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Most work on musical score models (a.k.a. musical language models) for music transcription has focused on describing the local sequential dependence of notes in musical scores and failed to capture their global repetitive structure, which…
We present an automatic piano transcription system that converts polyphonic audio recordings into musical scores. This has been a long-standing problem of music information processing, and recent studies have made remarkable progress in the…
In genomics, differential abundance and expression analyses are complicated by the compositional nature of sequence count data, which reflect only relative-not absolute-abundances or expression levels. Many existing methods attempt to…
Governments sometimes need to analyse sets of research papers within a field in order to monitor progress, assess the effect of recent policy changes, or identify areas of excellence. They may compare the average citation impacts of the…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
The challenges facing speech recognition systems, such as variations in pronunciations, adverse audio conditions, and the scarcity of labeled data, emphasize the necessity for a post-processing step that corrects recurring errors. Previous…
This paper proposes a novel batch normalization strategy for test-time adaptation. Recent test-time adaptation methods heavily rely on the modified batch normalization, i.e., transductive batch normalization (TBN), which calculates the mean…
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…
Estimating and testing for differences in molecular phenotypes (e.g. gene expression, chromatin accessibility, transcription factor binding) across conditions is an important part of understanding the molecular basis of gene regulation.…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
The rate of mRNA translation depends on the initiation, elongation, and termination rates of ribosomes along the mRNA. These rates depend on many "local" factors like the abundance of free ribosomes and tRNA molecules in the vicinity of the…
DNA samples are often pooled, either by experimental design, or because the sample itself is a mixture. For example, when population allele frequencies are of primary interest, individual samples may be pooled together to lower the cost of…
A density estimation method in a Bayesian nonparametric framework is presented when recorded data are not coming directly from the distribution of interest, but from a length biased version. From a Bayesian perspective, efforts to…
In this work, a Bayesian approach to speaker normalization is proposed to compensate for the degradation in performance of a speaker independent speech recognition system. The speaker normalization method proposed herein uses the technique…
Compositional generalization, the ability to predict complex meanings from training on simpler sentences, poses challenges for powerful pretrained seq2seq models. In this paper, we show that data augmentation methods that sample MRs and…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Predictive mean matching (PMM) is a popular imputation strategy that imputes missing values by borrowing observed values from other cases with similar expectations. We show that, unlike other imputation strategies, PMM is not guaranteed to…
We propose a method for detecting differential gene expression that exploits the correlation between genes. Our proposal averages the univariate scores of each feature with the scores in correlation neighborhoods. In a number of real and…
Diagnostic datasets that can detect biased models are an important prerequisite for bias reduction within natural language processing. However, undesired patterns in the collected data can make such tests incorrect. For example, if the…
The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks. We investigate the propagation of bursting noise between different levels of mathematical modelling, and demonstrate that conventional…