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Formalin-fixed paraffin-embedded (FFPE) samples have great potential for biomarker discovery, retrospective studies and diagnosis or prognosis of diseases. Their application, however, is hindered by the unsatisfactory performance of…
Accurate phase estimation -- the process of assigning phase values between $0$ and $2\pi$ to repetitive or periodic signals -- is a cornerstone in the analysis of oscillatory signals across diverse fields, from neuroscience to robotics,…
In this study, we propose a machine learning-based method for noise reduction and disease-causing gene feature extraction in gene sequencing DeepSeqDenoise algorithm combines CNN and RNN to effectively remove the sequencing noise, and…
Gene regulation is central to understanding cellular processes and development, potentially leading to the discovery of new treatments for diseases and personalized medicine. Inferring gene regulatory networks (GRNs) from single-cell RNA…
Nuclear Magnetic Resonance (NMR) spectroscopy is essential for revealing molecular structure, electronic environment, and dynamics. Accurate NMR shift prediction allows researchers to validate structures by comparing predicted and observed…
In the framework of three-active-neutrino mixing, the charge parity phase, the neutrino mass ordering, and the octant of $\theta_{23}$ remain unknown. The Deep Underground Neutrino Experiment (DUNE) is a next-generation long-baseline…
Given the output of a data source taking values in a finite alphabet, we wish to detect change-points, that is times when the statistical properties of the source change. Motivated by ideas of match lengths in information theory, we…
Raman spectroscopy can provide insight into the molecular composition of cells and tissue. Consequently, it can be used as a powerful diagnostic tool, e.g. to help identify changes in molecular contents with the onset of disease. But robust…
There have been significant advancements in anomaly detection in an unsupervised manner, where only normal images are available for training. Several recent methods aim to detect anomalies based on a memory, comparing or reconstructing the…
Prompt learning has attracted increasing attention in the graph domain as a means to bridge the gap between pretext and downstream tasks. Existing studies on heterogeneous graph prompting typically use feature prompts to modify node…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
In the absence of ground truth it is not possible to automatically determine the exact spectrum and occurrences of OCR errors in an OCR'ed text. Yet, for interactive postcorrection of OCR'ed historical printings it is extremely useful to…
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
Neural networks have revolutionized numerous fields, yet they remain vulnerable to a critical flaw: the tendency to learn implicit biases, spurious correlations between certain attributes and target labels in training data. These biases are…
Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…