literature relates to image segmentation methods that use deep neural networks (DNNs), less attention has been paid to assessing the statistical reliability of segmentation results. In this study, we interpret the…
Pooling genome-wide association studies of multiple related traits can substantially increase power for detecting genetic variants with pleiotropic effects. ASSET, which exhaustively searches all subsets of studies for association signals,…
Effective disinfection is essential for maintaining water quality standards in distribution networks. Chlorination, as the most used technique, ensures safe water by maintaining sufficient chlorine residuals but also leads to the formation…
Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have…
Current popular methods in literature of RNA sequencing normalisation do not account for gene length when compared across samples, whilst adjusting for count biases in the data. This creates a gap in the normalisation as bigger genes in RNA…
We develop differentially private hypothesis testing methods for the small sample regime. Given a sample $\cal D$ from a categorical distribution $p$ over some domain $\Sigma$, an explicitly described distribution $q$ over $\Sigma$, some…
This paper introduces SelfMatch, a semi-supervised learning method that combines the power of contrastive self-supervised learning and consistency regularization. SelfMatch consists of two stages: (1) self-supervised pre-training based on…
While the evaluation of explanations is an important step towards trustworthy models, it needs to be done carefully, and the employed metrics need to be well-understood. Specifically model randomization testing is often overestimated and…
In this paper, we study a class of two sample test statistics based on inter-point distances in the high dimensional and low sample size setting. Our test statistics include the well-known energy distance and maximum mean discrepancy with…
We study the fundamental problems of identity testing (goodness of fit), and closeness testing (two sample test) of distributions over $k$ elements, under differential privacy. While the problems have a long history in statistics, finite…
We study properties of two resampling scenarios: Conditional Randomisation and Conditional Permutation schemes, which are relevant for testing conditional independence of discrete random variables $X$ and $Y$ given a random variable $Z$.…
Previous divide-and-conquer segmentation analyses of DNA sequences do not provide a satisfactory stopping criterion for the recursion. This paper proposes that segmentation be considered as a model selection process. Using the tools in…
As high-throughput sequencing has become common practice, the cost of sequencing large amounts of genetic data has been drastically reduced, leading to much larger data sets for analysis. One important task is to identify biological…