Related papers: Counting unique molecular identifiers in sequencin…
We analyse the scaling of the weights added by invasion percolation on a branching process tree. This process is a paradigm model of self-organised criticality, where criticality is approach without a prespecified parameter. In this paper,…
Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…
Models of counts-of-counts data have been extensively used in the biological sciences, for example in cancer, population genetics, sampling theory and ecology. In this paper we explore properties of one model that is embedded into a…
Source code clones pose risks ranging from intellectual property violations to unintended vulnerabilities. Effective and efficient scalable clone detection, especially for diverged clones, remains challenging. Large language models (LLMs)…
In order to obtain morphological information of unlabeled galaxies, we present an unsupervised machine-learning (UML) method for morphological classification of galaxies, which can be summarized as two aspects: (1) the methodology of…
Consider a structured population consisting of $d$ colonies, with migration rates proportional to a positive parameter $K$. We sample $N_K$ individuals, distributed evenly across the $d$ colonies, and trace their ancestral lineages backward…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Cancer genomes exhibit a large number of different alterations that affect many genes in a diverse manner. It is widely believed that these alterations follow combinatorial patterns that have a strong connection with the underlying…
Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Consider the Markov process taking values in the partitions of N such that each pair of blocks merges at rate one, and each integer is eroded, i.e., becomes a singleton block, at rate d. This is a special case of exchangeable…
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to…
The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events -- choices of gene templates, base pair…
Neuroevolution is one of the methodologies that can be used for learning optimal architecture during training. It uses evolutionary algorithms to generate the topology of artificial neural networks and its parameters. The main benefits are…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
Missing input sequences are common in medical imaging data, posing a challenge for deep learning models reliant on complete input data. In this work, inspired by MultiMAE [2], we develop a masked autoencoder (MAE) paradigm for multi-modal,…
Urothelial cell carcinoma (UCC) is the ninth most common cancer that accounts for 4.7% of all the new cancer cases globally. UCC development and progression are due to complex and stochastic genetic programmes. To study the cascades of…
Cancer is a complex disease driven by genomic alterations, and tumor sequencing is becoming a mainstay of clinical care for cancer patients. The emergence of multi-institution sequencing data presents a powerful resource for learning…
Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…