Related papers: RNA-Seq Mapping Errors When Using Incomplete Refer…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
Completely random measures (CRMs) and their normalizations are a rich source of Bayesian nonparametric priors. Examples include the beta, gamma, and Dirichlet processes. In this paper we detail two major classes of sequential CRM…
We investigate random feature models in which neural networks sampled from a prescribed initialization ensemble are frozen and used as random features, with only the readout weights optimized. Adopting a statistical-physics viewpoint, we…
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic…
Generalized linear models usually assume a common dispersion parameter, an assumption that is seldom true in practice. Consequently, standard parametric methods may suffer appreciable loss of type I error control. As an alternative, we…
For randomized controlled trials to be conclusive, it is important to set the target sample size accurately at the design stage. Comparing two normal populations, the sample size calculation requires specification of the variance other than…
The capture-recapture method can be applied to measure the coverage of administrative and big data sources, in official statistics. In its basic form, it involves the linkage of two sources while assuming a perfect linkage and other…
Single-cell transcriptomic data approximates the abundance of proteins at a high resolution, but its noisiness necessitates transformation by a pipeline of methods before analysis and inference. In the absence of robust validation of these…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Measurement error in count data is common but underexplored in the literature, particularly in contexts where observed scores are bounded and arise from discrete scoring processes. Motivated by applications in oral reading fluency…
Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher.…
Modern stream processing systems often need to track the frequency of distinct keys in a data stream in real-time. Since maintaining exact counts can require a prohibitive amount of memory, many applications rely on compact, probabilistic…
Diagnostic tests are almost never perfect. Studies quantifying their performance use knowledge of the true health status, measured with a reference diagnostic test. Researchers commonly assume that the reference test is perfect, which is…
Machine-translated benchmarks are widely used to assess the multilingual capabilities of large language models (LLMs), yet translation errors in these benchmarks remain underexplored, raising concerns about the reliability and comparability…
Accurately inferring the root causes of disease from sequencing data can improve the discovery of novel therapeutic targets. However, existing root causal inference algorithms require perfectly measured continuous random variables. Single…
The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and…
Minimum Bayes-risk (MBR) decoding has recently gained renewed attention in text generation. MBR decoding considers texts sampled from a model as pseudo-references and selects the text with the highest similarity to the others. Therefore,…
Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect…
Spatial studies of transcriptome provide biologists with gene expression maps of heterogeneous and complex tissues. However, most experimental protocols for spatial transcriptomics suffer from the need to select beforehand a small fraction…
Automatic piano transcription models are typically evaluated using simple frame- or note-wise information retrieval (IR) metrics. Such benchmark metrics do not provide insights into the transcription quality of specific musical aspects such…